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Conserved domains on  [gi|382933115|gb|AFG30998|]
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gag polyprotein [Avian leukosis virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-86 2.15e-38

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


:

Pssm-ID: 460707  Cd Length: 86  Bit Score: 137.21  E-value: 2.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115    1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSSSDLYSPGSWDPITAALSQRAMVLGKSGELKTWGLVLGA 80
Cdd:pfam02813   1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSPGGSDDIIAAALQQAAMLGGKGEEKKTGGLLGAA 80


                  ....*.
gi 382933115   81 LKAARE 86
Cdd:pfam02813  81 KAAAEE 86
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 586-701 2.47e-31

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


:

Pssm-ID: 425454  Cd Length: 101  Bit Score: 117.47  E-value: 2.47e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  586 HKDRPLVRVILTNTgshpvkqrsvYITALLDSGADITIISEEDWPTDWPVVDtANPQIHGIGGGIpMRKSRDMIEVGVIN 665
Cdd:pfam00077   1 AEQRPLLTVKIGGK----------YFTALLDTGADDTVISQNDWPTNWPKQK-ATTNIQGIGGGI-NVRQSDQILILIGE 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 382933115  666 RDGSLERPLLLFPavaMVRGSILGRDCLQGLGLRLT 701
Cdd:pfam00077  69 DKFRGTVSPLILP---TCPVNIIGRDLLQQLGGRLT 101
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-384 1.96e-20

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: 87.72  E-value: 1.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  251 AWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSS-PLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAaatrdp 329
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSnALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQAR------ 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 382933115  330 RHPANGQGRGerTNLDRLKGlaDGMVGNPDGQAAlLRPGELVAITASALQAFREV 384
Cdd:pfam00607  75 RNQRAGPDRG--ITLDMLTG--TGQYATPQAQAQ-LPPEVLEQIKALALRAWKKL 124
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 499-564 3.25e-08

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: 53.27  E-value: 3.25e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 382933115 499 GQTGSGGRArglCYTCGSPGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQCRkrdgNQGQRPGRG 564
Cdd:PTZ00368  71 APPGSGPRS---CYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP----NAGKRPGGD 129
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 388-448 1.63e-04

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: 40.54  E-value: 1.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 382933115  388 AEPTDpWAEITQGPSESFVDFANRLIKAVEGSDLPPTARAPVIIDCFRQKSQPDIQQLIRA 448
Cdd:pfam19317   2 YKPTS-LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKP 61
 
Name Accession Description Interval E-value
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-86 2.15e-38

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


Pssm-ID: 460707  Cd Length: 86  Bit Score: 137.21  E-value: 2.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115    1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSSSDLYSPGSWDPITAALSQRAMVLGKSGELKTWGLVLGA 80
Cdd:pfam02813   1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSPGGSDDIIAAALQQAAMLGGKGEEKKTGGLLGAA 80


                  ....*.
gi 382933115   81 LKAARE 86
Cdd:pfam02813  81 KAAAEE 86
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 586-701 2.47e-31

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 117.47  E-value: 2.47e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  586 HKDRPLVRVILTNTgshpvkqrsvYITALLDSGADITIISEEDWPTDWPVVDtANPQIHGIGGGIpMRKSRDMIEVGVIN 665
Cdd:pfam00077   1 AEQRPLLTVKIGGK----------YFTALLDTGADDTVISQNDWPTNWPKQK-ATTNIQGIGGGI-NVRQSDQILILIGE 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 382933115  666 RDGSLERPLLLFPavaMVRGSILGRDCLQGLGLRLT 701
Cdd:pfam00077  69 DKFRGTVSPLILP---TCPVNIIGRDLLQQLGGRLT 101
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-384 1.96e-20

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: 87.72  E-value: 1.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  251 AWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSS-PLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAaatrdp 329
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSnALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQAR------ 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 382933115  330 RHPANGQGRGerTNLDRLKGlaDGMVGNPDGQAAlLRPGELVAITASALQAFREV 384
Cdd:pfam00607  75 RNQRAGPDRG--ITLDMLTG--TGQYATPQAQAQ-LPPEVLEQIKALALRAWKKL 124
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 607-694 5.11e-20

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 85.01  E-value: 5.11e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115 607 RSVYITALLDSGADITIISEEDWPTDWPvVDTANPQIHGIGGGIPMRKSRdmieVGVINRDGSlerPLLLFPAVAM--VR 684
Cdd:cd05482    6 NGKLFEGLLDTGADVSIIAENDWPKNWP-IQPAPSNLTGIGGAITPSQSS----VLLLEIDGE---GHLGTILVYVlsLP 77

                         90
                 ....*....|
gi 382933115 685 GSILGRDCLQ 694
Cdd:cd05482   78 VNLWGRDILS 87
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 499-564 3.25e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 53.27  E-value: 3.25e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 382933115 499 GQTGSGGRArglCYTCGSPGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQCRkrdgNQGQRPGRG 564
Cdd:PTZ00368  71 APPGSGPRS---CYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP----NAGKRPGGD 129
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 510-567 9.32e-05

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: 44.07  E-value: 9.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 382933115 510 LCYTCGSPGHYQAQC-PKKRKsgnsRERCQLCDGMGHNAKQCRKRDGNQGQRPGRGLFS 567
Cdd:COG5082   99 KCYNCGETGHLSRDCnPSKDQ----QKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPI 153
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 388-448 1.63e-04

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: 40.54  E-value: 1.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 382933115  388 AEPTDpWAEITQGPSESFVDFANRLIKAVEGSDLPPTARAPVIIDCFRQKSQPDIQQLIRA 448
Cdd:pfam19317   2 YKPTS-LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKP 61
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 511-526 3.13e-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: 38.28  E-value: 3.13e-04
                          10
                  ....*....|....*.
gi 382933115  511 CYTCGSPGHYQAQCPK 526
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
511-526 9.04e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 9.04e-04
                           10
                   ....*....|....*.
gi 382933115   511 CYTCGSPGHYQAQCPK 526
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 1-86 2.15e-38

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


Pssm-ID: 460707  Cd Length: 86  Bit Score: 137.21  E-value: 2.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115    1 MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSSSDLYSPGSWDPITAALSQRAMVLGKSGELKTWGLVLGA 80
Cdd:pfam02813   1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSPGGSDDIIAAALQQAAMLGGKGEEKKTGGLLGAA 80


                  ....*.
gi 382933115   81 LKAARE 86
Cdd:pfam02813  81 KAAAEE 86
Retro_M pfam02813
Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein ...
 2-87 1.54e-37

Retroviral M domain; Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure.


Pssm-ID: 460707  Cd Length: 86  Bit Score: 134.51  E-value: 1.54e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115    2 EAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLTSSSDLYSPGSWDPITAALSQRAMVLGKSGELKTWGLVLGAL 81
Cdd:pfam02813   1 EAAIIKIISAACKTCCGKSPPKKEEGAALLLLLKEEGLLMPPDDLSPGGSDDIIAAALQQAAMLGGKGEEKKTGGLLGAA 80


                  ....*.
gi 382933115   82 KAAREE 87
Cdd:pfam02813  81 KAAAEE 86
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 586-701 2.47e-31

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 117.47  E-value: 2.47e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  586 HKDRPLVRVILTNTgshpvkqrsvYITALLDSGADITIISEEDWPTDWPVVDtANPQIHGIGGGIpMRKSRDMIEVGVIN 665
Cdd:pfam00077   1 AEQRPLLTVKIGGK----------YFTALLDTGADDTVISQNDWPTNWPKQK-ATTNIQGIGGGI-NVRQSDQILILIGE 68

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 382933115  666 RDGSLERPLLLFPavaMVRGSILGRDCLQGLGLRLT 701
Cdd:pfam00077  69 DKFRGTVSPLILP---TCPVNIIGRDLLQQLGGRLT 101
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-384 1.96e-20

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: 87.72  E-value: 1.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115  251 AWTPLEPKLITRLADTVRTKGLRSPITMAEVEALMSS-PLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAaatrdp 329
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSnALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQAR------ 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 382933115  330 RHPANGQGRGerTNLDRLKGlaDGMVGNPDGQAAlLRPGELVAITASALQAFREV 384
Cdd:pfam00607  75 RNQRAGPDRG--ITLDMLTG--TGQYATPQAQAQ-LPPEVLEQIKALALRAWKKL 124
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 607-694 5.11e-20

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 85.01  E-value: 5.11e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 382933115 607 RSVYITALLDSGADITIISEEDWPTDWPvVDTANPQIHGIGGGIPMRKSRdmieVGVINRDGSlerPLLLFPAVAM--VR 684
Cdd:cd05482    6 NGKLFEGLLDTGADVSIIAENDWPKNWP-IQPAPSNLTGIGGAITPSQSS----VLLLEIDGE---GHLGTILVYVlsLP 77

                         90
                 ....*....|
gi 382933115 685 GSILGRDCLQ 694
Cdd:cd05482   78 VNLWGRDILS 87
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 499-564 3.25e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 53.27  E-value: 3.25e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 382933115 499 GQTGSGGRArglCYTCGSPGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQCRkrdgNQGQRPGRG 564
Cdd:PTZ00368  71 APPGSGPRS---CYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP----NAGKRPGGD 129
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 500-561 1.38e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 1.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 382933115 500 QTGSGGRArglCYTCGSPGHYQAQCPKKRKSGNSReRCQLCDGMGHNAKQC-RKRDGNQGQRP 561
Cdd:PTZ00368  47 PGGRGERS---CYNCGKTGHLSRECPEAPPGSGPR-SCYNCGQTGHISRECpNRAKGGAARRA 105
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 503-550 4.04e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.03  E-value: 4.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 382933115 503 SGGRARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQC 550
Cdd:PTZ00368  98 KGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDC 145
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 510-567 9.32e-05

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: 44.07  E-value: 9.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 382933115 510 LCYTCGSPGHYQAQC-PKKRKsgnsRERCQLCDGMGHNAKQCRKRDGNQGQRPGRGLFS 567
Cdd:COG5082   99 KCYNCGETGHLSRDCnPSKDQ----QKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPI 153
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 388-448 1.63e-04

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: 40.54  E-value: 1.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 382933115  388 AEPTDpWAEITQGPSESFVDFANRLIKAVEGSDLPPTARAPVIIDCFRQKSQPDIQQLIRA 448
Cdd:pfam19317   2 YKPTS-LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKP 61
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 511-560 2.93e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 41.72  E-value: 2.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 382933115 511 CYTCGSPGHYQAQCPKKRKSGNSRErCQLCDGMGHNAKQCRKRDGNQGQR 560
Cdd:PTZ00368  30 CYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAPPGSGPR 78
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 511-526 3.13e-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: 38.28  E-value: 3.13e-04
                          10
                  ....*....|....*.
gi 382933115  511 CYTCGSPGHYQAQCPK 526
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 510-550 4.21e-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: 42.15  E-value: 4.21e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 382933115 510 LCYTCGSPGHYQAQCPKKRKsgnsrerCQLCDGMGHNAKQC 550
Cdd:COG5082   80 ICYNCSWDGHRSNHCPKPKK-------CYNCGETGHLSRDC 113
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 511-561 5.34e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 5.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 382933115 511 CYTCGSPGHYQAQCPKKRKSGNSRER-CQLCDGMGHNAKQCRKRDGNQGQRP 561
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARpCYKCGEPGHLSRECPSAPGGRGERS 54
ZnF_C2HC smart00343
zinc finger;
511-526 9.04e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.04  E-value: 9.04e-04
                           10
                   ....*....|....*.
gi 382933115   511 CYTCGSPGHYQAQCPK 526
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
 
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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