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Conserved domains on  [gi|1034644875|ref|XP_016864933|]
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E3 ubiquitin-protein ligase TRIM23 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
406-550 2.61e-96

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd04158:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 169  Bit Score: 290.78  E-value: 2.61e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd04158     1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 486 RISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGCDARS 550
Cdd:cd04158    81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRSWYIQGCDARS 145
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
226-370 3.57e-26

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


:

Pssm-ID: 128778  Cd Length: 127  Bit Score: 103.50  E-value: 3.57e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  226 IRASILDMAHCIRTFTEEISDYSRKLVGIVQHIEGgeqivedgigmahtehvpgTAENARSCIRAYFYDLHETLCRQEEM 305
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEE-------------------NAADVEAQIKAAFDELRNALNKRKKQ 61
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875  306 ALSVVDAHVREKLIWLRQQQEDMTILLSEVSAACLHCEKTLQQDDC-RVVLAKQEITRLLETLQKQ 370
Cdd:smart00502  62 LLEDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTEEALNSGDPtELLLSKKLIIERLQNLLKQ 127
mRING-HC-C3HC3D_TRIM23_C-IX cd16645
Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein ...
28-77 7.35e-26

Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


:

Pssm-ID: 438307 [Multi-domain]  Cd Length: 50  Bit Score: 99.83  E-value: 7.35e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875  28 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAIRCPFDRQ 77
Cdd:cd16645     1 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAVRCPFDRQ 50
Bbox2_TRIM23_C-IX_rpt1 cd19773
first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
123-172 1.18e-24

first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


:

Pssm-ID: 380831  Cd Length: 50  Bit Score: 96.64  E-value: 1.18e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 123 SIIRCDEDEAHLASVYCTVCATHLCSECSQVTHSTKTLAKHRRVPLADKP 172
Cdd:cd19773     1 PSIPCDENEDHEATLYCTVCSTNLCEECFTSTHSTKTLSKHRRVPLSEKP 50
Bbox2_TRIM23_C-IX_rpt2 cd19774
second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
174-223 4.76e-21

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


:

Pssm-ID: 380832  Cd Length: 50  Bit Score: 86.31  E-value: 4.76e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 174 EKTMCSQHQVHAIEFVCLEEGCQTSPLMCCVCKEYGKHQGHKHSVLEPEA 223
Cdd:cd19774     1 EKPKCPIHPDHLIEFVCLEEDCQESPLMCIICKEYGKHQGHKHELLEEEA 50
 
Name Accession Description Interval E-value
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
406-550 2.61e-96

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 290.78  E-value: 2.61e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd04158     1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 486 RISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGCDARS 550
Cdd:cd04158    81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRSWYIQGCDARS 145
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
405-550 5.01e-83

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 256.00  E-value: 5.01e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875 485 DRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHEL-KDRPWEIQGCSAVT 145
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
402-550 4.11e-71

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 225.88  E-value: 4.11e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:PTZ00133   15 KKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDS 94
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:PTZ00133   95 NDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSV-RQRNWYIQGCCATT 162
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
402-550 2.01e-67

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 216.33  E-value: 2.01e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:smart00177  11 NKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875  482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSI-RDRNWYIQPTCATS 158
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
226-370 3.57e-26

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 103.50  E-value: 3.57e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  226 IRASILDMAHCIRTFTEEISDYSRKLVGIVQHIEGgeqivedgigmahtehvpgTAENARSCIRAYFYDLHETLCRQEEM 305
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEE-------------------NAADVEAQIKAAFDELRNALNKRKKQ 61
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875  306 ALSVVDAHVREKLIWLRQQQEDMTILLSEVSAACLHCEKTLQQDDC-RVVLAKQEITRLLETLQKQ 370
Cdd:smart00502  62 LLEDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTEEALNSGDPtELLLSKKLIIERLQNLLKQ 127
mRING-HC-C3HC3D_TRIM23_C-IX cd16645
Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein ...
28-77 7.35e-26

Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 438307 [Multi-domain]  Cd Length: 50  Bit Score: 99.83  E-value: 7.35e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875  28 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAIRCPFDRQ 77
Cdd:cd16645     1 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAVRCPFDRQ 50
Bbox2_TRIM23_C-IX_rpt1 cd19773
first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
123-172 1.18e-24

first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 380831  Cd Length: 50  Bit Score: 96.64  E-value: 1.18e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 123 SIIRCDEDEAHLASVYCTVCATHLCSECSQVTHSTKTLAKHRRVPLADKP 172
Cdd:cd19773     1 PSIPCDENEDHEATLYCTVCSTNLCEECFTSTHSTKTLSKHRRVPLSEKP 50
Bbox2_TRIM23_C-IX_rpt2 cd19774
second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
174-223 4.76e-21

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 380832  Cd Length: 50  Bit Score: 86.31  E-value: 4.76e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 174 EKTMCSQHQVHAIEFVCLEEGCQTSPLMCCVCKEYGKHQGHKHSVLEPEA 223
Cdd:cd19774     1 EKPKCPIHPDHLIEFVCLEEDCQESPLMCIICKEYGKHQGHKHELLEEEA 50
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
404-532 2.57e-12

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 65.39  E-value: 2.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFMQP--IPTIGFNVETVEYK----NLKFTIWDVGG---KHKLRPLWKHYYLNTQA 474
Cdd:COG1100     3 EKKIVVVGTGGVGKTSLVNRLVGDIFSLEkyLSTNGVTIDKKELKldglDVDLVIWDTPGqdeFRETRQFYARQLTGASL 82
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 475 VVFVVDSSHRD-RISEAhsELAKLLTEKELRDALLLIFaNKQDVAGALSVEEITELLSL 532
Cdd:COG1100    83 YLFVVDGTREEtLQSLY--ELLESLRRLGKKSPIILVL-NKIDLYDEEEIEDEERLKEA 138
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
404-516 2.03e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 62.39  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFM--QPIPTIGFNVET--VEYKNL--KFTIWDVGGKHKLRPLWKHYYLNTQAVVF 477
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSitEYYPGTTRNYVTtvIEEDGKtyKFNLLDTAGQEDYDAIRRLYYPQVERSLR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1034644875 478 VVD-SSHRDRISEahselAKLLTEKELRDAL-----LLIFANKQD 516
Cdd:TIGR00231  81 VFDiVILVLDVEE-----ILEKQTKEIIHHAdsgvpIILVGNKID 120
BBOX smart00336
B-Box-type zinc finger;
173-219 8.69e-05

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 40.01  E-value: 8.69e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034644875  173 HEKTMCSQHQVHAIEFVCLEegCQTspLMCCVCKEYgKHQGHKHSVL 219
Cdd:smart00336   1 QRAPKCDSHGDEPAEFFCEE--CGA--LLCRTCDEA-EHRGHTVVLL 42
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
31-74 2.62e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 38.64  E-value: 2.62e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1034644875   31 CGVCEDVFSlqgdKVPRLLLCGHTVCHDCLTRLpLHGRAIRCPF 74
Cdd:smart00184   1 CPICLEEYL----KDPVILPCGHTFCRSCIRKW-LESGNNTCPI 39
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
29-104 3.97e-04

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 43.07  E-value: 3.97e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTR-LPLHGRAIRCPFDRQVTDlgdsgvwgLKKNFALLELLERLQN 104
Cdd:TIGR00599  27 LRCHICKDFF-----DVPVLTSCSHTFCSLCIRRcLSNQPKCPLCRAEDQESK--------LRSNWLVSEIVESFKN 90
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
31-73 1.85e-03

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 36.22  E-value: 1.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1034644875  31 CGVCEDVFslqgdKVPRLLlCGHTVCHDCLTRL-PLHGRAIRCP 73
Cdd:pfam13445   1 CPICLELF-----TDPVLP-CGHTFCRECLEEMsQKKGGKFKCP 38
zf-B_box pfam00643
B-box zinc finger;
125-168 2.85e-03

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 35.91  E-value: 2.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1034644875 125 IRCDEDEAHLASVYCTVCATHLCSECSQVTHStktlaKHRRVPL 168
Cdd:pfam00643   4 RLCPEHEEEPLTLYCNDCQELLCEECSVGEHR-----GHTVVPL 42
 
Name Accession Description Interval E-value
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
406-550 2.61e-96

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 290.78  E-value: 2.61e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd04158     1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 486 RISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGCDARS 550
Cdd:cd04158    81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRSWYIQGCDARS 145
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
405-550 5.01e-83

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 256.00  E-value: 5.01e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875 485 DRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHEL-KDRPWEIQGCSAVT 145
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
406-550 3.62e-81

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 251.34  E-value: 3.62e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd00878     1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRE 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 486 RISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKlCCGRSWYIQGCDARS 550
Cdd:cd00878    81 RIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLES-IKGRRWHIQPCSAVT 144
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
402-550 4.11e-71

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 225.88  E-value: 4.11e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:PTZ00133   15 KKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDS 94
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:PTZ00133   95 NDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSV-RQRNWYIQGCCATT 162
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
405-550 2.12e-70

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 223.44  E-value: 2.12e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:cd04150     1 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875 485 DRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:cd04150    81 ERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSL-RNRNWYIQATCATS 145
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
402-550 7.95e-70

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 222.53  E-value: 7.95e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:PLN00223   15 KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:PLN00223   95 NDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RQRHWYIQSTCATS 162
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
402-550 2.01e-67

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 216.33  E-value: 2.01e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:smart00177  11 NKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875  482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSI-RDRNWYIQPTCATS 158
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
404-550 1.70e-66

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 213.48  E-value: 1.70e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSH 483
Cdd:cd04149     9 EMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSAD 88
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034644875 484 RDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:cd04149    89 RDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRI-RDRNWYVQPSCATS 154
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
406-548 8.80e-65

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 208.80  E-value: 8.80e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd04151     1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034644875 486 RISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDA 548
Cdd:cd04151    81 RLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSEL-KDRTWQIFKTSA 142
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
400-548 1.19e-56

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 187.94  E-value: 1.19e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 400 GPKMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd04153    11 FPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVI 90
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 480 DSSHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDA 548
Cdd:cd04153    91 DSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSI-RDHTWHIQGCCA 158
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
406-548 2.00e-56

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 186.85  E-value: 2.00e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEY-KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:cd04156     1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLeKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034644875 485 DRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGCDA 548
Cdd:cd04156    81 ARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDRDWYVQPCSA 144
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
401-550 2.10e-56

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 187.22  E-value: 2.10e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 401 PKMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd04155    12 SRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVID 91
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 481 SSHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDARS 550
Cdd:cd04155    92 SADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDI-RDRSWHIQACSAKT 160
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
404-548 6.18e-53

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 177.90  E-value: 6.18e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSH 483
Cdd:cd04154    14 EMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSD 93
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 484 RDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLcCGRSWYIQGCDA 548
Cdd:cd04154    94 RARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSI-KSHHWRIFGCSA 157
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
407-548 2.70e-44

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 155.34  E-value: 2.70e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEY-----KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:cd04152     6 IVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVslgnaKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDS 85
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGCDA 548
Cdd:cd04152    86 VDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELSSSTPWHVQPACA 152
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
402-538 5.07e-36

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 133.17  E-value: 5.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 402 KMEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:cd00879    17 KKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDA 96
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCG 538
Cdd:cd00879    97 ADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTG 153
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
407-548 2.16e-35

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 130.54  E-value: 2.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLK-----QDEFMQP---IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFV 478
Cdd:cd04160     2 VLILGLDNAGKTTFLEQTKtkfskNYKGLNPskiTPTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYV 81
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034644875 479 VDSSHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWY-IQGCDA 548
Cdd:cd04160    82 IDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDClVQPVSA 152
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
407-546 6.30e-35

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 129.10  E-value: 6.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD 485
Cdd:cd04162     2 ILVLGLDGAGKTSLLHSLSSERSLESvVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSE 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034644875 486 RISEAHSELAKLLTEKElrDALLLIFANKQDVAGALSVEEITELLSLHKLCCGRSWYIQGC 546
Cdd:cd04162    82 RLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSVQEIHKELELEPIARGRRWILQGT 140
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
407-548 6.59e-35

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 129.09  E-value: 6.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLKQDEFM--QPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:cd04157     2 ILVLGLDNSGKTTIINQLKPSNAQsqNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDR 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875 485 DRISEAHSELAKLLTEKEL--RDALLLIFANKQDVAGALSVEEITELLSLhKLCCGRSWYIQGCDA 548
Cdd:cd04157    82 LRMVVAKDELELLLNHPDIkhRRIPILFYANKMDLPDALTAVKITQLLCL-ENIKDKPWHIFASSA 146
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
404-537 8.83e-28

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 108.94  E-value: 8.83e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVtlGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSS 482
Cdd:cd04159     1 EITLV--GLQNSGKTTLVNVIASGQFSEDtIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAA 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 483 HRDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKL-----CC 537
Cdd:cd04159    79 DREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSItdrevSC 138
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
407-535 9.85e-27

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 106.32  E-value: 9.85e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRDR 486
Cdd:cd04161     2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDR 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1034644875 487 ISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKL 535
Cdd:cd04161    82 VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKL 130
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
404-539 3.45e-26

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 105.40  E-value: 3.45e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  404 EIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSH 483
Cdd:smart00178  17 HAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYD 96
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875  484 RDRISEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEITELLSLHKLCCGR 539
Cdd:smart00178  97 KERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGK 152
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
226-370 3.57e-26

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 103.50  E-value: 3.57e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  226 IRASILDMAHCIRTFTEEISDYSRKLVGIVQHIEGgeqivedgigmahtehvpgTAENARSCIRAYFYDLHETLCRQEEM 305
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEE-------------------NAADVEAQIKAAFDELRNALNKRKKQ 61
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034644875  306 ALSVVDAHVREKLIWLRQQQEDMTILLSEVSAACLHCEKTLQQDDC-RVVLAKQEITRLLETLQKQ 370
Cdd:smart00502  62 LLEDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTEEALNSGDPtELLLSKKLIIERLQNLLKQ 127
mRING-HC-C3HC3D_TRIM23_C-IX cd16645
Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein ...
28-77 7.35e-26

Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 438307 [Multi-domain]  Cd Length: 50  Bit Score: 99.83  E-value: 7.35e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875  28 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAIRCPFDRQ 77
Cdd:cd16645     1 VLECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRLPLHGRAVRCPFDRQ 50
Bbox2_TRIM23_C-IX_rpt1 cd19773
first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
123-172 1.18e-24

first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 380831  Cd Length: 50  Bit Score: 96.64  E-value: 1.18e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 123 SIIRCDEDEAHLASVYCTVCATHLCSECSQVTHSTKTLAKHRRVPLADKP 172
Cdd:cd19773     1 PSIPCDENEDHEATLYCTVCSTNLCEECFTSTHSTKTLSKHRRVPLSEKP 50
Bbox2_TRIM23_C-IX_rpt2 cd19774
second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
174-223 4.76e-21

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 380832  Cd Length: 50  Bit Score: 86.31  E-value: 4.76e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 174 EKTMCSQHQVHAIEFVCLEEGCQTSPLMCCVCKEYGKHQGHKHSVLEPEA 223
Cdd:cd19774     1 EKPKCPIHPDHLIEFVCLEEDCQESPLMCIICKEYGKHQGHKHELLEEEA 50
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
407-535 5.19e-17

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 79.67  E-value: 5.19e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 407 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETV---EYKNLKFTIWDVGGKHKLRP-LWKHYYLNTQAVVFVVDSS 482
Cdd:cd04105     3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFysnSSKGKKLTLVDVPGHEKLRDkLLEYLKASLKAIVFVVDSA 82
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034644875 483 HRDR-ISEAHSELAKLLTEKELRDAL--LLIFANKQDVAGALSVEEITELL--SLHKL 535
Cdd:cd04105    83 TFQKnIRDVAEFLYDILTDLEKIKNKipILIACNKQDLFTAKPAKKIKELLekEINTL 140
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
404-532 2.57e-12

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 65.39  E-value: 2.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFMQP--IPTIGFNVETVEYK----NLKFTIWDVGG---KHKLRPLWKHYYLNTQA 474
Cdd:COG1100     3 EKKIVVVGTGGVGKTSLVNRLVGDIFSLEkyLSTNGVTIDKKELKldglDVDLVIWDTPGqdeFRETRQFYARQLTGASL 82
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 475 VVFVVDSSHRD-RISEAhsELAKLLTEKELRDALLLIFaNKQDVAGALSVEEITELLSL 532
Cdd:COG1100    83 YLFVVDGTREEtLQSLY--ELLESLRRLGKKSPIILVL-NKIDLYDEEEIEDEERLKEA 138
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
405-516 2.92e-12

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 65.02  E-value: 2.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVE--TVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd01863     1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLsSTIGvdFKVKtvTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVY 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1034644875 480 DSSHRDRISEAHSELAKLLTEKELRDALLLIFANKQD 516
Cdd:cd01863    81 DVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKID 117
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
404-535 1.18e-11

Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206653 [Multi-domain]  Cd Length: 163  Bit Score: 62.95  E-value: 1.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFV 478
Cdd:cd01860     1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQeSTIGaaFLTQTVNLddTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVV 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034644875 479 VDSSHRDRISEAHSELakllteKELR-----DALLLIFANKQDVAG--ALSVEEITELLSLHKL 535
Cdd:cd01860    81 YDITSEESFEKAKSWV------KELQehgppNIVIALAGNKADLESkrQVSTEEAQEYADENGL 138
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
404-516 2.03e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 62.39  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEFM--QPIPTIGFNVET--VEYKNL--KFTIWDVGGKHKLRPLWKHYYLNTQAVVF 477
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSitEYYPGTTRNYVTtvIEEDGKtyKFNLLDTAGQEDYDAIRRLYYPQVERSLR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1034644875 478 VVD-SSHRDRISEahselAKLLTEKELRDAL-----LLIFANKQD 516
Cdd:TIGR00231  81 VFDiVILVLDVEE-----ILEKQTKEIIHHAdsgvpIILVGNKID 120
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
408-535 3.15e-11

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 61.70  E-value: 3.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 408 VTLGLDGAGKTTILFKLKQDEFMQ----PIPTIGFNVETVEY--KNLKFTIWDVGGKHKLRPLW-----KHYYLNTQAVV 476
Cdd:cd00882     1 VVVGRGGVGKSSLLNALLGGEVGEvsdvPGTTRDPDVYVKELdkGKVKLVLVDTPGLDEFGGLGreelaRLLLRGADLIL 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034644875 477 FVVDSSHRDRISEAHSELAKLLtekELRDALLLIFANKQDVAGALSVEEITELLSLHKL 535
Cdd:cd00882    81 LVVDSTDRESEEDAKLLILRRL---RKEGIPIILVGNKIDLLEEREVEELLRLEELAKI 136
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
406-516 8.68e-11

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 59.06  E-value: 8.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGFNVETVEY-------KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVF 477
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTFdPKYKSTIGVDFKTKTVlenddngKKIKLNIWDTAGQERFRSLHPFYYRGAAAALL 80
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1034644875 478 VVDSSHRDRISEAHSELaklltEKELRDALLLIFANKQD 516
Cdd:pfam08477  81 VYDSRTFSNLKYWLREL-----KKYAGNSPVILVGNKID 114
PLN03118 PLN03118
Rab family protein; Provisional
403-516 1.28e-10

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 61.22  E-value: 1.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 403 MEIRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVE----TVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFV 478
Cdd:PLN03118   13 LSFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKikqlTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILV 92
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1034644875 479 VDSSHRDRISEAHSELAKlltEKEL----RDALLLIFANKQD 516
Cdd:PLN03118   93 YDVTRRETFTNLSDVWGK---EVELystnQDCVKMLVGNKVD 131
RING-HC_TRIM32_C-VII cd16587
RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...
29-78 1.83e-10

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.


Pssm-ID: 438249 [Multi-domain]  Cd Length: 51  Bit Score: 56.26  E-value: 1.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1034644875  29 LECGVCEDVFSlQGDKVPRLLLCGHTVCHDCLTRLP--LHGRAIRCPFDRQV 78
Cdd:cd16587     1 LECPICLESFD-EGQLRPKLLHCGHTICEQCLEKLLasLSINGVRCPFCRKV 51
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
405-485 2.85e-10

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 59.01  E-value: 2.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd00154     1 FKIVLIGDSGVGKTSLLLRFVDNKFsENYKSTIGvdFKSKTIEVdgKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVY 80

                  ....*.
gi 1034644875 480 DSSHRD 485
Cdd:cd00154    81 DVTNRE 86
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
405-485 2.95e-09

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 56.36  E-value: 2.95e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  405 IRVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEQyKSTIGvdFKTKTIEVdgKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVY 80

                   ....*.
gi 1034644875  480 DSSHRD 485
Cdd:smart00175  81 DITNRE 86
mRING-HC-C3HC3D_arc-1-like cd23124
Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative ...
29-79 3.81e-09

Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative GTP-binding protein trim-23 homolog (arc-1) and similar proteins; arc-1, also called RING-type E3 ubiquitin transferase arc-1, is an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. arc-1 contains a modified C3HC3D-type RING-HC finger.


Pssm-ID: 438486 [Multi-domain]  Cd Length: 55  Bit Score: 52.89  E-value: 3.81e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1034644875  29 LECGVCEDVFSLQGD-KVPRLLL-CGHTVCHDCL-TRLPLHGRAIRCPFDRQVT 79
Cdd:cd23124     2 LECGICQQEYSADDPlLIPRILTeCGHTICTNCAgTILGQSSGSIFCPFDRIVT 55
RING-HC_malin cd16516
RING finger, HC subclass, found in malin and similar proteins; Malin ("mal" for seizure in ...
29-79 3.55e-08

RING finger, HC subclass, found in malin and similar proteins; Malin ("mal" for seizure in French), also known as NHL repeat-containing protein 1 (NHLRC1), or EPM2B, is a nuclear E3 ubiquitin-protein ligase that ubiquitinates and promotes the degradation of laforin (EPM2A encoding protein phosphatase). Malin and laforin operate as a functional complex that play key roles in regulating cellular functions such as glycogen metabolism, unfolded cellular stress response, and proteolytic processes. They act as pro-survival factors that negatively regulate the Hipk2-p53 cell death pathway. They also negatively regulate cellular glucose uptake by preventing plasma membrane targeting of glucose transporters. Moreover, they degrade polyglucosan bodies in concert with glycogen debranching enzyme and brain isoform glycogen phosphorylase. Furthermore, they, together with Hsp70, form a new functional complex that suppress the cellular toxicity of misfolded proteins by promoting their degradation through the ubiquitin-proteasome system. Defects in either malin or laforin may cause Lafora disease (LD), a fatal form of teenage-onset autosomal recessive progressive myoclonus epilepsy. In addition, malin may have function, independent of laforin, in lysosomal biogenesis and/or lysosomal glycogen disposal. Malin contains six NHL-repeat protein-protein interaction domains and a C3HC4-type RING-HC finger.


Pssm-ID: 438179 [Multi-domain]  Cd Length: 52  Bit Score: 49.81  E-value: 3.55e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1034644875  29 LECGVCEDVFSLQGDKVPRLLLCGHTVCHDCLTRL--PLHgRAIRCPFDRQVT 79
Cdd:cd16516     1 LECKVCFEKYSHQQEHRPRNLPCGHVLCRECVTALahPRR-SKLECPFCRKAC 52
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
406-481 4.27e-08

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 52.90  E-value: 4.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQA--VVFV 478
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFpEEYIPTIGvdFYTKTIEVdgKTVKLQIWDTAGQERFRALRPLYYRGADGflLVYD 80

                  ...
gi 1034644875 479 VDS 481
Cdd:pfam00071  81 ITS 83
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
406-484 1.10e-07

Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206698 [Multi-domain]  Cd Length: 164  Bit Score: 51.90  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEYKNLK--FTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd04117     2 RLLLIGDSGVGKTCLLCRFTDNEFHSShISTIGvdFKMKTIEVDGIKvrIQIWDTAGQERYQTITKQYYRRAQGIFLVYD 81

                  ....*
gi 1034644875 481 -SSHR 484
Cdd:cd04117    82 iSSER 86
PLN03110 PLN03110
Rab GTPase; Provisional
406-525 1.37e-07

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 52.24  E-value: 1.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGFNVET----VEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:PLN03110   14 KIVLIGDSGVGKSNILSRFTRNEFcLESKSTIGVEFATrtlqVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYD 93
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 481 SSHRDRISEAHSELakllteKELRD-----ALLLIFANKQDVAGALSVEE 525
Cdd:PLN03110   94 ITKRQTFDNVQRWL------RELRDhadsnIVIMMAGNKSDLNHLRSVAE 137
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
405-535 1.61e-07

Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 51.11  E-value: 1.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd01867     4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSfISTIGidFKIRTIELdgKKIKLQIWDTAGQERFRTITTSYYRGAMGIILVY 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034644875 480 DSSHR---DRISEAHSELAKLLTEkelrDALLLIFANKQDVAG--ALSVEEITELLSLHKL 535
Cdd:cd01867    84 DITDEksfENIKNWMRNIDEHASE----DVERMLVGNKCDMEEkrVVSKEEGEALAREYGI 140
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
405-516 1.76e-07

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 51.94  E-value: 1.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPIPT---IGFNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd04120     1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKStvgVDFKIKTVELrgKKIRLQIWDTAGQERFNSITSAYYRSAKGIILVY 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1034644875 480 DSSHRDRISEAhSELAKLLTEKELRDALLLIFANKQD 516
Cdd:cd04120    81 DITKKETFDDL-PKWMKMIDKYASEDAELLLVGNKLD 116
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
406-530 2.32e-07

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 51.29  E-value: 2.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF----MQPIPTIGFNVETVeyKNLKFTIWDVGGKHKLRPLWKHYYL---NTQAVVFV 478
Cdd:pfam09439   5 AVIIAGLCDSGKTSLFTLLTTDSVrptvTSQEPSAAYRYMLN--KGNSFTLIDFPGHVKLRYKLLETLKdssSLKGIVFV 82
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875 479 VDSS-HRDRISEAHSELAKLLTEKEL-RDAL-LLIFANKQDVAGALSVEEITELL 530
Cdd:pfam09439  83 VDSTiFPKEVTDTAEFLYDILSITELlKNGIdILIACNKQESFTARPPKKIKQAL 137
RING-HC_RNF183-like cd16556
RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar ...
29-82 2.39e-07

RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar proteins; RNF183 is an E3 ubiquitin-protein ligase that is upregulated during intestinal inflammation and is negatively regulated by miR-7. It promotes intestinal inflammation by increasing the ubiquitination and degradation of inhibitor of kappa B, thereby resulting in secondary activation of the Nuclear factor-kappaB (NF-kB) pathway. The interaction between RNF183-mediated ubiquitination and miRNA may be an important novel epigenetic mechanism in the pathogenesis of inflammatory bowel disease (IBD). The biological function of RNF223 and RNF225 remains unclear. Members of this family contain an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438218 [Multi-domain]  Cd Length: 57  Bit Score: 47.75  E-value: 2.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034644875  29 LECGVC----EDVFslqgdKVPRLLLCGHTVCHDCLTRL----PLHGRAIRCPFDRQVTDLG 82
Cdd:cd16556     1 LECSICfssyDNTF-----KTPKLLDCGHTFCLECLARLslasPPQAERVPCPLCRQPTVLP 57
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
433-517 3.13e-07

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 52.21  E-value: 3.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 433 IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD----------RISEAHSELAKLLTEKE 502
Cdd:pfam00503 152 VKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDqvlyeddstnRMEESLKLFEEICNSPW 231
                          90
                  ....*....|....*
gi 1034644875 503 LRDALLLIFANKQDV 517
Cdd:pfam00503 232 FKNTPIILFLNKKDL 246
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
406-519 4.03e-07

Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206695 [Multi-domain]  Cd Length: 191  Bit Score: 50.63  E-value: 4.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFM--QPIPTIGFN----VETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd04112     2 KVMLVGDSGVGKTCLLVRFKDGAFLagSFIATVGIQftnkVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLY 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1034644875 480 DSSHRDRISEAHSELAKLLTEKElRDALLLIFANKQDVAG 519
Cdd:cd04112    82 DVTNKSSFDNIRAWLTEILEYAQ-SDVVIMLLGNKADMSG 120
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
405-484 9.17e-07

Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus.


Pssm-ID: 206643 [Multi-domain]  Cd Length: 166  Bit Score: 49.22  E-value: 9.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGFNVETVEYKN----LKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd00877     1 FKLVLVGDGGTGKTTFVKRHLTGEFeKKYVATLGVEVHPLDFHTnrgkIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMF 80

                  ....*
gi 1034644875 480 DSSHR 484
Cdd:cd00877    81 DVTSR 85
Srp102 COG2229
Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, ...
398-555 1.07e-06

Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441830 [Multi-domain]  Cd Length: 189  Bit Score: 49.44  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 398 HIGPKMEIRVVTLGLDGAGKTTILFKLKQDEfmqPIPTIGFNVE-TVEYKN-----LKFTIWDVGGKHKLR----P---- 463
Cdd:COG2229     6 VAAREITVKIVYAGPFGAGKTTFVRSISEIE---PLSTEGRLTDaSLETKTtttvaFDFGRLTLGDGLRLHlfgtPgqvr 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 464 ---LWKHYYLNTQAVVFVVDSSHRDRISEAHSeLAKLltEKELRDALLLIFANKQDVAGALSVEEITELLSLhklccGRS 540
Cdd:COG2229    83 fdfMWDILLRGADGVVFLADSRRLEDSFNAES-LDFF--EERLEKLPFVVAVNKRDLPDALSLEELREALDL-----GPD 154
                         170
                  ....*....|....*...
gi 1034644875 541 WYIQGCDAR---SVFQII 555
Cdd:COG2229   155 VPVVEADARdgeSVKETL 172
Rab20 cd04126
Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be ...
405-519 1.32e-06

Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133326 [Multi-domain]  Cd Length: 220  Bit Score: 49.52  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:cd04126     1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQWGPYNISIWDTAGREQFHGLGSMYCRGAAAVILTYDVSNV 80
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1034644875 485 DRISEAHSELAKlLTEKELRDALLLIFANKQDVAG 519
Cdd:cd04126    81 QSLEELEDRFLG-LTDTANEDCLFAVVGNKLDLTE 114
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
406-518 1.53e-06

Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 48.39  E-value: 1.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd01861     2 KLVFLGDQSVGKTSIITRFMYDTFdNQYQATIGidFLSKTMYVddKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYD 81
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1034644875 481 sshrdrISEAHS-----ELAKLLTEKELRDALLLIFANKQDVA 518
Cdd:cd01861    82 ------ITNRQSfdntdKWIDDVRDERGNDVIIVLVGNKTDLS 118
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
406-480 2.11e-06

Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133315 [Multi-domain]  Cd Length: 170  Bit Score: 48.20  E-value: 2.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFM-QPIPTIG--FNVETVEY--KNLKFTIWDVGGKHKLR-PLWKHYYLNTQAVVFVV 479
Cdd:cd04115     4 KIIVIGDSNVGKTCLTYRFCAGRFPeRTEATIGvdFRERTVEIdgERIKVQLWDTAGQERFRkSMVQHYYRNVHAVVFVY 83

                  .
gi 1034644875 480 D 480
Cdd:cd04115    84 D 84
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
406-485 2.92e-06

Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 47.71  E-value: 2.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd01869     4 KLLLIGDSGVGKSCLLLRFADDTYTESyISTIGvdFKIRTIELdgKTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYD 83

                  ....*
gi 1034644875 481 SSHRD 485
Cdd:cd01869    84 VTDQE 88
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
406-523 3.45e-06

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 47.52  E-value: 3.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPIP-TIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd04122     4 KYIIIGDMGVGKSCLLHQFTEKKFMADCPhTIGveFGTRIIEVngQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYD 83
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1034644875 481 SSHRDRISEAHSEL--AKLLTEKelrDALLLIFANKQDVAGALSV 523
Cdd:cd04122    84 ITRRSTYNHLSSWLtdARNLTNP---NTVIFLIGNKADLEAQRDV 125
PLN03108 PLN03108
Rab family protein; Provisional
406-535 3.82e-06

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 48.01  E-value: 3.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFmQPIPTIGFNVE------TVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:PLN03108    8 KYIIIGDTGVGKSCLLLQFTDKRF-QPVHDLTIGVEfgarmiTIDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVY 86
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034644875 480 DSSHRDRISEAHSELAKLLTEKELRDALLLIfANKQDVAG--ALSVEEITELLSLHKL 535
Cdd:PLN03108   87 DITRRETFNHLASWLEDARQHANANMTIMLI-GNKCDLAHrrAVSTEEGEQFAKEHGL 143
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
406-482 5.02e-06

Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133314 [Multi-domain]  Cd Length: 169  Bit Score: 46.81  E-value: 5.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFmqpiP-----TIG--FNVETVEYKN--LKFTIWDVGGKHKLRPLWKHYYLNTQAVV 476
Cdd:cd04114     9 KIVLIGNAGVGKTCLVRRFTQGLF----PpgqgaTIGvdFMIKTVEIKGekIKLQIWDTAGQERFRSITQSYYRSANALI 84

                  ....*.
gi 1034644875 477 FVVDSS 482
Cdd:cd04114    85 LTYDIT 90
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
406-480 5.57e-06

Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 47.54  E-value: 5.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd04110     8 KLLIIGDSGVGKSSLLLRFADNTFSGSyITTIGvdFKIRTVEIngERVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYD 87
RING-HC_RNF224 cd16565
RING finger, HC subclass, found in RING finger protein RNF224 and similar proteins; RNF224 is ...
29-79 2.75e-05

RING finger, HC subclass, found in RING finger protein RNF224 and similar proteins; RNF224 is uncharacterized C3HC4-type RING-HC finger-containing proteins. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438227 [Multi-domain]  Cd Length: 59  Bit Score: 42.12  E-value: 2.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1034644875  29 LECGVCEDVFSLqGDKVPRLLLCGHTVCHDCLTRLPL---HGRAIRCPFDRQVT 79
Cdd:cd16565     1 LDCIICYSAYDL-STRLPRRLYCGHTFCQACLKRLDTvinEQRWIPCPQCRQNT 53
RING-HC_RNF152 cd16548
RING finger, HC subclass, found in RING finger protein 152 (RNF152) and similar proteins; ...
29-76 2.99e-05

RING finger, HC subclass, found in RING finger protein 152 (RNF152) and similar proteins; RNF152 is a lysosome-anchored E3 ubiquitin-protein ligase involved in apoptosis. It is polyubiquitinated through K48 linkage. It negatively regulates the activation of the mTORC1 pathway by targeting RagA GTPase for K63-linked ubiquitination. It interacts with and ubiquitinates RagA in an amino-acid-sensitive manner. The ubiquitination of RagA recruits its inhibitor GATOR1, a GAP complex for Rag GTPases, to the Rag complex, thereby inactivating mTORC1 signaling. RNF152 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal transmembrane domain, both of which are responsible for its E3 ligase activity.


Pssm-ID: 438210 [Multi-domain]  Cd Length: 46  Bit Score: 41.52  E-value: 2.99e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1034644875  29 LECGVCEDVFSLQgdKVPRLLLCGHTVCHDCLTRLPLHGRAIRCPFDR 76
Cdd:cd16548     1 LECQICFNYYSPR--RRPKLLDCKHTCCSVCLQQMRTSQKDLRCPWCR 46
mRING-HC-C3HC3D_Roquin cd16638
Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar ...
29-75 3.73e-05

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins; The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition.


Pssm-ID: 438300 [Multi-domain]  Cd Length: 44  Bit Score: 41.18  E-value: 3.73e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1034644875  29 LECGVCEDVFSlQGDKVPRLLLCGHTVCHDCLTRlpLHGRAirCPFD 75
Cdd:cd16638     2 LSCPVCTNEFD-GTQRKPISLGCGHTVCKTCLSK--LHRKQ--CPFD 43
Bbox2 cd19756
B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of ...
177-219 4.41e-05

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2).


Pssm-ID: 380814 [Multi-domain]  Cd Length: 39  Bit Score: 40.86  E-value: 4.41e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1034644875 177 MCSQHQVHAIEFVCLEEGCqtspLMCCVCKEYGKHQGHKHSVL 219
Cdd:cd19756     1 LCPEHPEEPLKLFCETCQE----LVCVLCLLSGEHRGHKVVPL 39
PLN03071 PLN03071
GTP-binding nuclear protein Ran; Provisional
405-484 4.77e-05

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 178620 [Multi-domain]  Cd Length: 219  Bit Score: 44.74  E-value: 4.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQ-PIPTIGFNVETVEYKN----LKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:PLN03071   14 FKLVIVGDGGTGKTTFVKRHLTGEFEKkYEPTIGVEVHPLDFFTncgkIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMF 93

                  ....*
gi 1034644875 480 DSSHR 484
Cdd:PLN03071   94 DVTAR 98
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
30-82 4.94e-05

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 40.85  E-value: 4.94e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1034644875  30 ECGVCEDVFslqgDKVPRLLLCGHTVCHDCLTRLpLHGRAIRCPFDRQVTDLG 82
Cdd:cd16564     2 ECPVCYEDF----DDAPRILSCGHSFCEDCLVKQ-LVSMTISCPICRRVTFIS 49
RING-HC_RNF182 cd16555
RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; ...
29-79 5.34e-05

RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; RNF182 is a brain-enriched E3 ubiquitin-protein ligase that stimulates E2-dependent polyubiquitination in vitro. It is upregulated in Alzheimer"s disease (AD) brains and neuronal cells exposed to injurious insults. It interacts with ATP6V0C and promotes its degradation by the ubiquitin-proteosome pathway, suggesting a very specific role in controlling the turnover of an essential component of the neurotransmitter release machinery. RNF182 contains an N-terminal C3HC4-type RING-HC finger, and a C-terminal transmembrane domain.


Pssm-ID: 438217 [Multi-domain]  Cd Length: 55  Bit Score: 40.88  E-value: 5.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875  29 LECGVCEDVFSLQGDKvPRLLLCGHTVCHDCLTRLPLHG----RAIRCPFDRQVT 79
Cdd:cd16555     2 LECKICYNRYDLRQRR-PKVLECCHRVCAKCLYKIVDLGdsspSVLVCPFCRFET 55
Rab23_like cd04106
Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family ...
405-559 6.27e-05

Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133306 [Multi-domain]  Cd Length: 162  Bit Score: 43.58  E-value: 6.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFM-QPIPTIGfnVETVEYK--------NLKFTIWDVGGKHKLRPLWKHYYLNTQAV 475
Cdd:cd04106     1 IKVIVVGNGNVGKSSMIQRFVKGIFTkDYKKTIG--VDFLEKQiflrqsdeDVRLMLWDTAGQEEFDAITKAYYRGAQAC 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 476 VFVVdsSHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVA--GALSVEEITELLSLHKLCCGRSWYIQGCDARSVFQ 553
Cdd:cd04106    79 ILVF--STTDRESFEAIESWKEKVEAECGDIPMVLVQTKIDLLdqAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFE 156

                  ....*.
gi 1034644875 554 IICDQY 559
Cdd:cd04106   157 YLAEKC 162
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
406-493 6.59e-05

Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 44.37  E-value: 6.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQ-PIPTIGFN-----VETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd04111     4 RLIVIGDSTVGKSSLLKRFTEGRFAEvSDPTVGVDffsrlIEIEPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVF 83
                          90
                  ....*....|....*..
gi 1034644875 480 DSSHR---DRISEAHSE 493
Cdd:cd04111    84 DITNResfEHVHDWLEE 100
Rab4 cd04113
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ...
410-485 6.69e-05

Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206696 [Multi-domain]  Cd Length: 161  Bit Score: 43.58  E-value: 6.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 410 LGLDGAGKTTILFKLKQDEFMQPIP-TIGFN----VETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:cd04113     6 IGSAGTGKSCLLHQFIENKFKQDSNhTIGVEfgsrVVNVGGKSVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSR 85

                  .
gi 1034644875 485 D 485
Cdd:cd04113    86 E 86
BBOX smart00336
B-Box-type zinc finger;
173-219 8.69e-05

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 40.01  E-value: 8.69e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034644875  173 HEKTMCSQHQVHAIEFVCLEegCQTspLMCCVCKEYgKHQGHKHSVL 219
Cdd:smart00336   1 QRAPKCDSHGDEPAEFFCEE--CGA--LLCRTCDEA-EHRGHTVVLL 42
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
406-517 8.70e-05

Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 43.36  E-value: 8.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETV--EYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd01865     3 KLLIIGNSSVGKTSFLFRYADDSFTSAfVSTVGidFKVKTVyrNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYD 82
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1034644875 481 SSHRDRISEAHSELAKLLTeKELRDALLLIFANKQDV 517
Cdd:cd01865    83 ITNEESFNAVQDWSTQIKT-YSWDNAQVILVGNKCDM 118
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
410-497 1.15e-04

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 43.46  E-value: 1.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  410 LGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKN----LKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHR 484
Cdd:smart00176   1 VGDGGTGKTTFVKRHLTGEFEKKyVATLGVEVHPLVFHTnrgpIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTAR 80
                           90
                   ....*....|....*.
gi 1034644875  485 ---DRISEAHSELAKL 497
Cdd:smart00176  81 vtyKNVPNWHRDLVRV 96
RING-HC_KEG-like cd23140
RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and ...
28-83 1.25e-04

RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and similar proteins; KEG, also called RING-type E3 ubiquitin transferase KEG, is a RING E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It is essential for Arabidopsis growth and development. It acts as a negative regulator of abscisic acid signaling. It is required for ABSCISIC ACID-INSENSITIVE5 (ABI5) degradation, by mediating its ubiquitination. Together with EDR1, KEG may regulate endocytic trafficking and/or the formation of signaling complexes on trans-Golgi network (TGN)/ early endosome (EE) vesicles during stress responses. KEG is a multidomain protein that includes a C3HC4-type RING-HC finger, a kinase domain, ankyrin repeats, and 12 HERC2-like (for HECT and RCC1-like) repeats.


Pssm-ID: 438502 [Multi-domain]  Cd Length: 57  Bit Score: 39.93  E-value: 1.25e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034644875  28 VLECGVCEDVFSLQGdKVPRLLLCGHTVCHDCLTRLPLHGRA--IRCPFDRQVTDLGD 83
Cdd:cd23140     1 VPECSVCSEGYNEDE-RVPLLLQCGHTFCKDCLSQMFIRCTDltLKCPRCRQSVLVGN 57
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
408-517 1.62e-04

Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206658 [Multi-domain]  Cd Length: 168  Bit Score: 42.41  E-value: 1.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 408 VTLGLDGAGKTTILFKLkQDEFMQPIPTIGFNVE------TVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDS 481
Cdd:cd01866     8 IIIGDTGVGKSCLLLQF-TDKRFQPVHDLTIGVEfgarmiTIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDI 86
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1034644875 482 SHRDRISEAHSELAKLLTEKELRDALLLIfANKQDV 517
Cdd:cd01866    87 TRRETFNHLTSWLEDARQHSNSNMTIMLI-GNKCDL 121
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
405-525 1.75e-04

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 42.34  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 405 IRVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETVEYKNL--KFTIWDVGGKHKLRPLWKHYYLNTQAVVFVV 479
Cdd:cd04119     1 IKVISMGNSGVGKSCIIKRYCEGRFVSKyLPTIGidYGVKKVSVRNKevRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVY 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034644875 480 DSSHRDRISEAHSELAKLLTE----KELRDALLLIFANKQDVAGALSVEE 525
Cdd:cd04119    81 DVTDRQSFEALDSWLKEMKQEggphGNMENIVVVVCANKIDLTKHRAVSE 130
Bbox1_RNF207-like cd19814
B-box-type 1 zinc finger found in RING finger protein 207 (RNF207) and similar proteins; ...
127-171 1.95e-04

B-box-type 1 zinc finger found in RING finger protein 207 (RNF207) and similar proteins; RNF207 is a cardiac-specific E3 ubiquitin-protein ligase that plays an important role in the regulation of cardiac repolarization. It regulates action potential duration, likely via effects on human ether-a-go-go-related gene (HERG) trafficking and localization, in a heat shock protein-dependent manner. RNF207 contains a RING finger, a B-box motif and Bbox C-terminal (BBC) domain, as well as a C-terminal non-homologous region (CNHR). The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380872  Cd Length: 49  Bit Score: 39.26  E-value: 1.95e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1034644875 127 CDEDEahLASVYCTVCATHLCSECSQVTHSTKTLAKHRRVPLADK 171
Cdd:cd19814     5 CDSEC--LAMFYCNTCGQPLCDDCREETHRAKMFSKHEVVSLSKR 47
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
29-75 1.99e-04

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 39.01  E-value: 1.99e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTRLpLHGRAIRCPFD 75
Cdd:cd16449     1 LECPICLERL-----KDPVLLPCGHVFCRECIRRL-LESGSIKCPIC 41
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
31-74 2.62e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 38.64  E-value: 2.62e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1034644875   31 CGVCEDVFSlqgdKVPRLLLCGHTVCHDCLTRLpLHGRAIRCPF 74
Cdd:smart00184   1 CPICLEEYL----KDPVILPCGHTFCRSCIRKW-LESGNNTCPI 39
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
127-168 2.96e-04

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).


Pssm-ID: 380815 [Multi-domain]  Cd Length: 44  Bit Score: 38.63  E-value: 2.96e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1034644875 127 CDEDEAHLASVYCTVCATHLCSECSQVTHS-TKTLAKHRRVPL 168
Cdd:cd19757     2 CDECEEREATVYCLECEEFLCDDCSDAIHRrGKLTRSHKLVPL 44
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
29-104 3.97e-04

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 43.07  E-value: 3.97e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTR-LPLHGRAIRCPFDRQVTDlgdsgvwgLKKNFALLELLERLQN 104
Cdd:TIGR00599  27 LRCHICKDFF-----DVPVLTSCSHTFCSLCIRRcLSNQPKCPLCRAEDQESK--------LRSNWLVSEIVESFKN 90
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
406-484 5.83e-04

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 40.88  E-value: 5.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVETVEY--KNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd01864     5 KIILIGDSNVGKTCVVQRFKSGTFSERQgNTIGvdFTMKTLEIqgKRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYD 84

                  ....
gi 1034644875 481 SSHR 484
Cdd:cd01864    85 ITRR 88
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
404-485 6.27e-04

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 41.60  E-value: 6.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGFNVETVE-YKN---LKFTIWDVGGKHKLRPLWKHYYLNTQAVVFV 478
Cdd:PTZ00132    9 EFKLILVGDGGVGKTTFVKRHLTGEFeKKYIPTLGVEVHPLKfYTNcgpICFNVWDTAGQEKFGGLRDGYYIKGQCAIIM 88

                  ....*..
gi 1034644875 479 VDSSHRD 485
Cdd:PTZ00132   89 FDVTSRI 95
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
406-518 6.70e-04

Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206693 [Multi-domain]  Cd Length: 170  Bit Score: 40.63  E-value: 6.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVETVEYKNLKFT--IWDVGGKHKLRPLWKHYYLNTQAVVFVVD 480
Cdd:cd04108     2 KVIVVGDLSVGKTCLINRFCKDVFDKNYkATIGvdFEMERFEVLGVPFSlqLWDTAGQERFKCIASTYYRGAQAIIIVFD 81
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1034644875 481 SSHRDRISEAHSELAKLLTEKELRDALLLIFANKQDVA 518
Cdd:cd04108    82 LTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLS 119
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
433-517 1.03e-03

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 41.41  E-value: 1.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875  433 IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVVDSSHRD----------RISEAHSELAKLLTEKE 502
Cdd:smart00275 169 VPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDqvleedestnRMQESLNLFESICNSRW 248
                           90
                   ....*....|....*
gi 1034644875  503 LRDALLLIFANKQDV 517
Cdd:smart00275 249 FANTSIILFLNKIDL 263
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
406-469 1.58e-03

Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206660 [Multi-domain]  Cd Length: 165  Bit Score: 39.47  E-value: 1.58e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034644875 406 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGfnVE------TVEYKNLKFTIWDVGGKHKLRPLWKHYY 469
Cdd:cd01868     5 KIVLIGDSGVGKSNLLSRFTRNEFnLDSKSTIG--VEfatrtiQIDGKTIKAQIWDTAGQERYRAITSAYY 73
RocCOR cd09914
Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ...
404-479 1.61e-03

Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease.


Pssm-ID: 206741 [Multi-domain]  Cd Length: 161  Bit Score: 39.63  E-value: 1.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034644875 404 EIRVVTLGLDGAGKTTILFKLKQDEF--MQPIpTIGFNVET-----VEYKNLKFTIWDVGGKHKLRPLWKHyYLNTQAVV 476
Cdd:cd09914     1 EAKLMLVGQGGVGKTSLCKQLIGEKFdgDESS-THGINVQDwkipaPERKKIRLNVWDFGGQEIYHATHQF-FLTSRSLY 78

                  ...
gi 1034644875 477 FVV 479
Cdd:cd09914    79 LLV 81
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
31-73 1.85e-03

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 36.22  E-value: 1.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1034644875  31 CGVCEDVFslqgdKVPRLLlCGHTVCHDCLTRL-PLHGRAIRCP 73
Cdd:pfam13445   1 CPICLELF-----TDPVLP-CGHTFCRECLEEMsQKKGGKFKCP 38
Bbox2_TRIM2_C-VII cd19824
B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar ...
125-170 2.03e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 Semi-independent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Aim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380882 [Multi-domain]  Cd Length: 42  Bit Score: 36.19  E-value: 2.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1034644875 125 IRCDEDEAHLASVYCTVCATHLCSECSQVTHstktlAKHRRVPLAD 170
Cdd:cd19824     2 LSCPNHDGNVMEFYCQSCETAMCQECTEGEH-----AEHPTVPLKD 42
Bbox1_BBX-like cd19821
B-box-type 1 zinc finger found in B-box (BBX) family of plant transcription factors and ...
127-168 2.14e-03

B-box-type 1 zinc finger found in B-box (BBX) family of plant transcription factors and similar proteins; The BBX family includes a group of zinc finger transcription factors that contain one or two B-box motifs, and sometimes also feature a CCT (CONSTANS, CO-like, and TOC1) domain. They play important roles in plant growth and development, including seedling photomorphogenesis, photoperiodic regulation of flowering, shade avoidance, and responses to biotic and abiotic stresses. Their B-box motifs show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs) and are involved in mediating transcriptional regulation and protein-protein interaction in plant signaling. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif; this family contains a modified motif, C3XC2H2, where X can be D, E, C or H.


Pssm-ID: 380879  Cd Length: 44  Bit Score: 36.12  E-value: 2.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1034644875 127 CDEDEAHLASVYCTVCATHLCSECSQVTHSTKTLA-KHRRVPL 168
Cdd:cd19821     2 CDSCESAPAVVYCRADRASLCRACDAKVHSANKLAsRHQRVPL 44
zf-B_box pfam00643
B-box zinc finger;
125-168 2.85e-03

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 35.91  E-value: 2.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1034644875 125 IRCDEDEAHLASVYCTVCATHLCSECSQVTHStktlaKHRRVPL 168
Cdd:pfam00643   4 RLCPEHEEEPLTLYCNDCQELLCEECSVGEHR-----GHTVVPL 42
mRING-HC-C3HC3D_Roquin1 cd16781
Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1; Roquin-1, also known as ...
29-76 2.95e-03

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1; Roquin-1, also known as RING finger and C3H zinc finger protein 1 (RC3H1), or RING finger protein 198 (RNF198), is a ubiquitously expressed RNA-binding protein essential for degradation of inflammation-related mRNAs and maintenance of immune homeostasis. It is localized in cytoplasmic granules and binds to the 3' untranslated region (3'UTR) of inducible costimulator (Icos) mRNA to post-transcriptionally repress its expression. Roquin-1 interacts with the 3'UTR of tumor necrosis factor receptor superfamily member 4 (TNFRSF4) and tumor-necrosis factor-alpha (TNFalpha), and post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway. Moreover, Roquin-1 shares functions with its paralog Roquin-2 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Roquin-1 contains an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 ubiquitin-ligase function, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger that is involved in RNA recognition, typically contacting AU-rich elements. In addition, both N- and C-terminal to the ROQ domain are combined to form a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain that is highly likely to function as an RNA-binding domain.


Pssm-ID: 438436 [Multi-domain]  Cd Length: 49  Bit Score: 36.14  E-value: 2.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1034644875  29 LECGVCEDVFSlQGDKVPRLLLCGHTVCHDCLTRlpLHGRAirCPFDR 76
Cdd:cd16781     7 LSCPICTQTFD-ETIRKPISLGCGHTVCKMCLNK--LHRKA--CPFDQ 49
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
29-78 4.76e-03

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 35.50  E-value: 4.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTRL-PLHGRAIRCPFDRQV 78
Cdd:cd16611     5 LHCPLCLDFF-----RDPVMLSCGHNFCQSCITGFwELQAEDTTCPECREL 50
Bbox1_TRIM9-like_C-I cd19803
B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM9, TRIM67 and ...
127-164 6.44e-03

B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM9, TRIM67 and similar proteins; This family includes a group of tripartite motif-containing proteins, including TRIM9 and TRIM67, both of which belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. It plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis.


Pssm-ID: 380861  Cd Length: 47  Bit Score: 34.97  E-value: 6.44e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1034644875 127 CDEDEAHLASVYCTVCATHLCSECSQVTH-STKTLAKHR 164
Cdd:cd19803     5 CEKSPPKEASVFCEQCEVFYCDSCRESCHpPRGPLAKHT 43
Bbox1_TRIM67_C-I cd19844
B-box-type 1 zinc finger found in tripartite motif-containing protein 67 (TRIM67) and similar ...
127-167 6.52e-03

B-box-type 1 zinc finger found in tripartite motif-containing protein 67 (TRIM67) and similar proteins; TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380902  Cd Length: 49  Bit Score: 35.02  E-value: 6.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1034644875 127 CDEDEAHLASVYCTVCATHLCSECSQVTHSTK-TLAKHRRVP 167
Cdd:cd19844     7 CDRNPPEPAAVLCEQCDVLYCSACQLKCHPTRgPFAKHRLVP 48
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
27-78 6.73e-03

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 34.84  E-value: 6.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1034644875  27 KVLECGVCedvfsLQGDKVPRLLLCGHTVCHDCLTRL---PLHGRAIRCPFDRQV 78
Cdd:cd16579     3 KFLRCPGC-----KAEYKCPKLLPCLHTVCSGCLEALaeqASETTEFQCPICKAS 52
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
29-77 6.87e-03

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 34.70  E-value: 6.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTRLPLH--GRAIRCPFDRQ 77
Cdd:cd16604     1 LSCPICLDLL-----KDPVTLPCGHSFCMGCLGALWGAgrGGRASCPLCRQ 46
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
29-77 7.21e-03

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 34.64  E-value: 7.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1034644875  29 LECGVCEDVFslqgdKVPRLLLCGHTVCHDCLTrlplHGRAIRCPFDRQ 77
Cdd:cd16644     6 LYCPLCQRVF-----KDPVITSCGHTFCRRCAL----TAPGEKCPVDNM 45
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
127-168 9.37e-03

B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, also termed protein associated with Myc (Pam), is an atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues. MYCBP2 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380857  Cd Length: 50  Bit Score: 34.68  E-value: 9.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1034644875 127 CD--EDEAHLASVYCTVCATHLCSECSQVTHSTKTLAKHRRVPL 168
Cdd:cd19799     3 CDnhDDGETAAIIFCCDCGNYLCAECDRFLHLHRKNRSHQRQVF 46
Bbox1_ZFYVE1_rpt2 cd19820
second B-box-type 1 zinc finger found in zinc finger FYVE domain-containing protein 1 (ZFYVE1) ...
118-163 9.88e-03

second B-box-type 1 zinc finger found in zinc finger FYVE domain-containing protein 1 (ZFYVE1) and similar proteins; ZFYVE1 also termed double FYVE-containing protein 1 (DFCP1), or SR3, or tandem FYVE fingers-1, is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYVE1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by Wortmannin, a PI3-kinase inhibitor. ZFYVE1 harbors two B-box motifs, both of which show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380878  Cd Length: 59  Bit Score: 34.93  E-value: 9.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1034644875 118 GISGESIIRCDEDEAHLASVYCTVCATHLCSECSQVTHSTKTLAKH 163
Cdd:cd19820     8 GGNGNSMHSSTAGSRQRAAVRCQSCKINLCPECQKRTHSGGNKRKH 53
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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