NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907128181|ref|XP_036016797|]
View 

igE-binding protein-like [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 274-401 5.46e-31

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 117.38  E-value: 5.46e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907128181 274 VHAPVEYLQIKEIAESVCKYGTNANFTLVQLDRLA-GMALTPADWQTVVKAALPSmGKYMEWRALWHEtaQAQARANAAA 352
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQE--LAQEQARRNQ 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907128181 353 LTPEQRDWTFDLLTGQGAYSA--DQTNYHWGAYAQISSTAIRAWKALSRAG 401
Cdd:pfam00607  78 RAGPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 401-472 4.97e-15

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


The actual alignment was detected with superfamily member pfam19317:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 70.20  E-value: 4.97e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907128181 401 GETTGQLTKVVQGPQESFSDFVARMTEAAERIFGDSEQAAPLVEQLIYEQATKECRAAIAPRKNKG-LQDWLR 472
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 496-549 7.38e-07

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.03  E-value: 7.38e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907128181 496 RSMSRNNQRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 549
Cdd:PTZ00368   20 APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAP 72
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 274-401 5.46e-31

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 117.38  E-value: 5.46e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907128181 274 VHAPVEYLQIKEIAESVCKYGTNANFTLVQLDRLA-GMALTPADWQTVVKAALPSmGKYMEWRALWHEtaQAQARANAAA 352
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQE--LAQEQARRNQ 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907128181 353 LTPEQRDWTFDLLTGQGAYSA--DQTNYHWGAYAQISSTAIRAWKALSRAG 401
Cdd:pfam00607  78 RAGPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 401-472 4.97e-15

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 70.20  E-value: 4.97e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907128181 401 GETTGQLTKVVQGPQESFSDFVARMTEAAERIFGDSEQAAPLVEQLIYEQATKECRAAIAPRKNKG-LQDWLR 472
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 496-549 7.38e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.03  E-value: 7.38e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907128181 496 RSMSRNNQRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 549
Cdd:PTZ00368   20 APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAP 72
ZnF_C2HC smart00343
zinc finger;
505-520 1.09e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 1.09e-04
                           10
                   ....*....|....*.
gi 1907128181  505 TCFNCGKPGHFKKDCR 520
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 504-519 1.20e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 39.43  E-value: 1.20e-04
                          10
                  ....*....|....*.
gi 1907128181 504 RTCFNCGKPGHFKKDC 519
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 492-550 5.38e-04

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 41.37  E-value: 5.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907128181 492 QSQNRSMSRNNQRTCFNCGKPGHFKKDCRAP-----DKQGGTLT------LCSKCGKGYHRADQCRSVRD 550
Cdd:COG5082    49 SVEDVSAIREENPVCFNCGQNGHLRRDCPHSicyncSWDGHRSNhcpkpkKCYNCGETGHLSRDCNPSKD 118
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 274-401 5.46e-31

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 117.38  E-value: 5.46e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907128181 274 VHAPVEYLQIKEIAESVCKYGTNANFTLVQLDRLA-GMALTPADWQTVVKAALPSmGKYMEWRALWHEtaQAQARANAAA 352
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQE--LAQEQARRNQ 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907128181 353 LTPEQRDWTFDLLTGQGAYSA--DQTNYHWGAYAQISSTAIRAWKALSRAG 401
Cdd:pfam00607  78 RAGPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 401-472 4.97e-15

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 70.20  E-value: 4.97e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907128181 401 GETTGQLTKVVQGPQESFSDFVARMTEAAERIFGDSEQAAPLVEQLIYEQATKECRAAIAPRKNKG-LQDWLR 472
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 496-549 7.38e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.03  E-value: 7.38e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907128181 496 RSMSRNNQRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 549
Cdd:PTZ00368   20 APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAP 72
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 495-547 3.10e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 47.11  E-value: 3.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907128181 495 NRSMSRNNQRTCFNCGKPGHFKKDCRAPDKQGGTLTLCSKCGKGYHRADQCRS 547
Cdd:PTZ00368   95 NRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 504-545 1.74e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 45.18  E-value: 1.74e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1907128181 504 RTCFNCGKPGHFKKDCRAPDKQGGTLTLCSKCGKGYHRADQC 545
Cdd:PTZ00368   78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDC 119
ZnF_C2HC smart00343
zinc finger;
505-520 1.09e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 1.09e-04
                           10
                   ....*....|....*.
gi 1907128181  505 TCFNCGKPGHFKKDCR 520
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 504-519 1.20e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 39.43  E-value: 1.20e-04
                          10
                  ....*....|....*.
gi 1907128181 504 RTCFNCGKPGHFKKDC 519
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
531-560 4.68e-04

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 37.92  E-value: 4.68e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907128181 531 LCSKCGKGYHRADQCRSVRDIKGRVLPPPD 560
Cdd:pfam14787   4 LCPRCKKGKHWARDCHSKFDKNGNPLSPNE 33
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 492-550 5.38e-04

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 41.37  E-value: 5.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907128181 492 QSQNRSMSRNNQRTCFNCGKPGHFKKDCRAP-----DKQGGTLT------LCSKCGKGYHRADQCRSVRD 550
Cdd:COG5082    49 SVEDVSAIREENPVCFNCGQNGHLRRDCPHSicyncSWDGHRSNhcpkpkKCYNCGETGHLSRDCNPSKD 118
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 504-548 7.05e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 37.91  E-value: 7.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907128181 504 RTCFNCGKPGHFKKDCR-APDKQggtlTLCSKCGKGYHRADQCRSV 548
Cdd:COG5082    98 KKCYNCGETGHLSRDCNpSKDQQ----KSCFDCNSTRHSSEDCPSI 139
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH