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Conserved domains on  [gi|148670202|gb|EDL02149|]
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HIV-1 Rev binding protein, partial [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ArfGap super family cl28907
GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs); ArfGAPs are a family ...
 3-82 3.74e-53

GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs); ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. Like all GTP-binding proteins, Arf proteins function as molecular switches, cycling between GTP (active-membrane bound) and GDP (inactive-cytosolic) form. Conversion to the GTP-bound form requires a guanine nucleotide exchange factor (GEF), whereas conversion to the GDP-bound form is catalyzed by a GTPase activating protein (GAP). In that sense, ArfGAPs were originally proposed to function as terminators of Arf signaling, which is mediated by regulating Arf family GTP-binding proteins. However, recent studies suggest that ArfGAPs can also function as Arf effectors, independently of their GAP enzymatic activity to transduce signals in cells. The ArfGAP domain contains a C4-type zinc finger motif and a conserved arginine that is required for activity, within a specific spacing (CX2CX16CX2CX4R). ArfGAPs, which have multiple functional domains, regulate the membrane trafficking and actin cytoskeleton remodeling via specific interactions with signaling lipids such as phosphoinositides and trafficking proteins, which consequently affect cellular events such as cell growth, migration, and cancer invasion. The ArfGAP family, which includes 31 human ArfGAP-domain containing proteins, is divided into 10 subfamilies based on domain structure and sequence similarity. The ArfGAP nomenclature is mainly based on the protein domain structure. For example, ASAP1 contains ArfGAP, SH3, ANK repeat and PH domains; ARAPs contain ArfGAP, Rho GAP, ANK repeat and PH domains; ACAPs contain ArfGAP, BAR (coiled coil), ANK repeat and PH domains; and AGAPs contain Arf GAP, GTP-binding protein-like, ANK repeat and PH domains. Furthermore, the ArfGAPs can be classified into two major types of subfamilies, according to the overall domain structure: the ArfGAP1 type includes 6 subfamilies (ArfGAP1, ArfGAP2/3, ADAP, SMAP, AGFG, and GIT), which contain the ArfGAP domain at the N-terminus of the protein; and the AZAP type includes 4 subfamilies (ASAP, ACAP, AGAP, and ARAP), which contain an ArfGAP domain between the PH and ANK repeat domains.


The actual alignment was detected with superfamily member cd08857:

Pssm-ID: 355783 [Multi-domain]  Cd Length: 116  Bit Score: 175.23  E-value: 3.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 82
Cdd:cd08857   37 CTSCSGILRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 116
COG5347 super family cl34987
GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ...
 18-222 2.67e-04

GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion];


The actual alignment was detected with superfamily member COG5347:

Pssm-ID: 227651 [Multi-domain]  Cd Length: 319  Bit Score: 43.23  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  18 RVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGlfDDRSSAIPDFR---DPQKVKEFLQEKYEKKRWYVPPEQAKVVASvh 94
Cdd:COG5347   59 KVKSLTLDNWTEEELRRMEVGGNSNANRFYEK--NLLDQLLLPIKakyDSSVAKKYIRKKYELKKFIDDSSSPSDFSS-- 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  95 asisgssaSSTSSTPEVKPLKSLL-GESAPALHLNKGTPSQSP--VVGRSQGQQQEKKQFDLLSDL---GSDIFAAPAPQ 168
Cdd:COG5347  135 --------FSASSTRTVDSVDDRLdSESQSRSSSASLGNSNRPddELNVESFQSTGSKPRSLTSTKsnkDNLLNSELLTL 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 148670202 169 STATANFAN--FAHFNSHAAQNSANADFANFDAFGQSSGSSNFGGFPTASHSSFQP 222
Cdd:COG5347  207 NSLLSSNSEvgSGTKSRSDAQEKSSTKATESVKPGPVNTSSTSSLPPAIKRSPVQQ 262
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 341-509 6.83e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 6.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  341 AATSSNAYTPTSNASSSVFGTVPVGASAQTQPASSGPAPFGATPSTNpfvAATGPSAASSTNPFQTNARGATAATFGTAS 420
Cdd:PHA03247 2674 AQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATP---LPPGPAAARQASPALPAAPAPPAVPAGPAT 2750

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  421 MSMPAGFGTPAQYSLPTSFSGsfqqPAFPAQAAFPQQTAFSQQPNGFATFGQTKPVVTPFGQVAAAGVSSNPFMTGAPTG 500
Cdd:PHA03247 2751 PGGPARPARPPTTAGPPAPAP----PAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAG 2826


                  ....*....
gi 148670202  501 QLPTGSSST 509
Cdd:PHA03247 2827 PLPPPTSAQ 2835
 
Name Accession Description Interval E-value
ArfGap_AGFG1 cd08857
ArfGAP domain of AGFG1 (ArfGAP domain and FG repeat-containing protein 1); The ArfGAP domain ...
 3-82 3.74e-53

ArfGAP domain of AGFG1 (ArfGAP domain and FG repeat-containing protein 1); The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG1 (alias: HIV-1 Rev binding protein, HRB; Rev interacting protein, RIP; Rev/Rex activating domain-binding protein, RAB) and AGFG2 are involved in the maintenance and spread of immunodeficiency virus type 1 (HIV-1) infection. The ArfGAP domain of AGFG1 is related to nucleoporins, which is a class of proteins that mediate nucleocytoplasmic transport. AGFG1 plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs, possibly together by the nuclear export receptor CRM1. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG1 promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication.


Pssm-ID: 350082 [Multi-domain]  Cd Length: 116  Bit Score: 175.23  E-value: 3.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 82
Cdd:cd08857   37 CTSCSGILRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 116
ArfGap smart00105
Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with ...
 3-89 1.22e-23

Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.


Pssm-ID: 214518 [Multi-domain]  Cd Length: 119  Bit Score: 95.87  E-value: 1.22e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202     3 CRTTASVSRGLNPpHR--VKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRW 80
Cdd:smart00105  33 CIECSGIHRSLGV-HIskVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSLKPPDDDDQQKYESFIAAKYEEKLF 111


                   ....*....
gi 148670202    81 yVPPEQAKV 89
Cdd:smart00105 112 -VPPESAEE 119
ArfGap pfam01412
Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating ...
 7-84 2.05e-18

Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.


Pssm-ID: 460200 [Multi-domain]  Cd Length: 117  Bit Score: 81.12  E-value: 2.05e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148670202    7 ASVSRGL-NPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDrSSAIPDFRDPQKVKEFLQEKYEKKRWYVPP 84
Cdd:pfam01412  40 SGVHRSLgVHISKVRSLTLDTWTDEQLELMKAGGNDRANEFWEANLPP-SYKPPPSSDREKRESFIRAKYVEKKFAKPG 117
PLN03131 PLN03131
hypothetical protein; Provisional
 3-80 3.28e-09

hypothetical protein; Provisional


Pssm-ID: 178677 [Multi-domain]  Cd Length: 705  Bit Score: 59.41  E-value: 3.28e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148670202   3 CRTTASVSRGLNppHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRW 80
Cdd:PLN03131  46 CMTCSGIHREFT--HRVKSVSMSKFTSQDVEALQNGGNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKY 121
COG5347 COG5347
GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ...
 18-222 2.67e-04

GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion];


Pssm-ID: 227651 [Multi-domain]  Cd Length: 319  Bit Score: 43.23  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  18 RVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGlfDDRSSAIPDFR---DPQKVKEFLQEKYEKKRWYVPPEQAKVVASvh 94
Cdd:COG5347   59 KVKSLTLDNWTEEELRRMEVGGNSNANRFYEK--NLLDQLLLPIKakyDSSVAKKYIRKKYELKKFIDDSSSPSDFSS-- 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  95 asisgssaSSTSSTPEVKPLKSLL-GESAPALHLNKGTPSQSP--VVGRSQGQQQEKKQFDLLSDL---GSDIFAAPAPQ 168
Cdd:COG5347  135 --------FSASSTRTVDSVDDRLdSESQSRSSSASLGNSNRPddELNVESFQSTGSKPRSLTSTKsnkDNLLNSELLTL 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 148670202 169 STATANFAN--FAHFNSHAAQNSANADFANFDAFGQSSGSSNFGGFPTASHSSFQP 222
Cdd:COG5347  207 NSLLSSNSEvgSGTKSRSDAQEKSSTKATESVKPGPVNTSSTSSLPPAIKRSPVQQ 262
PHA03247 PHA03247
large tegument protein UL36; Provisional
 341-509 6.83e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 6.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  341 AATSSNAYTPTSNASSSVFGTVPVGASAQTQPASSGPAPFGATPSTNpfvAATGPSAASSTNPFQTNARGATAATFGTAS 420
Cdd:PHA03247 2674 AQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATP---LPPGPAAARQASPALPAAPAPPAVPAGPAT 2750

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  421 MSMPAGFGTPAQYSLPTSFSGsfqqPAFPAQAAFPQQTAFSQQPNGFATFGQTKPVVTPFGQVAAAGVSSNPFMTGAPTG 500
Cdd:PHA03247 2751 PGGPARPARPPTTAGPPAPAP----PAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAG 2826


                  ....*....
gi 148670202  501 QLPTGSSST 509
Cdd:PHA03247 2827 PLPPPTSAQ 2835
 
Name Accession Description Interval E-value
ArfGap_AGFG1 cd08857
ArfGAP domain of AGFG1 (ArfGAP domain and FG repeat-containing protein 1); The ArfGAP domain ...
 3-82 3.74e-53

ArfGAP domain of AGFG1 (ArfGAP domain and FG repeat-containing protein 1); The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG1 (alias: HIV-1 Rev binding protein, HRB; Rev interacting protein, RIP; Rev/Rex activating domain-binding protein, RAB) and AGFG2 are involved in the maintenance and spread of immunodeficiency virus type 1 (HIV-1) infection. The ArfGAP domain of AGFG1 is related to nucleoporins, which is a class of proteins that mediate nucleocytoplasmic transport. AGFG1 plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs, possibly together by the nuclear export receptor CRM1. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG1 promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication.


Pssm-ID: 350082 [Multi-domain]  Cd Length: 116  Bit Score: 175.23  E-value: 3.74e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 82
Cdd:cd08857   37 CTSCSGILRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 116
ArfGap_AGFG2 cd17903
ArfGAP domain of AGFG2 (ArfGAP domain and FG repeat-containing protein 2); The ArfGAP domain ...
 3-82 2.52e-46

ArfGAP domain of AGFG2 (ArfGAP domain and FG repeat-containing protein 2); The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG2 is a member of the HIV-1 Rev binding protein (HRB) family and contains one Arf-GAP zinc finger domain, several Phe-Gly (FG) motifs, and four Asn-Pro-Phe (NPF) motifs. AGFG2 interacts with Eps15 homology (EH) domains and plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication.


Pssm-ID: 350090 [Multi-domain]  Cd Length: 116  Bit Score: 157.46  E-value: 2.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 82
Cdd:cd17903   37 CTTCSGLLRGLNPPHRVKSISMTTFTEPEVLFLQARGNEVCRKIWLGLFDARTSLIPDSRDPQKVKEFLQEKYEKKRWYV 116
ArfGap_AGFG cd08838
ArfGAP domain of the AGFG subfamily (ArfGAP domain and FG repeat-containing proteins); The ...
 3-82 1.42e-36

ArfGAP domain of the AGFG subfamily (ArfGAP domain and FG repeat-containing proteins); The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG1 (alias: HIV-1 Rev binding protein, HRB; Rev interacting protein, RIP; Rev/Rex activating domain-binding protein, RAB) and AGFG2 are involved in the maintenance and spread of immunodeficiency virus type 1 (HIV-1) infection. The ArfGAP domain of AGFG is related to nucleoporins, which is a class of proteins that mediate nucleocytoplasmic transport. AGFG plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs, possibly together by the nuclear export receptor CRM1. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication.


Pssm-ID: 350067 [Multi-domain]  Cd Length: 113  Bit Score: 131.16  E-value: 1.42e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNppHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYV 82
Cdd:cd08838   36 CTTCSGIHREFN--HRVKSISMSTFTPEEVEFLQAGGNEVARKIWLAKWDPRTDPEPDSGDDQKIREFIRLKYVDKRWYD 113
ArfGap smart00105
Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with ...
 3-89 1.22e-23

Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.


Pssm-ID: 214518 [Multi-domain]  Cd Length: 119  Bit Score: 95.87  E-value: 1.22e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202     3 CRTTASVSRGLNPpHR--VKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRW 80
Cdd:smart00105  33 CIECSGIHRSLGV-HIskVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSLKPPDDDDQQKYESFIAAKYEEKLF 111


                   ....*....
gi 148670202    81 yVPPEQAKV 89
Cdd:smart00105 112 -VPPESAEE 119
ArfGap pfam01412
Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating ...
 7-84 2.05e-18

Putative GTPase activating protein for Arf; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.


Pssm-ID: 460200 [Multi-domain]  Cd Length: 117  Bit Score: 81.12  E-value: 2.05e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148670202    7 ASVSRGL-NPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDrSSAIPDFRDPQKVKEFLQEKYEKKRWYVPP 84
Cdd:pfam01412  40 SGVHRSLgVHISKVRSLTLDTWTDEQLELMKAGGNDRANEFWEANLPP-SYKPPPSSDREKRESFIRAKYVEKKFAKPG 117
ArfGap cd08204
GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs); ArfGAPs are a family ...
 7-75 1.20e-12

GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs); ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. Like all GTP-binding proteins, Arf proteins function as molecular switches, cycling between GTP (active-membrane bound) and GDP (inactive-cytosolic) form. Conversion to the GTP-bound form requires a guanine nucleotide exchange factor (GEF), whereas conversion to the GDP-bound form is catalyzed by a GTPase activating protein (GAP). In that sense, ArfGAPs were originally proposed to function as terminators of Arf signaling, which is mediated by regulating Arf family GTP-binding proteins. However, recent studies suggest that ArfGAPs can also function as Arf effectors, independently of their GAP enzymatic activity to transduce signals in cells. The ArfGAP domain contains a C4-type zinc finger motif and a conserved arginine that is required for activity, within a specific spacing (CX2CX16CX2CX4R). ArfGAPs, which have multiple functional domains, regulate the membrane trafficking and actin cytoskeleton remodeling via specific interactions with signaling lipids such as phosphoinositides and trafficking proteins, which consequently affect cellular events such as cell growth, migration, and cancer invasion. The ArfGAP family, which includes 31 human ArfGAP-domain containing proteins, is divided into 10 subfamilies based on domain structure and sequence similarity. The ArfGAP nomenclature is mainly based on the protein domain structure. For example, ASAP1 contains ArfGAP, SH3, ANK repeat and PH domains; ARAPs contain ArfGAP, Rho GAP, ANK repeat and PH domains; ACAPs contain ArfGAP, BAR (coiled coil), ANK repeat and PH domains; and AGAPs contain Arf GAP, GTP-binding protein-like, ANK repeat and PH domains. Furthermore, the ArfGAPs can be classified into two major types of subfamilies, according to the overall domain structure: the ArfGAP1 type includes 6 subfamilies (ArfGAP1, ArfGAP2/3, ADAP, SMAP, AGFG, and GIT), which contain the ArfGAP domain at the N-terminus of the protein; and the AZAP type includes 4 subfamilies (ASAP, ACAP, AGAP, and ARAP), which contain an ArfGAP domain between the PH and ANK repeat domains.


Pssm-ID: 350058 [Multi-domain]  Cd Length: 106  Bit Score: 64.06  E-value: 1.20e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148670202   7 ASVSRGLnPPH--RVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKY 75
Cdd:cd08204   37 SGIHRSL-GVHisKVRSLTLDSWTPEQVELMKAIGNARANAYYEANLPPGFKKPTPDSSDEEREQFIRAKY 106
PLN03131 PLN03131
hypothetical protein; Provisional
 3-80 3.28e-09

hypothetical protein; Provisional


Pssm-ID: 178677 [Multi-domain]  Cd Length: 705  Bit Score: 59.41  E-value: 3.28e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148670202   3 CRTTASVSRGLNppHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRW 80
Cdd:PLN03131  46 CMTCSGIHREFT--HRVKSVSMSKFTSQDVEALQNGGNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKY 121
PLN03119 PLN03119
putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
 17-80 4.74e-07

putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional


Pssm-ID: 178666  Cd Length: 648  Bit Score: 52.54  E-value: 4.74e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 148670202  17 HRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRW 80
Cdd:PLN03119  58 HRVKSVSMSKFTSKEVEVLQNGGNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKY 121
ArfGap_SMAP2 cd08859
Stromal membrane-associated protein 2; a subfamily of the ArfGAP family; The SMAP subfamily of ...
 3-79 7.99e-06

Stromal membrane-associated protein 2; a subfamily of the ArfGAP family; The SMAP subfamily of Arf GTPase-activating proteins consists of the two structurally-related members, SMAP1 and SMAP2. Each SMAP member exhibits common and distinct functions in vesicle trafficking. They both bind to clathrin heavy chain molecules and are involved in the trafficking of clathrin-coated vesicles. SMAP1 preferentially exhibits GAP toward Arf6, while SMAP2 prefers Arf1 as a substrate. SMAP1 is involved in Arf6-dependent vesicle trafficking, but not Arf6-mediated actin cytoskeleton reorganization, and regulates clathrin-dependent endocytosis of the transferrin receptors and E-cadherin. SMAP2 regulates Arf1-dependent retrograde transport of TGN38/46 from the early endosome to the trans-Golgi network (TGN). SMAP2 has the Clathrin Assembly Lymphoid Myeloid (CALM)-binding domain, but SMAP1 does not.


Pssm-ID: 350083 [Multi-domain]  Cd Length: 107  Bit Score: 44.98  E-value: 7.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLNPP-HRVKSISMTTFTQQEIEFLQKHGNEVCKQIWlglfddrSSAIPD-FRDPQ---KVKEFLQEKYEK 77
Cdd:cd08859   33 CIRCAGIHRNLGVHiSRVKSVNLDQWTQEQIQCMQEMGNGKANRLY-------EAFLPEnFRRPQtdqAVEGFIRDKYEK 105


                 ..
gi 148670202  78 KR 79
Cdd:cd08859  106 KK 107
ArfGap_ADAP cd08832
ArfGap with dual PH domains; The ADAP subfamily, ArfGAPs with dual pleckstrin homology (PH) ...
 3-75 1.10e-04

ArfGap with dual PH domains; The ADAP subfamily, ArfGAPs with dual pleckstrin homology (PH) domains, includes two members: ADAP1 and ADAP2. Both ADAP1 (also known as centaurin-alpha1, p42(IP4), or PIP3BP) and ADAP2 (centaurin-alpha2) display a GTPase-activating protein (GAP) activity toward Arf6 (ADP-ribosylation factor 6), which is involved in protein trafficking that regulates endocytic recycling, cytoskeleton remodeling, and neuronal differentiation. ADAP2 has high sequence similarity to the ADAP1 and they both contain a ArfGAP domain at the N-terminus, followed by two PH domains. However, ADAP1, unlike ADAP2, contains a putative N-terminal nuclear localization signal. The PH domains of ADAP1bind to the two second messenger molecules phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) with identical high affinity, whereas those of ADAP2 specifically binds phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) and PI(3,4,5)P3, which are produced by activated phosphatidylinositol 3-kinase. ADAP1 is predominantly expressed in the brain neurons, while ADAP2 is broadly expressed, including the adipocytes, heart, and skeletal muscle but not in the brain. The limited distribution and high expression of ADAP1 in the brain indicates that ADAP1 is important for neuronal functions. ADAP1 has been shown to highly expressed in the neurons and plagues of Alzheimer's disease patients. In other hand, ADAP2 gene deletion has been shown to cause circulatory deficiencies and heart shape defects in zebrafish, indicating that ADAP2 has a vital role in heart development. Taken together, the hemizygous deletion of ADAP2 gene may be contributing to the cardiovascular malformation in patients with neurofibromatosis type 1 (NF1) microdeletions.


Pssm-ID: 350061 [Multi-domain]  Cd Length: 113  Bit Score: 41.48  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202   3 CRTTASVSRGLnPPH--RVKSISMTTFTQQEIEFLQKHGNEVCKQIWlglfddrSSAIPDF------RDPQKVKE-FLQE 73
Cdd:cd08832   40 CLDCSGIHRSL-GTHisKVKSLRLDNWDDSQVEFMEENGNEKAKAKY-------EAHVPAFyrrptpTDPQVLREqWIRA 111


                 ..
gi 148670202  74 KY 75
Cdd:cd08832  112 KY 113
COG5347 COG5347
GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ...
 18-222 2.67e-04

GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion];


Pssm-ID: 227651 [Multi-domain]  Cd Length: 319  Bit Score: 43.23  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  18 RVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGlfDDRSSAIPDFR---DPQKVKEFLQEKYEKKRWYVPPEQAKVVASvh 94
Cdd:COG5347   59 KVKSLTLDNWTEEELRRMEVGGNSNANRFYEK--NLLDQLLLPIKakyDSSVAKKYIRKKYELKKFIDDSSSPSDFSS-- 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  95 asisgssaSSTSSTPEVKPLKSLL-GESAPALHLNKGTPSQSP--VVGRSQGQQQEKKQFDLLSDL---GSDIFAAPAPQ 168
Cdd:COG5347  135 --------FSASSTRTVDSVDDRLdSESQSRSSSASLGNSNRPddELNVESFQSTGSKPRSLTSTKsnkDNLLNSELLTL 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 148670202 169 STATANFAN--FAHFNSHAAQNSANADFANFDAFGQSSGSSNFGGFPTASHSSFQP 222
Cdd:COG5347  207 NSLLSSNSEvgSGTKSRSDAQEKSSTKATESVKPGPVNTSSTSSLPPAIKRSPVQQ 262
PHA03247 PHA03247
large tegument protein UL36; Provisional
 341-509 6.83e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.54  E-value: 6.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  341 AATSSNAYTPTSNASSSVFGTVPVGASAQTQPASSGPAPFGATPSTNpfvAATGPSAASSTNPFQTNARGATAATFGTAS 420
Cdd:PHA03247 2674 AQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATP---LPPGPAAARQASPALPAAPAPPAVPAGPAT 2750

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  421 MSMPAGFGTPAQYSLPTSFSGsfqqPAFPAQAAFPQQTAFSQQPNGFATFGQTKPVVTPFGQVAAAGVSSNPFMTGAPTG 500
Cdd:PHA03247 2751 PGGPARPARPPTTAGPPAPAP----PAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAG 2826


                  ....*....
gi 148670202  501 QLPTGSSST 509
Cdd:PHA03247 2827 PLPPPTSAQ 2835
PHA03247 PHA03247
large tegument protein UL36; Provisional
 372-513 7.50e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.15  E-value: 7.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148670202  372 PASSGPAPFGATPSTNPFVAATGPSAASSTNPFQTNARGATAATFGTASMSMPAGFGTPAqyslptsfsgsfqQPAFPAQ 451
Cdd:PHA03247 2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGP-------------PRRLTRP 2786

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 148670202  452 AAFPQQTAFSQQPNGFATFGQTKPVVTPFGQVAAAGVSSNPFMTgaPTGQLPTGSSSTNPFL 513
Cdd:PHA03247 2787 AVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPP 2846
 
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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