Psyllid ID: psy9877
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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Close Homologs for Annotation Transfer
Close Homologs in SWISS-PROT Database Detected by BLAST 
Original result of BLAST against SWISS-PROT Database
No hits with e-value below 0.001 by BLAST
Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1447 | ||||||
| 345483499 | 1570 | PREDICTED: hypothetical protein LOC10011 | 0.440 | 0.406 | 0.386 | 1e-134 | |
| 427798445 | 1510 | Putative tick transposon, partial [Rhipi | 0.803 | 0.769 | 0.276 | 1e-132 | |
| 339261098 | 1532 | zinc knuckle protein [Trichinella spiral | 0.796 | 0.752 | 0.270 | 1e-123 | |
| 427791819 | 1682 | Putative tick transposon, partial [Rhipi | 0.798 | 0.687 | 0.265 | 1e-123 | |
| 427782459 | 1593 | Putative tick transposon [Rhipicephalus | 0.797 | 0.724 | 0.273 | 1e-121 | |
| 339259576 | 1520 | putative integrase core domain protein [ | 0.774 | 0.736 | 0.277 | 1e-113 | |
| 339264368 | 1624 | Pao retrotransposon peptidase superfamil | 0.778 | 0.693 | 0.268 | 1e-113 | |
| 339261110 | 1116 | zinc knuckle protein [Trichinella spiral | 0.694 | 0.900 | 0.283 | 1e-107 | |
| 339241105 | 1759 | zinc knuckle protein [Trichinella spiral | 0.745 | 0.613 | 0.281 | 1e-107 | |
| 340385703 | 1252 | PREDICTED: hypothetical protein LOC10063 | 0.576 | 0.666 | 0.317 | 1e-105 |
| >gi|345483499|ref|XP_001602535.2| PREDICTED: hypothetical protein LOC100118603 [Nasonia vitripennis] | Back alignment and taxonomy information |
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Score = 488 bits (1255), Expect = e-134, Method: Compositional matrix adjust.
Identities = 277/716 (38%), Positives = 414/716 (57%), Gaps = 78/716 (10%)
Query: 3 GTPARELVDSYPATGNMYNQVVEALKARFGREDLLTEVYIRELLKLVLANTASHDKLPIV 62
G+ A ELV S+P TG+ Y +V+E+L RFGR+D+ EVY+RELL+LVL N S +++ +
Sbjct: 398 GSRAAELVKSFPPTGDNYGKVIESLTKRFGRDDIQIEVYVRELLQLVLQNAMSSNEIELA 457
Query: 63 ILYDRLQSHLRNLESLGVSADRCAPILMPLVSSSLPQDLLQMWERCSVTQLHATQPSAGC 122
LYD+++S+LR+LE+LGV+ D+CA +L PLV S+LP+DLL++W+R S+G
Sbjct: 458 SLYDKIESYLRSLETLGVTTDKCAAMLFPLVESTLPEDLLRVWQR-----------SSGS 506
Query: 123 KEYLDSLMNFLKAEVEGVQKLELAKSGFGVVSSANKVESNNRRKDKHVKSPEKMNFLKAE 182
E V ++ N +++ R +K +K FL+++
Sbjct: 507 SE---------------------------VSAAGNSSDASKTRLEKLIK------FLESK 533
Query: 183 VEGVQKLELAKSGFGVVSSANKVESNNRRKDKHVKSPEKVPTATGLVNSTPKGESCIFCS 242
V+ ++ +A GF + + E +K K + ++V +A L+ S K CIFC
Sbjct: 534 VQNELRISMAVQGFSLKEDS---EKERVKKSKGQSAGKEVASARNLLASKGKENVCIFCE 590
Query: 243 QG-HYSGDC--QKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLKCEKCGSRHLT 299
+G H S C KDM++S++Q I++ K+ C+ CLKF H +KC KC RH+
Sbjct: 591 KGDHESAKCYMAKDMSISEKQAIVKQKRACFNCLKFVHNYRMYHVN--VKCSKCNRRHVD 648
Query: 300 ILCPRDSK-------SDIVTRTFVNTK------SSN----VLLQTLVVKIRGKDGKQDKL 342
++C + K + + + VN + SSN +QTL VKIR + + +
Sbjct: 649 VMCFAEEKCTGSQNAKTVNSVSAVNIQEECSLASSNEIPSTFMQTLRVKIR--NDATEII 706
Query: 343 ARLMIDTGSQQSYVLEQTMNSLSYTPITKQSMRHALFGGSITDAMDHNLFKIVISNLDNT 402
R +IDT SQ SYV N L+Y P+ +Q+M H LFGG + HN + + I +LDN
Sbjct: 707 VRAVIDTVSQNSYVFRDVANKLNYEPLEQQNMVHLLFGGDKSRVATHNKYLVRIGSLDNN 766
Query: 403 FACDFDVFGQSKICSTIPSIPSGPWIDELKQHNIELTDLQHPSTTVDILVGADIAGKFYT 462
+ +F Q+ IC+ +P++ G W+ ELK N+ LTD+ +V +L+GAD+AGK +T
Sbjct: 767 YRFNFQALDQNIICADVPTVTEGSWLQELKSFNVNLTDVCSKEKSVALLIGADVAGKLFT 826
Query: 463 GKRVELPSGLVAMETCMGWTLSGKMPTRYGSIDSSVATLVTSLLIKDANISDLWSLDVLG 522
G+ L SGL A+ET +GWTL GK+P G I+ +++ + + KDA+I DLWSLDVLG
Sbjct: 827 GRIHVLKSGLTAIETHLGWTLMGKVPVIKGRINLAMSAIF--MYAKDADIKDLWSLDVLG 884
Query: 523 IQDPMD-KSKADLAEAARKHFLDTVQVNSDNRFEVHLPWIEGHPPLASNLLLSQKRLEGT 581
I++P++ K++ K F +++ N++ R+EV LPW+E HP L N ++ +RLE
Sbjct: 885 IRNPIEHKTQEQHNSQVIKAFRESIIKNAEGRYEVKLPWLECHPELRDNKGMAIQRLESM 944
Query: 582 VKKLRRDQYYADYKRVLDTWEMDKIIERVPQEELDNPGYYMPHHHVVKPGSTTPVRPVFD 641
V+KL Y +Y + W IIERVP E+ + G Y+PH + K STT RP++D
Sbjct: 945 VRKLHATSKYEEYDGIFQEWLRAGIIERVPLEKEAHHGNYLPHRPIYKDNSTTTTRPIYD 1004
Query: 642 ASAKDNGV-SLNDCLEKGPNLIETIPTSLAKFRINKIGISGDIAKAFLQISVSPQD 696
ASA GV SLN CLEKGPNLIE + L +FR IG+ DI KAFLQISV+P D
Sbjct: 1005 ASA---GVPSLNRCLEKGPNLIEQVVDILLRFREGTIGVIADIKKAFLQISVNPAD 1057
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Source: Nasonia vitripennis Species: Nasonia vitripennis Genus: Nasonia Family: Pteromalidae Order: Hymenoptera Class: Insecta Phylum: Arthropoda Superkingdom: Eukaryota |
| >gi|427798445|gb|JAA64674.1| Putative tick transposon, partial [Rhipicephalus pulchellus] | Back alignment and taxonomy information |
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| >gi|339261098|ref|XP_003368076.1| zinc knuckle protein [Trichinella spiralis] gi|316964821|gb|EFV49757.1| zinc knuckle protein [Trichinella spiralis] | Back alignment and taxonomy information |
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| >gi|427791819|gb|JAA61361.1| Putative tick transposon, partial [Rhipicephalus pulchellus] | Back alignment and taxonomy information |
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| >gi|427782459|gb|JAA56681.1| Putative tick transposon [Rhipicephalus pulchellus] | Back alignment and taxonomy information |
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| >gi|339259576|ref|XP_003368837.1| putative integrase core domain protein [Trichinella spiralis] gi|316964514|gb|EFV49584.1| putative integrase core domain protein [Trichinella spiralis] | Back alignment and taxonomy information |
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| >gi|339264368|ref|XP_003366690.1| Pao retrotransposon peptidase superfamily [Trichinella spiralis] gi|316964699|gb|EFV49685.1| Pao retrotransposon peptidase superfamily [Trichinella spiralis] | Back alignment and taxonomy information |
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| >gi|339261110|ref|XP_003368070.1| zinc knuckle protein [Trichinella spiralis] gi|316963673|gb|EFV49170.1| zinc knuckle protein [Trichinella spiralis] | Back alignment and taxonomy information |
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| >gi|339241105|ref|XP_003376478.1| zinc knuckle protein [Trichinella spiralis] gi|316974804|gb|EFV58277.1| zinc knuckle protein [Trichinella spiralis] | Back alignment and taxonomy information |
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| >gi|340385703|ref|XP_003391348.1| PREDICTED: hypothetical protein LOC100639084, partial [Amphimedon queenslandica] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1447 | ||||||
| DICTYBASE|DDB_G0293328 | 131 | DDB_G0293328 "Cellular nucleic | 0.045 | 0.503 | 0.342 | 0.00091 |
| DICTYBASE|DDB_G0293328 DDB_G0293328 "Cellular nucleic acid-binding protein" [Dictyostelium discoideum (taxid:44689)] | Back alignment and assigned GO terms |
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Score = 99 (39.9 bits), Expect = 0.00091, P = 0.00091
Identities = 25/73 (34%), Positives = 34/73 (46%)
Query: 237 SCIFCSQ-GHYSGDC-QKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLKCEKCG 294
+C C+ GH S +C Q +++D I+ CY C FGH CR KC CG
Sbjct: 32 ACYVCNVVGHLSRECPQNPQPTFEKKDPIK----CYQCNGFGHFARDCRRGRDNKCYNCG 87
Query: 295 SR-HLTILCPRDS 306
H++ CP S
Sbjct: 88 GLGHISKDCPSPS 100
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.319 0.133 0.404 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 1447 1407 0.00091 124 3 11 22 0.39 34
39 0.45 37
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 1
No. of states in DFA: 642 (68 KB)
Total size of DFA: 664 KB (2288 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:03
No. of threads or processors used: 24
Search cpu time: 120.93u 0.11s 121.04t Elapsed: 00:01:31
Total cpu time: 120.93u 0.11s 121.04t Elapsed: 00:01:34
Start: Thu Aug 15 12:05:25 2013 End: Thu Aug 15 12:06:59 2013
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Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
No confident hit for EC number transfering in SWISSPROT detected by BLAST
EC Number Prediction by EFICAz Software
No EC number assignment, probably not an enzyme!
Prediction of Functionally Associated Proteins
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 1447 | |||
| cd01644 | 213 | cd01644, RT_pepA17, RT_pepA17: Reverse transcripta | 7e-55 | |
| pfam05380 | 159 | pfam05380, Peptidase_A17, Pao retrotransposon pept | 1e-36 | |
| pfam03564 | 146 | pfam03564, DUF1759, Protein of unknown function (D | 7e-08 | |
| pfam05585 | 164 | pfam05585, DUF1758, Putative peptidase (DUF1758) | 2e-05 | |
| pfam00078 | 194 | pfam00078, RVT_1, Reverse transcriptase (RNA-depen | 0.001 | |
| COG5082 | 190 | COG5082, AIR1, Arginine methyltransferase-interact | 0.001 | |
| cd09275 | 120 | cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase | 0.002 | |
| PTZ00368 | 148 | PTZ00368, PTZ00368, universal minicircle sequence | 0.002 |
| >gnl|CDD|238822 cd01644, RT_pepA17, RT_pepA17: Reverse transcriptase (RTs) in retrotransposons | Back alignment and domain information |
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Score = 190 bits (484), Expect = 7e-55
Identities = 90/236 (38%), Positives = 124/236 (52%), Gaps = 42/236 (17%)
Query: 620 YYMPHHHVVKPGS-TTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKFRINKIG 678
+Y+PHH V+KP TT +R VFDASA+ NGVSLND L KGP+L+ ++ L +FR KI
Sbjct: 2 WYLPHHAVIKPSKTTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIA 61
Query: 679 ISGDIAKAFLQISVSPQDRDCLSMRQPRIMVSRDCLRFLWQDENG--RVITYRHCRVVFG 736
+S DI K F Q+ V P+D RD LRFLW+ + + I YR V FG
Sbjct: 62 VSADIEKMFHQVKVRPED--------------RDVLRFLWRKDGDEPKPIEYRMTVVPFG 107
Query: 737 VSSSPFLLESCLKLHLELTLTDCREGKSSWPIHLVELLKDSFYVDNCLVSTDSQAEAEQF 796
+S+PFL LK H E D +++K +FYVD+ LVSTD+ EA
Sbjct: 108 AASAPFLANRALKQHAE----DHPHEA------AAKIIKRNFYVDDILVSTDTLNEAVNV 157
Query: 797 IQVASSIMKEKGFDLRGWE--------------LTGDKDDKPTN-VLGLLWDKSSD 837
+ +++K+ GF+LR W + D+D T LGL W+ +D
Sbjct: 158 AKRLIALLKKGGFNLRKWASNSQEVLDDLPEERVLLDRDSDVTEKTLGLRWNPKTD 213
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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. Length = 213 |
| >gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase | Back alignment and domain information |
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| >gnl|CDD|202685 pfam03564, DUF1759, Protein of unknown function (DUF1759) | Back alignment and domain information |
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| >gnl|CDD|147642 pfam05585, DUF1758, Putative peptidase (DUF1758) | Back alignment and domain information |
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| >gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase) | Back alignment and domain information |
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| >gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] | Back alignment and domain information |
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| >gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase HI in long-term repeat retroelements | Back alignment and domain information |
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| >gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional | Back alignment and domain information |
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Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1447 | |||
| cd01644 | 213 | RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) i | 100.0 | |
| PF05380 | 159 | Peptidase_A17: Pao retrotransposon peptidase ; Int | 100.0 | |
| cd03715 | 210 | RT_ZFREV_like RT_ZFREV_like: A subfamily of revers | 99.95 | |
| cd01645 | 213 | RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r | 99.93 | |
| PF05585 | 164 | DUF1758: Putative peptidase (DUF1758); InterPro: I | 99.87 | |
| cd01647 | 177 | RT_LTR RT_LTR: Reverse transcriptases (RTs) from r | 99.84 | |
| PF03564 | 145 | DUF1759: Protein of unknown function (DUF1759); In | 99.64 | |
| cd03714 | 119 | RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc | 99.63 | |
| PF00078 | 214 | RVT_1: Reverse transcriptase (RNA-dependent DNA po | 99.04 | |
| cd00304 | 98 | RT_like RT_like: Reverse transcriptase (RT, RNA-de | 98.7 | |
| .; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336 | 245 | DNA_pol_viral_C: DNA polymerase (viral) C-terminal | 98.7 | |
| PF08284 | 135 | RVP_2: Retroviral aspartyl protease; InterPro: IPR | 98.5 | |
| cd05484 | 91 | retropepsin_like_LTR_2 Retropepsins_like_LTR, peps | 98.47 | |
| PF12384 | 177 | Peptidase_A2B: Ty3 transposon peptidase; InterPro: | 98.37 | |
| cd05479 | 124 | RP_DDI RP_DDI; retropepsin-like domain of DNA dama | 98.32 | |
| cd06222 | 130 | RnaseH RNase H (RNase HI) is an endonuclease that | 98.24 | |
| PF13650 | 90 | Asp_protease_2: Aspartyl protease | 98.14 | |
| PF00077 | 100 | RVP: Retroviral aspartyl protease The Prosite entr | 98.08 | |
| PF09668 | 124 | Asp_protease: Aspartyl protease; InterPro: IPR0191 | 98.06 | |
| PF00075 | 132 | RNase_H: RNase H; InterPro: IPR002156 The RNase H | 98.02 | |
| PRK07708 | 219 | hypothetical protein; Validated | 97.81 | |
| PRK13907 | 128 | rnhA ribonuclease H; Provisional | 97.81 | |
| TIGR02281 | 121 | clan_AA_DTGA clan AA aspartic protease, TIGR02281 | 97.74 | |
| cd06095 | 86 | RP_RTVL_H_like Retropepsin of the RTVL_H family of | 97.72 | |
| cd01648 | 119 | TERT TERT: Telomerase reverse transcriptase (TERT) | 97.72 | |
| cd05481 | 93 | retropepsin_like_LTR_1 Retropepsins_like_LTR; peps | 97.72 | |
| cd05483 | 96 | retropepsin_like_bacteria Bacterial aspartate prot | 97.71 | |
| COG0328 | 154 | RnhA Ribonuclease HI [DNA replication, recombinati | 97.59 | |
| PF13975 | 72 | gag-asp_proteas: gag-polyprotein putative aspartyl | 97.57 | |
| cd05480 | 103 | NRIP_C NRIP_C; putative nuclear receptor interacti | 97.52 | |
| PF07727 | 246 | RVT_2: Reverse transcriptase (RNA-dependent DNA po | 97.46 | |
| cd03487 | 214 | RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr | 97.42 | |
| cd01650 | 220 | RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea | 97.22 | |
| PRK00203 | 150 | rnhA ribonuclease H; Reviewed | 97.12 | |
| PF13456 | 87 | RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH | 97.1 | |
| PRK07238 | 372 | bifunctional RNase H/acid phosphatase; Provisional | 97.06 | |
| PRK08719 | 147 | ribonuclease H; Reviewed | 97.04 | |
| PF00098 | 18 | zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi | 97.01 | |
| cd01646 | 158 | RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip | 96.87 | |
| TIGR03698 | 107 | clan_AA_DTGF clan AA aspartic protease, AF_0612 fa | 96.85 | |
| KOG0012|consensus | 380 | 96.6 | ||
| PF14223 | 119 | UBN2: gag-polypeptide of LTR copia-type | 96.59 | |
| cd00303 | 92 | retropepsin_like Retropepsins; pepsin-like asparta | 96.43 | |
| COG5082 | 190 | AIR1 Arginine methyltransferase-interacting protei | 96.35 | |
| PRK06548 | 161 | ribonuclease H; Provisional | 96.29 | |
| COG5082 | 190 | AIR1 Arginine methyltransferase-interacting protei | 96.24 | |
| PF02160 | 201 | Peptidase_A3: Cauliflower mosaic virus peptidase ( | 96.14 | |
| PF14227 | 119 | UBN2_2: gag-polypeptide of LTR copia-type | 96.12 | |
| cd06094 | 89 | RP_Saci_like RP_Saci_like, retropepsin family. Ret | 96.1 | |
| cd01651 | 226 | RT_G2_intron RT_G2_intron: Reverse transcriptases | 95.99 | |
| PTZ00368 | 148 | universal minicircle sequence binding protein (UMS | 94.83 | |
| PTZ00368 | 148 | universal minicircle sequence binding protein (UMS | 94.72 | |
| cd05482 | 87 | HIV_retropepsin_like Retropepsins, pepsin-like asp | 94.71 | |
| PF12382 | 137 | Peptidase_A2E: Retrotransposon peptidase; InterPro | 94.65 | |
| PF09337 | 39 | zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR0 | 94.56 | |
| KOG3752|consensus | 371 | 94.12 | ||
| PF14787 | 36 | zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: | 91.66 | |
| KOG4400|consensus | 261 | 91.23 | ||
| PF13696 | 32 | zf-CCHC_2: Zinc knuckle | 89.83 | |
| COG3577 | 215 | Predicted aspartyl protease [General function pred | 88.1 | |
| PF13917 | 42 | zf-CCHC_3: Zinc knuckle | 87.44 | |
| cd01709 | 346 | RT_like_1 RT_like_1: A subfamily of reverse transc | 85.15 | |
| KOG0119|consensus | 554 | 84.63 | ||
| smart00343 | 26 | ZnF_C2HC zinc finger. | 84.25 | |
| KOG4400|consensus | 261 | 82.75 |
| >cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons | Back alignment and domain information |
|---|
Probab=100.00 E-value=7.2e-41 Score=366.14 Aligned_cols=195 Identities=45% Similarity=0.767 Sum_probs=180.4
Q ss_pred eeeecCceeccCCC-CCCeEEEEcCCCCCCCcccCccccCCCCcccchhHHHhhcccccceeecccccceeeeEeCCCCC
Q psy9877 619 GYYMPHHHVVKPGS-TTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKFRINKIGISGDIAKAFLQISVSPQDR 697 (1447)
Q Consensus 619 ~~~~P~~~V~k~~~-t~k~R~v~D~~~~~~~~slN~~~~~g~~~~~~l~~~l~~~r~~~~~~~~Di~~af~qi~l~~~dr 697 (1447)
+||+|||||++++| +||+|+|+|||++.+|.|||+.+.+||+++++|.++|++||++++++++||++|||||+|+|+||
T Consensus 1 ~~y~ph~~V~~~~~~~~k~R~V~D~s~~~~g~sLN~~l~~gp~~~~~l~~iL~~~R~~~~~~~~Di~~af~qI~i~~~d~ 80 (213)
T cd01644 1 VWYLPHHAVIKPSKTTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDR 80 (213)
T ss_pred CcccCCceecCCCCCCCccEEEEecccccCCchhhHHhccCCccccchhhhheeeecCceeEehhHHHhhhheecCcccC
Confidence 49999999999999 99999999999998999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccccccceeEEEEecC-CCC-cEEEEEEeeecCccCChHHHHHHHHHHHHHhhcccCCCCCCCchhHHHhhh
Q psy9877 698 DCLSMRQPRIMVSRDCLRFLWQDE-NGR-VITYRHCRVVFGVSSSPFLLESCLKLHLELTLTDCREGKSSWPIHLVELLK 775 (1447)
Q Consensus 698 ~~~~~~~~~~~~~~~~~~f~w~~~-~~~-~~~y~~~~~pfGl~~sP~~~~~~l~~~l~~~~~~~~~~~~~~p~~~~~~~~ 775 (1447)
+ +++|+|+.. +.+ ++.|+|++||||+++||++|+++|++++.++... . +++.+.
T Consensus 81 ~--------------~~~F~w~~~~~~~~~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~--~--------~~~~i~ 136 (213)
T cd01644 81 D--------------VLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHE--A--------AAKIIK 136 (213)
T ss_pred c--------------eEEEEEeCCCCCCcceEEEEEEEccCCccchHHHHHHHHHHHhhcchh--h--------HHHHHH
Confidence 9 999999987 444 4999999999999999999999999999887654 2 566778
Q ss_pred ccccccccccccCcHHHHHHHHHHHHHHHHhcCCccccccccC--------C-------CCCCCcceeceeeecCCC
Q psy9877 776 DSFYVDNCLVSTDSQAEAEQFIQVASSIMKEKGFDLRGWELTG--------D-------KDDKPTNVLGLLWDKSSD 837 (1447)
Q Consensus 776 ~~~YvDDil~~~~s~~e~~~~~~~~~~~l~~~g~~l~k~~snp--------~-------~~~~~~k~LG~~w~~~~d 837 (1447)
..+|||||++++++.+||...++++.++|+++||+++||.||. . ..+...|.||+.|++..|
T Consensus 137 ~~~YvDDili~~~s~~e~~~~~~~v~~~L~~~Gf~l~kw~sn~~~~l~~~~~~~~~~~~~~~~~~k~LGl~W~~~~D 213 (213)
T cd01644 137 RNFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWASNSQEVLDDLPEERVLLDRDSDVTEKTLGLRWNPKTD 213 (213)
T ss_pred HeeecccceecCCCHHHHHHHHHHHHHHHHhCCccchhcccCchhhhhcccccccccccccccchhcccceeeccCC
Confidence 8999999999999999999999999999999999999999992 1 234579999999999876
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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. |
| >PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family | Back alignment and domain information |
|---|
| >cd03715 RT_ZFREV_like 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 | Back alignment and domain information |
|---|
| >cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs) | Back alignment and domain information |
|---|
| >PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function [] | Back alignment and domain information |
|---|
| >cd01647 RT_LTR 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 | Back alignment and domain information |
|---|
| >PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function | Back alignment and domain information |
|---|
| >cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons | Back alignment and domain information |
|---|
| >PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons | Back alignment and domain information |
|---|
| >cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family | Back alignment and domain information |
|---|
| >PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein | Back alignment and domain information |
|---|
| >PF08284 RVP_2: Retroviral aspartyl protease; InterPro: IPR013242 This region defines single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses) | Back alignment and domain information |
|---|
| >cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases | Back alignment and domain information |
|---|
| >PF12384 Peptidase_A2B: Ty3 transposon peptidase; InterPro: IPR024650 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families | Back alignment and domain information |
|---|
| >cd05479 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein | Back alignment and domain information |
|---|
| >cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner | Back alignment and domain information |
|---|
| >PF13650 Asp_protease_2: Aspartyl protease | Back alignment and domain information |
|---|
| >PF00077 RVP: Retroviral aspartyl protease The Prosite entry also includes Pfam:PF00026; InterPro: IPR018061 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families | Back alignment and domain information |
|---|
| >PF09668 Asp_protease: Aspartyl protease; InterPro: IPR019103 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families | Back alignment and domain information |
|---|
| >PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site | Back alignment and domain information |
|---|
| >PRK07708 hypothetical protein; Validated | Back alignment and domain information |
|---|
| >PRK13907 rnhA ribonuclease H; Provisional | Back alignment and domain information |
|---|
| >TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family | Back alignment and domain information |
|---|
| >cd06095 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements | Back alignment and domain information |
|---|
| >cd01648 TERT TERT: Telomerase reverse transcriptase (TERT) | Back alignment and domain information |
|---|
| >cd05481 retropepsin_like_LTR_1 Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats | Back alignment and domain information |
|---|
| >cd05483 retropepsin_like_bacteria Bacterial aspartate proteases, retropepsin-like protease family | Back alignment and domain information |
|---|
| >COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease | Back alignment and domain information |
|---|
| >cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein | Back alignment and domain information |
|---|
| >PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus | Back alignment and domain information |
|---|
| >cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons | Back alignment and domain information |
|---|
| >cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT) | Back alignment and domain information |
|---|
| >PRK00203 rnhA ribonuclease H; Reviewed | Back alignment and domain information |
|---|
| >PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B | Back alignment and domain information |
|---|
| >PRK07238 bifunctional RNase H/acid phosphatase; Provisional | Back alignment and domain information |
|---|
| >PRK08719 ribonuclease H; Reviewed | Back alignment and domain information |
|---|
| >PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule | Back alignment and domain information |
|---|
| >cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons | Back alignment and domain information |
|---|
| >TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family | Back alignment and domain information |
|---|
| >KOG0012|consensus | Back alignment and domain information |
|---|
| >PF14223 UBN2: gag-polypeptide of LTR copia-type | Back alignment and domain information |
|---|
| >cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases | Back alignment and domain information |
|---|
| >COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] | Back alignment and domain information |
|---|
| >PRK06548 ribonuclease H; Provisional | Back alignment and domain information |
|---|
| >COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] | Back alignment and domain information |
|---|
| >PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families | Back alignment and domain information |
|---|
| >PF14227 UBN2_2: gag-polypeptide of LTR copia-type | Back alignment and domain information |
|---|
| >cd06094 RP_Saci_like RP_Saci_like, retropepsin family | Back alignment and domain information |
|---|
| >cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin | Back alignment and domain information |
|---|
| >PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional | Back alignment and domain information |
|---|
| >PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional | Back alignment and domain information |
|---|
| >cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases | Back alignment and domain information |
|---|
| >PF12382 Peptidase_A2E: Retrotransposon peptidase; InterPro: IPR024648 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families | Back alignment and domain information |
|---|
| >PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule | Back alignment and domain information |
|---|
| >KOG3752|consensus | Back alignment and domain information |
|---|
| >PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A | Back alignment and domain information |
|---|
| >KOG4400|consensus | Back alignment and domain information |
|---|
| >PF13696 zf-CCHC_2: Zinc knuckle | Back alignment and domain information |
|---|
| >COG3577 Predicted aspartyl protease [General function prediction only] | Back alignment and domain information |
|---|
| >PF13917 zf-CCHC_3: Zinc knuckle | Back alignment and domain information |
|---|
| >cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs) | Back alignment and domain information |
|---|
| >KOG0119|consensus | Back alignment and domain information |
|---|
| >smart00343 ZnF_C2HC zinc finger | Back alignment and domain information |
|---|
| >KOG4400|consensus | Back alignment and domain information |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
No homologous structure with e-value below 0.005
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
Score = 59.1 bits (142), Expect = 1e-08
Identities = 108/705 (15%), Positives = 204/705 (28%), Gaps = 224/705 (31%)
Query: 99 QDLLQMWERCSVTQLHATQPSAGCKEYLDSLMNFL-KAEVEGVQKLELAKSG----FGVV 153
+D+L ++E V CK+ D + L K E++ + + A SG F +
Sbjct: 19 KDILSVFEDAFVDNFD-------CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 154 SSANKVESNNRRKDKHVKSPEKMN--FLKAEVEGVQKLELAKSGFGV--VSSANKVESNN 209
S K V+ ++N FL + ++ + S + +++ ++N
Sbjct: 72 LS-----KQEEMVQKFVEEVLRINYKFL---MSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 210 RRKDK-HVKSPEKVPTA-TGLVNSTPKGESCIFCSQGHYSGDCQK-----DMTLSQRQDI 262
+ K +V + L+ P I K D+ LS +
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLI-----DGVLGSGKTWVALDVCLSYKVQC 178
Query: 263 IRNKQVCYACLKFGHRVSRCRTKSRLKCEKCGSRHLTILCPRDSKSDIVTRTFVNTKSSN 322
+ ++ + L + ++ L E I S+SD + + S
Sbjct: 179 KMDFKIFW--LNLKN---CNSPETVL--EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI- 230
Query: 323 VLLQTLVVKIRGKDGKQDKLARLMIDTGSQQSYVLEQTMNSLSYTPITKQSMRHALFGGS 382
Q +L RL+ + Y N L
Sbjct: 231 ----------------QAELRRLL----KSKPYE-----NCL------------------ 247
Query: 383 ITDAMDHNLFKIVISNLDNTFACD------FDVFGQSKICSTIPSIPSGPWIDELKQHNI 436
+V L N + F++ KI T
Sbjct: 248 -----------LV---LLNV--QNAKAWNAFNL--SCKILLT--------------TRFK 275
Query: 437 ELTDLQHPSTTVDILVGADIAGKFYTGKRVELPSGLVAMETCMGWTLSGKMPTRYGSIDS 496
++TD +TT I + + L + +P + +
Sbjct: 276 QVTDFLSAATTTHISLDHHSMT-LTPDEVKSLLLKYLDCRP-------QDLPREVLTTNP 327
Query: 497 SVATLVTSLLIKDANISDLW--------------SLDVLGIQDPMDKSKADLAEAARKHF 542
+++ + D W SL+VL +P + RK F
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL---EPAE---------YRKMF 375
Query: 543 LDTVQVNSDNRFEVHLP-------WIEGHP--------PLASNLLLSQKRLEGTV----- 582
H+P W + L L+ ++ E T+
Sbjct: 376 DRLSVFPPS----AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 583 ---KKLRRDQYYADYKRVLDTWEMDKIIERVPQEELDNP---GYYMPH--HHVVK---PG 631
K++ + YA ++ ++D + I + ++L P Y+ H HH+ P
Sbjct: 432 YLELKVKLENEYALHRSIVDHY---NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE 488
Query: 632 STTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKFRINKI--GISGDIAKAFLQ 689
T R VF L+ +E K R + SG I Q
Sbjct: 489 RMTLFRMVF----------LDF------RFLE------QKIRHDSTAWNASGSILNTLQQ 526
Query: 690 ISVSPQDRDCLSMRQPRIMVSRDCLRFLWQDENGRVITYRHCRVV 734
+ + C + + +V L FL + E +I ++ ++
Sbjct: 527 LKFY-KPYICDNDPKYERLV-NAILDFLPKIEE-NLICSKYTDLL 568
|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1447 | |||
| 1rw3_A | 455 | POL polyprotein; RNA and DNA dependent DNA polymer | 100.0 | |
| 2zd1_B | 428 | P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid | 100.0 | |
| 1mu2_A | 555 | HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym | 100.0 | |
| 2zd1_A | 557 | Reverse transcriptase/ribonuclease H; P51/P66, het | 100.0 | |
| 3fsi_A | 255 | RT, reverse transcriptase domain; transferase/DNA | 99.97 | |
| 2ehg_A | 149 | Ribonuclease HI; RNAse HI, hyperthermophilic archa | 98.36 | |
| 3hst_B | 141 | Protein RV2228C/MT2287; ribonuclease H1, RV2228C N | 98.35 | |
| 3u3g_D | 140 | Ribonuclease H, RNAse H1; hydrolase, cleave the RN | 98.25 | |
| 3s8i_A | 148 | Protein DDI1 homolog 1; protease, structural genom | 98.08 | |
| 2kq2_A | 147 | Ribonuclease H-related protein; PSI, NESG, protein | 97.91 | |
| 2i1a_A | 148 | DNA damage-inducible protein DDI1; acid protease f | 97.87 | |
| 2bl6_A | 37 | Nucleocapsid protein P11; lentivirus, polyprotein, | 97.52 | |
| 3p1g_A | 165 | Xenotropic murine leukemia virus-related virus (X | 97.48 | |
| 2qkb_A | 154 | Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy | 97.45 | |
| 2cqf_A | 63 | RNA-binding protein LIN-28; CCHC zinc-finger, stru | 97.44 | |
| 3qio_A | 150 | GAG-POL polyprotein; RNAse H, inhibitor, nuclease, | 97.43 | |
| 3h08_A | 146 | RNH (ribonuclease H); RNAse H, 3D-structure, endon | 97.36 | |
| 2e4l_A | 158 | Ribonuclease HI, RNAse HI; hydrolase, endoribonucl | 97.36 | |
| 2ec7_A | 49 | GAG polyprotein (PR55GAG); nucleocapsid protein, H | 97.36 | |
| 2a51_A | 39 | Nucleocapsid protein; sivlhoest, structure, NCP8, | 97.35 | |
| 1fmb_A | 104 | EIAV protease; hydrolase (acid proteinase), RNA-di | 97.29 | |
| 1jl1_A | 155 | Ribonuclease HI; RNAse HI, protein stability, ther | 97.25 | |
| 2lsn_A | 165 | Reverse transcriptase; RNAse H, viral protein; NMR | 97.21 | |
| 3nyb_B | 83 | Protein AIR2; polya RNA polymerase, zinc knuckle p | 97.19 | |
| 1a1t_A | 55 | Nucleocapsid protein; stem-loop RNA, viral protein | 97.18 | |
| 2zd1_A | 557 | Reverse transcriptase/ribonuclease H; P51/P66, het | 97.13 | |
| 2ihx_A | 61 | Nucleocapsid (NC) protein; protein-RNA complex, vi | 97.12 | |
| 2bl6_A | 37 | Nucleocapsid protein P11; lentivirus, polyprotein, | 97.11 | |
| 1ril_A | 166 | Ribonuclease H; hydrolase(endoribonuclease); 2.80A | 97.06 | |
| 2li8_A | 74 | Protein LIN-28 homolog A; zinc finger, micro RNA, | 97.04 | |
| 1cl4_A | 60 | Protein (GAG polyprotein); nucleocapsid protein, R | 96.96 | |
| 2a51_A | 39 | Nucleocapsid protein; sivlhoest, structure, NCP8, | 96.95 | |
| 4htu_A | 134 | Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, | 96.88 | |
| 2li8_A | 74 | Protein LIN-28 homolog A; zinc finger, micro RNA, | 96.86 | |
| 2lli_A | 124 | Protein AIR2; RNA surveillance, RNA degradation, R | 96.84 | |
| 2ec7_A | 49 | GAG polyprotein (PR55GAG); nucleocapsid protein, H | 96.81 | |
| 1zbf_A | 142 | Ribonuclease H-related protein; RNAse H, RNA/DNA h | 96.69 | |
| 1dsq_A | 26 | Nucleic acid binding protein P14; CCHC type zinc f | 96.64 | |
| 1a1t_A | 55 | Nucleocapsid protein; stem-loop RNA, viral protein | 96.64 | |
| 3ts2_A | 148 | Protein LIN-28 homolog A; microrna biogenesis, pro | 96.54 | |
| 1nc8_A | 29 | Nucleocapsid protein; HIV-2, RNA recognition, zinc | 96.48 | |
| 2lli_A | 124 | Protein AIR2; RNA surveillance, RNA degradation, R | 96.46 | |
| 2ihx_A | 61 | Nucleocapsid (NC) protein; protein-RNA complex, vi | 96.28 | |
| 2cqf_A | 63 | RNA-binding protein LIN-28; CCHC zinc-finger, stru | 96.1 | |
| 3nyb_B | 83 | Protein AIR2; polya RNA polymerase, zinc knuckle p | 95.98 | |
| 1cl4_A | 60 | Protein (GAG polyprotein); nucleocapsid protein, R | 95.97 | |
| 1a6b_B | 40 | Momulv, zinc finger protein NCP10; nucleocapsid pr | 95.92 | |
| 3ts2_A | 148 | Protein LIN-28 homolog A; microrna biogenesis, pro | 95.56 | |
| 1u6p_A | 56 | GAG polyprotein; MLV, A-minor K-turn, stem loop, b | 95.41 | |
| 3ec0_A | 99 | Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1 | 95.36 | |
| 3slz_A | 132 | GAG-Pro-POL polyprotein; beta sheet and dimer, pro | 94.59 | |
| 2hs1_A | 99 | HIV-1 protease; ultra-high resolution active site | 94.58 | |
| 2hah_A | 116 | Protease, retropepsin; retroviral, aspartyl, hydro | 94.3 | |
| 3ka2_A | 203 | [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro | 93.8 | |
| 2ysa_A | 55 | Retinoblastoma-binding protein 6; zinc finger, CCH | 93.32 | |
| 2rsp_A | 124 | RSV protease; hydrolase(aspartyl proteinase); 2.00 | 90.01 | |
| 3liy_A | 116 | Protease; hydrolase, hydrolase-hydrolase inhibitor | 85.32 | |
| 3ka2_A | 203 | [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydro | 85.01 | |
| 3kyl_A | 596 | Telomerase reverse transcriptase; reverse transcri | 84.06 | |
| 3sqf_A | 114 | Protease; folded monomer, retropepsin, D-type retr | 82.53 | |
| 3oym_A | 395 | PFV integrase, P42IN; protein-DNA complex; HET: DN | 80.65 |
| >1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2 | Back alignment and structure |
|---|
Probab=100.00 E-value=2e-47 Score=470.78 Aligned_cols=399 Identities=16% Similarity=0.138 Sum_probs=317.4
Q ss_pred ChhH-HHHHHHHHHHHHcCcEEecCCCCCCCCeeeecCceeccCCCCCCeEEEEcCCCCCCCcccCccccCCCCcccchh
Q psy9877 588 DQYY-ADYKRVLDTWEMDKIIERVPQEELDNPGYYMPHHHVVKPGSTTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIP 666 (1447)
Q Consensus 588 ~~~~-~~y~~~i~~~l~~G~i~~~~~~~~~~~~~~~P~~~V~k~~~t~k~R~v~D~~~~~~~~slN~~~~~g~~~~~~l~ 666 (1447)
+++. ++++++|++|++.|+|+++.++ |++|+++|.|++ +|++|+|+|||. ||+.+.++++++|.+.
T Consensus 48 ~~~~~~~~~~~i~~ll~~G~I~~~~sp------~~spv~~V~Kk~-~g~~R~~~D~r~------LN~~~~~~~~~lp~~~ 114 (455)
T 1rw3_A 48 SQEARLGIKPHIQRLLDQGILVPCQSP------WNTPLLPVKKPG-TNDYRPVQDLRE------VNKRVEDIHPTVPNPY 114 (455)
T ss_dssp CTTHHHHSHHHHHHHHHTTSEEEECCS------CBBCEECCCCSS-SSCCCCEECTHH------HHHTBCCCCCCCCCHH
T ss_pred CHHHHHHHHHHHHHHHhCCCEEecCCc------ccCceEEEeccC-CCcEEEchhHHH------HHhhccCCCCCCCCHH
Confidence 3556 8999999999999999998654 999999998863 599999999998 9999999999999999
Q ss_pred HHHhhcc-cccceeecccccceeeeEeCCCCCCcccccccccccccceeEEEEecC-CCCcEEEEEEeeecCccCChHHH
Q psy9877 667 TSLAKFR-INKIGISGDIAKAFLQISVSPQDRDCLSMRQPRIMVSRDCLRFLWQDE-NGRVITYRHCRVVFGVSSSPFLL 744 (1447)
Q Consensus 667 ~~l~~~r-~~~~~~~~Di~~af~qi~l~~~dr~~~~~~~~~~~~~~~~~~f~w~~~-~~~~~~y~~~~~pfGl~~sP~~~ 744 (1447)
++|.+++ ++++++++|+++|||||+|+|+|++ +++|.|+.. .++.+.|+|+|||||+++||++|
T Consensus 115 ~ll~~l~~~~~~~s~lDl~~~y~qi~l~~~d~~--------------~taF~~~~p~~~~~g~y~~~~mpfGl~naP~~f 180 (455)
T 1rw3_A 115 NLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQP--------------LFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLF 180 (455)
T ss_dssp HHHTTCCTTCCEEEEEEBTTGGGGSBBCSTTSG--------------GGCEEECTTSSSCCEEEEESBCCSSCTTHHHHH
T ss_pred HHhhhhccCCceEEecchhhhheeEeccccccc--------------eeEEeecCCCCCCCceEEEEecCCCCCCcHHHH
Confidence 9999997 8999999999999999999999999 999999744 45679999999999999999999
Q ss_pred HHHHHHHHHHhhcccCCCCCCCchhHHHhhhccccccccccccCcHHHHHHHHHHHHHHHHhcCCccccccccCCCCCCC
Q psy9877 745 ESCLKLHLELTLTDCREGKSSWPIHLVELLKDSFYVDNCLVSTDSQAEAEQFIQVASSIMKEKGFDLRGWELTGDKDDKP 824 (1447)
Q Consensus 745 ~~~l~~~l~~~~~~~~~~~~~~p~~~~~~~~~~~YvDDil~~~~s~~e~~~~~~~~~~~l~~~g~~l~k~~snp~~~~~~ 824 (1447)
|++|+.++.++...++. ..+.+|||||+|++++.++|.++++.+.+.|+++||.++..+|. .....
T Consensus 181 q~~m~~~l~~~~~~~~~------------~~v~~YvDDili~s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~--f~~~~ 246 (455)
T 1rw3_A 181 DEALHRDLADFRIQHPD------------LILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRASAKKAQ--ICQKQ 246 (455)
T ss_dssp HHHHHHHHHHHHHTCTT------------CEEEEETTEEEEEESSHHHHHHHHHHHHHHHHHHTCCBCGGGCC--CSBSS
T ss_pred HHHHHHHHHHhhhhCCC------------ceEEEEcCCEEEecCCHHHHHHHHHHHHHHHHHcCCccCccchh--hhccc
Confidence 99999999987644433 23458999999999999999999999999999999999866665 23457
Q ss_pred cceeceeeecCCCeEEEeecccccc--CcCCchHHHHHhhhhhhcCccccccceeehhHHHHHHHHh-cCCCCCccCChh
Q psy9877 825 TNVLGLLWDKSSDTLAINIDRLTSM--HIEKITKKVMLSAAHRIFDPIGVICAFALIPKLLIQKTWE-TGLAWNDEVDEN 901 (1447)
Q Consensus 825 ~k~LG~~w~~~~d~~~~~~~~~~~~--~~~~~TkR~~~s~~~~~~dplg~~~p~~~~~k~llq~l~~-~~~~Wd~~l~~~ 901 (1447)
.++||+.|+..+ +.+...+...+ -+.+.|++++.+++|.+-.+..++..+...++.+.+.+.+ ..+.|++ +
T Consensus 247 ~~fLG~~i~~~g--i~~~~~kv~~i~~~~~p~t~k~l~~flG~~~y~r~fi~~~~~~~~pL~~llkk~~~~~W~~----~ 320 (455)
T 1rw3_A 247 VKYLGYLLKEGQ--RWLTEARKETVMGQPTPKTPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFNWGP----D 320 (455)
T ss_dssp CEETTEEESSSE--ECCCTTCCCCCCCCCTTTHHHHHHHTTTTTCCCSSCCCCCGGGCCTTCC--------CCCC----C
T ss_pred eeEeeeeccCCe--eEEChhHhhhhccCCCCCCHHHhhhhcccchHHHHHHhhhhhhcccHHHHhcCCCCcCchH----H
Confidence 899999988543 44333211111 1457899999999987555555554444444444333333 2577877 6
Q ss_pred hHHHHHHHHhhcCccceeecceeeeCCCCCCCCcceEEEEecccccceeeEEEEEEEecCCceEEEEEeeecccccCCCC
Q psy9877 902 TKTKFVQWMAEVPDIAEIRVPRWISEPNVESRESWSLHVFSDASKLAYAAAVFLRVEHSKTKVSLHLLAARARVAPSSKS 981 (1447)
Q Consensus 902 ~~~~~~~~~~~l~~l~~~~ipR~~~~~~~~~~~~~~L~vftDAS~~g~gavly~r~~~~~g~~~~~~~~sksr~~p~k~~ 981 (1447)
+..+|+.+++.|.+.+.+..|+. ..++++|||||..|+|||+++. .+|..++..++||+...+.+
T Consensus 321 ~~~af~~lK~~l~~~pvL~~p~~----------~~~~~l~~DAS~~~~gavL~q~---~~~~~~~i~y~Sk~l~~~e~-- 385 (455)
T 1rw3_A 321 QQKAYQEIKQALLTAPALGLPDL----------TKPFELFVDEKQGYAKGVLTQK---LGPWRRPVAYLSKKLDPVAA-- 385 (455)
T ss_dssp CSSSCCHHHHHTCSSCCSCCSSS----------CCTTSCEEEEEECSSSBEECCB---CTTTTCCCCCCCBCSCSSCS--
T ss_pred HHHHHHHHHHHhhcCcccccCCC----------CCcEEEEEeccCCcceeEEEEe---cCCcEEEEEEEcccCCcccc--
Confidence 77889999999998777777663 3467889999999999999875 46667788889998888887
Q ss_pred CCcccchhHhHHHHHHHHHHHHHHHHhccccccceEEEechHHHHHHHhcC-CCcchhhhhhHHHhhhcCC-CceEEEc
Q psy9877 982 KSTLTIPRLELLAASIATRLCQTVVKDYKLQDVRTTFWTDATTVLAWIRRN-EPWNVFVMNRITEIRNLSQ-EHEWRHV 1058 (1447)
Q Consensus 982 ~~~~siprlEL~A~~~a~~~~~~l~~~l~~~~~~~~~~tDs~~~l~~i~~~-~~~~~~v~nrv~~I~~~~~-~~~~~hv 1058 (1447)
+|+++++||+|++.|++.+..++ ....++++|||. +++|+.+. .+| +..+|+.++...+. .+.+.++
T Consensus 386 --~ys~~ekEllAi~~a~~~~~~yl-----~g~~~~v~tDh~-~~~~l~~~~~~~--~~~~Rl~rW~~~L~e~~~i~~~ 454 (455)
T 1rw3_A 386 --GWPPCLRMVAAIAVLTKDAGKLT-----MGQPLVIKAPHA-VEALVKQPPDRW--LSNARMTHYQALLLDTDRVQFG 454 (455)
T ss_dssp --SSCCSSHHHHHHHHHHHHHHGGG-----CSSCEEEECSSC-TTTTSSSTTTTT--CCCCCCSCCCCCCCCCCSSSSC
T ss_pred --ccchHHHHHHHHHHHHHHHHHHc-----CCCcEEEEecCh-HHHHhCCCcccc--ccchHHHHHHHHhCcCCCeEee
Confidence 99999999999999999777666 346899999998 99999987 444 33455555555544 3444443
|
| >2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ... | Back alignment and structure |
|---|
| >1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B | Back alignment and structure |
|---|
| >2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... | Back alignment and structure |
|---|
| >3fsi_A RT, reverse transcriptase domain; transferase/DNA MMLV RT, protein-DNA complex, drug-DNA complex; HET: OWL; 1.75A {Moloney murine leukemia virus} SCOP: e.8.1.2 PDB: 1d1u_A 1n4l_A* 1ztt_A 2fjv_A* 2fjw_A 2fjx_A* 2fvp_A 2fvq_A 2fvr_A 2fvs_A 2r2r_A* 2r2s_A* 2r2t_A* 2r2u_A* 1ztw_A* 1i6j_A 1qaj_A* 1d0e_A* 1nnd_A 1mml_A ... | Back alignment and structure |
|---|
| >2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A | Back alignment and structure |
|---|
| >3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} | Back alignment and structure |
|---|
| >3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} | Back alignment and structure |
|---|
| >3s8i_A Protein DDI1 homolog 1; protease, structural genomics, structural genomics consortiu retropepsin-like domain, protein turnover, hydrolase; 1.70A {Homo sapiens} | Back alignment and structure |
|---|
| >2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A | Back alignment and structure |
|---|
| >2i1a_A DNA damage-inducible protein DDI1; acid protease fold, dimer, retroviral protease domain, protein turnover; HET: DNA; 2.30A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} | Back alignment and structure |
|---|
| >3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A | Back alignment and structure |
|---|
| >2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* | Back alignment and structure |
|---|
| >2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A | Back alignment and structure |
|---|
| >3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} | Back alignment and structure |
|---|
| >2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A | Back alignment and structure |
|---|
| >2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 | Back alignment and structure |
|---|
| >2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} | Back alignment and structure |
|---|
| >1fmb_A EIAV protease; hydrolase (acid proteinase), RNA-directed DNA polymerase, AS protease, endonuclease, polyprotein; HET: HYB; 1.80A {Equine infectious anemia virus} SCOP: b.50.1.1 PDB: 2fmb_A* | Back alignment and structure |
|---|
| >1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ... | Back alignment and structure |
|---|
| >2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus} | Back alignment and structure |
|---|
| >3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A | Back alignment and structure |
|---|
| >2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... | Back alignment and structure |
|---|
| >2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} | Back alignment and structure |
|---|
| >2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} | Back alignment and structure |
|---|
| >1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A | Back alignment and structure |
|---|
| >2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A | Back alignment and structure |
|---|
| >2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} | Back alignment and structure |
|---|
| >4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A | Back alignment and structure |
|---|
| >2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 | Back alignment and structure |
|---|
| >1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A* | Back alignment and structure |
|---|
| >1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A | Back alignment and structure |
|---|
| >3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* | Back alignment and structure |
|---|
| >1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A | Back alignment and structure |
|---|
| >2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} | Back alignment and structure |
|---|
| >2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A | Back alignment and structure |
|---|
| >1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1 | Back alignment and structure |
|---|
| >3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* | Back alignment and structure |
|---|
| >1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A | Back alignment and structure |
|---|
| >3ec0_A Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1.18A {Human immunodeficiency virus type 2} SCOP: b.50.1.1 PDB: 1hii_A* 1hsi_A 1hsh_A* 1idb_A* 1jld_A* 2mip_A 1ida_A* 3ebz_A* 3ecg_A* 3s45_A* 4upj_A* 1ivq_A* 1ivp_A 2hpf_A 3upj_A* 2hpe_A* 5upj_A* 6upj_A* 1sip_A 1tcw_A* ... | Back alignment and structure |
|---|
| >3slz_A GAG-Pro-POL polyprotein; beta sheet and dimer, protease, peptide inhibitor, TL-3 PEPS virus, hydrolase-hydrolase inhibitor complex; HET: 3TL; 1.40A {Dg-75 murine leukemia virus} PDB: 3nr6_A* 3sm1_A* 3sm2_A* 4exh_A* | Back alignment and structure |
|---|
| >2hs1_A HIV-1 protease; ultra-high resolution active site surface binding site, HYDR; HET: 017; 0.84A {Human immunodeficiency virus 1} PDB: 3nu4_A* 3tl9_A* 3tkw_A* 3tkg_A* 3ndu_A* 3ndt_A* 3k4v_A* 3a2o_A* 1fgc_C* 2a1e_A* 2aod_A* 2aoi_A* 2aoj_A* 2hb3_A* 2ien_A* 1sdt_A* 2z4o_A* 2zye_A* 2nmw_A* 3b7v_A* ... | Back alignment and structure |
|---|
| >2hah_A Protease, retropepsin; retroviral, aspartyl, hydrolase-hydrolase complex; HET: 3TL; 1.70A {Feline immunodeficiency virus} PDB: 3ogp_A* 3ogq_A* 2fiv_A* 6fiv_A* 3fiv_A* 5fiv_A* 4fiv_A* 1fiv_A* 1b11_A* | Back alignment and structure |
|---|
| >3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB: 3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A* 3nxn_A* 4epj_A 4ep2_A 4ep3_A 4eq0_A 4eqj_A 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A 3kt2_A ... | Back alignment and structure |
|---|
| >2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} | Back alignment and structure |
|---|
| >2rsp_A RSV protease; hydrolase(aspartyl proteinase); 2.00A {Rous sarcoma virus} SCOP: b.50.1.1 PDB: 1mvp_A 1bai_A* | Back alignment and structure |
|---|
| >3liy_A Protease; hydrolase, hydrolase-hydrolase inhibitor complex; HET: STA; 1.86A {Human t-lymphotropic virus 1} PDB: 2b7f_A* 3liq_A* 3lit_A* 3liv_A* 3lix_A* 3lin_A* | Back alignment and structure |
|---|
| >3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB: 3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A* 3nxn_A* 4epj_A 4ep2_A 4ep3_A 4eq0_A 4eqj_A 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A 3kt2_A ... | Back alignment and structure |
|---|
| >3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A {Tribolium castaneum} PDB: 3du5_A 3du6_A | Back alignment and structure |
|---|
| >3sqf_A Protease; folded monomer, retropepsin, D-type retrovirus; 1.63A {Mason-pfizer monkey virus} SCOP: b.50.1.1 PDB: 1nso_A | Back alignment and structure |
|---|
| >3oym_A PFV integrase, P42IN; protein-DNA complex; HET: DNA; 2.02A {Human spumaretrovirus} PDB: 3oyn_A* 3s3o_A* 4be2_A* 3l2q_A 3l2s_A 3l2r_A* 3l2u_A* 3l2v_A* 3l2w_A* 3l2t_A* 3os1_A* 3os2_A* 3os0_A* 3oya_A* 3oy9_A* 3oyc_A* 3oyd_A* 3oye_A* 3oyb_A* 3oyg_A* ... | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 1447 | ||||
| d2exfa1 | 42 | g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod | 0.002 |
| >d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 | Back information, alignment and structure |
|---|
class: Small proteins fold: Retrovirus zinc finger-like domains superfamily: Retrovirus zinc finger-like domains family: Retrovirus zinc finger-like domains domain: HIV nucleocapsid species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]
Score = 35.2 bits (81), Expect = 0.002
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCGSR-HLTILCP 303
C+ C K GH CR + C KCG H C
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1447 | |||
| d2zd1b1 | 424 | HIV-1 reverse transcriptase {Human immunodeficienc | 100.0 | |
| d1mu2a2 | 427 | HIV-1 reverse transcriptase {Human immunodeficienc | 100.0 | |
| d1ztwa1 | 255 | MMLV reverse transcriptase {Moloney murine leukemi | 99.96 | |
| d1hara_ | 216 | HIV-1 reverse transcriptase {Human immunodeficienc | 99.96 | |
| d2exfa1 | 42 | HIV nucleocapsid {Human immunodeficiency virus typ | 97.6 | |
| d1s1ta1 | 110 | HIV RNase H (Domain of reverse transcriptase) {Hum | 97.6 | |
| d1mu2a1 | 126 | HIV RNase H (Domain of reverse transcriptase) {Hum | 97.53 | |
| d1nc8a_ | 29 | HIV nucleocapsid {Human immunodeficiency virus typ | 97.36 | |
| d2exfa1 | 42 | HIV nucleocapsid {Human immunodeficiency virus typ | 97.35 | |
| d1jl1a_ | 152 | RNase H (RNase HI) {Escherichia coli [TaxId: 562]} | 96.92 | |
| d1zbfa1 | 132 | BH0863-like Ribonuclease H {Bacillus halodurans [T | 96.8 | |
| d2fmba_ | 104 | EIAV protease {Equine infectious anemia virus [Tax | 96.55 | |
| d1rila_ | 147 | RNase H (RNase HI) {Thermus thermophilus [TaxId: 2 | 96.52 | |
| d4fiva_ | 113 | Feline immunodeficiency virus (FIV) protease {Feli | 96.3 | |
| d1dsqa_ | 26 | Nucleic acid binding protein p14 {Mouse mammary tu | 95.57 | |
| d2rspa_ | 124 | Rous sarcoma virus protease {Rous sarcoma virus, s | 94.93 | |
| d2nmza1 | 99 | Human immunodeficiency virus type 1 protease {Huma | 94.0 | |
| d1nsoa_ | 107 | Mason-Pfizer monkey virus protease {Simian retrovi | 93.99 | |
| d3ecga1 | 99 | Human immunodeficiency virus type 2 (HIV-2) protea | 93.33 | |
| d1hvca_ | 203 | Human immunodeficiency virus type 1 protease {Huma | 91.91 | |
| d1cl4a_ | 32 | Nucleocapsid protein from mason-pfizer monkey viru | 89.01 | |
| d1dsva_ | 31 | Nucleic acid binding protein p14 {Mouse mammary tu | 88.0 | |
| d1a6bb_ | 40 | Zinc finger protein ncp10 {Moloney murine leukemia | 86.37 | |
| d1a6bb_ | 40 | Zinc finger protein ncp10 {Moloney murine leukemia | 83.89 |
| >d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]} | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: DNA/RNA polymerases superfamily: DNA/RNA polymerases family: Reverse transcriptase domain: HIV-1 reverse transcriptase species: Human immunodeficiency virus type 1 [TaxId: 11676]
Probab=100.00 E-value=7.7e-36 Score=351.82 Aligned_cols=322 Identities=13% Similarity=0.062 Sum_probs=241.5
Q ss_pred hhH-HHHHHHHHHHHHcCcEEecCCCCCCCCeeeecCceeccCCCCCCeEEEEcCCCCCCCcccCccccCCCCcccchhH
Q psy9877 589 QYY-ADYKRVLDTWEMDKIIERVPQEELDNPGYYMPHHHVVKPGSTTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPT 667 (1447)
Q Consensus 589 ~~~-~~y~~~i~~~l~~G~i~~~~~~~~~~~~~~~P~~~V~k~~~t~k~R~v~D~~~~~~~~slN~~~~~g~~~~~~l~~ 667 (1447)
++. ++++++|++|++.|+|+++.+. ..|.+|+|+|.|++ .+|+|+|+|||. ||+.+ .+.++.+...+
T Consensus 24 ~ek~~al~~~i~~ll~~G~I~~~~s~----Sp~~sPvf~V~KKd-g~k~R~~iDyR~------LN~~t-~d~~~~~~~~~ 91 (424)
T d2zd1b1 24 EEKIKALVEICTEMEKEGKISKIGPE----NPYNTPVFAIKKKD-STKWRKLVDFRE------LNKRT-QDFWEVQLGIP 91 (424)
T ss_dssp HHHHHHHHHHHHHHHHTTSEEECCTT----CCCBBCEEEECCTT-CSSCEEEECTHH------HHHHB-CCCCCTTSCCC
T ss_pred HHHHHHHHHHHHHHHHCCeeEecCCC----CCCcCCeEEEEeCC-CCceEEEEccHH------HHHhc-CCCCCCCCcCc
Confidence 444 8999999999999999997532 24999999999987 358999999999 99998 56677777788
Q ss_pred HHhhcccccceeecccccceeeeEeCCCCCCcccccccccccccceeEEEEecC--CCCcEEEEEEeeecCccCChHHHH
Q psy9877 668 SLAKFRINKIGISGDIAKAFLQISVSPQDRDCLSMRQPRIMVSRDCLRFLWQDE--NGRVITYRHCRVVFGVSSSPFLLE 745 (1447)
Q Consensus 668 ~l~~~r~~~~~~~~Di~~af~qi~l~~~dr~~~~~~~~~~~~~~~~~~f~w~~~--~~~~~~y~~~~~pfGl~~sP~~~~ 745 (1447)
++..+.++++|+++|+++|||||+|+|+||+ +++|.+... .++.+.|+|+|||||+++||++||
T Consensus 92 ~~~~L~~~~~ft~lDl~~ay~qIpl~e~~r~--------------~tAF~~p~~~f~T~~g~y~~~vlPfGl~nsPa~Fq 157 (424)
T d2zd1b1 92 HPAGLKKKKSVTVLDVGDAYFSVPLDEDFRK--------------YTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQ 157 (424)
T ss_dssp CCTTGGGSSEEEEEECGGGGGGSBCCTTTGG--------------GGCEEECCGGGCSCCEEEEESBCCTTCTHHHHHHH
T ss_pred ChHHhcCCceEeeccccccccccCCChhhcc--------------ceeccccCcccccCCceEEEEecCCcccCcHHHHH
Confidence 8999999999999999999999999999999 999998655 578899999999999999999999
Q ss_pred HHHHHHHHHhhcccCCCCCCCchhHHHhhhccccccccccccCc-HHHHHHHHHHHHHHHHhcCCccccccccCCCCCCC
Q psy9877 746 SCLKLHLELTLTDCREGKSSWPIHLVELLKDSFYVDNCLVSTDS-QAEAEQFIQVASSIMKEKGFDLRGWELTGDKDDKP 824 (1447)
Q Consensus 746 ~~l~~~l~~~~~~~~~~~~~~p~~~~~~~~~~~YvDDil~~~~s-~~e~~~~~~~~~~~l~~~g~~l~k~~snp~~~~~~ 824 (1447)
++|+.++.++...++. +.+..|||||+|++++ .++|.+.++.|++.|.++||.+++.++ ....+
T Consensus 158 r~m~~il~~~~~~~~~------------~~i~~Y~DDIlI~S~~~~eeH~~~l~~vl~~L~~~gl~l~~Kk~---f~~~~ 222 (424)
T d2zd1b1 158 SSMTKILEPFKKQNPD------------IVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKH---QKEPP 222 (424)
T ss_dssp HHHHHHHHHHHHHCTT------------CEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHHHHC---------------
T ss_pred HHHHHHcccccccCcc------------eeEEeccceEEEecCchhHHHHHHHHHHHHHHHHhCCccchhhh---hhhcc
Confidence 9999999987765443 2345899999999984 899999999999999999998863332 23557
Q ss_pred cceeceeeecCCCeEEEeeccccccC-cCCchHHHHHhhhhhhcCccccccceeehhHHHHHHHHhcCCCCCc--cCChh
Q psy9877 825 TNVLGLLWDKSSDTLAINIDRLTSMH-IEKITKKVMLSAAHRIFDPIGVICAFALIPKLLIQKTWETGLAWND--EVDEN 901 (1447)
Q Consensus 825 ~k~LG~~w~~~~d~~~~~~~~~~~~~-~~~~TkR~~~s~~~~~~dplg~~~p~~~~~k~llq~l~~~~~~Wd~--~l~~~ 901 (1447)
++||||.+...+- .+.. .++. ..+.|.+++.+++|.+--+..++..+. ++. +..+.+....++. .++++
T Consensus 223 v~~LG~~is~~gi--~~~~---~kl~~~~p~t~kelq~fLG~~n~~r~fIp~~s--~~~-L~~ll~~~~~~~~~~~Wt~e 294 (424)
T d2zd1b1 223 FLWMGYELHPDKW--TVQP---IVLPEKDSWTVNDIQKLVGKLNWASQIYPGIK--VRQ-LSKLLRGTKALTEVIPLTEE 294 (424)
T ss_dssp CTTCCEEECGGGC--CCCC---CCCCCCSSEEHHHHHHHHHHHHHHTTTCTTCC--CHH-HHHTTCSCCCTTCEECCCHH
T ss_pred cccceeeecCCcE--eCCH---HHhccccCCCHHHHHHHHHHHHHHHHhcccch--HHH-HHHHhhhhccCCCCccCCHH
Confidence 9999999887553 3333 2222 467799999999987432223332222 222 3333333333332 24569
Q ss_pred hHHHHHHHHhhcCccceeecceeeeCCCCCCCCcceEEEEecccccceeeEEEEEEEecCCceEEEEEeee
Q psy9877 902 TKTKFVQWMAEVPDIAEIRVPRWISEPNVESRESWSLHVFSDASKLAYAAAVFLRVEHSKTKVSLHLLAAR 972 (1447)
Q Consensus 902 ~~~~~~~~~~~l~~l~~~~ipR~~~~~~~~~~~~~~L~vftDAS~~g~gavly~r~~~~~g~~~~~~~~sk 972 (1447)
.+.+|+.+++.|.+.+.+..|+ ++.+|++.+||| |+|+++|+... .+++.+....+++
T Consensus 295 ~~~af~~lK~~l~~~p~L~~~D----------p~kp~~~~~das--~~g~~~~~~~q-~~~~~~~~~~~~~ 352 (424)
T d2zd1b1 295 AELELAENREILKEPVHGVYYD----------PSKDLIAEIQKQ--GQGQWTYQIYQ-EPFKNLKTGKYAR 352 (424)
T ss_dssp HHHHHHHHHHHTTSCCTTCCCC----------TTSCCEEEEEEE--ETTEEEEEEES-STTCEEEEEEEEC
T ss_pred HHHHHHHHHHHhcccccccCCC----------CCCCEEEEEecC--CCCceEEEEEc-CCCcccceEEecc
Confidence 9999999999998855555554 456799999999 56777777764 3445655555554
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| >d1mu2a2 e.8.1.2 (A:3-429) HIV-1 reverse transcriptase {Human immunodeficiency virus type 2 [TaxId: 11709]} | Back information, alignment and structure |
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| >d1ztwa1 e.8.1.2 (A:24-278) MMLV reverse transcriptase {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} | Back information, alignment and structure |
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| >d1hara_ e.8.1.2 (A:) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]} | Back information, alignment and structure |
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| >d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} | Back information, alignment and structure |
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| >d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} | Back information, alignment and structure |
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| >d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} | Back information, alignment and structure |
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| >d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} | Back information, alignment and structure |
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| >d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} | Back information, alignment and structure |
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| >d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
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| >d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]} | Back information, alignment and structure |
|---|
| >d2fmba_ b.50.1.1 (A:) EIAV protease {Equine infectious anemia virus [TaxId: 11665]} | Back information, alignment and structure |
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| >d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
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| >d4fiva_ b.50.1.1 (A:) Feline immunodeficiency virus (FIV) protease {Feline immunodeficiency virus [TaxId: 11673]} | Back information, alignment and structure |
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| >d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} | Back information, alignment and structure |
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| >d2rspa_ b.50.1.1 (A:) Rous sarcoma virus protease {Rous sarcoma virus, strain pr-C [TaxId: 11886]} | Back information, alignment and structure |
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| >d2nmza1 b.50.1.1 (A:1-99) Human immunodeficiency virus type 1 protease {Human immunodeficiency virus type 1 [TaxId: 11676]} | Back information, alignment and structure |
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| >d1nsoa_ b.50.1.1 (A:) Mason-Pfizer monkey virus protease {Simian retrovirus 1, SRV-1 [TaxId: 11942]} | Back information, alignment and structure |
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| >d3ecga1 b.50.1.1 (A:1-99) Human immunodeficiency virus type 2 (HIV-2) protease {Human immunodeficiency virus type 2 [TaxId: 11709]} | Back information, alignment and structure |
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| >d1hvca_ b.50.1.1 (A:) Human immunodeficiency virus type 1 protease {Human immunodeficiency virus type 1 [TaxId: 11676]} | Back information, alignment and structure |
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| >d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]} | Back information, alignment and structure |
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| >d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} | Back information, alignment and structure |
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| >d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} | Back information, alignment and structure |
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| >d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} | Back information, alignment and structure |
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