Psyllid ID: psy3902

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-
TPAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPHN
cccccccEEEEEccccccccccccccccccccccEEEEccccEEEcccEEcccccccccccccccccEEEEcccccccHHHHHHHHHcccccccEEEEEccccccccEEEcHHHHHccccccHHHHHHcccccccccccccccccccccccccHHHHHccHHHHHHHcHHHHHcccccccc
cccccEEEEEEEcccccccccccccHHHHccccccEEEcccccEEEEEEEcccccHHHcccccccEEEEEEEccccccccccEEEEEEEEccccEEEEEcccHccccEEccHHHHHccccHHHHHHHHHcccccccHHHccccccccccHHHHHHHHHcccHHHHHcccHccEccccEccc
tpagyfthcvideagqatepevlvpisllhrdnghvvlagdplqlgptvFSKLGqqlelstpsgyfthcvideagqatepevlvpisllhrdnghvvlagdplqlgptvFSKLGQQLELRISLLERLtgrflysrdmsrfyatggydprlVTRLVNNYRTMPEILKISsdlfydaslvphn
tpagyfthcvideagqatePEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERltgrflysrdmsrfyatggydprlvTRLVNNYRTMPEILkissdlfydaslvphn
TPAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPHN
***GYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDAS*****
TPAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLV***
TPAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPHN
**AGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLV***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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TPAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPHN
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query181 2.2.26 [Sep-21-2011]
Q6J5K9 1274 Probable RNA helicase arm yes N/A 0.712 0.101 0.472 8e-31
Q99MV5 1187 Putative helicase Mov10l1 yes N/A 0.801 0.122 0.441 8e-29
Q9BXT6 1211 Putative helicase Mov10l1 yes N/A 0.801 0.119 0.420 6e-27
Q1LXK4 1013 Putative helicase mov-10- no N/A 0.607 0.108 0.457 1e-20
Q8GYD9 1002 Probable RNA helicase SDE yes N/A 0.580 0.104 0.486 1e-20
Q5ZKD7 967 Putative helicase MOV-10 no N/A 0.718 0.134 0.406 7e-19
Q9HCE1 1003 Putative helicase MOV-10 no N/A 0.839 0.151 0.390 8e-18
Q0V8H6 1003 Putative helicase MOV-10 no N/A 0.607 0.109 0.463 9e-18
P23249 1004 Putative helicase MOV-10 no N/A 0.602 0.108 0.443 3e-17
Q1LXK5 1015 Putative helicase mov-10- no N/A 0.591 0.105 0.452 1e-16
>sp|Q6J5K9|ARMI_DROME Probable RNA helicase armi OS=Drosophila melanogaster GN=armi PE=2 SV=3 Back     alignment and function desciption
 Score =  133 bits (334), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/129 (47%), Positives = 85/129 (65%)

Query: 51   SKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVF 110
            + LG  L+L  P+G+FTH + DEAGQ TEPE +VPI +L +    VVL+GDP QL   V 
Sbjct: 927  TTLGNFLQLGFPAGHFTHVLFDEAGQCTEPETMVPIVMLTKKRSQVVLSGDPRQLQSIVT 986

Query: 111  SKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSD 170
            S++  ++   IS LERL  R  Y +D+ RF  + GY+P ++T+L+ NYR +P I+ I S 
Sbjct: 987  SRIASKMGFSISFLERLLERSPYRKDLQRFPESSGYNPLVLTKLLYNYRALPSIMSIYSR 1046

Query: 171  LFYDASLVP 179
            LFYD  L+P
Sbjct: 1047 LFYDDELIP 1055
Probable RNA helicase required for axial polarization of the oocyte during early and mid oogenesis. Plays a central role in RNA interference (RNAi) process, a process that mediates mRNA destruction of translational repression. Required for the assembly of the RISC complex, a complex required for target RNA destruction or repression. May be required in the RISC assembly to unwind miRNAs, in the production of single-stranded miRNA from the double-stranded miRNA, a key step in RISC formation. Required both for the translational control of oskar (osk) mRNA and cytoskeletal polarization in the oocyte.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3
>sp|Q99MV5|M10L1_MOUSE Putative helicase Mov10l1 OS=Mus musculus GN=Mov10l1 PE=1 SV=1 Back     alignment and function description
>sp|Q9BXT6|M10L1_HUMAN Putative helicase Mov10l1 OS=Homo sapiens GN=MOV10L1 PE=1 SV=1 Back     alignment and function description
>sp|Q1LXK4|M10B1_DANRE Putative helicase mov-10-B.1 OS=Danio rerio GN=mov10b.1 PE=2 SV=2 Back     alignment and function description
>sp|Q8GYD9|SDE3_ARATH Probable RNA helicase SDE3 OS=Arabidopsis thaliana GN=SDE3 PE=1 SV=1 Back     alignment and function description
>sp|Q5ZKD7|MOV10_CHICK Putative helicase MOV-10 OS=Gallus gallus GN=MOV10 PE=2 SV=1 Back     alignment and function description
>sp|Q9HCE1|MOV10_HUMAN Putative helicase MOV-10 OS=Homo sapiens GN=MOV10 PE=1 SV=2 Back     alignment and function description
>sp|Q0V8H6|MOV10_BOVIN Putative helicase MOV-10 OS=Bos taurus GN=MOV10 PE=2 SV=1 Back     alignment and function description
>sp|P23249|MOV10_MOUSE Putative helicase MOV-10 OS=Mus musculus GN=Mov10 PE=1 SV=2 Back     alignment and function description
>sp|Q1LXK5|M10B2_DANRE Putative helicase mov-10-B.2 OS=Danio rerio GN=mov10b.2 PE=3 SV=1 Back     alignment and function description

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 ?
Query181
383861120 3858 PREDICTED: uncharacterized protein LOC10 0.823 0.038 0.462 9e-34
307184311 1196 Putative helicase Mov10l1 [Camponotus fl 0.696 0.105 0.511 2e-31
340709376 1193 PREDICTED: probable RNA helicase armi-li 0.690 0.104 0.519 3e-31
328792831 1138 PREDICTED: probable RNA helicase armi [A 0.801 0.127 0.462 3e-31
332019918 1240 Putative helicase Mov10l1 [Acromyrmex ec 0.696 0.101 0.515 5e-31
322800122 1309 hypothetical protein SINV_80088 [Solenop 0.707 0.097 0.5 7e-31
380023614 1261 PREDICTED: LOW QUALITY PROTEIN: probable 0.801 0.114 0.455 1e-30
307213130 711 Probable RNA helicase armi [Harpegnathos 0.707 0.180 0.5 3e-30
350420467 1154 PREDICTED: probable RNA helicase armi-li 0.690 0.108 0.511 3e-30
242005506 1199 conserved hypothetical protein [Pediculu 0.712 0.107 0.488 7e-30
>gi|383861120|ref|XP_003706034.1| PREDICTED: uncharacterized protein LOC100877332 [Megachile rotundata] Back     alignment and taxonomy information
 Score =  148 bits (373), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 75/162 (46%), Positives = 106/162 (65%), Gaps = 13/162 (8%)

Query: 17   ATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQ 76
             T P +  P+S++ R   H +  G  + LG  + + +G       P G+F+H ++DEAGQ
Sbjct: 3497 GTGPRLNCPMSVIGR---HRITVGTCIALG--ILNNMG------FPRGHFSHVLVDEAGQ 3545

Query: 77   ATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRD 136
            ATEPE+++P++ +H D G V+LAGDPLQLGP V S+L +   L  S L RL   F Y RD
Sbjct: 3546 ATEPEIMIPLNFVHSDYGQVILAGDPLQLGPVVQSRLAKNFGLDESFLTRLLRHFPYQRD 3605

Query: 137  MSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLV 178
             + F +   YDPRLVT+LV NYR++PEIL++SS LFYD+ L+
Sbjct: 3606 PNGFESQ--YDPRLVTKLVINYRSLPEILELSSSLFYDSELI 3645

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|307184311|gb|EFN70769.1| Putative helicase Mov10l1 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|340709376|ref|XP_003393286.1| PREDICTED: probable RNA helicase armi-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|328792831|ref|XP_001121242.2| PREDICTED: probable RNA helicase armi [Apis mellifera] Back     alignment and taxonomy information
>gi|332019918|gb|EGI60378.1| Putative helicase Mov10l1 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|322800122|gb|EFZ21228.1| hypothetical protein SINV_80088 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|380023614|ref|XP_003695612.1| PREDICTED: LOW QUALITY PROTEIN: probable RNA helicase armi-like [Apis florea] Back     alignment and taxonomy information
>gi|307213130|gb|EFN88652.1| Probable RNA helicase armi [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|350420467|ref|XP_003492518.1| PREDICTED: probable RNA helicase armi-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|242005506|ref|XP_002423606.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212506754|gb|EEB10868.1| conserved hypothetical protein [Pediculus humanus corporis] Back     alignment and taxonomy information

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 ?
Query181
RGD|1304735 550 Mov10l1 "Mov10l1, Moloney leuk 0.872 0.287 0.427 1.9e-27
UNIPROTKB|E1BZJ8 1192 MOV10L1 "Uncharacterized prote 0.718 0.109 0.492 3.4e-27
FB|FBgn0041164 1274 armi "armitage" [Drosophila me 0.701 0.099 0.480 1.3e-26
MGI|MGI:1891384 1187 Mov10l1 "Moloney leukemia viru 0.718 0.109 0.484 1.5e-26
UNIPROTKB|F1RXR7 1211 MOV10L1 "Uncharacterized prote 0.872 0.130 0.421 1.8e-25
UNIPROTKB|G3X7G5 1214 MOV10L1 "Uncharacterized prote 0.718 0.107 0.469 3.7e-25
UNIPROTKB|Q9BXT6 1211 MOV10L1 "Putative helicase Mov 0.718 0.107 0.461 7.7e-25
ZFIN|ZDB-GENE-061013-333 1106 zgc:154086 "zgc:154086" [Danio 0.668 0.109 0.472 1.2e-22
ZFIN|ZDB-GENE-030131-9089 1013 mov10b.1 "Moloney leukemia vir 0.607 0.108 0.457 1e-19
ZFIN|ZDB-GENE-091230-8 1001 mov10a "Moloney leukemia virus 0.613 0.110 0.508 2.1e-19
RGD|1304735 Mov10l1 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
 Score = 313 (115.2 bits), Expect = 1.9e-27, P = 1.9e-27
 Identities = 68/159 (42%), Positives = 92/159 (57%)

Query:    19 EPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQAT 78
             E  ++  I    RD G  +      ++  T  S  G   ++    GYFTH  +DEAGQA+
Sbjct:   199 EETIIEAIKPYCRD-GEDIWRASRFRIIITTCSSAGLFYQIGVRVGYFTHVFVDEAGQAS 257

Query:    79 EPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMS 138
             EPE L+P+ L+   NG +VLAGDP+QLGP + S+L     L +S+LERL  R  Y RD +
Sbjct:   258 EPECLIPLGLISDINGQIVLAGDPMQLGPVIKSRLAMAYGLNVSMLERLMSRPAYLRDEN 317

Query:   139 RFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASL 177
              F A G Y+P LVT+LV NYR+   +L + S LFY   L
Sbjct:   318 AFGACGAYNPLLVTKLVKNYRSHSALLALPSRLFYHREL 356
GO:0007281 "germ cell development" evidence=ISO
GO:0007283 "spermatogenesis" evidence=ISO
GO:0007517 "muscle organ development" evidence=ISO
GO:0008283 "cell proliferation" evidence=ISO
GO:0045786 "negative regulation of cell cycle" evidence=ISO
UNIPROTKB|E1BZJ8 MOV10L1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
FB|FBgn0041164 armi "armitage" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
MGI|MGI:1891384 Mov10l1 "Moloney leukemia virus 10-like 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1RXR7 MOV10L1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|G3X7G5 MOV10L1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9BXT6 MOV10L1 "Putative helicase Mov10l1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-061013-333 zgc:154086 "zgc:154086" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-9089 mov10b.1 "Moloney leukemia virus 10, homolog, b.1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-091230-8 mov10a "Moloney leukemia virus 10, homolog, a" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

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 ?
Query181
pfam13086220 pfam13086, AAA_11, AAA domain 5e-18
pfam13086220 pfam13086, AAA_11, AAA domain 5e-18
COG1112 767 COG1112, COG1112, Superfamily I DNA and RNA helica 5e-17
TIGR00376 637 TIGR00376, TIGR00376, DNA helicase, putative 5e-13
COG1112 767 COG1112, COG1112, Superfamily I DNA and RNA helica 2e-10
TIGR00376 637 TIGR00376, TIGR00376, DNA helicase, putative 6e-08
pfam13604195 pfam13604, AAA_30, AAA domain 0.003
pfam13604195 pfam13604, AAA_30, AAA domain 0.003
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain Back     alignment and domain information 
 Score = 77.8 bits (192), Expect = 5e-18
 Identities = 25/47 (53%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 6   FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSK 52
           F   +IDEA QATEPE L+P+ L  +    VVL GD  QL PTV S 
Sbjct: 177 FDVVIIDEAAQATEPETLIPLLLGCK---KVVLVGDHKQLPPTVLSP 220

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Length = 220
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain Back     alignment and domain information
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative Back     alignment and domain information
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative Back     alignment and domain information
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain Back     alignment and domain information
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 181
KOG1802|consensus 935 99.97
KOG1803|consensus 649 99.97
TIGR00376 637 DNA helicase, putative. The gene product may repre 99.95
KOG1805|consensus 1100 99.94
COG1112 767 Superfamily I DNA and RNA helicases and helicase s 99.86
KOG1804|consensus 775 99.81
KOG1801|consensus 827 99.76
KOG1807|consensus 1025 99.74
PF13086236 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV 99.68
KOG1806|consensus 1320 99.24
PF13604196 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL 98.8
TIGR01447 586 recD exodeoxyribonuclease V, alpha subunit. This f 98.32
TIGR01448 720 recD_rel helicase, putative, RecD/TraA family. Thi 98.25
KOG1803|consensus 649 98.22
PRK10875 615 recD exonuclease V subunit alpha; Provisional 98.21
PRK10919 672 ATP-dependent DNA helicase Rep; Provisional 98.08
PRK13889 988 conjugal transfer relaxase TraA; Provisional 98.02
PRK13826 1102 Dtr system oriT relaxase; Provisional 98.01
KOG1804|consensus 775 98.0
TIGR02768 744 TraA_Ti Ti-type conjugative transfer relaxase TraA 97.96
TIGR01073 726 pcrA ATP-dependent DNA helicase PcrA. Designed to 97.96
PRK13909 910 putative recombination protein RecB; Provisional 97.88
TIGR01075 715 uvrD DNA helicase II. Designed to identify uvrD me 97.86
PRK11773 721 uvrD DNA-dependent helicase II; Provisional 97.86
PRK14712 1623 conjugal transfer nickase/helicase TraI; Provision 97.84
COG1074 1139 RecB ATP-dependent exoDNAse (exonuclease V) beta s 97.81
TIGR00609 1087 recB exodeoxyribonuclease V, beta subunit. All pro 97.8
PF01443234 Viral_helicase1: Viral (Superfamily 1) RNA helicas 97.76
TIGR02785 1232 addA_Gpos recombination helicase AddA, Firmicutes 97.76
TIGR00376 637 DNA helicase, putative. The gene product may repre 97.76
TIGR02784 1141 addA_alphas double-strand break repair helicase Ad 97.75
TIGR01074 664 rep ATP-dependent DNA helicase Rep. Designed to id 97.74
PRK13709 1747 conjugal transfer nickase/helicase TraI; Provision 97.68
PRK10876 1181 recB exonuclease V subunit beta; Provisional 97.56
PRK11054 684 helD DNA helicase IV; Provisional 97.53
KOG1802|consensus 935 97.51
KOG1805|consensus 1100 97.37
PF09848 352 DUF2075: Uncharacterized conserved protein (DUF207 97.36
TIGR02760 1960 TraI_TIGR conjugative transfer relaxase protein Tr 97.32
PF05970 364 PIF1: PIF1-like helicase; InterPro: IPR010285 This 97.32
TIGR02760 1960 TraI_TIGR conjugative transfer relaxase protein Tr 97.3
COG0210 655 UvrD Superfamily I DNA and RNA helicases [DNA repl 97.12
PRK10536262 hypothetical protein; Provisional 96.74
PF00580315 UvrD-helicase: UvrD/REP helicase N-terminal domain 96.5
COG1112 767 Superfamily I DNA and RNA helicases and helicase s 95.86
PF02562205 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH 95.32
COG0507 696 RecD ATP-dependent exoDNAse (exonuclease V), alpha 94.61
PF13604196 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL 93.69
KOG1801|consensus 827 92.74
COG1875436 NYN ribonuclease and ATPase of PhoH family domains 92.02
PRK13709 1747 conjugal transfer nickase/helicase TraI; Provision 91.77
PF05127177 Helicase_RecD: Helicase; InterPro: IPR007807 This 90.71
COG3973 747 Superfamily I DNA and RNA helicases [General funct 89.28
KOG0387|consensus 923 84.35
PRK14712 1623 conjugal transfer nickase/helicase TraI; Provision 83.73
TIGR01447 586 recD exodeoxyribonuclease V, alpha subunit. This f 82.3
PF00580315 UvrD-helicase: UvrD/REP helicase N-terminal domain 80.89
>KOG1802|consensus Back     alignment and domain information 
Probab=99.97  E-value=1e-32  Score=240.24  Aligned_cols=145  Identities=32%  Similarity=0.446  Sum_probs=126.3

Q ss_pred             EEecCCCCCCccccccccccccCCCceEecCCCcccccceecccccccccCCCCCccceeeeccccCCCcchhhhhhhcc
Q psy3902          10 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLL   89 (181)
Q Consensus        10 ~~de~~q~~e~~~~~~l~~~~~~~~~~~l~~d~~~vv~~T~~~~~~~~~~~~~~~~fd~vIIDEAsq~~e~~~l~~l~~~   89 (181)
                      +.||.|+.+..+..+... +.+...+.++..  ++||+|||.+++...   +...+|..|+||||.|++||++|+||.+ 
T Consensus       519 lkde~gelS~sD~~k~~~-lk~~~e~ell~~--AdVIccTcv~Agd~r---l~~~kfr~VLiDEaTQatEpe~LiPlvl-  591 (935)
T KOG1802|consen  519 LKDEGGELSSSDEKKYRK-LKRAAEKELLNQ--ADVICCTCVGAGDRR---LSKFKFRTVLIDEATQATEPECLIPLVL-  591 (935)
T ss_pred             hhhhcccccchhhHHHHH-HHHHHHHHHHhh--cCEEEEecccccchh---hccccccEEEEecccccCCcchhhhhhh-
Confidence            569999999998866554 455666667764  899999999999754   3456799999999999999999999998 


Q ss_pred             ccCCCeEEEEcCCCCCCceEeccchhccchhhhHHHHHhcCcccccccccccccCCcCCccccchhhhhcChhHHHHhhh
Q psy3902          90 HRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISS  169 (181)
Q Consensus        90 ~~~~~~~vlvGD~~QL~P~v~~~~~~~~~~~~slf~rl~~~~~~~~~~~~~~~~~~~~~~~~~~L~~qyR~~~~I~~~~s  169 (181)
                        ++|++||||||+||+|++....+...++.+|||+||+..+.              .|   ++|.+||||||.|++|+|
T Consensus       592 --G~kq~VlVGDh~QLgpvi~~kK~a~Agl~qsLferli~lg~--------------~P---~~L~vQYRmhP~lSefps  652 (935)
T KOG1802|consen  592 --GAKQLVLVGDHKQLGPVIMCKKAATAGLSQSLFERLISLGI--------------KP---IRLQVQYRMHPALSEFPS  652 (935)
T ss_pred             --cceeEEEeccccccCceeeeHHHHHhHHHHHHHHHHHhccC--------------Cc---eEEEEeeeeChhhhhcch
Confidence              58999999999999999999888888999999999998853              34   679999999999999999


Q ss_pred             hhhcCCCcccC
Q psy3902         170 DLFYDASLVPH  180 (181)
Q Consensus       170 ~~fY~g~L~~~  180 (181)
                      ..||+|.|.+.
T Consensus       653 n~fY~G~LqnG  663 (935)
T KOG1802|consen  653 NMFYEGELQNG  663 (935)
T ss_pred             hhhccchhhcC
Confidence            99999999864

>KOG1803|consensus Back     alignment and domain information
>TIGR00376 DNA helicase, putative Back     alignment and domain information
>KOG1805|consensus Back     alignment and domain information
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG1804|consensus Back     alignment and domain information
>KOG1801|consensus Back     alignment and domain information
>KOG1807|consensus Back     alignment and domain information
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A Back     alignment and domain information
>KOG1806|consensus Back     alignment and domain information
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A Back     alignment and domain information
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit Back     alignment and domain information
>TIGR01448 recD_rel helicase, putative, RecD/TraA family Back     alignment and domain information
>KOG1803|consensus Back     alignment and domain information
>PRK10875 recD exonuclease V subunit alpha; Provisional Back     alignment and domain information
>PRK10919 ATP-dependent DNA helicase Rep; Provisional Back     alignment and domain information
>PRK13889 conjugal transfer relaxase TraA; Provisional Back     alignment and domain information
>PRK13826 Dtr system oriT relaxase; Provisional Back     alignment and domain information
>KOG1804|consensus Back     alignment and domain information
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA Back     alignment and domain information
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA Back     alignment and domain information
>PRK13909 putative recombination protein RecB; Provisional Back     alignment and domain information
>TIGR01075 uvrD DNA helicase II Back     alignment and domain information
>PRK11773 uvrD DNA-dependent helicase II; Provisional Back     alignment and domain information
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00609 recB exodeoxyribonuclease V, beta subunit Back     alignment and domain information
>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases Back     alignment and domain information
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type Back     alignment and domain information
>TIGR00376 DNA helicase, putative Back     alignment and domain information
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type Back     alignment and domain information
>TIGR01074 rep ATP-dependent DNA helicase Rep Back     alignment and domain information
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>PRK10876 recB exonuclease V subunit beta; Provisional Back     alignment and domain information
>PRK11054 helD DNA helicase IV; Provisional Back     alignment and domain information
>KOG1802|consensus Back     alignment and domain information
>KOG1805|consensus Back     alignment and domain information
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10536 hypothetical protein; Provisional Back     alignment and domain information
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA Back     alignment and domain information
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli [] Back     alignment and domain information
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair] Back     alignment and domain information
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A Back     alignment and domain information
>KOG1801|consensus Back     alignment and domain information
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only] Back     alignment and domain information
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase Back     alignment and domain information
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only] Back     alignment and domain information
>KOG0387|consensus Back     alignment and domain information
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit Back     alignment and domain information
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query181
2wjv_A 800 Crystal Structure Of The Complex Between Human Nons 9e-09
2xzo_A 623 Upf1 Helicase - Rna Complex Length = 623 9e-09
2gjk_A 624 Structural And Functional Insights Into The Human U 9e-09
2xzl_A 802 Upf1-Rna Complex Length = 802 2e-08
4b3g_A 646 Crystal Structure Of Ighmbp2 Helicase In Complex Wi 7e-08
4b3f_X 646 Crystal Structure Of 1ghmbp2 Helicase Length = 646 7e-08
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense Mediated Decay Factors Upf1 And Upf2 Length = 800 Back     alignment and structure 
Iteration: 1

 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 40/112 (35%), Positives = 52/112 (46%), Gaps = 20/112 (17%)
Query: 66  FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLE 125
           F   +IDE+ QATEPE +VP+ L  +    ++L GD  QLGP V  K   +  L  SL E
Sbjct: 516 FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFE 572
Query: 126 RLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASL 177
           RL                 G  P    RL   YR  P +    S++FY+ SL
Sbjct: 573 RLV--------------VLGIRP---IRLQVQYRMHPALSAFPSNIFYEGSL 607
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex Length = 623 Back     alignment and structure
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1 Helicase Core Length = 624 Back     alignment and structure
>pdb|2XZL|A Chain A, Upf1-Rna Complex Length = 802 Back     alignment and structure
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna Length = 646 Back     alignment and structure
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase Length = 646 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query181
2wjy_A 800 Regulator of nonsense transcripts 1; nonsense medi 3e-32
2wjy_A 800 Regulator of nonsense transcripts 1; nonsense medi 2e-20
2gk6_A 624 Regulator of nonsense transcripts 1; UPF1, helicas 7e-32
2gk6_A 624 Regulator of nonsense transcripts 1; UPF1, helicas 4e-20
2xzl_A 802 ATP-dependent helicase NAM7; hydrolase-RNA complex 2e-31
2xzl_A 802 ATP-dependent helicase NAM7; hydrolase-RNA complex 9e-20
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800 Back     alignment and structure
 Score =  120 bits (303), Expect = 3e-32
 Identities = 38/119 (31%), Positives = 51/119 (42%), Gaps = 20/119 (16%)

Query: 62  PSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
               F   +IDE+ QATEPE +VP+ L  +    ++L GD  QLGP V  K   +  L  
Sbjct: 512 AKMQFRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQ 568

Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
           SL ERL    +                    RL   YR  P +    S++FY+ SL   
Sbjct: 569 SLFERLVVLGIR-----------------PIRLQVQYRMHPALSAFPSNIFYEGSLQNG 610
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800 Back     alignment and structure
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Length = 624 Back     alignment and structure
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Length = 624 Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Length = 802 Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Length = 802 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query181
4b3f_X 646 DNA-binding protein smubp-2; hydrolase, helicase; 99.95
2gk6_A 624 Regulator of nonsense transcripts 1; UPF1, helicas 99.92
2wjy_A 800 Regulator of nonsense transcripts 1; nonsense medi 99.91
2xzl_A 802 ATP-dependent helicase NAM7; hydrolase-RNA complex 99.89
3vkw_A 446 Replicase large subunit; alpha/beta domain, helica 99.04
1w36_D 608 RECD, exodeoxyribonuclease V alpha chain; recombin 98.86
3e1s_A 574 Exodeoxyribonuclease V, subunit RECD; alpha and be 98.55
3lfu_A 647 DNA helicase II; SF1 helicase, ATP-binding, DNA da 98.55
3upu_A 459 ATP-dependent DNA helicase DDA; RECA-like domain, 98.5
1uaa_A 673 REP helicase, protein (ATP-dependent DNA helicase 98.06
1pjr_A 724 PCRA; DNA repair, DNA replication, SOS response, h 98.0
4b3f_X 646 DNA-binding protein smubp-2; hydrolase, helicase; 97.84
3u4q_A 1232 ATP-dependent helicase/nuclease subunit A; helicas 97.29
1w36_B 1180 RECB, exodeoxyribonuclease V beta chain; recombina 97.24
2gk6_A 624 Regulator of nonsense transcripts 1; UPF1, helicas 96.92
2wjy_A 800 Regulator of nonsense transcripts 1; nonsense medi 96.57
2xzl_A 802 ATP-dependent helicase NAM7; hydrolase-RNA complex 96.18
2l8b_A189 Protein TRAI, DNA helicase I; RECD, hydrolase; NMR 93.33
2zpa_A 671 Uncharacterized protein YPFI; RNA modification enz 92.13
3u4q_B 1166 ATP-dependent helicase/deoxyribonuclease subunit; 91.26
1w36_D 608 RECD, exodeoxyribonuclease V alpha chain; recombin 85.18
2b8t_A223 Thymidine kinase; deoxyribonucleoside kinase, zinc 84.38
2j9r_A214 Thymidine kinase; TK1, DNK, lasso, transferase, AT 83.45
3upu_A 459 ATP-dependent DNA helicase DDA; RECA-like domain, 83.05
1xx6_A191 Thymidine kinase; NESG, northeast structural genom 81.98
1z3i_X 644 Similar to RAD54-like; recombination ATPase helica 80.58
3e1s_A 574 Exodeoxyribonuclease V, subunit RECD; alpha and be 80.47
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A Back     alignment and structure
Probab=99.95  E-value=1.4e-29  Score=226.61  Aligned_cols=120  Identities=32%  Similarity=0.445  Sum_probs=104.1

Q ss_pred             cccccceecccccccc-cCCCCCccceeeeccccCCCcchhhhhhhccccCCCeEEEEcCCCCCCceEeccchhccchhh
Q psy3902          43 LQLGPTVFSKLGQQLE-LSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI  121 (181)
Q Consensus        43 ~~vv~~T~~~~~~~~~-~~~~~~~fd~vIIDEAsq~~e~~~l~~l~~~~~~~~~~vlvGD~~QL~P~v~~~~~~~~~~~~  121 (181)
                      ++||++|+++++.... ..+....||+||||||+|++||++|+|+.    +++++||||||+||||++.+..+...+++.
T Consensus       343 ~~vv~~t~~~a~~~~~~~~~~~~~Fd~vIIDEAsQ~~e~~~lipL~----~~~~~ILVGD~~QLpP~v~~~~a~~~gl~~  418 (646)
T 4b3f_X          343 ANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLL----KARKCILAGDHKQLPPTTVSHKAALAGLSL  418 (646)
T ss_dssp             CSEEEEETTTTCSSSGGGGSCTTCCSEEEETTGGGSCHHHHTTTGG----GSSEEEEEECTTSCCCCCSCHHHHHTTTTC
T ss_pred             cceeeeehhhhhhhhHHHhhhhccCCEEEEcCccccchHHHHhhcc----ccceEEEcCCccccCceecchhhhhccccc
Confidence            6799999998876432 22456789999999999999999999997    468999999999999999998888889999


Q ss_pred             hHHHHHhcCcccccccccccccCCcCCccccchhhhhcChhHHHHhhhhhhcCCCcccCC
Q psy3902         122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPHN  181 (181)
Q Consensus       122 slf~rl~~~~~~~~~~~~~~~~~~~~~~~~~~L~~qyR~~~~I~~~~s~~fY~g~L~~~~  181 (181)
                      |+|+|+...               +.+....+|++||||||+|++|+|+.||+|+|++++
T Consensus       419 SlferL~~~---------------~~~~~v~~L~~qYRmhp~I~~f~n~~fY~g~L~~~~  463 (646)
T 4b3f_X          419 SLMERLAEE---------------YGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHS  463 (646)
T ss_dssp             CHHHHHHHH---------------HGGGTEEECCEESSSCHHHHHHHHHHHSTTCCEECT
T ss_pred             hHHHHHHHh---------------cCCceeeecccccCCcHHHHhhhHHhhcCCccccCc
Confidence            999999875               234456789999999999999999999999998753
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Back     alignment and structure
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus} Back     alignment and structure
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D* Back     alignment and structure
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Back     alignment and structure
>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A* Back     alignment and structure
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4} Back     alignment and structure
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 Back     alignment and structure
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B* Back     alignment and structure
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A Back     alignment and structure
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A* Back     alignment and structure
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B* Back     alignment and structure
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Back     alignment and structure
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli} Back     alignment and structure
>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12} Back     alignment and structure
>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B* Back     alignment and structure
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D* Back     alignment and structure
>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A* Back     alignment and structure
>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A* Back     alignment and structure
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4} Back     alignment and structure
>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14 Back     alignment and structure
>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19 Back     alignment and structure
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_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 ?
Query 181
d1w36d1359 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha c 3e-09
d1w36d1359 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha c 2e-05
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Length = 359 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

 Score = 52.6 bits (125), Expect = 3e-09
 Identities = 23/103 (22%), Positives = 33/103 (32%), Gaps = 14/103 (13%)

Query: 66  FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP----TVFSKLGQQLE--- 118
               V+DEA     P +   I  L  D+  V+  GD  QL       V   +        
Sbjct: 262 LDVLVVDEASMIDLPMMSRLIDAL-PDHARVIFLGDRDQLASVEAGAVLGDICAYANAGF 320

Query: 119 --LRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYR 159
              R   L RLTG  + +   +            +  L  +YR
Sbjct: 321 TAERARQLSRLTGTHVPAGTGT----EAASLRDSLCLLQKSYR 359
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Length = 359 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query181
d1w36d1359 Exodeoxyribonuclease V alpha chain (RecD) {Escheri 99.05
d1uaaa1306 DEXX box DNA helicase {Escherichia coli, RepD [Tax 98.68
d1pjra1318 DEXX box DNA helicase {Bacillus stearothermophilus 98.58
d1w36b1485 Exodeoxyribonuclease V beta chain (RecB), N-termin 98.26
g1qhh.1 623 DEXX box DNA helicase {Bacillus stearothermophilus 96.0
d1w36d1359 Exodeoxyribonuclease V alpha chain (RecD) {Escheri 93.67
d1z63a1230 Helicase of the SNF2/Rad54 hamily {Sulfolobus solf 82.59
d1yksa1140 YFV helicase domain {Yellow fever virus [TaxId: 11 80.15
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=99.05  E-value=2.3e-11  Score=99.85  Aligned_cols=48  Identities=27%  Similarity=0.257  Sum_probs=38.7

Q ss_pred             CCccceeeeccccCCCcchhhhhhhccccCCCeEEEEcCCCCCCceEec
Q psy3902          63 SGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFS  111 (181)
Q Consensus        63 ~~~fd~vIIDEAsq~~e~~~l~~l~~~~~~~~~~vlvGD~~QL~P~v~~  111 (181)
                      ...+|++|||||||++++.+...+.... ...++||+||+.|||||-.+
T Consensus       259 ~l~~d~lIIDEaSmv~~~l~~~ll~~~~-~~~~lILvGD~~QLppV~~G  306 (359)
T d1w36d1         259 PLHLDVLVVDEASMIDLPMMSRLIDALP-DHARVIFLGDRDQLASVEAG  306 (359)
T ss_dssp             CCSCSEEEECSGGGCBHHHHHHHHHTCC-TTCEEEEEECTTSGGGTSTT
T ss_pred             ccccceeeehhhhccCHHHHHHHHHHhc-CCCEEEEECChhhccCCCCC
Confidence            3469999999999999887665555443 46899999999999998443
>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} Back     information, alignment and structure
>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Back     information, alignment and structure
>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Back     information, alignment and structure