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Conserved domains on  [gi|1316032196|sp|P25059|]
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RecName: Full=Gag-Pro-Pol polyprotein; Contains: RecName: Full=Matrix protein p15; Short=MA; Contains: RecName: Full=Capsid protein p24; Short=CA; Contains: RecName: Full=Nucleocapsid protein p12-pro; Contains: RecName: Full=Protease; Contains: RecName: Full=Reverse transcriptase/ribonuclease H; Short=RT; Contains: RecName: Full=Integrase; Short=IN

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 570-773 2.06e-59

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd01645:

Pssm-ID: 477363 [Multi-domain]  Cd Length: 213  Bit Score: 203.28  E-value: 2.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  570 LNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPTHLPHII 649
Cdd:cd01645      9 LTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  650 cLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDI 729
Cdd:cd01645     89 -LDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDI 167

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1316032196  730 LYVSPTEEQRLQCYQTMAAHLRDLGFQVASEKTrQTPSPVPFLG 773
Cdd:cd01645    168 LIASDLEGQLREIYEELRQTLLRWGLTIPPEKV-QKEPPFQYLG 210
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1183-1276 3.10e-22

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 92.38  E-value: 3.10e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1183 PNHIWQADITHYKY--KQFTYALHVFVDTYSGATHASA-KRGLTTQTTIEGLLEAIVHLG-RPKKLNTDQGANYTSKTFV 1258
Cdd:pfam00665    1 PNQLWQGDFTYIRIpgGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1316032196 1259 RFCQQFGISLSHHVPYNP 1276
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Gag_p24_C super family cl44748
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 1.52e-16

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: 75.59  E-value: 1.52e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032196  241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317    7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1002-1119 6.87e-10

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd09273:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 131  Bit Score: 58.50  E-value: 6.87e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1002 LFSDGAARR-GAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAPPEPLNIWVDSKYLYSLLRTL--VLGAWLQPDP 1078
Cdd:cd09273      2 VFTDGSSFKaGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLetIGIERGFLKS 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1316032196 1079 VPSYAL---LYKSLLRHPAIFVGHVRSHSSASHPIASLNNYVDQ 1119
Cdd:cd09273     82 IKNLSLflqLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADA 125
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1356-1398 3.74e-06

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


The actual alignment was detected with superfamily member pfam00552:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 45.08  E-value: 3.74e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196 1356 YKLPGQNNRRWLGPLPALVEASGGALLAT--NPPVWVPWRLLKAF 1398
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQdaSDPQWVPERLLKRI 45
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 347-387 3.00e-05

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: 45.57  E-value: 3.00e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368    30 CYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 450-533 5.45e-05

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member pfam00077:

Pssm-ID: 472175  Cd Length: 101  Bit Score: 43.51  E-value: 5.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  450 LVDTGAENTVLPQNWLVRDYPR--TPAAVLGAGGISRNRYNWLQGPLTLALKPEGP--FITIPKILVDtfdkwqILGRDV 525
Cdd:pfam00077   19 LLDTGADDTVISQNDWPTNWPKqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTvsPLILPTCPVN------IIGRDL 92


                   ....*...
gi 1316032196  526 LSRLQASI 533
Cdd:pfam00077   93 LQQLGGRL 100
Gag_p19 super family cl03491
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 5.64e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


The actual alignment was detected with superfamily member pfam02228:

Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.41  E-value: 5.64e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196    4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228   10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
Gag_p24 super family cl02908
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 4.08e-04

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.


The actual alignment was detected with superfamily member pfam00607:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 41.88  E-value: 4.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1316032196  190 EAANT----LQGFNPQnGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607   81 PDRGItldmLTGTGQY-ATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 570-773 2.06e-59

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 203.28  E-value: 2.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  570 LNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPTHLPHII 649
Cdd:cd01645      9 LTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  650 cLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDI 729
Cdd:cd01645     89 -LDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDI 167

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1316032196  730 LYVSPTEEQRLQCYQTMAAHLRDLGFQVASEKTrQTPSPVPFLG 773
Cdd:cd01645    168 LIASDLEGQLREIYEELRQTLLRWGLTIPPEKV-QKEPPFQYLG 210
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 605-776 1.99e-41

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 150.92  E-value: 1.99e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  605 VRKPN-GAWRFV----HDLRVTNALTKP-------IPALSPGPPDLTAIPTHLPHIICLDLKDAFFQIPVEDRFRSYFAF 672
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  673 TLPTP----GGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVsYMDDILYVSPTEEQRLQCYQTMAA 748
Cdd:pfam00078   81 TTPPIninwNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLTLVR-YADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 1316032196  749 HLRDLGFQVASEKTRQT--PSPVPFLGQMV 776
Cdd:pfam00078  160 WLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1183-1276 3.10e-22

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 92.38  E-value: 3.10e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1183 PNHIWQADITHYKY--KQFTYALHVFVDTYSGATHASA-KRGLTTQTTIEGLLEAIVHLG-RPKKLNTDQGANYTSKTFV 1258
Cdd:pfam00665    1 PNQLWQGDFTYIRIpgGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1316032196 1259 RFCQQFGISLSHHVPYNP 1276
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1182-1290 3.53e-18

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 87.13  E-value: 3.53e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1182 APNHIWQADITHYKYKQ-FTYaLHVFVDTYSG-ATHASAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTF 1257
Cdd:COG2801    147 APNQVWVTDITYIPTAEgWLY-LAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGPPKPLilHSDNGSQYTSKAY 225

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1316032196 1258 VRFCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:COG2801    226 QELLKKLGITQSMSRPGNPQDNAFIESFFGTLK 258
transpos_IS3 NF033516
IS3 family transposase;
1182-1290 1.30e-16

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 83.38  E-value: 1.30e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1182 APNHIWQADITHYKYKQFTYALHVFVDTYSG-ATHASAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTFV 1258
Cdd:NF033516   214 RPNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPEGLilHSDNGSQYTSKAYR 293

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1316032196 1259 RFCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:NF033516   294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 1.52e-16

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: 75.59  E-value: 1.52e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032196  241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317    7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1002-1119 6.87e-10

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 58.50  E-value: 6.87e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1002 LFSDGAARR-GAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAPPEPLNIWVDSKYLYSLLRTL--VLGAWLQPDP 1078
Cdd:cd09273      2 VFTDGSSFKaGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLetIGIERGFLKS 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1316032196 1079 VPSYAL---LYKSLLRHPAIFVGHVRSHSSASHPIASLNNYVDQ 1119
Cdd:cd09273     82 IKNLSLflqLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADA 125
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1356-1398 3.74e-06

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 45.08  E-value: 3.74e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196 1356 YKLPGQNNRRWLGPLPALVEASGGALLAT--NPPVWVPWRLLKAF 1398
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQdaSDPQWVPERLLKRI 45
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-387 3.00e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 45.57  E-value: 3.00e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368    30 CYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
ZnF_C2HC smart00343
zinc finger;
347-361 3.99e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 3.99e-05
                            10
                    ....*....|....*
gi 1316032196   347 CYRCLKEGHWARDCP 361
Cdd:smart00343    2 CYNCGKEGHIARDCP 16
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 450-533 5.45e-05

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: 43.51  E-value: 5.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  450 LVDTGAENTVLPQNWLVRDYPR--TPAAVLGAGGISRNRYNWLQGPLTLALKPEGP--FITIPKILVDtfdkwqILGRDV 525
Cdd:pfam00077   19 LLDTGADDTVISQNDWPTNWPKqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTvsPLILPTCPVN------IIGRDL 92


                   ....*...
gi 1316032196  526 LSRLQASI 533
Cdd:pfam00077   93 LQQLGGRL 100
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 5.64e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.41  E-value: 5.64e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196    4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228   10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1183-1290 3.56e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 44.09  E-value: 3.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1183 PNHIWQADITHYKYKQFTYALHVFVDTYSGATHA-SAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTFVR 1259
Cdd:PHA02517   109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGGLihHSDKGSQYVSLAYTQ 188

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1316032196 1260 FCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:PHA02517   189 RLKEAGIRASTGSRGDSYDNAPAESINGLYK 219
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 4.08e-04

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: 41.88  E-value: 4.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1316032196  190 EAANT----LQGFNPQnGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607   81 PDRGItldmLTGTGQY-ATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
transpos_IS21 NF033546
IS21 family transposase;
1203-1290 5.57e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 43.74  E-value: 5.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1203 LHVFVDT--YSGATHASAKRGLTTQTTIEGLLEAIVHLG------RP-------KKLNTDQGANYTsKTFVRFCQQFGIS 1267
Cdd:NF033546   138 LHVFVAVlgYSRYTYVEATPSESQEDLLDGHQRAFEFFGgvpreiVYdnlktavDKRDRYEEPRLN-PRFAAFAAHYGFE 216

                           90       100
                   ....*....|....*....|...
gi 1316032196 1268 LSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:NF033546   217 PRPCRPYRPQEKGKVERAVGYVR 239
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 347-361 8.34e-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: 37.89  E-value: 8.34e-04
                           10
                   ....*....|....*
gi 1316032196  347 CYRCLKEGHWARDCP 361
Cdd:pfam00098    3 CYNCGEPGHIARDCP 17
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 997-1104 3.71e-03

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 39.28  E-value: 3.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  997 PAALCLFSDGA------ARRGAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAP-PEPLNIWVDSKYLYSLLRTLV 1069
Cdd:pfam00075    1 PKAVTVYTDGSclgnpgPGGAGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITQWV 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196 1070 LG----AW---LQPDPVPS---YALLYKSLLRHPaIFVGHVRSHS 1104
Cdd:pfam00075   81 HGwkknGWpttSEGKPVKNkdlWQLLKALCKKHQ-VYWQWVKGHA 124
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 570-773 2.06e-59

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 203.28  E-value: 2.06e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  570 LNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPTHLPHII 649
Cdd:cd01645      9 LTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAALPKGWPLIV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  650 cLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDI 729
Cdd:cd01645     89 -LDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDI 167

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1316032196  730 LYVSPTEEQRLQCYQTMAAHLRDLGFQVASEKTrQTPSPVPFLG 773
Cdd:cd01645    168 LIASDLEGQLREIYEELRQTLLRWGLTIPPEKV-QKEPPFQYLG 210
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 605-776 1.99e-41

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 150.92  E-value: 1.99e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  605 VRKPN-GAWRFV----HDLRVTNALTKP-------IPALSPGPPDLTAIPTHLPHIICLDLKDAFFQIPVEDRFRSYFAF 672
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  673 TLPTP----GGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVsYMDDILYVSPTEEQRLQCYQTMAA 748
Cdd:pfam00078   81 TTPPIninwNGELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRAGLTLVR-YADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 1316032196  749 HLRDLGFQVASEKTRQT--PSPVPFLGQMV 776
Cdd:pfam00078  160 WLKESGLKINPEKTQFFlkSKEVKYLGVTL 189
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 570-773 2.87e-39

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 145.57  E-value: 2.87e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  570 LNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGA-WRFVHDLRVTNALTKPIPALSPGPPD-LTAIPTHLPH 647
Cdd:cd03715      9 LPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNdYRMVQDLRLVNQAVLPIHPAVPNPYTlLSLLPPKHQW 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  648 IICLDLKDAFFQIPVEDRFRSYFAFTLPTpgglqphRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMD 727
Cdd:cd03715     89 YTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVD 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1316032196  728 DILYVSPTEEQRLQCYQTMAAHLRDLGFQVASEKTRQTPSPVPFLG 773
Cdd:cd03715    162 DLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLG 207
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 589-776 1.02e-31

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 122.70  E-value: 1.02e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  589 GYISPWDGPGNNPVFPVRKPNGAWRFVHDLRVTNALTKPIPALSPGPPDLTAIPTHLPHIICLDLKDAFFQIPVEDRFRS 668
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  669 YFAFTlpTPGGLqphrrFAWRVLPQGFINSPALFERALQEPLRQVSAAFsqslLVSYMDDILYVSPTEE---QRLQcyQT 745
Cdd:cd01647     81 KTAFR--TPFGL-----YEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKTEEehlEHLR--EV 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1316032196  746 MAAhLRDLGFQVASEKTRQTPSPVPFLGQMV 776
Cdd:cd01647    148 LER-LREAGLKLNPEKCEFGVPEVEFLGHIV 177
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1183-1276 3.10e-22

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 92.38  E-value: 3.10e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1183 PNHIWQADITHYKY--KQFTYALHVFVDTYSGATHASA-KRGLTTQTTIEGLLEAIVHLG-RPKKLNTDQGANYTSKTFV 1258
Cdd:pfam00665    1 PNQLWQGDFTYIRIpgGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 1316032196 1259 RFCQQFGISLSHHVPYNP 1276
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1182-1290 3.53e-18

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 87.13  E-value: 3.53e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1182 APNHIWQADITHYKYKQ-FTYaLHVFVDTYSG-ATHASAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTF 1257
Cdd:COG2801    147 APNQVWVTDITYIPTAEgWLY-LAAVIDLFSReIVGWSVSDSMDAELVVDALEMAIERRGPPKPLilHSDNGSQYTSKAY 225

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1316032196 1258 VRFCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:COG2801    226 QELLKKLGITQSMSRPGNPQDNAFIESFFGTLK 258
transpos_IS3 NF033516
IS3 family transposase;
1182-1290 1.30e-16

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 83.38  E-value: 1.30e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1182 APNHIWQADITHYKYKQFTYALHVFVDTYSG-ATHASAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTFV 1258
Cdd:NF033516   214 RPNQVWVTDITYIRTAEGWLYLAVVLDLFSReIVGWSVSTSMSAELVLDALEMAIEWRGKPEGLilHSDNGSQYTSKAYR 293

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1316032196 1259 RFCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:NF033516   294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 241-297 1.52e-16

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: 75.59  E-value: 1.52e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1316032196  241 WSTIVQGPAESYVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANKECQQILQGRG 297
Cdd:pfam19317    7 LADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLG 63
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 651-773 3.77e-14

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 70.07  E-value: 3.77e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  651 LDLKDAFFQIPVEDRFRSYFAFTLPTPgglqphrRFAWRVLPQGFINSPALFER---ALQEPLRQVSaafsqSLLVSYMD 727
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGE-------TYQFKALPFGLSLAPRVFTKvveALLAPLRLLG-----VRIFSYLD 68

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1316032196  728 DILYVSPTEEQRLQCYQTMAA-HLRDLGFQVASEKTRQTPSP-VPFLG 773
Cdd:cd03714     69 DLLIIASSIKTSEAVLRHLRAtLLANLGFTLNLEKSKLGPTQrITFLG 116
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1002-1119 6.87e-10

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 58.50  E-value: 6.87e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1002 LFSDGAARR-GAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAPPEPLNIWVDSKYLYSLLRTL--VLGAWLQPDP 1078
Cdd:cd09273      2 VFTDGSSFKaGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLetIGIERGFLKS 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1316032196 1079 VPSYAL---LYKSLLRHPAIFVGHVRSHSSASHPIASLNNYVDQ 1119
Cdd:cd09273     82 IKNLSLflqLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADA 125
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 651-773 6.34e-08

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 51.97  E-value: 6.34e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  651 LDLKDAFFQIPvedrfrsyfaftlptpgglqphrrfawrvLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDIL 730
Cdd:cd00304      1 FDVKSFFTSIP-----------------------------LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196  731 YVSPTEEQRlQCYQTMAAHLRDLGFQVASEKTRQTPS--PVPFLG 773
Cdd:cd00304     52 VIAKSEQQA-VKKRELEEFLARLGLNLSDEKTQFTEKekKFKFLG 95
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1356-1398 3.74e-06

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 45.08  E-value: 3.74e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196 1356 YKLPGQNNRRWLGPLPALVEASGGALLAT--NPPVWVPWRLLKAF 1398
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVPQdaSDPQWVPERLLKRI 45
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-387 3.00e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 45.57  E-value: 3.00e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCPT 387
Cdd:PTZ00368    30 CYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE 70
ZnF_C2HC smart00343
zinc finger;
347-361 3.99e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 3.99e-05
                            10
                    ....*....|....*
gi 1316032196   347 CYRCLKEGHWARDCP 361
Cdd:smart00343    2 CYNCGKEGHIARDCP 16
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 450-533 5.45e-05

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: 43.51  E-value: 5.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  450 LVDTGAENTVLPQNWLVRDYPR--TPAAVLGAGGISRNRYNWLQGPLTLALKPEGP--FITIPKILVDtfdkwqILGRDV 525
Cdd:pfam00077   19 LLDTGADDTVISQNDWPTNWPKqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTvsPLILPTCPVN------IIGRDL 92


                   ....*...
gi 1316032196  526 LSRLQASI 533
Cdd:pfam00077   93 LQQLGGRL 100
Gag_p19 pfam02228
Major core protein p19; p19 is a component of the inner protein layer of the viral ...
 4-44 5.64e-05

Major core protein p19; p19 is a component of the inner protein layer of the viral nucleocapsid.


Pssm-ID: 460500  Cd Length: 92  Bit Score: 43.41  E-value: 5.64e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196    4 SPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYI 44
Cdd:pfam02228   10 SPIPRPPRGLAAHHWLNFLQAAYRLEPGPSSYDFHQLKKFL 50
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 630-755 6.41e-05

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 45.76  E-value: 6.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  630 ALSPGP---PDLTAIPTHL---PHIICLDLKDAFFQIPVEDRFRSYFAFTLPTPGGLQPHRRFAWRVLPQGFINSPALFE 703
Cdd:cd01644     37 MLLKGPdllNSLFGVLLRFrqgKIAVSADIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLAN 116

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1316032196  704 RALQEPLRQV-SAAFSQSLLVS-YMDDILYVSPTEEQRLQCYQTMAAHLRDLGF 755
Cdd:cd01644    117 RALKQHAEDHpHEAAAKIIKRNfYVDDILVSTDTLNEAVNVAKRLIALLKKGGF 170
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1183-1290 3.56e-04

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 44.09  E-value: 3.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1183 PNHIWQADITHYKYKQFTYALHVFVDTYSGATHA-SAKRGLTTQTTIEGLLEAIVHLGRPKKL--NTDQGANYTSKTFVR 1259
Cdd:PHA02517   109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGwRVSSSMDTDFVLDALEQALWARGRPGGLihHSDKGSQYVSLAYTQ 188

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1316032196 1260 FCQQFGISLSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:PHA02517   189 RLKEAGIRASTGSRGDSYDNAPAESINGLYK 219
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 119-233 4.08e-04

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: 41.88  E-value: 4.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  119 RHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQT---------AHMTSLTAAIAA 189
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALASSNALTPYDWRTLAKAVLSPGQYLlwkaewqelAQEQARRNQRAG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1316032196  190 EAANT----LQGFNPQnGTLTQQSAQPNagDLRSQYQNLWLQAWKNLP 233
Cdd:pfam00607   81 PDRGItldmLTGTGQY-ATPQAQAQLPP--EVLEQIKALALRAWKKLP 125
transpos_IS21 NF033546
IS21 family transposase;
1203-1290 5.57e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 43.74  E-value: 5.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1203 LHVFVDT--YSGATHASAKRGLTTQTTIEGLLEAIVHLG------RP-------KKLNTDQGANYTsKTFVRFCQQFGIS 1267
Cdd:NF033546   138 LHVFVAVlgYSRYTYVEATPSESQEDLLDGHQRAFEFFGgvpreiVYdnlktavDKRDRYEEPRLN-PRFAAFAAHYGFE 216

                           90       100
                   ....*....|....*....|...
gi 1316032196 1268 LSHHVPYNPTSSGLVERTNGLLK 1290
Cdd:NF033546   217 PRPCRPYRPQEKGKVERAVGYVR 239
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 347-361 8.34e-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: 37.89  E-value: 8.34e-04
                           10
                   ....*....|....*
gi 1316032196  347 CYRCLKEGHWARDCP 361
Cdd:pfam00098    3 CYNCGEPGHIARDCP 17
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1187-1289 1.11e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 42.95  E-value: 1.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196 1187 WQADITHYKYKQftYALHVFVDTYSGATHASAKRGLTTQTTIEGLLEAIVHLGRP--KKLNTDQGANYTSktFVRFCQQF 1264
Cdd:COG2826    175 WEGDLIIGKRGK--SALLTLVERKSRFVILLKLPDKTAESVADALIRLLRKLPAFlrKSITTDNGKEFAD--HKEIEAAL 250

                           90       100
                   ....*....|....*....|....*..
gi 1316032196 1265 GIS--LSHhvPYNPTSSGLVERTNGLL 1289
Cdd:COG2826    251 GIKvyFAD--PYSPWQRGTNENTNGLL 275
RT_Bac_retron_II cd03487
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 648-763 1.19e-03

RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.


Pssm-ID: 239569 [Multi-domain]  Cd Length: 214  Bit Score: 41.79  E-value: 1.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  648 IICLDLKDaFFQ-IPvEDRFRSYFaFTLPTPGGLQpHRRFAW-----RVLPQGFINSPAL-------FERALQEPLRQVS 714
Cdd:cd03487     59 VLKLDIKD-FFPsIT-FERVRGVF-RSLGYFSPDV-ATILAKlctynGHLPQGAPTSPALsnlvfrkLDERLSKLAKSNG 134

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1316032196  715 AAFSQsllvsYMDDILyVSPTEEQRLQCYQT---MAAHLRDLGFQVASEKTR 763
Cdd:cd03487    135 LTYTR-----YADDIT-FSSNKKLKEALDKLleiIRSILSEEGFKINKSKTR 180
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 692-773 1.93e-03

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 41.42  E-value: 1.93e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  692 PQGFINSPAL-------FERALQEPLRQVSAAFSQSL----LVSYMDDILYVSPTEEQRLQCYQTMAAHLRDLGFQVASE 760
Cdd:cd01651    128 PQGGVISPLLaniylheLDKFVEEKLKEYYDTSDPKFrrlrYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPE 207

                           90
                   ....*....|....*.
gi 1316032196  761 KTR---QTPSPVPFLG 773
Cdd:cd01651    208 KTRithFKSEGFDFLG 223
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-386 2.69e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 2.69e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPCPICKDPSHWKRDCP 386
Cdd:PTZ00368    55 CYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECP 94
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-386 3.04e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 39.79  E-value: 3.04e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPC-PICKDPSHWKRDCP 386
Cdd:PTZ00368   106 CYNCGGEGHISRDCPNAGKRPGGDKTcYNCGQTGHLSRDCP 146
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 997-1104 3.71e-03

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 39.28  E-value: 3.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1316032196  997 PAALCLFSDGA------ARRGAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAP-PEPLNIWVDSKYLYSLLRTLV 1069
Cdd:pfam00075    1 PKAVTVYTDGSclgnpgPGGAGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKALKsPSKVNIYTDSQYVIGGITQWV 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1316032196 1070 LG----AW---LQPDPVPS---YALLYKSLLRHPaIFVGHVRSHS 1104
Cdd:pfam00075   81 HGwkknGWpttSEGKPVKNkdlWQLLKALCKKHQ-VYWQWVKGHA 124
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-387 7.56e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 38.63  E-value: 7.56e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1316032196  347 CYRCLKEGHWARDCPTKTTGPPPGPCPICK--DPSHWKRDCPT 387
Cdd:PTZ00368     3 CYRCGGVGHQSRECPNSAPAGAAKARPCYKcgEPGHLSRECPS 45
 
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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