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Conserved domains on  [gi|9627212|ref|NP_056892|]
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Pr95 [Mason-Pfizer monkey virus]

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 ...
 314-438 1.51e-49

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: 170.92  E-value: 1.51e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9627212    393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607  81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 5.11e-36

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: 130.85  E-value: 5.11e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                ....*...
gi 9627212  851 LWGRDLLS 858
Cdd:cd05482  80 LWGRDILS 87
trimeric_dUTPase super family cl00493
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 638-756 5.77e-31

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: 118.16  E-value: 5.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692   6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 9627212    718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692  85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
Gag_p10 super family cl03546
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 5.21e-24

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


The actual alignment was detected with superfamily member pfam02337:

Pssm-ID: 426727  Cd Length: 85  Bit Score: 96.65  E-value: 5.21e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212      8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337   2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                  ....
gi 9627212     88 ELID 91
Cdd:pfam02337  82 AVLD 85
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 6.54e-23

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: 92.93  E-value: 6.54e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212    443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317   6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 3.51e-13

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 64.11  E-value: 3.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9627212    575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787   2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 2.45e-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: 62.18  E-value: 2.45e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 9627212     865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
ZnF_C2HC smart00343
zinc finger;
548-562 5.02e-04

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 5.02e-04
                           10
                   ....*....|....*
gi 9627212     548 CCFKCGKKGHFAKNC 562
Cdd:smart00343   1 KCYNCGKEGHIARDC 15
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 510-591 1.95e-03

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: 39.79  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   510 RLCSDIGPSyqqglAMAAAFS-------GQTVKDFLNNKNKEKGGCCFKCGKKGHFAKNChehahNNAEPKVPGL-CPRC 581
Cdd:PTZ00368  14 RECPNSAPA-----GAAKARPcykcgepGHLSRECPSAPGGRGERSCYNCGKTGHLSREC-----PEAPPGSGPRsCYNC 83

                         90
                 ....*....|
gi 9627212   582 KRGKHWANEC 591
Cdd:PTZ00368  84 GQTGHISREC 93
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 314-438 1.51e-49

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: 170.92  E-value: 1.51e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9627212    393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607  81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 5.11e-36

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: 130.85  E-value: 5.11e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                ....*...
gi 9627212  851 LWGRDLLS 858
Cdd:cd05482  80 LWGRDILS 87
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 638-756 5.77e-31

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 118.16  E-value: 5.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692   6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 9627212    718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692  85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 767-861 2.45e-28

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: 109.38  E-value: 2.45e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    767 QKPSLTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPN 846
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPT 82

                          90
                  ....*....|....*
gi 9627212    847 LPVNLWGRDLLSQMK 861
Cdd:pfam00077  83 CPVNIIGRDLLQQLG 97
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 5.21e-24

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 96.65  E-value: 5.21e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212      8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337   2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                  ....
gi 9627212     88 ELID 91
Cdd:pfam02337  82 AVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 6.54e-23

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: 92.93  E-value: 6.54e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212    443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317   6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 639-756 2.81e-22

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: 93.84  E-value: 2.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    639 TRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKG---LQVYPGVIDNDYTGEIK-IMAK 714
Cdd:TIGR00576  15 TYATEGAAGYDLRAAEDVTIPP-GERALVPTGIAIELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKvILIN 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9627212    715 AVNNIVTVSQGNRIAQLILLPlIETDNKVQQPY------RGQGSFGSS 756
Cdd:TIGR00576  94 LGKEDFTVKKGDRIAQLVVEK-IVTEVEFEEVEeldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 639-756 2.54e-20

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: 88.15  E-value: 2.54e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  639 TRATPGSAGLDLCSTSH--TVLTPemGPQAL-STGIYGPLPPNTFGLILGRSSITMK-GLQVY--PGVIDNDYTGEIKIM 712
Cdd:COG0756  15 AYATPGSAGLDLRAALDepVTLKP--GERALvPTGLAIALPPGYEAQVRPRSGLALKhGITLLnsPGTIDSDYRGEIKVI 92

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212  713 akAVN---NIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:COG0756  93 --LINlgdEPFTIERGDRIAQLVIAPvvqaefeeveeLDETE-------RGAGGFGST 141
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 646-733 3.05e-19

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: 83.31  E-value: 3.05e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  646 AGLDLCS---TSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVY-PGVIDNDYTGEIKIMAKAVNNI-V 720
Cdd:cd07557   1 AGYDLRLgedFEGIVLPP-GETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpV 79

                        90
                ....*....|...
gi 9627212  721 TVSQGNRIAQLIL 733
Cdd:cd07557  80 VIKKGDRIAQLVF 92
dut PRK00601
dUTP diphosphatase;
639-756 6.29e-18

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 81.36  E-value: 6.29e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   639 TRATPGSAGLDLCSTSHTVLTPEMGPQAL-STGIYGPLPPNTFGLILGRS------SITMKGLqvyPGVIDNDYTGEIK- 710
Cdd:PRK00601  21 AYATEGSAGLDLRACLDEPVTLAPGERALvPTGLAIHIPDGYEAQILPRSglahkhGIVLGNL---PGTIDSDYRGELKv 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627212   711 IMAKAVNNIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:PRK00601  98 SLWNRGQEPFTIEPGERIAQLVIVPvvqaefeeveeFDETE-------RGAGGFGST 147
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 3.51e-13

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 64.11  E-value: 3.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9627212    575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787   2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 2.45e-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: 62.18  E-value: 2.45e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 9627212     865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 875-909 1.61e-08

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: 51.36  E-value: 1.61e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9627212    875 MLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFG 909
Cdd:pfam01585   9 LQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLG 43
ZnF_C2HC smart00343
zinc finger;
548-562 5.02e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 5.02e-04
                           10
                   ....*....|....*
gi 9627212     548 CCFKCGKKGHFAKNC 562
Cdd:smart00343   1 KCYNCGKEGHIARDC 15
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 542-594 1.52e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 1.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627212   542 NKEKGGC----CFKCGKKGHFAKNCHEHAHNNAEPKvpgLCPRCKRGKHWANECKSK 594
Cdd:PTZ00368  95 NRAKGGAarraCYNCGGEGHISRDCPNAGKRPGGDK---TCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 510-591 1.95e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   510 RLCSDIGPSyqqglAMAAAFS-------GQTVKDFLNNKNKEKGGCCFKCGKKGHFAKNChehahNNAEPKVPGL-CPRC 581
Cdd:PTZ00368  14 RECPNSAPA-----GAAKARPcykcgepGHLSRECPSAPGGRGERSCYNCGKTGHLSREC-----PEAPPGSGPRsCYNC 83

                         90
                 ....*....|
gi 9627212   582 KRGKHWANEC 591
Cdd:PTZ00368  84 GQTGHISREC 93
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 529-598 2.76e-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: 39.83  E-value: 2.76e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212  529 FSGQTVKDFLNNKNKEKGgcCFKCGKKGHFAKNCHEHA--------HNNAEPKVPGLCPRCKRGKHWANECKSKTDNQ 598
Cdd:COG5082  45 YEDRSVEDVSAIREENPV--CFNCGQNGHLRRDCPHSIcyncswdgHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQ 120
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 549-562 2.86e-03

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: 35.97  E-value: 2.86e-03
                          10
                  ....*....|....
gi 9627212    549 CFKCGKKGHFAKNC 562
Cdd:pfam00098   3 CYNCGEPGHIARDC 16
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 314-438 1.51e-49

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: 170.92  E-value: 1.51e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    314 HHNGFDFAVIKELKTAASQYGATAPYTLAIVESVAD-NWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAG 392
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASsNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9627212    393 N--GWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKG 438
Cdd:pfam00607  81 PdrGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 771-858 5.11e-36

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: 130.85  E-value: 5.11e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  771 LTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPnLPVN 850
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS-LPVN 79


                ....*...
gi 9627212  851 LWGRDLLS 858
Cdd:cd05482  80 LWGRDILS 87
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 638-756 5.77e-31

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 118.16  E-value: 5.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    638 LTRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVN 717
Cdd:pfam00692   6 PTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVLFNLG 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 9627212    718 N-IVTVSQGNRIAQLILLP----LIETDNKVQQPYRGQGSFGSS 756
Cdd:pfam00692  85 KsDFTIKKGDRIAQLIFEPilhpELEPVETLDNTDRGDGGFGSS 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 767-861 2.45e-28

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: 109.38  E-value: 2.45e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    767 QKPSLTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPN 846
Cdd:pfam00077   3 QRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQILILIGEDKFRGTVSPLILPT 82

                          90
                  ....*....|....*
gi 9627212    847 LPVNLWGRDLLSQMK 861
Cdd:pfam00077  83 CPVNIIGRDLLQQLG 97
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-91 5.21e-24

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 96.65  E-value: 5.21e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212      8 HERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIK 87
Cdd:pfam02337   2 KQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALIR 81


                  ....
gi 9627212     88 ELID 91
Cdd:pfam02337  82 AVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 443-510 6.54e-23

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: 92.93  E-value: 6.54e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212    443 SLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIR 510
Cdd:pfam19317   6 SLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIR 73
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 639-756 2.81e-22

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: 93.84  E-value: 2.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    639 TRATPGSAGLDLCSTSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKG---LQVYPGVIDNDYTGEIK-IMAK 714
Cdd:TIGR00576  15 TYATEGAAGYDLRAAEDVTIPP-GERALVPTGIAIELPDGYYGRVAPRSGLALKHgvtIDNSPGVIDADYRGEIKvILIN 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9627212    715 AVNNIVTVSQGNRIAQLILLPlIETDNKVQQPY------RGQGSFGSS 756
Cdd:TIGR00576  94 LGKEDFTVKKGDRIAQLVVEK-IVTEVEFEEVEeldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 639-756 2.54e-20

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: 88.15  E-value: 2.54e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  639 TRATPGSAGLDLCSTSH--TVLTPemGPQAL-STGIYGPLPPNTFGLILGRSSITMK-GLQVY--PGVIDNDYTGEIKIM 712
Cdd:COG0756  15 AYATPGSAGLDLRAALDepVTLKP--GERALvPTGLAIALPPGYEAQVRPRSGLALKhGITLLnsPGTIDSDYRGEIKVI 92

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212  713 akAVN---NIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:COG0756  93 --LINlgdEPFTIERGDRIAQLVIAPvvqaefeeveeLDETE-------RGAGGFGST 141
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 646-733 3.05e-19

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: 83.31  E-value: 3.05e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  646 AGLDLCS---TSHTVLTPeMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVY-PGVIDNDYTGEIKIMAKAVNNI-V 720
Cdd:cd07557   1 AGYDLRLgedFEGIVLPP-GETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpV 79

                        90
                ....*....|...
gi 9627212  721 TVSQGNRIAQLIL 733
Cdd:cd07557  80 VIKKGDRIAQLVF 92
dut PRK00601
dUTP diphosphatase;
639-756 6.29e-18

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 81.36  E-value: 6.29e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   639 TRATPGSAGLDLCSTSHTVLTPEMGPQAL-STGIYGPLPPNTFGLILGRS------SITMKGLqvyPGVIDNDYTGEIK- 710
Cdd:PRK00601  21 AYATEGSAGLDLRACLDEPVTLAPGERALvPTGLAIHIPDGYEAQILPRSglahkhGIVLGNL---PGTIDSDYRGELKv 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627212   711 IMAKAVNNIVTVSQGNRIAQLILLP-----------LIETDnkvqqpyRGQGSFGSS 756
Cdd:PRK00601  98 SLWNRGQEPFTIEPGERIAQLVIVPvvqaefeeveeFDETE-------RGAGGFGST 147
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 639-774 1.55e-16

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 78.10  E-value: 1.55e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   639 TRATPGSAGLDLCSTSHTVLtPEMGPQALSTGIYGPLPPNTFGLILGRSSITMKG-LQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PHA02703  27 TRGSPGAAGLDLCSACDCIV-PAGCRCVVFTDLLIKLPDGCYGRIAPRSGLAVKHfIDVGAGVIDADYRGNVGvVLFNFG 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9627212   717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSSDIYwvqpiTCQKPSLTLW 774
Cdd:PHA02703 106 HNDFEVKKGDRIAQLICeraaFPAVEEVACLDDTDRGAGGFGSTGSG-----ACEGCGDTVW 162
PLN02547 PLN02547
dUTP pyrophosphatase
 639-756 1.91e-13

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 68.67  E-value: 1.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   639 TRATPGSAGLDLCSTSHTVLtPEMGPQALSTGIYGPLPPNTFGLILGRSSITMK-GLQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PLN02547  30 SRGSALAAGYDLSSAYDTVV-PARGKALVPTDLSIAIPEGTYARIAPRSGLAWKhSIDVGAGVIDADYRGPVGvILFNHS 108

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 9627212   717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSS 756
Cdd:PLN02547 109 DVDFEVKVGDRIAQLILekivTPEVVEVEDLDATVRGAGGFGST 152
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
575-609 3.51e-13

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 64.11  E-value: 3.51e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9627212    575 PGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGNR 609
Cdd:pfam14787   2 PGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 865-911 2.45e-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: 62.18  E-value: 2.45e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 9627212     865 CSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
PHA03094 PHA03094
dUTPase; Provisional
 639-758 7.40e-11

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 60.93  E-value: 7.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   639 TRATPGSAGLDLCStSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRSSITMK-GLQVYPGVIDNDYTGEIK-IMAKAV 716
Cdd:PHA03094  19 TRSSPKSAGYDLYS-AYDYTVPPKERILVKTDISLSIPKFCYGRIAPRSGLSLNyGIDIGGGVIDEDYRGNIGvIFINNG 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 9627212   717 NNIVTVSQGNRIAQLIL----LPLIETDNKVQQPYRGQGSFGSSDI 758
Cdd:PHA03094  98 KCTFNIKTGDRIAQIIFerieYPELKEVQSLDSTDRGDQGFGSSGL 143
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 875-909 1.61e-08

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: 51.36  E-value: 1.61e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9627212    875 MLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFG 909
Cdd:pfam01585   9 LQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLG 43
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 783-858 2.23e-06

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. 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: 133159  Cd Length: 86  Bit Score: 46.56  E-value: 2.23e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9627212  783 LIDTGADVTIIKlEDWPPNWPITDTLTNLRGI-GQSNNP-KQSSKYLTWRDKEnnsgLIKPF-VIPNLPVNLWGRDLLS 858
Cdd:cd06095  13 LVDTGATHSVLK-SDLGPKQELSTTSVLIRGVsGQSQQPvTTYRTLVDLGGHT----VSHSFlVVPNCPDPLLGRDLLS 86
PTZ00143 PTZ00143
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 643-758 1.67e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 240288 [Multi-domain]  Cd Length: 155  Bit Score: 45.88  E-value: 1.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   643 PGSAGLDLCSTSHTVLTP------EMGPQ--ALSTGIYGPLPPNTFGLILGRSSITMKGLQVYP--GVIDNDYTGEIKIm 712
Cdd:PTZ00143  24 EGDSGLDLFIVKDQTIKPgetafiKLGIKaaAFQKDEDGSDGKNVSWLLFPRSSISKTPLRLANsiGLIDAGYRGELIA- 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9627212   713 akAVNNI----VTVSQGNRIAQLILL---PL-IETDNKVQQPYRGQGSFGSSDI 758
Cdd:PTZ00143 103 --AVDNIkdepYTIKKGDRLVQLVSFdgePItFELVDELDETTRGEGGFGSTGR 154
PHA03124 PHA03124
dUTPase; Provisional
 643-756 8.57e-05

dUTPase; Provisional


Pssm-ID: 165396 [Multi-domain]  Cd Length: 418  Bit Score: 46.09  E-value: 8.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   643 PGSAGLDLCSTSHTVLTPEMG-----PQALSTGiygplpPNTFGLILGRSSITMKGLQVYP-GVIDNDYtgeikiMAKAV 716
Cdd:PHA03124 288 AEDAGYDIRAPEDCTILPGGStriilPQKLACG------KFRAAFILGRSSMNLKGLLVDPeHVQDDDW------ISFNI 355

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9627212   717 NNI----VTVSQGNRIAQLILLP-----LIETD-------NKVQQ-----PYRGQGSFGSS 756
Cdd:PHA03124 356 TNIrdaaAFFHAGDRIAQLIALEdklefLGEPDalpwkivNSVQDekknlSSRGDGGFGSS 416
dCTP_deam TIGR02274
deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli ...
 675-752 8.70e-05

deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli monofunctional deoxycytidine triphosphate deaminase (dCTP deaminase) and a Methanocaldococcus jannaschii bifunctional dCTP deaminase (3.5.4.13)/dUTP diphosphatase (EC 3.6.1.23), which has the EC number 3.5.4.30 for the overall operation. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274062  Cd Length: 179  Bit Score: 44.23  E-value: 8.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212    675 LPPNTFGLILGRSSITMKGLQVYP--GVIDNDYTGEIKI-MAKAVNNIVTVSQGNRIAQLILLPLIEtdnKVQQPYRGQG 751
Cdd:TIGR02274  89 LPDDVVGFLEGRSSLARLGLFIHVtaGRIDPGFEGNITLeLFNAGKLPVKLRPGMRIAQLVFERLSS---PAERPYNGRS 165


                  .
gi 9627212    752 S 752
Cdd:TIGR02274 166 G 166
Dcd COG0717
dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway ...
 675-752 1.15e-04

dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440481  Cd Length: 180  Bit Score: 43.66  E-value: 1.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212  675 LPPNTFGLILGRSSITMKGL--QVYPGVIDNDYTGEIKIMAKAVNNI-VTVSQGNRIAQLIllpLIETDNKVQQPYRGQG 751
Cdd:COG0717  88 LPDDLVAFLEGRSSLARLGLfvHTTAGVIDPGFEGRITLELSNTGPLpIKLYPGMRIAQLV---FFRLSGPAERPYGRGG 164


                .
gi 9627212  752 S 752
Cdd:COG0717 165 K 165
ZnF_C2HC smart00343
zinc finger;
548-562 5.02e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 5.02e-04
                           10
                   ....*....|....*
gi 9627212     548 CCFKCGKKGHFAKNC 562
Cdd:smart00343   1 KCYNCGKEGHIARDC 15
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 542-594 1.52e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 1.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9627212   542 NKEKGGC----CFKCGKKGHFAKNCHEHAHNNAEPKvpgLCPRCKRGKHWANECKSK 594
Cdd:PTZ00368  95 NRAKGGAarraCYNCGGEGHISRDCPNAGKRPGGDK---TCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 510-591 1.95e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   510 RLCSDIGPSyqqglAMAAAFS-------GQTVKDFLNNKNKEKGGCCFKCGKKGHFAKNChehahNNAEPKVPGL-CPRC 581
Cdd:PTZ00368  14 RECPNSAPA-----GAAKARPcykcgepGHLSRECPSAPGGRGERSCYNCGKTGHLSREC-----PEAPPGSGPRsCYNC 83

                         90
                 ....*....|
gi 9627212   582 KRGKHWANEC 591
Cdd:PTZ00368  84 GQTGHISREC 93
PHA03131 PHA03131
dUTPase; Provisional
 643-734 2.24e-03

dUTPase; Provisional


Pssm-ID: 222996 [Multi-domain]  Cd Length: 286  Bit Score: 41.13  E-value: 2.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9627212   643 PGSAGLDLCSTSHTVLTPEmgpQALSTGIYGPLP---PNTFGLILGRSSITMKGLQVYPGVIDND--------YTGEiki 711
Cdd:PHA03131 130 PDDAGFDVSLPQDLVIFPT---TTFTFTLSLCCPpisPHFVPVIFGRSGLASKGLTVKPTKWRRSglqlklynYTDE--- 203

                         90       100
                 ....*....|....*....|...
gi 9627212   712 makavnnIVTVSQGNRIAQLILL 734
Cdd:PHA03131 204 -------TIFLPAGSRICQVVFM 219
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 529-598 2.76e-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: 39.83  E-value: 2.76e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9627212  529 FSGQTVKDFLNNKNKEKGgcCFKCGKKGHFAKNCHEHA--------HNNAEPKVPGLCPRCKRGKHWANECKSKTDNQ 598
Cdd:COG5082  45 YEDRSVEDVSAIREENPV--CFNCGQNGHLRRDCPHSIcyncswdgHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQ 120
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 549-562 2.86e-03

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: 35.97  E-value: 2.86e-03
                          10
                  ....*....|....
gi 9627212    549 CFKCGKKGHFAKNC 562
Cdd:pfam00098   3 CYNCGEPGHIARDC 16
 
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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