Citrus Sinensis ID: 047960

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-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEKVSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIQKKQSSGGKGSPRLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCGSPNNTREGASRCKDVDWAAFSCTS
ccccccccccHHHHHcccHHHHccccccccccccccccccccccccccEEEEEcccccEEccccccccccHHHHHHHHHHHHHHHHHHHHcccccccEEEEccHHHHHHHHHHHHHHHHcccccccEEEccccccccccccEEEEEEcccccccEEEcccccHHHHHHHHcccccEEEEcccHHcccHHHHHHHHHHHHcccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccEEEEEEccccccEEcccccccccccccccccccccccccccccc
cccEEEEcccccHcccccHHHHcccccccccHHHHccccccccccccccEEEEEccccEEccccccccccHHHHHHHHHHHHHHHHHHHHcccccccEEEEcccHHHHHHHHHHHHHHHccHHEEEEEEEccccccccccEEEEEEEEEcccccEEEcccHHHHHHHHHHHccEEEEEccHHHHHccHHHHHHHHHHHHcccEEEcccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHEcccccccEEEEEccccccccccccccccEccccccccccccc
mllsvqyrmhphirdfpsrhfyqgrltdsesvinlpdevyykdpvlrpyvffdvihgreshrggsvsyqnvdeaKFGVCLYEHLQKTLKsmglgkvtvGIITPYKLQLKCLQHEFRNVlnseegkdlYINTVDafqgqerdVIIMSCVrasnhgvgfvADIRRMNVALTRARRALWVMgnagaltqsdDWAALIADSKArncymdmdslpKEFSVALAakapgygplqgkiphnarglrsagqrhrsfdmnmesrsgtpseddekvsrngnyrpfkpplenslddfdqsgeKYRDAWQHGIQkkqssggkgsprleDLVDAFWWVGLYYTLTLtgsegielshqvcgspnntregasrckdvdwaafscts
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLnseegkdlYINTVDAFQGQERDVIIMSCVRasnhgvgfvadIRRMNVALTRARRALWVMGnagaltqsddWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRSAGQRHRSfdmnmesrsgtpseddekvsrngnyrpfkpplensldDFDQSGEKYRDAWQHGIqkkqssggkgsprLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCGSpnntregasrckdvdwaafscts
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEKVSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIqkkqssggkgsPRLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCGSPNNTREGASRCKDVDWAAFSCTS
********MHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAK***********************************************************************************************EDLVDAFWWVGLYYTLTLTGSEGIELSHQVC**************DVDWAAF****
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVI****************DEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLP*************************************************************************************************************DAFWWVGLYYTLTL******************************WAAFSC**
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNA********RHRSFDMN***************SRNGNYRPFKPPLENSLDDFDQSGEKYRD*****************PRLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCG***********CKDVDWAAFSCTS
MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSV**************************************************************************************************RLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCGS**********C************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRSAGQRHRSFDMNMESRSGTPSEDDEKVSRNGNYRPFKPPLENSLDDFDQSGEKYRDAWQHGIQKKQSSGGKGSPRLEDLVDAFWWVGLYYTLTLTGSEGIELSHQVCGSPNNTREGASRCKDVDWAAFSCTS
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 ?
Query371 2.2.26 [Sep-21-2011]
Q00416 2231 Helicase SEN1 OS=Saccharo yes no 0.541 0.090 0.418 1e-42
O943871944 Uncharacterized ATP-depen yes no 0.547 0.104 0.435 1e-40
B6SFA4818 Probable helicase MAGATAM no no 0.536 0.243 0.396 2e-37
Q923551687 Helicase sen1 OS=Schizosa no no 0.517 0.113 0.401 3e-36
Q86AS0967 Probable helicase DDB_G02 yes no 0.501 0.192 0.405 2e-34
Q54I89 1331 Regulator of nonsense tra no no 0.638 0.178 0.347 7e-30
Q9FJR0 1254 Regulator of nonsense tra no no 0.536 0.158 0.367 1e-28
Q9EPU01124 Regulator of nonsense tra yes no 0.536 0.177 0.371 5e-28
Q929001129 Regulator of nonsense tra yes no 0.506 0.166 0.387 9e-28
Q9VYS3 1180 Regulator of nonsense tra yes no 0.536 0.168 0.359 9e-28
>sp|Q00416|SEN1_YEAST Helicase SEN1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SEN1 PE=1 SV=2 Back     alignment and function desciption
 Score =  174 bits (440), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 85/203 (41%), Positives = 126/203 (62%), Gaps = 2/203 (0%)

Query: 2    LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRESH 61
            LL VQYRMHP I  FPS  FYQGRL D   +  L    +++   L PY FFD+I GR+  
Sbjct: 1650 LLDVQYRMHPSISKFPSSEFYQGRLKDGPGMDILNKRPWHQLEPLAPYKFFDIISGRQEQ 1709

Query: 62   RGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNS 121
               ++SY N++E +  + L ++L +   +       +GII+PY+ Q++ ++ EF      
Sbjct: 1710 NAKTMSYTNMEEIRVAIELVDYLFRKFDNKIDFTGKIGIISPYREQMQKMRKEFARYFGG 1769

Query: 122  EEGKDLYINTVDAFQGQERDVIIMSCVRA--SNHGVGFVADIRRMNVALTRARRALWVMG 179
               K +  NT+D FQGQE+++I++SCVRA  +   VGF+ D RRMNVALTRA+ ++WV+G
Sbjct: 1770 MINKSIDFNTIDGFQGQEKEIILISCVRADDTKSSVGFLKDFRRMNVALTRAKTSIWVLG 1829

Query: 180  NAGALTQSDDWAALIADSKARNC 202
            +  +L +S  W  LI D+K R+C
Sbjct: 1830 HQRSLAKSKLWRDLIEDAKDRSC 1852
ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -
>sp|O94387|YGSA_SCHPO Uncharacterized ATP-dependent helicase C29A10.10c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC29A10.10c PE=3 SV=1 Back     alignment and function description
>sp|B6SFA4|MAA3_ARATH Probable helicase MAGATAMA 3 OS=Arabidopsis thaliana GN=MAA3 PE=2 SV=1 Back     alignment and function description
>sp|Q92355|SEN1_SCHPO Helicase sen1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sen1 PE=1 SV=1 Back     alignment and function description
>sp|Q86AS0|Y4399_DICDI Probable helicase DDB_G0274399 OS=Dictyostelium discoideum GN=DDB_G0274399 PE=3 SV=1 Back     alignment and function description
>sp|Q54I89|RENT1_DICDI Regulator of nonsense transcripts 1 OS=Dictyostelium discoideum GN=upf1 PE=3 SV=1 Back     alignment and function description
>sp|Q9FJR0|RENT1_ARATH Regulator of nonsense transcripts 1 homolog OS=Arabidopsis thaliana GN=UPF1 PE=1 SV=2 Back     alignment and function description
>sp|Q9EPU0|RENT1_MOUSE Regulator of nonsense transcripts 1 OS=Mus musculus GN=Upf1 PE=1 SV=2 Back     alignment and function description
>sp|Q92900|RENT1_HUMAN Regulator of nonsense transcripts 1 OS=Homo sapiens GN=UPF1 PE=1 SV=2 Back     alignment and function description
>sp|Q9VYS3|RENT1_DROME Regulator of nonsense transcripts 1 homolog OS=Drosophila melanogaster GN=Upf1 PE=1 SV=2 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 ?
Query371
225459354 1375 PREDICTED: uncharacterized ATP-dependent 0.824 0.222 0.802 1e-150
147779903 1408 hypothetical protein VITISV_009619 [Viti 0.824 0.217 0.802 1e-150
255545656 1352 splicing endonuclease positive effector 0.811 0.222 0.770 1e-141
224082154 1147 predicted protein [Populus trichocarpa] 0.819 0.265 0.763 1e-140
449465617 1363 PREDICTED: uncharacterized ATP-dependent 0.824 0.224 0.767 1e-140
449529064 1363 PREDICTED: LOW QUALITY PROTEIN: uncharac 0.824 0.224 0.767 1e-140
356522392 1388 PREDICTED: probable helicase senataxin-l 0.824 0.220 0.757 1e-138
356558781 1328 PREDICTED: uncharacterized ATP-dependent 0.824 0.230 0.757 1e-138
357513937 1516 Helicase sen1 [Medicago truncatula] gi|3 0.819 0.200 0.725 1e-132
15234617 1311 tRNA-splicing endonuclease positive effe 0.797 0.225 0.702 1e-124
>gi|225459354|ref|XP_002284214.1| PREDICTED: uncharacterized ATP-dependent helicase C29A10.10c-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  537 bits (1384), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 252/314 (80%), Positives = 279/314 (88%), Gaps = 8/314 (2%)

Query: 1    MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRES 60
            MLLSVQYRMHPHIRDFPSR+FYQGRLTDSESV NLPDE YYKDP+LRPYVF+D+ HGRES
Sbjct: 1058 MLLSVQYRMHPHIRDFPSRYFYQGRLTDSESVTNLPDEAYYKDPLLRPYVFYDITHGRES 1117

Query: 61   HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLN 120
            HRGGSVSYQN+ EA+  + LYEHLQKTLKS+G+GK++VGIITPYKLQLKCLQ EF +VL+
Sbjct: 1118 HRGGSVSYQNIHEAQICLRLYEHLQKTLKSLGMGKISVGIITPYKLQLKCLQREFDDVLS 1177

Query: 121  SEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGN 180
            SEEGKDLYINTVDAFQGQERDVIIMSCVRAS+HGVGFVADIRRMNVALTRARRALWVMGN
Sbjct: 1178 SEEGKDLYINTVDAFQGQERDVIIMSCVRASSHGVGFVADIRRMNVALTRARRALWVMGN 1237

Query: 181  AGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRS 240
            A AL QSDDWAALI+D++AR+CY+DMDSLPKEF   L  K P YGPL GK+  N RGLRS
Sbjct: 1238 ANALMQSDDWAALISDARARSCYLDMDSLPKEF---LVPKGPTYGPLSGKVSSNMRGLRS 1294

Query: 241  AGQRHRSFDMNMESRSGTPSEDDEK-----VSRNGNYRPFKPPLENSLDDFDQSGEKYRD 295
            AG RHR  DM++ES+SGTPSEDDEK     +SRNGNYRP KP +ENSLDDFDQS +K RD
Sbjct: 1295 AGPRHRQLDMHVESKSGTPSEDDEKSNASLISRNGNYRPLKPTMENSLDDFDQSADKSRD 1354

Query: 296  AWQHGIQKKQSSGG 309
            AWQ+GIQKKQSS G
Sbjct: 1355 AWQYGIQKKQSSAG 1368

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147779903|emb|CAN65841.1| hypothetical protein VITISV_009619 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255545656|ref|XP_002513888.1| splicing endonuclease positive effector sen1, putative [Ricinus communis] gi|223546974|gb|EEF48471.1| splicing endonuclease positive effector sen1, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224082154|ref|XP_002306584.1| predicted protein [Populus trichocarpa] gi|222856033|gb|EEE93580.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449465617|ref|XP_004150524.1| PREDICTED: uncharacterized ATP-dependent helicase C29A10.10c-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449529064|ref|XP_004171521.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized ATP-dependent helicase C29A10.10c-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356522392|ref|XP_003529830.1| PREDICTED: probable helicase senataxin-like [Glycine max] Back     alignment and taxonomy information
>gi|356558781|ref|XP_003547681.1| PREDICTED: uncharacterized ATP-dependent helicase C29A10.10c-like [Glycine max] Back     alignment and taxonomy information
>gi|357513937|ref|XP_003627257.1| Helicase sen1 [Medicago truncatula] gi|355521279|gb|AET01733.1| Helicase sen1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|15234617|ref|NP_194739.1| tRNA-splicing endonuclease positive effector-related protein [Arabidopsis thaliana] gi|4938486|emb|CAB43845.1| putative protein [Arabidopsis thaliana] gi|7269910|emb|CAB81003.1| putative protein [Arabidopsis thaliana] gi|332660321|gb|AEE85721.1| tRNA-splicing endonuclease positive effector-related protein [Arabidopsis thaliana] 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 ?
Query371
TAIR|locus:21264801311 AT4G30100 [Arabidopsis thalian 0.778 0.220 0.709 5.9e-112
TAIR|locus:20590881090 AT2G19120 "AT2G19120" [Arabido 0.603 0.205 0.744 3.9e-92
POMBASE|SPBC29A10.10c1944 SPBC29A10.10c "tRNA-splicing e 0.547 0.104 0.435 3.5e-39
UNIPROTKB|G4NIZ82037 MGG_02784 "DNA-binding protein 0.665 0.121 0.401 4.2e-39
CGD|CAL00033352018 SEN1 [Candida albicans (taxid: 0.533 0.098 0.438 2.9e-38
SGD|S000004422 2231 SEN1 "Presumed helicase and su 0.536 0.089 0.429 3.4e-38
TAIR|locus:2130384818 MAA3 "MAGATAMA 3" [Arabidopsis 0.536 0.243 0.396 8.1e-35
POMBASE|SPAC6G9.10c1687 sen1 "ATP-dependent 5' to 3' D 0.514 0.113 0.404 1.4e-33
TAIR|locus:2152627638 AT5G37030 [Arabidopsis thalian 0.544 0.316 0.401 1.1e-32
TAIR|locus:20185611050 AT1G65810 [Arabidopsis thalian 0.539 0.190 0.375 4.2e-32
TAIR|locus:2126480 AT4G30100 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1105 (394.0 bits), Expect = 5.9e-112, P = 5.9e-112
 Identities = 217/306 (70%), Positives = 253/306 (82%)

Query:     1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVYYKDPVLRPYVFFDVIHGRES 60
             +LL+VQYRMHP IRDFPSR+FYQGRLTDSESV   PDE+YYKD VL+PY+FFD+ HGRES
Sbjct:  1004 LLLTVQYRMHPQIRDFPSRYFYQGRLTDSESVSTAPDEIYYKDSVLKPYLFFDISHGRES 1063

Query:    61 HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLN 120
             HRGGSVSY+N+DEA+F V +Y HLQ+TLKS+G GKV+VG+ITPYKLQLKCL+ EF N L+
Sbjct:  1064 HRGGSVSYENIDEARFCVGVYLHLQRTLKSLGGGKVSVGVITPYKLQLKCLKIEFGNALS 1123

Query:   121 SEEGKDLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGN 180
              +E +++YINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRA+RALWVMGN
Sbjct:  1124 QDELQEIYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRAKRALWVMGN 1183

Query:   181 AGALTQSDDWAALIADSKARNCYMDMDSLPKEFSVALAAKAPGYGPLQGKIPHNARGLRS 240
             A AL + +DWAALI D+KARNC+M+M+SLPK+F V    K P + P   K P NARG RS
Sbjct:  1184 ASALMKCEDWAALITDAKARNCFMEMESLPKDFPVP---KVPSFIP---KAP-NARGFRS 1236

Query:   241 AGQRHRSFDMNMESRSGTPSEDDEKVS-----RNGNYRPFKPPLENSLDDFDQSGEKYRD 295
              G R RS DM+ ESRSGTPSEDD+K+S     RNGN R      ENS+DD D  G++YRD
Sbjct:  1237 GGPRTRSIDMHPESRSGTPSEDDKKLSTTTFPRNGNSRR-----ENSVDDSDPPGDRYRD 1291

Query:   296 AWQHGI 301
             AWQHGI
Sbjct:  1292 AWQHGI 1297
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
GO:0009506 "plasmodesma" evidence=IDA
TAIR|locus:2059088 AT2G19120 "AT2G19120" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
POMBASE|SPBC29A10.10c SPBC29A10.10c "tRNA-splicing endonuclease positive effector (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|G4NIZ8 MGG_02784 "DNA-binding protein SMUBP-2" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
CGD|CAL0003335 SEN1 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
SGD|S000004422 SEN1 "Presumed helicase and subunit of the Nrd1 complex (Nrd1p-Nab3p-Sen1p)" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
TAIR|locus:2130384 MAA3 "MAGATAMA 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
POMBASE|SPAC6G9.10c sen1 "ATP-dependent 5' to 3' DNA/RNA helicase Sen1" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
TAIR|locus:2152627 AT5G37030 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2018561 AT1G65810 [Arabidopsis thaliana (taxid:3702)] 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 Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query371
pfam13087195 pfam13087, AAA_12, AAA domain 2e-75
TIGR00376637 TIGR00376, TIGR00376, DNA helicase, putative 3e-40
COG1112767 COG1112, COG1112, Superfamily I DNA and RNA helica 7e-39
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain Back     alignment and domain information 
 Score =  231 bits (591), Expect = 2e-75
 Identities = 79/182 (43%), Positives = 108/182 (59%), Gaps = 8/182 (4%)

Query: 2   LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLP-DEVYYKDPVLRPYVFFDVIHGRES 60
           +L  QYRMHP I +FPS  FY G+L D ESV   P    ++    L P VF DV    E 
Sbjct: 19  MLDTQYRMHPDISEFPSELFYGGKLKDGESVAERPLPWDFHLPDPLGPLVFIDVDGSEEE 78

Query: 61  HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLN 120
               S SY N  EA+  V   + ++K LKS       +GIITPY+ Q++ ++   +    
Sbjct: 79  -EEKSTSYSNEAEAEL-VV--QLVEKLLKSGPEKNKDIGIITPYRAQVRLIKKLLKRKFG 134

Query: 121 SEEGKDLYINTVDAFQGQERDVIIMSCVRAS-NHGVGFVADIRRMNVALTRARRALWVMG 179
                D+ +NTVD FQG+E+DVII S VR++   G+GF++D RR+NVALTRA+R L ++G
Sbjct: 135 --GEPDIEVNTVDGFQGREKDVIIFSTVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVG 192

Query: 180 NA 181
           NA
Sbjct: 193 NA 194

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 = 195
>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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 371
KOG1802935 consensus RNA helicase nonsense mRNA reducing fact 100.0
PF13087200 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP 100.0
KOG1803649 consensus DNA helicase [Replication, recombination 100.0
TIGR00376637 DNA helicase, putative. The gene product may repre 100.0
COG1112767 Superfamily I DNA and RNA helicases and helicase s 99.97
KOG18071025 consensus Helicases [Replication, recombination an 99.96
KOG1801827 consensus tRNA-splicing endonuclease positive effe 99.96
KOG18051100 consensus DNA replication helicase [Replication, r 99.95
KOG1804775 consensus RNA helicase [RNA processing and modific 99.81
KOG18061320 consensus DEAD box containing helicases [Replicati 99.5
PRK11054684 helD DNA helicase IV; Provisional 98.6
PF13538104 UvrD_C_2: UvrD-like helicase C-terminal domain; PD 97.85
PRK13909910 putative recombination protein RecB; Provisional 97.57
COG1074 1139 RecB ATP-dependent exoDNAse (exonuclease V) beta s 97.57
COG3973747 Superfamily I DNA and RNA helicases [General funct 97.25
TIGR00609 1087 recB exodeoxyribonuclease V, beta subunit. All pro 97.23
TIGR01448720 recD_rel helicase, putative, RecD/TraA family. Thi 96.86
PF01443234 Viral_helicase1: Viral (Superfamily 1) RNA helicas 96.74
PF13361351 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 96.73
TIGR01447586 recD exodeoxyribonuclease V, alpha subunit. This f 96.73
PF13361351 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 96.58
cd00221115 Vsr Very Short Patch Repair (Vsr) Endonuclease. En 96.57
COG0507696 RecD ATP-dependent exoDNAse (exonuclease V), alpha 96.4
PRK10875615 recD exonuclease V subunit alpha; Provisional 96.34
cd01038108 Endonuclease_DUF559 Domain of unknown function, ap 96.16
TIGR02768744 TraA_Ti Ti-type conjugative transfer relaxase TraA 96.06
PRK09767117 hypothetical protein; Provisional 95.6
TIGR01075715 uvrD DNA helicase II. Designed to identify uvrD me 95.35
PRK10919672 ATP-dependent DNA helicase Rep; Provisional 95.3
TIGR02785 1232 addA_Gpos recombination helicase AddA, Firmicutes 95.1
TIGR01073726 pcrA ATP-dependent DNA helicase PcrA. Designed to 94.86
PRK11773721 uvrD DNA-dependent helicase II; Provisional 94.8
TIGR027841141 addA_alphas double-strand break repair helicase Ad 94.78
TIGR01073 726 pcrA ATP-dependent DNA helicase PcrA. Designed to 94.13
TIGR01074664 rep ATP-dependent DNA helicase Rep. Designed to id 94.03
KOG1804775 consensus RNA helicase [RNA processing and modific 93.55
PRK10876 1181 recB exonuclease V subunit beta; Provisional 93.3
PRK11773721 uvrD DNA-dependent helicase II; Provisional 93.16
TIGR01075715 uvrD DNA helicase II. Designed to identify uvrD me 93.0
PRK13889988 conjugal transfer relaxase TraA; Provisional 91.56
PRK13826 1102 Dtr system oriT relaxase; Provisional 91.5
TIGR01074664 rep ATP-dependent DNA helicase Rep. Designed to id 90.49
PRK10876 1181 recB exonuclease V subunit beta; Provisional 90.3
PF04480108 DUF559: Protein of unknown function (DUF559); Inte 89.64
COG0210655 UvrD Superfamily I DNA and RNA helicases [DNA repl 89.61
TIGR00632117 vsr DNA mismatch endonuclease Vsr. All proteins in 87.18
PRK10919672 ATP-dependent DNA helicase Rep; Provisional 86.05
TIGR02784 1141 addA_alphas double-strand break repair helicase Ad 84.59
PF09848352 DUF2075: Uncharacterized conserved protein (DUF207 84.41
TIGR02785 1232 addA_Gpos recombination helicase AddA, Firmicutes 82.6
PRK14712 1623 conjugal transfer nickase/helicase TraI; Provision 81.08
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=7.4e-41  Score=338.17  Aligned_cols=201  Identities=37%  Similarity=0.626  Sum_probs=171.2

Q ss_pred             CccccccCCchhhhhcchhhccCCccccCccccCC-CCcccCCCC-CCCcEEEEEcCCCeeeecCCCCCccCHHHHHHHH
Q 047960            1 MLLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINL-PDEVYYKDP-VLRPYVFFDVIHGRESHRGGSVSYQNVDEAKFGV   78 (371)
Q Consensus         1 i~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~-~~~~~~~~~-~~~p~~f~~v~~g~~~~~~~~~S~~N~~EA~~Vv   78 (371)
                      |||.+||||||.|++|+|..||+|.|.++-..... +....++.| ...|+.|+... |.++...+++|+.|..||..+.
T Consensus       635 ~~L~vQYRmhP~lSefpsn~fY~G~LqnGVT~~~R~~~g~~~pwp~p~~pl~fy~~~-g~eeisasGtSf~Nr~Ea~~~e  713 (935)
T KOG1802|consen  635 IRLQVQYRMHPALSEFPSNMFYEGELQNGVTEIERSPLGVDFPWPQPDKPLFFYVCY-GQEEISASGTSFLNRTEAANCE  713 (935)
T ss_pred             eEEEEeeeeChhhhhcchhhhccchhhcCcchhhhccCCCCCCCCCCCCccceEEec-cceeeeccccceecHHHHHHHH
Confidence            68999999999999999999999999987543322 222222222 24677777765 6777777788999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhh--hccCCCCCeEEccccCCCCccccEEEEEccccCCC-Cc
Q 047960           79 CLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNV--LNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GV  155 (371)
Q Consensus        79 ~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~--~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~-~~  155 (371)
                      .|+..|++.    |+.+.+|||||||.+|+.+|-+.|...  +..+....|.|.|||+|||+|+|+||+||||++.+ ++
T Consensus       714 kii~~l~~~----gv~~~qIGVITpYegQr~~i~~ym~~~gsl~~~ly~~veVasVDaFQGrEKdfIIlSCVRsn~~qgI  789 (935)
T KOG1802|consen  714 KIITKLLKS----GVKPSQIGVITPYEGQRSYIVNYMQTNGSLHKDLYKEVEVASVDAFQGREKDFIILSCVRSNEHQGI  789 (935)
T ss_pred             HHHHHHHHc----CCCHHHeeeecccchhHHHHHHHHHhcCccccchhheeEEEeeccccCcccceEEEEEeeccccccc
Confidence            999988663    799999999999999999999987542  33333567899999999999999999999999975 49


Q ss_pred             cCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceecc
Q 047960          156 GFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDM  206 (371)
Q Consensus       156 gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~  206 (371)
                      ||+.|+||||||+||||.+|+||||+..|++.++|.++|.|++++.+++..
T Consensus       790 GFl~d~RRlNVaLTRaK~glvivGN~~~L~k~~LW~~li~h~~eke~l~eg  840 (935)
T KOG1802|consen  790 GFLNDPRRLNVALTRAKYGLVIVGNPKVLRKHPLWGHLITHYKEKEVLVEG  840 (935)
T ss_pred             ccccCchhhhhhhhhcccceEEecCHHHhhhchHHHHHHHHhhcccceeec
Confidence            999999999999999999999999999999999999999999999999874

>PF13087 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A 2XZL_A Back     alignment and domain information
>KOG1803 consensus DNA helicase [Replication, recombination and repair] Back     alignment and domain information
>TIGR00376 DNA helicase, putative 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
>KOG1807 consensus Helicases [Replication, recombination and repair] Back     alignment and domain information
>KOG1801 consensus tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification] Back     alignment and domain information
>KOG1805 consensus DNA replication helicase [Replication, recombination and repair] Back     alignment and domain information
>KOG1804 consensus RNA helicase [RNA processing and modification] Back     alignment and domain information
>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair] Back     alignment and domain information
>PRK11054 helD DNA helicase IV; Provisional Back     alignment and domain information
>PF13538 UvrD_C_2: UvrD-like helicase C-terminal domain; PDB: 1W36_G 3K70_G 3DMN_A 3UPU_B 3GPL_A 3E1S_A 3GP8_A Back     alignment and domain information
>PRK13909 putative recombination protein RecB; 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
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only] Back     alignment and domain information
>TIGR00609 recB exodeoxyribonuclease V, beta subunit Back     alignment and domain information
>TIGR01448 recD_rel helicase, putative, RecD/TraA family 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
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A Back     alignment and domain information
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit Back     alignment and domain information
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A Back     alignment and domain information
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease 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
>PRK10875 recD exonuclease V subunit alpha; Provisional Back     alignment and domain information
>cd01038 Endonuclease_DUF559 Domain of unknown function, appears to be related to a diverse group of endonucleases Back     alignment and domain information
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA Back     alignment and domain information
>PRK09767 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01075 uvrD DNA helicase II Back     alignment and domain information
>PRK10919 ATP-dependent DNA helicase Rep; Provisional Back     alignment and domain information
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type Back     alignment and domain information
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA Back     alignment and domain information
>PRK11773 uvrD DNA-dependent helicase II; Provisional Back     alignment and domain information
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type Back     alignment and domain information
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA Back     alignment and domain information
>TIGR01074 rep ATP-dependent DNA helicase Rep Back     alignment and domain information
>KOG1804 consensus RNA helicase [RNA processing and modification] Back     alignment and domain information
>PRK10876 recB exonuclease V subunit beta; Provisional Back     alignment and domain information
>PRK11773 uvrD DNA-dependent helicase II; Provisional Back     alignment and domain information
>TIGR01075 uvrD DNA helicase II 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
>TIGR01074 rep ATP-dependent DNA helicase Rep Back     alignment and domain information
>PRK10876 recB exonuclease V subunit beta; Provisional Back     alignment and domain information
>PF04480 DUF559: Protein of unknown function (DUF559); InterPro: IPR007569 This entry represents a protein of unknown function, but is thought to be a DNA mismatch repair endonuclease Back     alignment and domain information
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00632 vsr DNA mismatch endonuclease Vsr Back     alignment and domain information
>PRK10919 ATP-dependent DNA helicase Rep; Provisional Back     alignment and domain information
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type 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
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type Back     alignment and domain information
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional 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 ?
Query371
2wjv_A800 Crystal Structure Of The Complex Between Human Nons 1e-28
2gjk_A624 Structural And Functional Insights Into The Human U 2e-28
2xzo_A623 Upf1 Helicase - Rna Complex Length = 623 2e-28
2xzl_A802 Upf1-Rna Complex Length = 802 3e-25
4b3g_A646 Crystal Structure Of Ighmbp2 Helicase In Complex Wi 9e-15
4b3f_X646 Crystal Structure Of 1ghmbp2 Helicase Length = 646 1e-14
>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 =  123 bits (309), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 76/196 (38%), Positives = 111/196 (56%), Gaps = 8/196 (4%)
Query: 3   LSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDEVY-YKDPVLRPYVFFDVIHGRESH 61
           L VQYRMHP +  FPS  FY+G L +  +  +   + + ++ P     +FF V  G+E  
Sbjct: 584 LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEI 643
Query: 62  RGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH--EFRNVL 119
                SY N  EA       E +   L   G     +GIITPY+ Q   L    +F   L
Sbjct: 644 ASSGTSYLNRTEAAN----VEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSL 699
Query: 120 NSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-GVGFVADIRRMNVALTRARRALWVM 178
           +++  +++ I +VDAFQG+E+D II+SCVRA+ H G+GF+ D RR+NVALTRAR  + ++
Sbjct: 700 HTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIV 759
Query: 179 GNAGALTQSDDWAALI 194
           GN  AL++   W  L+
Sbjct: 760 GNPKALSKQPLWNHLL 775
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1 Helicase Core Length = 624 Back     alignment and structure
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex Length = 623 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 ?
Query371
2gk6_A624 Regulator of nonsense transcripts 1; UPF1, helicas 6e-77
2xzl_A802 ATP-dependent helicase NAM7; hydrolase-RNA complex 3e-73
2wjy_A800 Regulator of nonsense transcripts 1; nonsense medi 7e-73
3vkw_A446 Replicase large subunit; alpha/beta domain, helica 3e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-05
>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
 Score =  248 bits (634), Expect = 6e-77
 Identities = 76/210 (36%), Positives = 113/210 (53%), Gaps = 8/210 (3%)

Query: 2   LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVIN-LPDEVYYKDPVLRPYVFFDVIHGRES 60
            L VQYRMHP +  FPS  FY+G L +  +  + +     ++ P     +FF V  G+E 
Sbjct: 407 RLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEE 466

Query: 61  HRGGSVSYQNVDEAKFGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQH--EFRNV 118
                 SY N  EA     +   L K     G     +GIITPY+ Q   L    +F   
Sbjct: 467 IASSGTSYLNRTEAANVEKITTKLLK----AGAKPDQIGIITPYEGQRSYLVQYMQFSGS 522

Query: 119 LNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNHG-VGFVADIRRMNVALTRARRALWV 177
           L+++  +++ I +VDAFQG+E+D II+SCVRA+ H  +GF+ D RR+NVALTRAR  + +
Sbjct: 523 LHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 582

Query: 178 MGNAGALTQSDDWAALIADSKARNCYMDMD 207
           +GN  AL++   W  L+   K +   ++  
Sbjct: 583 VGNPKALSKQPLWNHLLNYYKEQKVLVEGP 612
>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
>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
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus} Length = 446 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query371
4b3f_X646 DNA-binding protein smubp-2; hydrolase, helicase; 100.0
2gk6_A624 Regulator of nonsense transcripts 1; UPF1, helicas 100.0
2xzl_A802 ATP-dependent helicase NAM7; hydrolase-RNA complex 100.0
2wjy_A800 Regulator of nonsense transcripts 1; nonsense medi 100.0
3dmn_A174 Putative DNA helicase; APC89291.2, lactobacillus p 99.34
3lfu_A647 DNA helicase II; SF1 helicase, ATP-binding, DNA da 98.48
3e1s_A574 Exodeoxyribonuclease V, subunit RECD; alpha and be 98.48
1pjr_A724 PCRA; DNA repair, DNA replication, SOS response, h 98.11
3upu_A459 ATP-dependent DNA helicase DDA; RECA-like domain, 97.89
3vkw_A446 Replicase large subunit; alpha/beta domain, helica 97.78
1w36_D608 RECD, exodeoxyribonuclease V alpha chain; recombin 96.76
1uaa_A673 REP helicase, protein (ATP-dependent DNA helicase 95.85
3r3p_A105 MobIle intron protein; homing endonuclease, hydrol 95.77
3hrl_A104 Endonuclease-like protein; structural genomics, PS 95.14
1uaa_A673 REP helicase, protein (ATP-dependent DNA helicase 94.83
3u4q_A 1232 ATP-dependent helicase/nuclease subunit A; helicas 93.03
1w36_B 1180 RECB, exodeoxyribonuclease V beta chain; recombina 91.85
3u4q_A 1232 ATP-dependent helicase/nuclease subunit A; helicas 85.41
1cw0_A155 Protein (DNA mismatch endonuclease); protein-DNA c 83.21
1vsr_A136 Protein (VSR endonuclease); DNA repair, mismatch r 82.65
1w36_B 1180 RECB, exodeoxyribonuclease V beta chain; recombina 81.79
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A Back     alignment and structure
Probab=100.00  E-value=4.9e-40  Score=346.89  Aligned_cols=197  Identities=29%  Similarity=0.403  Sum_probs=164.2

Q ss_pred             ccccccCCchhhhhcchhhccCCccccCccccCCCCc----ccCCCCCCCcEEEEEcCCCe--eeecCCCCCccCHHHHH
Q 047960            2 LLSVQYRMHPHIRDFPSRHFYQGRLTDSESVINLPDE----VYYKDPVLRPYVFFDVIHGR--ESHRGGSVSYQNVDEAK   75 (371)
Q Consensus         2 ~L~~qYRmhp~I~~f~n~~FY~g~L~~~~s~~~~~~~----~~~~~~~~~p~~f~~v~~g~--~~~~~~~~S~~N~~EA~   75 (371)
                      +|++||||||+|++|+|+.||+|+|.+++++......    .........|+.|+++.+..  +.....+.|+.|..||+
T Consensus       435 ~L~~qYRmhp~I~~f~n~~fY~g~L~~~~~~~~~~~~~lp~~~~~~~~~~p~~f~d~~g~~~~~~~~~~~~s~~N~~EA~  514 (646)
T 4b3f_X          435 TLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVR  514 (646)
T ss_dssp             ECCEESSSCHHHHHHHHHHHSTTCCEECTTTTTCCGGGSTTCCCCTTTTCSEEEEECTTSSCCCCC-----CCCCHHHHH
T ss_pred             ecccccCCcHHHHhhhHHhhcCCccccCcchhhhhhccccccccccccCCceEEEecCCCccccccccCCccccCHHHHH
Confidence            7999999999999999999999999988766542211    11122335689999998642  23344456899999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCceEEEEcccHHHHHHHHHHHHhhhccCCCCCeEEccccCCCCccccEEEEEccccCCC-C
Q 047960           76 FGVCLYEHLQKTLKSMGLGKVTVGIITPYKLQLKCLQHEFRNVLNSEEGKDLYINTVDAFQGQERDVIIMSCVRASNH-G  154 (371)
Q Consensus        76 ~Vv~lv~~l~~~l~~~~~~~~sIgVITpy~aQ~~~I~~~L~~~~~~~~~~~i~V~TVd~fQG~ErDVIIiS~vrs~~~-~  154 (371)
                      .|+.+++.|.+.    |+++.+|||||||++|+.+|++.|.+.     ...+.|+|||+|||+|+||||||+|+++.. .
T Consensus       515 ~V~~~v~~L~~~----gv~~~dIgVItpYraQ~~~l~~~l~~~-----~~~i~v~TVd~fQG~E~dvII~S~vrsn~~~~  585 (646)
T 4b3f_X          515 LVSLHIQALVDA----GVPARDIAVVSPYNLQVDLLRQSLVHR-----HPELEIKSVDGFQGREKEAVILSFVRSNRKGE  585 (646)
T ss_dssp             HHHHHHHHHHHH----TCCGGGEEEEESCHHHHHHHHHHHTTT-----CTTCEEEEGGGGTTCCEEEEEEECCCCCTTCC
T ss_pred             HHHHHHHHHHhc----CCCcCcEEEECCCHHHHHHHHHHHHHh-----CCCCEECChhhcccccCCEEEEEeccCCCCCC
Confidence            999998887653    789999999999999999999888642     347899999999999999999999999864 4


Q ss_pred             ccCCCCCCchhhhhHhhcccEEEEeecccccCCchHHHHHHHHHhCCceeccC
Q 047960          155 VGFVADIRRMNVALTRARRALWVMGNAGALTQSDDWAALIADSKARNCYMDMD  207 (371)
Q Consensus       155 ~gfl~d~rRLNVAlSRAK~~liVvGn~~~L~~~~~w~~ll~~a~~~~~~~~~~  207 (371)
                      +||+.++||||||+||||.+||||||..+|+.++.|++|++|+++++++...-
T Consensus       586 iGFl~~~rRlNVAlTRAk~~liivGn~~~l~~~~~~~~li~~~~~~g~~~~~~  638 (646)
T 4b3f_X          586 VGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAF  638 (646)
T ss_dssp             CCSTTCHHHHHHHHHTEEEEEEEEECHHHHTTSHHHHHHHHHHHHSSEEEEGG
T ss_pred             ccccCCcCcEEeEhhhhhCeEEEEEchHHhcCCHHHHHHHHHHHHCCCEeeHH
Confidence            99999999999999999999999999999999999999999999999987653
>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
>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
>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
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, STR genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum} 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
>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
>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
>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
>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
>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
>3r3p_A MobIle intron protein; homing endonuclease, hydrolase; 2.20A {Bacillus phage 0305phi8-36} Back     alignment and structure
>3hrl_A Endonuclease-like protein; structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; 1.95A {Neisseria gonorrhoeae fa 1090} 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
>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
>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
>1cw0_A Protein (DNA mismatch endonuclease); protein-DNA complex, intercalation, zinc, hydrolase/DNA; HET: DNA; 2.30A {Escherichia coli} SCOP: c.52.1.15 Back     alignment and structure
>1vsr_A Protein (VSR endonuclease); DNA repair, mismatch recognition, hydrolase; 1.80A {Escherichia coli} SCOP: c.52.1.15 PDB: 1odg_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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query371
d1w36d2246 Exodeoxyribonuclease V alpha chain (RecD) {Escheri 97.6
g1qhh.1623 DEXX box DNA helicase {Bacillus stearothermophilus 97.56
d1w36b2395 Exodeoxyribonuclease V beta chain (RecB), N-termin 96.72
d1uaaa2333 DEXX box DNA helicase {Escherichia coli, RepD [Tax 96.45
d1pjra2333 DEXX box DNA helicase {Bacillus stearothermophilus 95.6
d1w36c2470 Exodeoxyribonuclease V gamma chain (RecC), N-termi 93.25
d1vsra_134 Very short patch repair (VSR) endonuclease {Escher 83.26
>d1w36d2 c.37.1.19 (D:361-606) 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=97.60  E-value=1.3e-05  Score=72.05  Aligned_cols=55  Identities=27%  Similarity=0.216  Sum_probs=44.6

Q ss_pred             CeEEccccCCCCccccEEEEEccccCCCCccCCCCCCchhhhhHhhcccEEEEeecccc
Q 047960          126 DLYINTVDAFQGQERDVIIMSCVRASNHGVGFVADIRRMNVALTRARRALWVMGNAGAL  184 (371)
Q Consensus       126 ~i~V~TVd~fQG~ErDVIIiS~vrs~~~~~gfl~d~rRLNVAlSRAK~~liVvGn~~~L  184 (371)
                      .-...|||..||.|.|.||+-+....    ..+.+.+.|.||+||||+.++|+|+...|
T Consensus       172 ~ayA~TiHkaQGse~~~v~~~l~~~~----~~~~~r~l~YtaiTRAk~~~~l~~~~~~l  226 (246)
T d1w36d2         172 TTWAMTVHKSQGSEFDHAALILPSQR----TPVVTRELVYTAVTRARRRLSLYADERIL  226 (246)
T ss_dssp             SCSEEETTTTTTCCBSEEEEECCSSC----CSSSCHHHHHHHHTTBSSCEEEECCTTHH
T ss_pred             hheeccHHHhccCCCCcceeccCccc----ccccchhhHHHHHhhhhCeEEEEECHHHH
Confidence            34677999999999999998764332    23567788999999999999999987653
>d1w36b2 c.37.1.19 (B:486-880) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1uaaa2 c.37.1.19 (A:308-640) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} Back     information, alignment and structure
>d1pjra2 c.37.1.19 (A:319-651) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Back     information, alignment and structure
>d1w36c2 c.37.1.19 (C:348-817) Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vsra_ c.52.1.15 (A:) Very short patch repair (VSR) endonuclease {Escherichia coli [TaxId: 562]} Back     information, alignment and structure