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Conserved domains on  [gi|418972|gb|S31035|]
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retrovirus-related gag polyprotein - mouse intracisternal A-particle MIAD8 (fragment)

Protein Classification

Graphical summary

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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 ...
 118-245 7.58e-34

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: 125.85  E-value: 7.58e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     118 VHAPVEYVQIKELAESVRKYGTMLNFTLVQLDRLA-GMALTPADWQTIVKAALPSmGKYMEWRALWHEAAQAQARTNADA 196
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 418972     197 ltPEQRDWTFDLLMGQGAYSA--DQTNYHWGAYAQISSTAIRAWNGLSRAG 245
Cdd:pfam00607  80 --GPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 570-656 1.88e-33

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: 123.15  E-value: 1.88e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972   570 LRLKINRKEFEGILDTGADKSIISTHWWPKAWPTTESSHSLQGLGyQSCPTI-SSIALTWESSEGQQGKFIPYVLPLPVN 648
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIG-GAITPSqSSVLLLEIDGEGHLGTILVYVLSLPVN 79


                ....*...
gi 418972   649 LWGRDIMQ 656
Cdd:cd05482  80 LWGRDILS 87
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-316 1.23e-14

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: 69.05  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 418972     251 LTKIIQGPQESFSDFVARMTEAAERIFGESEQAAPLIEQLIYEQATKECRAAIAPRKNKG-LQDWLR 316
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
trimeric_dUTPase super family cl00493
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 442-540 1.78e-14

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


The actual alignment was detected with superfamily member pfam00692:

Pssm-ID: 444938 [Multi-domain]  Cd Length: 129  Bit Score: 70.40  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     442 PGRPTRV--EPRAASDFLLRPqMSIQPVPVEPIPSLPPGTMGLILGRGSLTLQGLVVHPGVMDCQHSPEIQVLCSSPKGV 519
Cdd:pfam00692   8 PGSPGDAgyDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLGKS 86

                          90       100
                  ....*....|....*....|..
gi 418972     520 -FSISKGDRIAQLLLLPDNTRE 540
Cdd:pfam00692  87 dFTIKKGDRIAQLIFEPILHPE 108
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 671-716 5.18e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


:

Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 61.02  E-value: 5.18e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 418972      671 GYSAKANNIMAKMGYKEGKGLGHQEnNGRIEPISPNGNQDRQGLGF 716
Cdd:smart00443   2 STSNIGAKLLRKMGWKEGQGLGKNE-QGIVEPISAEIKKDRKGLGA 46
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 340-393 1.44e-06

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: 48.26  E-value: 1.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 418972    340 RSMGRNNHRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 393
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 ...
 118-245 7.58e-34

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: 125.85  E-value: 7.58e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     118 VHAPVEYVQIKELAESVRKYGTMLNFTLVQLDRLA-GMALTPADWQTIVKAALPSmGKYMEWRALWHEAAQAQARTNADA 196
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 418972     197 ltPEQRDWTFDLLMGQGAYSA--DQTNYHWGAYAQISSTAIRAWNGLSRAG 245
Cdd:pfam00607  80 --GPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 570-656 1.88e-33

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: 123.15  E-value: 1.88e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972   570 LRLKINRKEFEGILDTGADKSIISTHWWPKAWPTTESSHSLQGLGyQSCPTI-SSIALTWESSEGQQGKFIPYVLPLPVN 648
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIG-GAITPSqSSVLLLEIDGEGHLGTILVYVLSLPVN 79


                ....*...
gi 418972   649 LWGRDIMQ 656
Cdd:cd05482  80 LWGRDILS 87
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 566-662 2.21e-22

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: 92.05  E-value: 2.21e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     566 DRPKLRLKINRKEFEGILDTGADKSIISTHWWPKAWPTTESSHSLQGLGYQSCPTISSIALTWESSEGQQGKFIPYVLP- 644
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPt 82

                          90
                  ....*....|....*...
gi 418972     645 LPVNLWGRDIMQHLGLIL 662
Cdd:pfam00077  83 CPVNIIGRDLLQQLGGRL 100
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-316 1.23e-14

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: 69.05  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 418972     251 LTKIIQGPQESFSDFVARMTEAAERIFGESEQAAPLIEQLIYEQATKECRAAIAPRKNKG-LQDWLR 316
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 442-540 1.78e-14

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 70.40  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     442 PGRPTRV--EPRAASDFLLRPqMSIQPVPVEPIPSLPPGTMGLILGRGSLTLQGLVVHPGVMDCQHSPEIQVLCSSPKGV 519
Cdd:pfam00692   8 PGSPGDAgyDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLGKS 86

                          90       100
                  ....*....|....*....|..
gi 418972     520 -FSISKGDRIAQLLLLPDNTRE 540
Cdd:pfam00692  87 dFTIKKGDRIAQLIFEPILHPE 108
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 671-716 5.18e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 61.02  E-value: 5.18e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 418972      671 GYSAKANNIMAKMGYKEGKGLGHQEnNGRIEPISPNGNQDRQGLGF 716
Cdd:smart00443   2 STSNIGAKLLRKMGWKEGQGLGKNE-QGIVEPISAEIKKDRKGLGA 46
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 451-533 6.44e-10

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 56.35  E-value: 6.44e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972   451 RAASDFllrPQMSIQP-----VPVEPIPSLPPGTMGLILGRGSLTLQGLVVH-PGVMDCQHSPEIQVLCS--SPKGvFSI 522
Cdd:cd07557   6 RLGEDF---EGIVLPPgetvlVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYnlGPEP-VVI 81

                        90
                ....*....|.
gi 418972   523 SKGDRIAQLLL 533
Cdd:cd07557  82 KKGDRIAQLVF 92
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 672-715 7.21e-10

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 54.82  E-value: 7.21e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 418972     672 YSAKANNIMAKMGYKEGKGLGhQENNGRIEPISPNGNQDRQGLG 715
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLG-KNEQGIAEPIEAKIKKDRRGLG 43
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 340-393 1.44e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 1.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 418972    340 RSMGRNNHRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 393
Cdd:PTZ00368  20 APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAP 72
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 475-535 3.18e-06

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 47.32  E-value: 3.18e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 418972   475 LPPGTMGLILGRGSLTL-QGLVV--HPGVMDCQHSPEIQVLC----SSPkgvFSISKGDRIAQLLLLP 535
Cdd:COG0756  52 LPPGYEAQVRPRSGLALkHGITLlnSPGTIDSDYRGEIKVILinlgDEP---FTIERGDRIAQLVIAP 116
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 474-535 3.41e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 44.15  E-value: 3.41e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418972     474 SLPPGTMGLILGRGSLTLQG---LVVHPGVMDCQHSPEIQVLC----SSPkgvFSISKGDRIAQLLLLP 535
Cdd:TIGR00576  49 ELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKVILinlgKED---FTVKKGDRIAQLVVEK 114
ZnF_C2HC smart00343
zinc finger;
349-364 1.01e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 1.01e-04
                           10
                   ....*....|....*.
gi 418972      349 TCFNCGKPGHFKKDCR 364
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 348-363 1.44e-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: 39.05  E-value: 1.44e-04
                          10
                  ....*....|....*.
gi 418972     348 RTCFNCGKPGHFKKDC 363
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
PHA03094 PHA03094
dUTPase; Provisional
 445-550 1.58e-04

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 42.44  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972    445 PTRVEPRAAS-------DFLLRPQMSIQpVPVEPIPSLPPGTMGLILGRGSLTLQ-GLVVHPGVMDCQHSPEIQV-LCSS 515
Cdd:PHA03094  18 PTRSSPKSAGydlysayDYTVPPKERIL-VKTDISLSIPKFCYGRIAPRSGLSLNyGIDIGGGVIDEDYRGNIGViFINN 96

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 418972    516 PKGVFSISKGDRIAQLLLlpdntrEKFAGPEIKKM 550
Cdd:PHA03094  97 GKCTFNIKTGDRIAQIIF------ERIEYPELKEV 125
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 348-423 3.69e-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: 39.06  E-value: 3.69e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 418972   348 RTCFNCGKPGHFKKDCR-APDKQggtlTLCSKCGKGYHRADQCRSVRdiKGRILPPADSQSAYMPKNGSSGPRSQGP 423
Cdd:COG5082  98 KKCYNCGETGHLSRDCNpSKDQQ----KSCFDCNSTRHSSEDCPSIW--KHYVLNNGDGHPIKKFCYSCGSAGHFGD 168
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 118-245 7.58e-34

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: 125.85  E-value: 7.58e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     118 VHAPVEYVQIKELAESVRKYGTMLNFTLVQLDRLA-GMALTPADWQTIVKAALPSmGKYMEWRALWHEAAQAQARTNADA 196
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALAsSNALTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQARRNQRA 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 418972     197 ltPEQRDWTFDLLMGQGAYSA--DQTNYHWGAYAQISSTAIRAWNGLSRAG 245
Cdd:pfam00607  80 --GPDRGITLDMLTGTGQYATpqAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 570-656 1.88e-33

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: 123.15  E-value: 1.88e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972   570 LRLKINRKEFEGILDTGADKSIISTHWWPKAWPTTESSHSLQGLGyQSCPTI-SSIALTWESSEGQQGKFIPYVLPLPVN 648
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIG-GAITPSqSSVLLLEIDGEGHLGTILVYVLSLPVN 79


                ....*...
gi 418972   649 LWGRDIMQ 656
Cdd:cd05482  80 LWGRDILS 87
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 566-662 2.21e-22

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: 92.05  E-value: 2.21e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     566 DRPKLRLKINRKEFEGILDTGADKSIISTHWWPKAWPTTESSHSLQGLGYQSCPTISSIALTWESSEGQQGKFIPYVLP- 644
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPt 82

                          90
                  ....*....|....*...
gi 418972     645 LPVNLWGRDIMQHLGLIL 662
Cdd:pfam00077  83 CPVNIIGRDLLQQLGGRL 100
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 251-316 1.23e-14

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: 69.05  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 418972     251 LTKIIQGPQESFSDFVARMTEAAERIFGESEQAAPLIEQLIYEQATKECRAAIAPRKNKG-LQDWLR 316
Cdd:pfam19317   7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGtLSDMIR 73
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 442-540 1.78e-14

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 70.40  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972     442 PGRPTRV--EPRAASDFLLRPqMSIQPVPVEPIPSLPPGTMGLILGRGSLTLQGLVVHPGVMDCQHSPEIQVLCSSPKGV 519
Cdd:pfam00692   8 PGSPGDAgyDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLGKS 86

                          90       100
                  ....*....|....*....|..
gi 418972     520 -FSISKGDRIAQLLLLPDNTRE 540
Cdd:pfam00692  87 dFTIKKGDRIAQLIFEPILHPE 108
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 671-716 5.18e-12

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 61.02  E-value: 5.18e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 418972      671 GYSAKANNIMAKMGYKEGKGLGHQEnNGRIEPISPNGNQDRQGLGF 716
Cdd:smart00443   2 STSNIGAKLLRKMGWKEGQGLGKNE-QGIVEPISAEIKKDRKGLGA 46
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 451-533 6.44e-10

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 56.35  E-value: 6.44e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972   451 RAASDFllrPQMSIQP-----VPVEPIPSLPPGTMGLILGRGSLTLQGLVVH-PGVMDCQHSPEIQVLCS--SPKGvFSI 522
Cdd:cd07557   6 RLGEDF---EGIVLPPgetvlVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYnlGPEP-VVI 81

                        90
                ....*....|.
gi 418972   523 SKGDRIAQLLL 533
Cdd:cd07557  82 KKGDRIAQLVF 92
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 672-715 7.21e-10

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 54.82  E-value: 7.21e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 418972     672 YSAKANNIMAKMGYKEGKGLGhQENNGRIEPISPNGNQDRQGLG 715
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLG-KNEQGIAEPIEAKIKKDRRGLG 43
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 340-393 1.44e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 1.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 418972    340 RSMGRNNHRTCFNCGKPGHFKKDCRAPDKQGGTLTlCSKCGKGYHRADQCRSVR 393
Cdd:PTZ00368  20 APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS-CYNCGKTGHLSRECPEAP 72
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 339-391 1.60e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 48.26  E-value: 1.60e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 418972    339 NRSMGRNNHRTCFNCGKPGHFKKDCRAPDKQGGTLTLCSKCGKGYHRADQCRS 391
Cdd:PTZ00368  95 NRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 475-535 3.18e-06

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 47.32  E-value: 3.18e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 418972   475 LPPGTMGLILGRGSLTL-QGLVV--HPGVMDCQHSPEIQVLC----SSPkgvFSISKGDRIAQLLLLP 535
Cdd:COG0756  52 LPPGYEAQVRPRSGLALkHGITLlnSPGTIDSDYRGEIKVILinlgDEP---FTIERGDRIAQLVIAP 116
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 348-417 8.62e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.34  E-value: 8.62e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972    348 RTCFNCGKPGHFKKDCRAPDKQGGTLTLCSKCGKGYHRADQCRSVRDikgrilPPADSQSAYmpKNGSSG 417
Cdd:PTZ00368  78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGK------RPGGDKTCY--NCGQTG 139
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 474-535 3.41e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 44.15  E-value: 3.41e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418972     474 SLPPGTMGLILGRGSLTLQG---LVVHPGVMDCQHSPEIQVLC----SSPkgvFSISKGDRIAQLLLLP 535
Cdd:TIGR00576  49 ELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKVILinlgKED---FTVKKGDRIAQLVVEK 114
ZnF_C2HC smart00343
zinc finger;
349-364 1.01e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.73  E-value: 1.01e-04
                           10
                   ....*....|....*.
gi 418972      349 TCFNCGKPGHFKKDCR 364
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 348-363 1.44e-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: 39.05  E-value: 1.44e-04
                          10
                  ....*....|....*.
gi 418972     348 RTCFNCGKPGHFKKDC 363
Cdd:pfam00098   1 GKCYNCGEPGHIARDC 16
PHA03094 PHA03094
dUTPase; Provisional
 445-550 1.58e-04

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 42.44  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972    445 PTRVEPRAAS-------DFLLRPQMSIQpVPVEPIPSLPPGTMGLILGRGSLTLQ-GLVVHPGVMDCQHSPEIQV-LCSS 515
Cdd:PHA03094  18 PTRSSPKSAGydlysayDYTVPPKERIL-VKTDISLSIPKFCYGRIAPRSGLSLNyGIDIGGGVIDEDYRGNIGViFINN 96

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 418972    516 PKGVFSISKGDRIAQLLLlpdntrEKFAGPEIKKM 550
Cdd:PHA03094  97 GKCTFNIKTGDRIAQIIF------ERIEYPELKEV 125
dut PRK00601
dUTP diphosphatase;
451-535 8.25e-04

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 40.53  E-value: 8.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972    451 RAASDfllrPQMSIQPVPVEPIPS-----LPPGTMGLILGRGSLTL-QGLVV--HPGVMDCQHSPEIQVLC----SSPkg 518
Cdd:PRK00601  33 RACLD----EPVTLAPGERALVPTglaihIPDGYEAQILPRSGLAHkHGIVLgnLPGTIDSDYRGELKVSLwnrgQEP-- 106

                         90
                 ....*....|....*..
gi 418972    519 vFSISKGDRIAQLLLLP 535
Cdd:PRK00601 107 -FTIEPGERIAQLVIVP 122
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 445-550 8.71e-04

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 40.74  E-value: 8.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418972    445 PTRVEPRAASDFLLRPQMSIQP------VPVEPIPSLPPGTMGLILGRGSLTLQGLV-VHPGVMDCQHSPEIQV-LCSSP 516
Cdd:PHA02703  26 PTRGSPGAAGLDLCSACDCIVPagcrcvVFTDLLIKLPDGCYGRIAPRSGLAVKHFIdVGAGVIDADYRGNVGVvLFNFG 105

                         90       100       110
                 ....*....|....*....|....*....|....
gi 418972    517 KGVFSISKGDRIAQLLLlpdntrEKFAGPEIKKM 550
Cdd:PHA02703 106 HNDFEVKKGDRIAQLIC------ERAAFPAVEEV 133
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
375-402 3.58e-03

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 35.61  E-value: 3.58e-03
                          10        20
                  ....*....|....*....|....*...
gi 418972     375 LCSKCGKGYHRADQCRSVRDIKGRILPP 402
Cdd:pfam14787   4 LCPRCKKGKHWARDCHSKFDKNGNPLSP 31
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 348-423 3.69e-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: 39.06  E-value: 3.69e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 418972   348 RTCFNCGKPGHFKKDCR-APDKQggtlTLCSKCGKGYHRADQCRSVRdiKGRILPPADSQSAYMPKNGSSGPRSQGP 423
Cdd:COG5082  98 KKCYNCGETGHLSRDCNpSKDQQ----KSCFDCNSTRHSSEDCPSIW--KHYVLNNGDGHPIKKFCYSCGSAGHFGD 168
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 344-394 3.94e-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: 39.06  E-value: 3.94e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 418972   344 RNNHRTCFNCGKPGHFKKDCRAP-----DKQGGTLT------LCSKCGKGYHRADQCRSVRD 394
Cdd:COG5082  57 REENPVCFNCGQNGHLRRDCPHSicyncSWDGHRSNhcpkpkKCYNCGETGHLSRDCNPSKD 118
 
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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