254780823
double-strand break repair protein AddB
| GeneID in NCBI database: | 8209829 | Locus tag: | CLIBASIA_03580 |
| Protein GI in NCBI database: | 254780823 | Protein Accession: | YP_003065236.1 |
| Gene range: | +(426908, 430030) | Protein Length: | 1040aa |
| Gene description: | double-strand break repair protein AddB | ||
| COG prediction: | [L] Inactivated superfamily I helicase | ||
| KEGG prediction: | double-strand break repair protein AddB | ||
| SEED prediction: | FIG041266: ATP-dependent nuclease subunit B | ||
| Pathway involved in KEGG: | not defined | ||
| Subsystem involved in SEED: | - none - | ||
| sequence | sequence profile | ||
Prediction of Local Sequence Properties
| Source | Summary | Result |
|---|
|
|
Close Homologs Detected by BLAST or PSI-BLAST
Homolog within the Genome Detected by BLAST
Original result of BLAST against C. L. asiaticus genome
No hits with e-value below 0.05
Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations
Original result of PSI-BLAST first 2 iterations
| Identity | Alignment graph | Length | Definition | Round | E-value |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | |||
| 315122047 | 1050 | double-strand break repair protein AddB [Candidatus Lib | 1 | 0.0 | |
| 222084228 | 1063 | double-strand break repair protein AddB [Agrobacterium | 1 | 0.0 | |
| 150398435 | 1059 | double-strand break repair protein AddB [Sinorhizobium | 1 | 0.0 | |
| 222147061 | 1062 | double-strand break repair protein AddB [Agrobacterium | 1 | 0.0 | |
| 325291477 | 1061 | double-strand break repair protein AddB [Agrobacterium | 1 | 0.0 | |
| 15963788 | 1059 | hypothetical protein SMc02759 [Sinorhizobium meliloti 1 | 1 | 0.0 | |
| 307310976 | 1059 | double-strand break repair protein AddB [Sinorhizobium | 1 | 0.0 | |
| 209551531 | 1064 | double-strand break repair protein AddB [Rhizobium legu | 1 | 0.0 | |
| 15887383 | 1061 | hypothetical protein Atu0024 [Agrobacterium tumefaciens | 1 | 0.0 | |
| 116249793 | 1063 | hypothetical protein RL0027 [Rhizobium leguminosarum bv | 1 | 0.0 |
| >gi|315122047|ref|YP_004062536.1| double-strand break repair protein AddB [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 1050 | Back alignment and organism information |
|---|
Score = 1544 bits (3998), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 760/1051 (72%), Positives = 885/1051 (84%), Gaps = 12/1051 (1%)
Query: 1 MHNKKPNVFTIAPSSPFFREMIPALLNGTLVENFRYDPLNPLLLASVTIYVPTKRAIQEL 60
M NKKPN+FTIAPSS FFREM+ +LLNGTLVE+F+YDP NPL LAS+TIYVPTKRAIQ L
Sbjct: 1 MENKKPNIFTIAPSSSFFREMVLSLLNGTLVESFQYDPSNPLSLASITIYVPTKRAIQAL 60
Query: 61 RSEFIEITGKKSTILPIIKSLGDVVEEKFTADLLLSYNLNPPVSNIQRLLELARLILIWR 120
RSEF G+KS ILP+IK LGD+V+E F D LS NLNPP+SN++RLLELARLIL WR
Sbjct: 61 RSEFTAAIGEKSIILPVIKPLGDIVDENFNTDFPLSCNLNPPISNMKRLLELARLILAWR 120
Query: 121 NKLPDIIKDLYPESPLSLPISPANAIWLAKNLADIIDIIETEEKKWEDLHALKNEKYGMW 180
N+ P+ IKD+YPESPL LP SPA+AIWLAKNLADIID+IE EEKKWEDL+ L+N+KYGMW
Sbjct: 121 NQFPNKIKDIYPESPLILPASPADAIWLAKNLADIIDVIEIEEKKWEDLYTLENDKYGMW 180
Query: 181 WLLAADFLKIASKYWTERLVELNASSPVGYQIALMRAEAEHLMK--GTKGPIIIAGSTGS 238
WL A DFLKIAS+YW +RL EL+ SS V YQIALMRAEAE++ K GT GPII+AGSTGS
Sbjct: 181 WLFALDFLKIASEYWKDRLSELSVSSAVHYQIALMRAEAEYIAKRKGT-GPIIVAGSTGS 239
Query: 239 IPATARLMSTVANHPNGAIVLPGLDCHIPTAIWNTITEKSTNITSSNTTYSTHPQYSLAK 298
+PATARLMS VA+ PNGAIVLPG+D +P+ IW+TI+EKS NIT SN T+ +PQYSL+K
Sbjct: 240 MPATARLMSAVASDPNGAIVLPGVDVFMPSNIWDTISEKSNNITQSNATHPMNPQYSLSK 299
Query: 299 LLDFLDIKREDVKRLGNVSNEMYGRSMVISKSFLPPDTSDMRNTDILENKIPNIQKCFSD 358
LL FL IKREDVK LG V++EM RS++ISKSF P + + +TD +E+KI ++QK FSD
Sbjct: 300 LLHFLKIKREDVKCLGIVNDEMRMRSIIISKSFFPSGSFNTYDTDRMEDKILDLQKSFSD 359
Query: 359 VALIEADNEREEAISIAIALRMSLDENKK-KSALITADRNLARRVKLELTRFGINIDISA 417
VALIEA+NEREEA SIAIALRMSLDENKK KSALITADRNLARRVKLEL RFGI++DISA
Sbjct: 360 VALIEANNEREEATSIAIALRMSLDENKKTKSALITADRNLARRVKLELIRFGIDVDISA 419
Query: 418 GIPLSTTLHSSILTSLLNAIFKLNDFMAIATLVKHPLAKFGFPEKYLSRAKNALELVALR 477
GIPLSTTL SILTSLLNA+FK ND MA+A L+KHPLA FGFPEK+L +AKNALEL+ALR
Sbjct: 420 GIPLSTTLQGSILTSLLNAVFKTNDPMALAVLIKHPLATFGFPEKHLFKAKNALELIALR 479
Query: 478 GNKNSYDIMDLKSLVLDRIATQKNNTHVPHWQSRLSEEDKELAVLLVDHILQCITPLVTY 537
GN+N DI+DLKSLV+++I QKN+ ++P WQSRLSEEDK+L++ L DHI++ I PL Y
Sbjct: 480 GNRNPCDIIDLKSLVINKINEQKNDKYIPRWQSRLSEEDKKLSLWLADHIVKSIAPLAVY 539
Query: 538 KTNKNSTCGNLSISDWTKLTVTCLQNVCLDEHRKLPNLWFEEEGKTLSSLFSKIIETGSC 597
K N+NS +LS DWT+LT CLQNVCLDE++KLP+LW EEGK LS+LFSKIIE G C
Sbjct: 540 KMNENSIGDSLSTPDWTELTAACLQNVCLDENKKLPSLWLAEEGKALSALFSKIIEAGPC 599
Query: 598 IKANAIEWIDIITRLIDGETVKPKIEKSSTLFILGTLESRLLNFDTLILGGLNEGVWPKN 657
IKANAIEWIDIIT LI GETVKPKIEKSST+FILGTLESRLLNFDTLILGGLNEG+WPK
Sbjct: 600 IKANAIEWIDIITALIAGETVKPKIEKSSTIFILGTLESRLLNFDTLILGGLNEGIWPKY 659
Query: 658 TAKNPFLSRVMQSDLNLKTAEKYIGQAAHDFEMANGTRHLIYTRSLRENNIPTIASRWLQ 717
T KNPFLSR+MQSDL L+TAEKYIGQAAHDFEMA+GTRHLIYTRSL+ENNIPT+ASRWLQ
Sbjct: 660 TPKNPFLSRMMQSDLGLETAEKYIGQAAHDFEMASGTRHLIYTRSLQENNIPTVASRWLQ 719
Query: 718 RLLVLGGTDFFDNLKKRGQCYLDWTRKLDYTT-KQPHYKRPKPFPPLEAQPRTYSFSEIK 776
RLLV GG F ++LKK+G+ YLDW R+LD +T KQ KRP+PFPPLE QP+TYSFSEIK
Sbjct: 720 RLLVFGGNAFSNDLKKKGERYLDWARRLDDSTKKQIICKRPRPFPPLETQPKTYSFSEIK 779
Query: 777 QLINDPYAVYARRILKLDFIPHFKKDPDRTDRGTLFHNIITELIKKRINKNTPEINHLMK 836
+L++DPYA+YA++IL+LDF+P FK DP+ DRG LFH I+T LI+++INKNTPEI MK
Sbjct: 780 KLMSDPYAIYAQKILRLDFMPRFKNDPNPKDRGILFHKIVTGLIEEKINKNTPEITRRMK 839
Query: 837 QIIDSHFEKENLPPHIDIIWRHLFHKISHSFLEHEEKIQSSIEKIFVNIPAKMAIESIGI 896
IIDS FEKENLPPHIDIIWR+LFHKI+ FLE+EE+ Q IEK VN+PAKM I+SIGI
Sbjct: 840 DIIDSCFEKENLPPHIDIIWRYLFHKIALPFLEYEEQRQPLIEKTIVNVPAKMKIDSIGI 899
Query: 897 HLTGFADRIDLLKSGFVDITDYKTGDNPKKETAQKLIDPQLSLEAAALKAGSFSQIDCRK 956
HLTG ADRID+LKSG+ DI DYKTG+NP K+ AQ LIDPQLSLEA ALKAGSFSQIDCR+
Sbjct: 900 HLTGIADRIDILKSGYADIIDYKTGNNPTKKIAQNLIDPQLSLEAVALKAGSFSQIDCRE 959
Query: 957 VANLFYIRLKQKFK-------IDCITNDKKKYSADELSEKSLKNLIEIVTLLQNGEQPFI 1009
V L YIRLK K IDCI ++K SADELSE+SLKN IEI+ LQ+G++PFI
Sbjct: 960 VGKLVYIRLKLDHKRLKPRLIIDCIAGNEKDLSADELSEESLKNFIEIIKSLQSGKKPFI 1019
Query: 1010 SHLRLSEKSNIQSEYDHLARVAEWREEYDIS 1040
SHLR SE +NI SEYDHLARV EW+E YD S
Sbjct: 1020 SHLRFSENANIPSEYDHLARVEEWKENYDAS 1050
|
Species: Candidatus Liberibacter solanacearum Genus: Candidatus Liberibacter Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|222084228|ref|YP_002542754.1| double-strand break repair protein AddB [Agrobacterium radiobacter K84] Length = 1063 | Back alignment and organism information |
|---|
| >gi|150398435|ref|YP_001328902.1| double-strand break repair protein AddB [Sinorhizobium medicae WSM419] Length = 1059 | Back alignment and organism information |
|---|
| >gi|222147061|ref|YP_002548018.1| double-strand break repair protein AddB [Agrobacterium vitis S4] Length = 1062 | Back alignment and organism information |
|---|
| >gi|325291477|ref|YP_004277341.1| double-strand break repair protein AddB [Agrobacterium sp. H13-3] Length = 1061 | Back alignment and organism information |
|---|
| >gi|15963788|ref|NP_384141.1| hypothetical protein SMc02759 [Sinorhizobium meliloti 1021] Length = 1059 | Back alignment and organism information |
|---|
| >gi|307310976|ref|ZP_07590621.1| double-strand break repair protein AddB [Sinorhizobium meliloti BL225C] Length = 1059 | Back alignment and organism information |
|---|
| >gi|209551531|ref|YP_002283448.1| double-strand break repair protein AddB [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 1064 | Back alignment and organism information |
|---|
| >gi|15887383|ref|NP_353064.1| hypothetical protein Atu0024 [Agrobacterium tumefaciens str. C58] Length = 1061 | Back alignment and organism information |
|---|
| >gi|116249793|ref|YP_765631.1| hypothetical protein RL0027 [Rhizobium leguminosarum bv. viciae 3841] Length = 1063 | Back alignment and organism information |
|---|
Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| TIGR02786 | 1021 | TIGR02786, addB_alphas, double-strand break repair prot | 0.0 | |
| COG2887 | 269 | COG2887, COG2887, RecB family exonuclease [DNA replicat | 3e-29 | |
| COG3857 | 1108 | COG3857, AddB, ATP-dependent nuclease, subunit B [DNA r | 8e-05 | |
| TIGR03623 | 874 | TIGR03623, TIGR03623, probable DNA repair protein | 0.001 | |
| COG3893 | 697 | COG3893, COG3893, Inactivated superfamily I helicase [D | 1e-142 |
| >gnl|CDD|163020 TIGR02786, addB_alphas, double-strand break repair protein AddB, alphaproteobacterial type | Back alignment and domain information |
|---|
| >gnl|CDD|32713 COG2887, COG2887, RecB family exonuclease [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >gnl|CDD|33647 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >gnl|CDD|163360 TIGR03623, TIGR03623, probable DNA repair protein | Back alignment and domain information |
|---|
| >gnl|CDD|33681 COG3893, COG3893, Inactivated superfamily I helicase [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
| Identity | Alignment graph | Length | Definition | Probability |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| TIGR02786 | 1096 | addB_alphas double-strand break repair protein AddB; In | 100.0 | |
| TIGR03623 | 874 | probable DNA repair protein. Members of this protein fa | 100.0 | |
| COG3857 | 1108 | AddB ATP-dependent nuclease, subunit B [DNA replication | 100.0 | |
| COG3893 | 697 | Inactivated superfamily I helicase [DNA replication, re | 100.0 | |
| TIGR02773 | 1192 | addB_Gpos ATP-dependent nuclease subunit B; InterPro: I | 100.0 | |
| TIGR02784 | 1190 | addA_alphas double-strand break repair helicase AddA; I | 100.0 | |
| TIGR02785 | 1295 | addA_Gpos recombination helicase AddA; InterPro: IPR014 | 100.0 | |
| TIGR00609 | 1324 | recB exodeoxyribonuclease V, beta subunit; InterPro: IP | 99.97 | |
| PRK11069 | 1122 | recC exonuclease V subunit gamma; Provisional | 100.0 | |
| pfam04257 | 1008 | Exonuc_V_gamma Exodeoxyribonuclease V, gamma subunit. T | 100.0 | |
| TIGR02774 | 1116 | rexB_recomb ATP-dependent nuclease subunit B; InterPro: | 100.0 | |
| PRK10876 | 1181 | recB exonuclease V subunit beta; Provisional | 100.0 | |
| COG1074 | 1139 | RecB ATP-dependent exoDNAse (exonuclease V) beta subuni | 100.0 | |
| PRK13909 | 911 | putative recombination protein RecB; Provisional | 100.0 | |
| PRK11773 | 722 | uvrD DNA-dependent helicase II; Provisional | 100.0 | |
| PRK10919 | 672 | ATP-dependent DNA helicase Rep; Provisional | 100.0 | |
| COG0210 | 655 | UvrD Superfamily I DNA and RNA helicases [DNA replicati | 99.97 | |
| COG1330 | 1078 | RecC Exonuclease V gamma subunit [DNA replication, reco | 100.0 | |
| TIGR01073 | 811 | pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR0057 | 100.0 | |
| TIGR01075 | 741 | uvrD DNA helicase II; InterPro: IPR005753 The SOS respo | 100.0 | |
| TIGR01074 | 677 | rep ATP-dependent DNA helicase Rep; InterPro: IPR005752 | 100.0 | |
| pfam00580 | 494 | UvrD-helicase UvrD/REP helicase. The Rep family helicas | 99.98 | |
| COG2887 | 269 | RecB family exonuclease [DNA replication, recombination | 99.98 | |
| pfam10926 | 363 | DUF2800 Protein of unknown function (DUF2800). This is | 99.29 | |
| TIGR00372 | 206 | cas4 CRISPR-associated protein Cas4; InterPro: IPR01334 | 98.62 | |
| pfam06023 | 290 | DUF911 Archaeal protein of unknown function (DUF911). T | 98.39 | |
| COG4343 | 281 | CRISPR-associated protein, RecB family exonuclease [Def | 97.32 | |
| TIGR01896 | 295 | cas_AF1879 CRISPR-associated protein, Csa1 family; Inte | 97.14 | |
| COG1468 | 190 | CRISPR-associated protein Cas4 (RecB family exonuclease | 95.9 | |
| PRK11054 | 684 | helD DNA helicase IV; Provisional | 99.92 | |
| TIGR01450 | 1207 | recC exodeoxyribonuclease V, gamma subunit; InterPro: I | 99.22 | |
| KOG1805 | 1100 | consensus | 98.47 | |
| pfam09810 | 329 | Morph_protein1 Defects in morphology protein 1, mitocho | 98.24 | |
| pfam01930 | 162 | Cas_Cas4 Domain of unknown function DUF83. This domain | 98.11 | |
| PHA00619 | 210 | CRISPR-associated Cas4-like protein | 97.6 | |
| PHA01622 | 204 | CRISPR-associated Cas4-like protein | 97.12 | |
| TIGR03491 | 457 | RecB family nuclease, putative, TM0106 family. Members | 97.93 | |
| pfam08696 | 209 | Dna2 DNA replication factor Dna2. Dna2 is a DNA replica | 96.53 | |
| PRK09709 | 877 | exonuclease VIII; Reviewed | 95.88 |
| >TIGR02786 addB_alphas double-strand break repair protein AddB; InterPro: IPR014153 AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage | Back alignment and domain information |
|---|
| >TIGR03623 probable DNA repair protein | Back alignment and domain information |
|---|
| >COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >COG3893 Inactivated superfamily I helicase [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >TIGR02773 addB_Gpos ATP-dependent nuclease subunit B; InterPro: IPR014140 DNA repair is accomplished by several different systems in prokaryotes | Back alignment and domain information |
|---|
| >TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages | Back alignment and domain information |
|---|
| >TIGR02785 addA_Gpos recombination helicase AddA; InterPro: IPR014152 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages | Back alignment and domain information |
|---|
| >TIGR00609 recB exodeoxyribonuclease V, beta subunit; InterPro: IPR004586 Exodeoxyribonuclease V, or RecBCD holoenzyme, (3 | Back alignment and domain information |
|---|
| >PRK11069 recC exonuclease V subunit gamma; Provisional | Back alignment and domain information |
|---|
| >pfam04257 Exonuc_V_gamma Exodeoxyribonuclease V, gamma subunit | Back alignment and domain information |
|---|
| >TIGR02774 rexB_recomb ATP-dependent nuclease subunit B; InterPro: IPR014141 DNA repair is accomplished by several different systems in prokaryotes | Back alignment and domain information |
|---|
| >PRK10876 recB exonuclease V subunit beta; 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 |
|---|
| >PRK13909 putative recombination protein RecB; Provisional | Back alignment and domain information |
|---|
| >PRK11773 uvrD DNA-dependent helicase II; Provisional | Back alignment and domain information |
|---|
| >PRK10919 ATP-dependent DNA helicase Rep; Provisional | Back alignment and domain information |
|---|
| >COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >COG1330 RecC Exonuclease V gamma subunit [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751 The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli | Back alignment and domain information |
|---|
| >TIGR01075 uvrD DNA helicase II; InterPro: IPR005753 The SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesions | Back alignment and domain information |
|---|
| >TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752 RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring | Back alignment and domain information |
|---|
| >pfam00580 UvrD-helicase UvrD/REP helicase | Back alignment and domain information |
|---|
| >COG2887 RecB family exonuclease [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >pfam10926 DUF2800 Protein of unknown function (DUF2800) | Back alignment and domain information |
|---|
| >TIGR00372 cas4 CRISPR-associated protein Cas4; InterPro: IPR013343 This entry consists of conserved proteins found in many prokaryotic genomes whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats) | Back alignment and domain information |
|---|
| >pfam06023 DUF911 Archaeal protein of unknown function (DUF911) | Back alignment and domain information |
|---|
| >COG4343 CRISPR-associated protein, RecB family exonuclease [Defense mechanisms] | Back alignment and domain information |
|---|
| >TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family; InterPro: IPR009260 This family consists of several archaeal strongly conserved proteins whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats) | Back alignment and domain information |
|---|
| >COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms] | Back alignment and domain information |
|---|
| >PRK11054 helD DNA helicase IV; Provisional | Back alignment and domain information |
|---|
| >TIGR01450 recC exodeoxyribonuclease V, gamma subunit; InterPro: IPR006697 The exodeoxyribonuclease V enzyme is a multisubunit enzyme comprised of the proteins RecB (IPR004586 from INTERPRO), RecC (this family) and RecD (IPR006344 from INTERPRO) | Back alignment and domain information |
|---|
| >KOG1805 consensus | Back alignment and domain information |
|---|
| >pfam09810 Morph_protein1 Defects in morphology protein 1, mitochondrial precursor | Back alignment and domain information |
|---|
| >pfam01930 Cas_Cas4 Domain of unknown function DUF83 | Back alignment and domain information |
|---|
| >PHA00619 CRISPR-associated Cas4-like protein | Back alignment and domain information |
|---|
| >PHA01622 CRISPR-associated Cas4-like protein | Back alignment and domain information |
|---|
| >TIGR03491 RecB family nuclease, putative, TM0106 family | Back alignment and domain information |
|---|
| >pfam08696 Dna2 DNA replication factor Dna2 | Back alignment and domain information |
|---|
| >PRK09709 exonuclease VIII; Reviewed | Back alignment and domain information |
|---|
Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch
Homologous Structures Detected by PSI-BLAST against Nonredundant Database
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| 1w36_C | 1122 | Recbcd:dna Complex Length = 1122 | 2e-22 | |
| 3pjr_A | 724 | Helicase Substrate Complex Length = 724 | 1e-15 | |
| 2pjr_A | 548 | Helicase Product Complex Length = 548 | 3e-12 | |
| 1qhh_B | 273 | Structure Of Dna Helicase With Adpnp Length = 273 | 7e-10 |
| gi|56966627|pdb|1W36|C Chain C, Recbcd:dna Complex Length = 1122 | Back alignment and structure |
Score = 113 bits (281), Expect = 2e-22, Method: Composition-based stats.
Identities = 114/1086 (10%), Positives = 257/1086 (23%), Gaps = 165/1086 (15%)
Query: 20 EMIPALLNGTLVENFRYDPLNPLLLASVTIYVPTKRAIQELRSEFIEITGKKSTILPIIK 79
+++ AL+ + DP P I V + Q L+ + G + I
Sbjct: 11 DVLEALMEFIVERERLDDPFEPE-----MILVQSTGMAQWLQMTLSQKFGIAANID---F 62
Query: 80 SLGDVVEEKFTADLLLSYNLNPPVSNIQRLLELARLILIWRNKLPDIIKDLYPESPLSLP 139
L +L + +L L+ + + L+
Sbjct: 63 PLPASFIWDMFVRVLPEIPKESAFNKQSMSWKLMTLLPQLLEREDFTLL----RHYLTDD 118
Query: 140 ISPANAIWLAKNLADIIDIIETEEKKWEDLHALKNEKYGM---WWLLAADFLKIASKYWT 196
L+ AD+ D W L + L A +T
Sbjct: 119 SDKRKLFQLSSKAADLFDQYLVYRPDW--LAQWETGHLVEGLGEAQAWQAPLWKALVEYT 176
Query: 197 ERLVELNASSPVGYQIALMRAEAEHLMKGT--KGPIIIAGSTGSIPATARLMSTVANHPN 254
+L + + + I G + P + + + H
Sbjct: 177 HQLGQPRW-HRANLYQRFIETLESATTCPPGLPSRVFICGISALPPVYLQALQALGKHIE 235
Query: 255 GAIVLPGLDCHIPTAIWNTITEKSTNITSSNTTYSTHPQYSLA----------------- 297
++ + I + ++
Sbjct: 236 IHLLFTNPCRYYWGDIKDPAYLAKLLTRQRRHSFEDRELPLFRDSENAGQLFNSDGEQDV 295
Query: 298 --KLLDFLDIKREDVKRLGNVSNEMYGRSMVIS---------------KSFLPPDTSDMR 340
LL D L + + +
Sbjct: 296 GNPLLASWGKLGRDYIYLLSDLESSQELDAFVDVTPDNLLHNIQSDILELENRAVAGVNI 355
Query: 341 NTDILENKIPNIQKCFSDVALIEADNEREEAISIAIALRMSLDEN----KKKSALITADR 396
+ + S + + + E + L L+E+ + ++ AD
Sbjct: 356 EEFSRSDNKRPLDPLDSSITFHVCHSPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADI 415
Query: 397 NLARRVKLEL-----TRFGINIDISAGIPLSTTLHSSILTSLLNAIFKLNDFMAIATLVK 451
+ + + IS + SLL+ + L+
Sbjct: 416 DSYSPFIQAVFGSAPADRYLPYAISDRRARQSHPVLEAFISLLSLPDSRFVSEDVLALLD 475
Query: 452 HPLAKFGFP--EKYLSRAKNALELVALRGNKNSYDIMDLK-------SLVLDRIATQKNN 502
P+ F E+ L + + +R + ++ +L+ +
Sbjct: 476 VPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPATGQHTWRFGLTRMLLGY 535
Query: 503 THVPHWQSRLSEEDKELAVLL-VDHILQCITPLVTYKTNKNSTCGNLSISDWTKLTVTCL 561
S + + L + + + L+ + + +W + L
Sbjct: 536 AMESAQGEWQSVLPYDESSGLIAELVGHLASLLMQLNIWRRGLAQERPLEEWLPVCRDML 595
Query: 562 QNVCLDEHRKLPNLWFEEEGKTLSSLFSKIIETGSCIKANAIEWIDIITRLIDGETVKPK 621
L + + ++ ++ + D + + +D E + +
Sbjct: 596 NAFFLPDAETEAA--MTLIEQQWQAIIAEGLGAQYGDAVPLSLLRDELAQRLDQERISQR 653
Query: 622 IEKSSTLFILGTLESRLLNFDTLILGGLNEGVWPKNTAKNPFLSRVMQSDLNLKTAEKYI 681
+ I + R + F + L G+N+GV+P+ A F +M +
Sbjct: 654 FLAGP-VNICTLMPMRSIPFKVVCLLGMNDGVYPRQLAPLGF--DLMSQKPKRGDRSRRD 710
Query: 682 GQAAHDFEMANGTRH-LIYTRSLRE--NNIPTIASRWLQRLLVLGGTDF----------- 727
E + L + R +N S +Q L+ G
Sbjct: 711 DDRYLFLEALISAQQKLYISYIGRSIQDNSERFPSVLVQELIDYIGQSHYLPGDEALNCD 770
Query: 728 -------------------FDNLKKRGQCYLDWTRKLDYTTKQPHYKRPKPFPPLEAQPR 768
+ G+ L ++ P P
Sbjct: 771 ESEARVKAHLTCLHTRMPFDPQNYQPGERQSYAREWLPAASQAGKAHSEFVQPLPFTLPE 830
Query: 769 TYSFSEIKQLINDPYAVYARRILKLDFIPHFKKDPDRTDR---GTLFHNIITELIKKRIN 825
T +++ P + + L+++F + PD G + I +L+ +
Sbjct: 831 TVPLETLQRFWAHPVRAFFQMRLQVNFRTEDSEIPDTEPFILEGLSRYQINQQLLNALVE 890
Query: 826 KNTPEIN-HLMKQIIDSHFEKENLPPHIDIIWRHLFHKISHSFLEHEEKIQSSIEKIFVN 884
++ E + D +++ + Q
Sbjct: 891 QDDAERLFRRFRAAGD--LPYGAFGEIFWETQCQEMQQLADRVIA---CRQPG------- 938
Query: 885 IPAKMAIESIGIHLTG---FADRIDLLKSG--FVDITDYKTGDNPKKETAQKLIDPQLSL 939
++ + G+ +TG G P + + QL L
Sbjct: 939 QSMEIDLACNGVQITGWLPQV-----QPDGLLRWR---------PSLLSVAQG--MQLWL 982
Query: 940 EAAALKAGSFSQIDCRKVANLFYIRLKQKFKIDCITNDKKKYSADELSEKSLKNLIEIVT 999
E A + D + +E++L L +++
Sbjct: 983 EHLVYCASG-----------------GNGESRLFLRKDGEWRFPPLAAEQALHYLSQLIE 1025
Query: 1000 LLQNGE 1005
+ G
Sbjct: 1026 GYREGM 1031
|
| gi|4930230|pdb|3PJR|A Chain A, Helicase Substrate Complex Length = 724 | Back alignment and structure |
| >gi|9257172|pdb|2PJR|A Chain A, Helicase Product Complex Length = 548 | Back alignment and structure |
| >gi|5542369|pdb|1QHH|B Chain B, Structure Of Dna Helicase With Adpnp Length = 273 | Back alignment and structure |
Homologous Structures in PDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| 3h4r_A | 265 | Exodeoxyribonuclease 8; exonuclease, recombination, hyd | 5e-06 | |
| 2is6_A | 680 | DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2 | 4e-04 |
| >3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} Length = 265 | Back alignment and structure |
|---|
Score = 49.2 bits (116), Expect = 5e-06
Identities = 34/251 (13%), Positives = 63/251 (25%), Gaps = 14/251 (5%)
Query: 770 YSFSEIKQLINDPYAVYARRILKLDFIPHFKKDPDRTDRGTLFHNIITELIK-KRINKNT 828
S S++ + + P R+ +D D GT FH + EL +
Sbjct: 13 ISKSQLDDIADTPALYLWRKNAPVDT-----TKTKTLDLGTAFHCRVLELEEFSNRFIVA 67
Query: 829 PEINHLMKQIIDSHFEKENLPPHIDII-----WRHLFHKISHSFLEHEEKIQSSIEKIFV 883
PE N + + S +
Sbjct: 68 PEFNRRTNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHA 127
Query: 884 NIPAKMAIESIGIHLTGFADRIDLLKSGFVDITDYKTGDNPKKETAQKLIDPQLSLEAAA 943
GI D+I +D+ K Q + +
Sbjct: 128 ESSIYWEDPETGILCRCRPDKIIPEFHWIMDVKTTADIQRFKTAYYDYRYHVQDAFYSDG 187
Query: 944 LKAGSFSQIDCRKVANLFYIRLKQKFKIDCITNDKKKYSADELSEKSLKNLIEIVTLLQN 1003
+A Q + ++ ++ ++ A + ++ +NL + L
Sbjct: 188 YEAQFGVQPTFVFLVAS-TTIECGRYPVEIFMMGEEAKLAGQ--QEYHRNLRTLSDCLNT 244
Query: 1004 GEQPFISHLRL 1014
E P I L L
Sbjct: 245 DEWPAIKTLSL 255
|
| >2is6_A DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A {Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A* Length = 680 | Back alignment and structure |
|---|
Homologous Structures in PDB70 Database Detected by HHsearch
Original result of HHsearch against PDB70 database
| Identity | Alignment graph | Length | Definition | Probability |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| 1w36_C | 1122 | RECC, exodeoxyribonuclease V gamma chain; recombination | 100.0 | |
| 1w36_B | 1180 | RECB, exodeoxyribonuclease V beta chain; recombination, | 100.0 | |
| 1pjr_A | 724 | PCRA; DNA repair, DNA replication, SOS response, helica | 100.0 | |
| 2is6_A | 680 | DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2 | 100.0 | |
| 1uaa_A | 673 | REP helicase, protein (ATP-dependent DNA helicase REP.) | 100.0 | |
| 3h4r_A | 265 | Exodeoxyribonuclease 8; exonuclease, recombination, hyd | 99.64 | |
| 3l0a_A | 266 | Putative exonuclease; RER070207002219, structural genom | 99.49 | |
| 3dmn_A | 174 | Putative DNA helicase; APC89291.2, lactobacillus planta | 97.19 | |
| 2vld_A | 251 | NUCS, UPF0286 protein pyrab01260; endonuclease, hydrola | 93.6 |
| >1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C* | Back alignment and structure |
|---|
Probab=100.00 E-value=0 Score=351.57 Aligned_cols=910 Identities=12% Similarity=0.079 Sum_probs=500.0
Q ss_pred EEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCEEEEECCHHHHHHHHHHHHHHCCCCCEECCEEEEHHHHHHHH
Q ss_conf 98389889379999999711210112367898133222067627968999999999851188865140331257765655
Q gi|254780823|r 9 FTIAPSSPFFREMIPALLNGTLVENFRYDPLNPLLLASVTIYVPTKRAIQELRSEFIEITGKKSTILPIIKSLGDVVEEK 88 (1040)
Q Consensus 9 ~~~~~~~~fl~~~a~~l~~~~~~~~~~~~~~~p~~L~~v~vl~ptrraa~~Lr~~l~~~~~~~~~~~P~i~t~~~~~~~~ 88 (1040)
|+|..+.- ++.|++.|..-.... ...+| |...+|||||+.+++||+..|+++.|..+.+ ++.+.+.|....
T Consensus 2 l~~~~Sn~-~e~L~~~l~~~l~~~----~~~~p--f~~~~iiV~s~~~~~wL~~~lA~~~gi~an~--~f~~p~~~~~~~ 72 (1122)
T 1w36_C 2 LRVYHSNR-LDVLEALMEFIVERE----RLDDP--FEPEMILVQSTGMAQWLQMTLSQKFGIAANI--DFPLPASFIWDM 72 (1122)
T ss_dssp EEEEEESC-HHHHHHHHHHHHHSS----CCCCS--SCCCBEECSSHHHHHHHHHHHHHTTSCBCCC--BCCCHHHHHHHH
T ss_pred CEEECCCC-HHHHHHHHHHHHHHC----CCCCC--CCCCEEEECCHHHHHHHHHHHHHHHCCEEEE--CCCCHHHHHHHH
T ss_conf 77880589-999999999999858----78899--9999788797479999999999984907744--689999999999
Q ss_pred HHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 40454334677888881899999999999998631-00000012232111356978899989999999999997599978
Q gi|254780823|r 89 FTADLLLSYNLNPPVSNIQRLLELARLILIWRNKL-PDIIKDLYPESPLSLPISPANAIWLAKNLADIIDIIETEEKKWE 167 (1040)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~r~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~lA~~L~~l~d~~~~~~~~~~ 167 (1040)
...-...... ..+.++..-.+.+++++....... .... ...+....+..+.+.+|..|+++|++|..++.+|
T Consensus 73 ~~~~l~~~~~-~~~~~~~~l~w~l~~~L~~~~~~~~~~~l-----~~yl~~~~~~~r~~~la~~iA~lf~qY~~yRp~~- 145 (1122)
T 1w36_C 73 FVRVLPEIPK-ESAFNKQSMSWKLMTLLPQLLEREDFTLL-----RHYLTDDSDKRKLFQLSSKAADLFDQYLVYRPDW- 145 (1122)
T ss_dssp HHHHSSSCCS-SCTTCHHHHHHHHHHHHHHHCSSSTTHHH-----HHHTTSSCSSHHHHHHHHHHHHHHHHHTTSSHHH-
T ss_pred HHHHCCCCCC-CCCCCHHHHHHHHHHHHHHHHCCCCCHHH-----HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCHHH-
T ss_conf 9985389854-58997440399999998987528460999-----9987058740279999999999999998626999-
Q ss_pred HHHHCCH------HCCHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHC--CCCCEEEEEECCC
Q ss_conf 9874002------20207999999999999999999753248--889899999999874434422--7688099983456
Q gi|254780823|r 168 DLHALKN------EKYGMWWLLAADFLKIASKYWTERLVELN--ASSPVGYQIALMRAEAEHLMK--GTKGPIIIAGSTG 237 (1040)
Q Consensus 168 ~L~~l~~------~~~~~~w~~~~~fL~~~~~~~~~~l~~~g--~~d~~~~~~~~~~~~~~~~~~--~~~~~i~v~g~~~ 237 (1040)
|..-.. -.....||..+ ...+.+ .....+ ...+.......+......... .-+.+|+|+|.+.
T Consensus 146 -l~~W~~~~~~~~~~~~~~WQ~~L--wr~L~~----~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~lp~r~~vfg~s~ 218 (1122)
T 1w36_C 146 -LAQWETGHLVEGLGEAQAWQAPL--WKALVE----YTHQLGQPRWHRANLYQRFIETLESATTCPPGLPSRVFICGISA 218 (1122)
T ss_dssp -HHHHHTTCCCTTCCTTHHHHHHH--HHHHHH----HHHHTTCCCCCSTTTHHHHHHHHHSCTTCCCSCCSEEEEESCCC
T ss_pred -HHHHHCCCCCCCCCHHHHHHHHH--HHHHHH----HHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCC
T ss_conf -99987599876787235569999--999998----63002687567799999999987426666324886589850464
Q ss_pred CCHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCC-------------------------CCCCCCCCCCCH
Q ss_conf 6167999999986148968998248632107888643342012-------------------------333334446763
Q gi|254780823|r 238 SIPATARLMSTVANHPNGAIVLPGLDCHIPTAIWNTITEKSTN-------------------------ITSSNTTYSTHP 292 (1040)
Q Consensus 238 ~~~~~~~ll~al~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~-------------------------~~~~~~~~~~~~ 292 (1040)
+++.+..+++++++..+.+.++.++|..++.+.-......... .........+||
T Consensus 219 l~~~~l~~l~aLs~~~~v~l~~~~P~~~~w~di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p 298 (1122)
T 1w36_C 219 LPPVYLQALQALGKHIEIHLLFTNPCRYYWGDIKDPAYLAKLLTRQRRHSFEDRELPLFRDSENAGQLFNSDGEQDVGNP 298 (1122)
T ss_dssp CCHHHHHHHHHHTTTSEEEEEEECSCSSCCSCCCCHHHHTTTSCCBEESSSSCBCCSSTTHHHHSSTTCSSSSCSCCSCH
T ss_pred CCHHHHHHHHHHHCCCCEEEEECCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCHHHCCCCH
T ss_conf 89999999999853698699716868898864058888898999887653200111210122445420475212203786
Q ss_pred HHHHHHHHHHCCCCHHHCCC------------CCCCCCCCHHHHHHHHHHH--CCCCCCC-HHHCCCCCCCCCCCCCCCC
Q ss_conf 68999999762999666025------------7766645367777544420--1112210-0000012356765321337
Q gi|254780823|r 293 QYSLAKLLDFLDIKREDVKR------------LGNVSNEMYGRSMVISKSF--LPPDTSD-MRNTDILENKIPNIQKCFS 357 (1040)
Q Consensus 293 ~~~~~~l~~~l~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~--~~a~~~~-~~~~~~~~~~~~~~~~~~~ 357 (1040)
. +..+|...++... ..................+ .+..... ...................
T Consensus 299 l------La~~G~~gr~~~~l~~~~~~~~~~~~f~~~~~~sll~~~q~~il~l~~~~~~~~~~~~~~~~~~~~~~~~~D~ 372 (1122)
T 1w36_C 299 L------LASWGKLGRDYIYLLSDLESSQELDAFVDVTPDNLLHNIQSDILELENRAVAGVNIEEFSRSDNKRPLDPLDS 372 (1122)
T ss_dssp H------HHHHTHHHHHHHHHHTTCSSEEEEECCCCCCSCSHHHHHHHHHHHTCCCCCCCCSHHHHHCCTTSEECCTTCC
T ss_pred H------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHCCCCCHHHCCCCCCCCCCCCCC
T ss_conf 9------9987376799999986046642100257888630678788788752102111343011011002477888999
Q ss_pred CCEEEECCCHHHHHHHHHHHHHHHHHHC----CCEEEEEECCCCHHHHHHHH-HH----HHCCCCCCCCCCHHHHCHHHH
Q ss_conf 8159955998999999999999986422----98499980264113578884-35----513777665690035288989
Q gi|254780823|r 358 DVALIEADNEREEAISIAIALRMSLDEN----KKKSALITADRNLARRVKLE-LT----RFGINIDISAGIPLSTTLHSS 428 (1040)
Q Consensus 358 ~v~~~~a~~~~~Ea~~ia~~lr~~~~~~----~~~~avv~~d~~~~~~v~~~-L~----~~gipv~~s~g~pL~~~p~v~ 428 (1040)
+|+++.|+++.+|++.+++.|++..... +++|+|++||...+.++..+ +. ..+||++++++.++..+|.+.
T Consensus 373 SI~i~~~~s~~rEvE~l~~~Il~ll~~~~~l~p~DIaVl~pdi~~Y~p~I~avF~~~~~~~~IP~~i~~~~~~~~~pl~~ 452 (1122)
T 1w36_C 373 SITFHVCHSPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAISDRRARQSHPVLE 452 (1122)
T ss_dssp SSEEEEESSHHHHHHHHHHHHHHHHHHSTTCCGGGEEEEESCHHHHHHHHHHHTSCCSSTTCCCCEECSEETGGGCHHHH
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCCCCCEEECCCHHHHCCHHHH
T ss_conf 88999759989999999999999974288888212678728879889999998610245678872413520432058999
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCCC--CCCCHHHHHHHHHHHHHHHHCCCCC-------------CCCCC-CHHHHH
Q ss_conf 9999999983799978999986296545--6679389999999732232104557-------------77811-178887
Q gi|254780823|r 429 ILTSLLNAIFKLNDFMAIATLVKHPLAK--FGFPEKYLSRAKNALELVALRGNKN-------------SYDIM-DLKSLV 492 (1040)
Q Consensus 429 ~l~~ll~~~~~~~~~~~l~~LL~sPl~~--~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~-~l~~~~ 492 (1040)
.+++++++..++++..+++++|++|.+. ++.+.........-......+.+.. ...+. .+....
T Consensus 453 ~l~~lL~l~~~r~~~~~vl~lL~~p~l~~~f~l~~~~~~~l~~~~~~~gir~g~~~~~~~~~~~~~~~~~tw~~~l~Rll 532 (1122)
T 1w36_C 453 AFISLLSLPDSRFVSEDVLALLDVPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPATGQHTWRFGLTRML 532 (1122)
T ss_dssp HHHHHTTGGGCCCCHHHHHHHTTSHHHHHHTTCCHHHHHHHHHHHHHHTCCSCSCHHHHHHTTCCCCSSSSHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf 99999987417999999999976814232138987899999999998087657435667876045211134877677776
Q ss_pred HHHCCCCCCC-CCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 5220114444-345520101553432579999999899999987501100221023788999999999997236763211
Q gi|254780823|r 493 LDRIATQKNN-THVPHWQSRLSEEDKELAVLLVDHILQCITPLVTYKTNKNSTCGNLSISDWTKLTVTCLQNVCLDEHRK 571 (1040)
Q Consensus 493 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 571 (1040)
.......... ................ +...+...+..+... ........++.+|...+...++.........
T Consensus 533 lg~~~~~~~~~~~~~~p~~~~~~~~~~----~l~~~~~~l~~L~~~---~~~l~~~~t~~~w~~~l~~lL~~~~~~~~~~ 605 (1122)
T 1w36_C 533 LGYAMESAQGEWQSVLPYDESSGLIAE----LVGHLASLLMQLNIW---RRGLAQERPLEEWLPVCRDMLNAFFLPDAET 605 (1122)
T ss_dssp HHHSSCSTTCCSSSCCCCTTSCSSTHH----HHHHHHHHHHHHHHH---HHHTSSCEEHHHHTTHHHHHHHHHCCCCSHH
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHH----HHHHHHHHHHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHHHCCCHHH
T ss_conf 543201345564123450012222699----999999999999999---9997188989999999999999974888668
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCCCCCEEEECCCCC
Q ss_conf 14566577799999999866421376644778899999986224433566778773798034333566586378528631
Q gi|254780823|r 572 LPNLWFEEEGKTLSSLFSKIIETGSCIKANAIEWIDIITRLIDGETVKPKIEKSSTLFILGTLESRLLNFDTLILGGLNE 651 (1040)
Q Consensus 572 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~v~v~~~~~a~~~~~~~v~v~gl~e 651 (1040)
.. ........+....+..........++...+..++...+........... ++|+|++++.+++.+|++|+++|+||
T Consensus 606 ~~--~~~~~~~~l~~l~~~~~~~~~~~~l~l~~~~~~L~~~l~~~~~~~~~~~-~~V~v~tl~~~R~ipfkvVfllGlnd 682 (1122)
T 1w36_C 606 EA--AMTLIEQQWQAIIAEGLGAQYGDAVPLSLLRDELAQRLDQERISQRFLA-GPVNICTLMPMRSIPFKVVCLLGMND 682 (1122)
T ss_dssp HH--HHHHHHHHHHHHHHHHHHTCCCSEECHHHHHHHHHHHHHHCEECTTTTS-SSCEEECCCTTCCCCEEEEEEECCBT
T ss_pred HH--HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCCCC-CCEEEECCHHHCCCCCCEEEEEECCC
T ss_conf 99--9999999999999999872367643899999999987401345678989-97698112553578867699973366
Q ss_pred CCCCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHH-CCCEEEEEEECCC--CCCCCCCCHHHHHHHHCCCCCCH
Q ss_conf 13456666676489678856489996678889999999985-5985999920467--77665665378887731473100
Q gi|254780823|r 652 GVWPKNTAKNPFLSRVMQSDLNLKTAEKYIGQAAHDFEMAN-GTRHLIYTRSLRE--NNIPTIASRWLQRLLVLGGTDFF 728 (1040)
Q Consensus 652 ~~~P~~~~~~~~l~~~~r~~l~l~~~e~~~~~~~~~~~~~~-~a~~v~lt~~~~~--~~~~~~ps~~l~~l~~~~~~~~~ 728 (1040)
|.||.....++|.....+...|.+..... ..+.+|..++ +..++++||+..+ ++.+..||.++.++.........
T Consensus 683 g~fP~~~~~~~fdl~~~~~~~gd~~~~~e--dr~lfl~al~sA~~~L~lSy~~~~~~~~~~~~PS~~l~eL~d~l~~~~~ 760 (1122)
T 1w36_C 683 GVYPRQLAPLGFDLMSQKPKRGDRSRRDD--DRYLFLEALISAQQKLYISYIGRSIQDNSERFPSVLVQELIDYIGQSHY 760 (1122)
T ss_dssp TTSSCCCCCCSSCHHHHSCCTTCCCHHHH--HHHHHHHHHHHEEEEEEEEEECBCSSSCCBCCBCHHHHHHHHHHHTTEE
T ss_pred CCCCCCCCCCCCCCHHHCCCCCCCHHHHH--HHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 75766566666531544236688106578--9999999999754423144412327899834877899999999974235
Q ss_pred HHCCCC------------------------------C---CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 001136------------------------------5---3223478752101234345475567630012467780045
Q gi|254780823|r 729 DNLKKR------------------------------G---QCYLDWTRKLDYTTKQPHYKRPKPFPPLEAQPRTYSFSEI 775 (1040)
Q Consensus 729 ~~~~~~------------------------------~---~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~lS~S~l 775 (1040)
...... . .....+....... .........+.....+..+|+|.+
T Consensus 761 ~~~~~~~~~~~~~~~~~~~l~~~h~l~~fs~~~f~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~ls~s~L 837 (1122)
T 1w36_C 761 LPGDEALNCDESEARVKAHLTCLHTRMPFDPQNYQPGERQSYAREWLPAASQA---GKAHSEFVQPLPFTLPETVPLETL 837 (1122)
T ss_dssp CSSCSSSCHHHHHHHHHHHHCCBCCSSTTSGGGSSSSTTCCSCGGGHHHHTTC---CCCCCCSCCCCCCCCCSCEEHHHH
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCCHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf 77743346320046788654012667888855530043234409998763254---556764456899877884489999
Q ss_pred HHHHCCHHHHHHHHHCCCCCCCCCC-------CCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 7764283688897632888887212-------489988998999999999986125898347899999999999653279
Q gi|254780823|r 776 KQLINDPYAVYARRILKLDFIPHFK-------KDPDRTDRGTLFHNIITELIKKRINKNTPEINHLMKQIIDSHFEKENL 848 (1040)
Q Consensus 776 ~~~~~cP~~~~~~~~l~l~~~~~~~-------~~~~a~~~GtlvH~~Le~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 848 (1040)
++|.+||++||++++|++...+... ..+++..++++.|.+|+.+... ...+.....+.. ....+
T Consensus 838 ~~f~~~P~~~fl~~~L~~~~~~~~~~~~d~Ep~~ld~L~~~~l~~~ll~~~l~~---~~~~~~~~~~~~------~g~LP 908 (1122)
T 1w36_C 838 QRFWAHPVRAFFQMRLQVNFRTEDSEIPDTEPFILEGLSRYQINQQLLNALVEQ---DDAERLFRRFRA------AGDLP 908 (1122)
T ss_dssp HHHSSSHHHHHHHTTTCCCCCCSCCCCCSSCCSSCCHHHHHHHHHHHHHHHHTT---CCHHHHHHHHHH------HTCSC
T ss_pred HHHHHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC---CCHHHHHHHHHH------CCCCC
T ss_conf 999979689999974488886212245556866677065524999999998718---999999999997------59999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCEEEEECCCCCCCCHHH
Q ss_conf 86699999999999999999999732468859999965688978823799999978888799858999726853468879
Q gi|254780823|r 849 PPHIDIIWRHLFHKISHSFLEHEEKIQSSIEKIFVNIPAKMAIESIGIHLTGFADRIDLLKSGFVDITDYKTGDNPKKET 928 (1040)
Q Consensus 849 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~E~~~~~~i~~~~~~l~GrIDRid~~~dG~~~IvDYKTG~~p~~~~ 928 (1040)
+......++.+....+..++.......... .+.++.+.++ +++|+|+||+|. +|| +|.|++|+... ++
T Consensus 909 ~g~~g~~~~~~~~~~~~~l~~~~~~~~~~~----~~~~~~l~~~--~~~L~G~l~~v~--~~~---~v~~~~~~~~~-~~ 976 (1122)
T 1w36_C 909 YGAFGEIFWETQCQEMQQLADRVIACRQPG----QSMEIDLACN--GVQITGWLPQVQ--PDG---LLRWRPSLLSV-AQ 976 (1122)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHTTCCCC----EEEEEEEEET--TEEEEEEEEEEC--SSE---EEEECSSCCCH-HH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCEEEEEEEC--CEEEEEEECCCC--CCC---EEEEEECCCCH-HH
T ss_conf 825569999999999999999998706888----8634898409--889999889862--683---59997278987-88
Q ss_pred HHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 84230121699999998288677785574213888606866554345654558988899999999999999984889
Q gi|254780823|r 929 AQKLIDPQLSLEAAALKAGSFSQIDCRKVANLFYIRLKQKFKIDCITNDKKKYSADELSEKSLKNLIEIVTLLQNGE 1005 (1040)
Q Consensus 929 ~~~~~~~QL~lY~~~~~~~~~~~~~~~~~~~~~y~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 1005 (1040)
. .++.++-+++...+. ......++ +.+...... ..+ .++....|..++.-|..|.
T Consensus 977 ~-----l~~wl~hL~~~a~~~------~~~~~~~~--~~~~~~~~~-----p~~----~~~A~~~L~~l~~~~~~g~ 1031 (1122)
T 1w36_C 977 G-----MQLWLEHLVYCASGG------NGESRLFL--RKDGEWRFP-----PLA----AEQALHYLSQLIEGYREGM 1031 (1122)
T ss_dssp H-----HHHHHHHHHHHHTSC------CCEEEEEC--GGGCEEEEC-----CCC----HHHHHHHHHHHHHHHHHTT
T ss_pred H-----HHHHHHHHHHHHCCC------CCCEEEEE--ECCCEEEEC-----CCC----HHHHHHHHHHHHHHHHHHH
T ss_conf 9-----999999999982699------99728999--769679989-----989----7999999999999999983
|
| >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 |
|---|
| >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 |
|---|
| >2is6_A DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A {Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A* | 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 |
|---|
| >3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} | Back alignment and structure |
|---|
| >3l0a_A Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale} | Back alignment and structure |
|---|
| >3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, structural genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum} | Back alignment and structure |
|---|
| >2vld_A NUCS, UPF0286 protein pyrab01260; endonuclease, hydrolase; 2.60A {Pyrococcus abyssi} | Back alignment and structure |
|---|
Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
No hit with e-value below 0.005
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| Identity | Alignment graph | Length | Definition | Probability |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| d1w36c2 | 470 | Exodeoxyribonuclease V gamma chain (RecC), N-terminal d | 99.96 | |
| d1uaaa2 | 333 | DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 5 | 99.86 | |
| d1pjra2 | 333 | DEXX box DNA helicase {Bacillus stearothermophilus, Pcr | 99.81 | |
| g1qhh.1 | 623 | DEXX box DNA helicase {Bacillus stearothermophilus, Pcr | 99.95 | |
| d1w36b2 | 395 | Exodeoxyribonuclease V beta chain (RecB), N-terminal do | 99.78 | |
| d1w36c1 | 347 | Exodeoxyribonuclease V gamma chain (RecC), N-terminal d | 99.42 | |
| d1pjra1 | 318 | DEXX box DNA helicase {Bacillus stearothermophilus, Pcr | 98.47 | |
| d1uaaa1 | 306 | DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 5 | 98.1 | |
| d1w36b3 | 276 | Exodeoxyribonuclease V beta chain (RecB), C-terminal do | 99.28 | |
| d1w36b1 | 485 | Exodeoxyribonuclease V beta chain (RecB), N-terminal do | 99.15 | |
| d1w36c3 | 304 | Exodeoxyribonuclease V beta chain (RecC), C-terminal do | 97.48 |
| >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 |
|---|
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 gamma chain (RecC), N-terminal domain species: Escherichia coli [TaxId: 562]
Probab=99.96 E-value=4e-26 Score=184.77 Aligned_cols=360 Identities=14% Similarity=0.115 Sum_probs=223.5
Q ss_pred CCCCCEEEECCCHHHHHHHHHHHHHHHHHH-C---CCEEEEEECCCCHHHHHHHH-----HHHHCCCCCCCCCCHHHHCH
Q ss_conf 337815995599899999999999998642-2---98499980264113578884-----35513777665690035288
Q gi|254780823|r 355 CFSDVALIEADNEREEAISIAIALRMSLDE-N---KKKSALITADRNLARRVKLE-----LTRFGINIDISAGIPLSTTL 425 (1040)
Q Consensus 355 ~~~~v~~~~a~~~~~Ea~~ia~~lr~~~~~-~---~~~~avv~~d~~~~~~v~~~-----L~~~gipv~~s~g~pL~~~p 425 (1040)
...+|+++.|+++.+|++.|++.|++.... + +++|+|++|+...+.++..+ +...+||+.++++.++..+|
T Consensus 23 ~D~si~i~~c~~~~rEvE~l~~~I~~~l~~~~~~~~~DIaVl~r~~~~Y~~~I~~vF~~~~~~~~IPy~i~~~~~~~~~p 102 (470)
T d1w36c2 23 LDSSITFHVCHSPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAISDRRARQSHP 102 (470)
T ss_dssp TCCSSEEEEESSHHHHHHHHHHHHHHHHHHSTTCCGGGEEEEESCHHHHHHHHHHHTSCCSSTTCCCCEECSEETGGGCH
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCH
T ss_conf 99988999799869999999999999997785979050788859768879999999815443578786985884122179
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCC--CCCCCHHHHHHHHHHHHHHHHCCCCC----------CCCCCCHHHHHH
Q ss_conf 989999999998379997899998629654--56679389999999732232104557----------778111788875
Q gi|254780823|r 426 HSSILTSLLNAIFKLNDFMAIATLVKHPLA--KFGFPEKYLSRAKNALELVALRGNKN----------SYDIMDLKSLVL 493 (1040)
Q Consensus 426 ~v~~l~~ll~~~~~~~~~~~l~~LL~sPl~--~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~l~~~~~ 493 (1040)
.+.+++++|+++.++++..+++++|++|++ ..+..................+.... ......+.....
T Consensus 103 ~i~~ll~lL~l~~~~~~~~~l~~lL~~p~~~~~~~i~~~~~~~l~~~~~~~~i~~~~~~~~~~~~~~~~~~~~s~~~~~~ 182 (470)
T d1w36c2 103 VLEAFISLLSLPDSRFVSEDVLALLDVPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPATGQHTWRFGLT 182 (470)
T ss_dssp HHHHHHHHTTGGGCCCCHHHHHHHTTSHHHHHHTTCCHHHHHHHHHHHHHHTCCSCSCHHHHHHTTCCCCSSSSHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHCCHHHHHH
T ss_conf 99999999997608998189999868715310258987799999999998454324678878760231010124998876
Q ss_pred HHCCCCCCCCCCCCHHHC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 220114444345520101-5534325799999998999999875011002210237889999999999972367632111
Q gi|254780823|r 494 DRIATQKNNTHVPHWQSR-LSEEDKELAVLLVDHILQCITPLVTYKTNKNSTCGNLSISDWTKLTVTCLQNVCLDEHRKL 572 (1040)
Q Consensus 494 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~l~~~l~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 572 (1040)
..............+... ...............+...+..+... .........+..|...+..............
T Consensus 183 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~- 258 (470)
T d1w36c2 183 RMLLGYAMESAQGEWQSVLPYDESSGLIAELVGHLASLLMQLNIW---RRGLAQERPLEEWLPVCRDMLNAFFLPDAET- 258 (470)
T ss_dssp HHHHHHSSCSTTCCSSSCCCCTTSCSSTHHHHHHHHHHHHHHHHH---HHHTSSCEEHHHHTTHHHHHHHHHCCCCSHH-
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf 543321000134555333346554335799999999999999999---9987344779999999998888874100345-
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCCCCCEEEECCCCCC
Q ss_conf 45665777999999998664213766447788999999862244335667787737980343335665863785286311
Q gi|254780823|r 573 PNLWFEEEGKTLSSLFSKIIETGSCIKANAIEWIDIITRLIDGETVKPKIEKSSTLFILGTLESRLLNFDTLILGGLNEG 652 (1040)
Q Consensus 573 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~v~v~~~~~a~~~~~~~v~v~gl~e~ 652 (1040)
..........+....+..........++...+..++...+........... ++|+|||+|.++|++|++|||+|+|||
T Consensus 259 -~~~~~~~~~~l~~l~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~-d~V~v~tih~akglef~vVfl~Gl~eg 336 (470)
T d1w36c2 259 -EAAMTLIEQQWQAIIAEGLGAQYGDAVPLSLLRDELAQRLDQERISQRFLA-GPVNICTLMPMRSIPFKVVCLLGMNDG 336 (470)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTCCCSEECHHHHHHHHHHHHHHCEECTTTTS-SSCEEECCCTTCCCCEEEEEEECCBTT
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCC-CCCEEECCHHHCCCCCCEEEEEEECCC
T ss_conf -678999999999999999975113313699999999854321002445756-783773315324888888999983376
Q ss_pred CCCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHCCC-EEEEEEECCC--CCCCCCCCHHHHHHHHC
Q ss_conf 3456666676489678856489996678889999999985598-5999920467--77665665378887731
Q gi|254780823|r 653 VWPKNTAKNPFLSRVMQSDLNLKTAEKYIGQAAHDFEMANGTR-HLIYTRSLRE--NNIPTIASRWLQRLLVL 722 (1040)
Q Consensus 653 ~~P~~~~~~~~l~~~~r~~l~l~~~e~~~~~~~~~~~~~~~a~-~v~lt~~~~~--~~~~~~ps~~l~~l~~~ 722 (1040)
.||.....+++.....+...+.+..... ..+++|..+++++ ++++||+..+ .+.+..||+|+.++...
T Consensus 337 ~fP~~~~~~~~~~~~~~~~~~~~~~~~e--er~lfy~altrA~~~L~lSy~~~~~~~g~~~~PS~~i~el~~~ 407 (470)
T d1w36c2 337 VYPRQLAPLGFDLMSQKPKRGDRSRRDD--DRYLFLEALISAQQKLYISYIGRSIQDNSERFPSVLVQELIDY 407 (470)
T ss_dssp TSSCCCCCCSSCHHHHSCCTTCCCHHHH--HHHHHHHHHHHEEEEEEEEEECBCSSSCCBCCBCHHHHHHHHH
T ss_pred EEECCCCCCHHHHHHHHHHCCCCHHHHH--HHHHHHHHHHHHHCEEEEEEECCCCCCCCCCCCCHHHHHHHHH
T ss_conf 1205556100002788776066112478--9999999998444049999824656687974887899999999
|
| >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 |
|---|
| >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 |
|---|
| >d1w36c1 c.37.1.19 (C:1-347) Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain {Escherichia coli [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 |
|---|
| >d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d1w36b3 c.52.1.24 (B:899-1174) Exodeoxyribonuclease V beta chain (RecB), C-terminal domain {Escherichia coli [TaxId: 562]} | 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 |
|---|
| >d1w36c3 c.52.1.25 (C:818-1121) Exodeoxyribonuclease V beta chain (RecC), C-terminal domain {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 1040 | double-strand break repair protein AddB [Candidatu | ||
| 3h4r_A_ | 265 | (A:) Exodeoxyribonuclease 8; exonuclease, recombin | 5e-21 | |
| 3l0a_A_ | 266 | (A:) Putative exonuclease; RER070207002219, struct | 6e-09 | |
| 1w36_B_444-587_727-885 | 303 | (B:444-587,B:727-885) RECB, exodeoxyribonuclease V | 0.001 |
| >3h4r_A (A:) Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12}Length = 265 | Back alignment and structure |
|---|
Score = 98.2 bits (243), Expect = 5e-21
Identities = 33/256 (12%), Positives = 59/256 (23%), Gaps = 20/256 (7%)
Query: 761 PPLEAQPRTYSFSEIKQLINDPYAVYARRILKLDFIPHFKKDPDRTDRGTLFHNIITELI 820
S S++ + + P R+ +D D GT FH + EL
Sbjct: 4 MENYHAGPGISKSQLDDIADTPALYLWRKNAPVD-----TTKTKTLDLGTAFHCRVLELE 58
Query: 821 KKRINKNTPE-INHLMKQIIDSHFEKE-----NLPPHIDIIWRHLFHKISHSFLEHEEKI 874
+ N + I + S +
Sbjct: 59 EFSNRFIVAPEFNRRTNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQ 118
Query: 875 QSSIEKIFVNIPAKMAIESIGIHLTGFADRIDLLKSGFVDITDYKTGDNPKKETAQKLI- 933
GI D+I F I D KT + ++
Sbjct: 119 WLVESAGHAESSIYWEDPETGILCRCRPDKII---PEFHWIMDVKTTADIQRFKTAYYDY 175
Query: 934 --DPQLSLEAAALKAGSFSQIDCRKVANLFYIRLKQKFKIDCITNDKKKYSADELSEKSL 991
Q + + +A Q L + + + + ++
Sbjct: 176 RYHVQDAFYSDGYEAQFGVQPT---FVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYH 232
Query: 992 KNLIEIVTLLQNGEQP 1007
+NL + L E P
Sbjct: 233 RNLRTLSDCLNTDEWP 248
|
| >3l0a_A (A:) Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale}Length = 266 | Back alignment and structure |
|---|
| >1w36_B (B:444-587,B:727-885) RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}Length = 303 | Back alignment and structure |
|---|
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
| Identity | Alignment graph | Length | Definition | Probability |
| Target | 1040 | double-strand break repair protein AddB [Candidatus Lib | ||
| 3h4r_A_ | 265 | Exodeoxyribonuclease 8; exonuclease, recombination | 99.94 | |
| 3l0a_A_ | 266 | Putative exonuclease; RER070207002219, structural | 99.9 | |
| 1w36_C_808-1035 | 228 | RECC, exodeoxyribonuclease V gamma chain; recombin | 97.71 | |
| 1w36_B_444-587_727-885 | 303 | RECB, exodeoxyribonuclease V beta chain; recombina | 99.31 | |
| 1w36_C_371-446_653-739_781-807 | 190 | RECC, exodeoxyribonuclease V gamma chain; recombin | 99.28 | |
| 3dmn_A_ | 174 | Putative DNA helicase; APC89291.2, lactobacillus p | 97.25 | |
| 1w36_D_361-595 | 235 | RECD, exodeoxyribonuclease V alpha chain; recombin | 95.58 | |
| 1uaa_A_278-376_544-673 | 229 | REP helicase, protein (ATP-dependent DNA helicase | 99.2 | |
| 1pjr_A_287-385_549-724 | 275 | PCRA; DNA repair, DNA replication, SOS response, h | 99.13 | |
| 1w36_B_886-964_1014-1180 | 246 | RECB, exodeoxyribonuclease V beta chain; recombina | 99.14 | |
| 2is6_A_284-381_547-680 | 232 | DNA helicase II; hydrolase/DNA complex; HET: DNA A | 98.85 | |
| 1uaa_A_1-102_185-277 | 195 | REP helicase, protein (ATP-dependent DNA helicase | 98.27 | |
| 2is6_A_1-106_189-283 | 201 | DNA helicase II; hydrolase/DNA complex; HET: DNA A | 98.16 | |
| 1pjr_A_1-107_194-286 | 200 | PCRA; DNA repair, DNA replication, SOS response, h | 97.55 | |
| 1w36_C_1-82_185-330 | 228 | RECC, exodeoxyribonuclease V gamma chain; recombin | 98.23 | |
| 1w36_B_1-148_349-443 | 243 | RECB, exodeoxyribonuclease V beta chain; recombina | 98.2 | |
| 1uaa_A_377-543 | 167 | REP helicase, protein (ATP-dependent DNA helicase | 96.05 | |
| 2is6_A_382-524 | 143 | DNA helicase II; hydrolase/DNA complex; HET: DNA A | 96.05 | |
| 1w36_B_588-726 | 139 | RECB, exodeoxyribonuclease V beta chain; recombina | 95.83 | |
| 1pjr_A_386-548 | 163 | PCRA; DNA repair, DNA replication, SOS response, h | 95.03 | |
| 2vld_A_122-251 | 130 | NUCS, UPF0286 protein pyrab01260; endonuclease, hy | 95.46 |
| >3h4r_A (A:) Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} | Back alignment and structure |
|---|
Probab=99.94 E-value=1.5e-27 Score=196.62 Aligned_cols=244 Identities=13% Similarity=-0.046 Sum_probs=151.5
Q ss_pred CCCCCCCCCCHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 01246778004577642836888976328888872124899889989999999999861258983478999999999996
Q gi|254780823|r 764 EAQPRTYSFSEIKQLINDPYAVYARRILKLDFIPHFKKDPDRTDRGTLFHNIITELIKKRINKNTPEINHLMKQIIDSHF 843 (1040)
Q Consensus 764 ~~~~~~lS~S~l~~~~~cP~~~~~~~~l~l~~~~~~~~~~~a~~~GtlvH~~Le~~~~~~~~~~~~~~~~~l~~~~~~~~ 843 (1040)
...+..+|+|.+++|..||++||+++++++++... .++.+||++|.+|+.++..............+........
T Consensus 7 ~~~~~~~S~S~l~~~~~Cp~~~~~~~~~~~~~~~~-----~~~~~G~~~H~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (265)
T 3h4r_A 7 YHAGPGISKSQLDDIADTPALYLWRKNAPVDTTKT-----KTLDLGTAFHCRVLELEEFSNRFIVAPEFNRRTNAGKEEE 81 (265)
T ss_dssp ----CCBCHHHHHHHHHCHHHHHHHTTSCCCCCCC-----SCCTHHHHHHHHHSSHHHHTCC------------------
T ss_pred HCCCCCCCHHHHHHHHHCHHHHHHHHHCCCCCCCC-----HHHHHHHHHHHHHHCHHHHCCCCCCCCCHHHHHHHHHHHH
T ss_conf 44899839889999985999999997378999997-----7998729999987472232123324663023456666799
Q ss_pred HHCCC------CHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCEEE
Q ss_conf 53279------866999999999999999999997324--6885999996568897882379999997888879985899
Q gi|254780823|r 844 EKENL------PPHIDIIWRHLFHKISHSFLEHEEKIQ--SSIEKIFVNIPAKMAIESIGIHLTGFADRIDLLKSGFVDI 915 (1040)
Q Consensus 844 ~~~~~------~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~E~~~~~~i~~~~~~l~GrIDRid~~~dG~~~I 915 (1040)
..... .......+..++..++.++...+.... ....... .+..+.++..++.++|+||||+ +|.+.|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~e~~~~~~~~~~~l~G~iD~i~---~~~~~I 156 (265)
T 3h4r_A 82 KAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAE--SSIYWEDPETGILCRCRPDKII---PEFHWI 156 (265)
T ss_dssp ----------------CCCTTHHHHHHHHHTTSHHHHHHHSSSCBSS--CCEEEECTTTCCEEEECCSEEE---GGGTEE
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCE--EEEEEEECCCCEEEEEEEEEEE---CCCCEE
T ss_conf 99986555316542129999999999999982954676654202314--7899997676648888899997---799748
Q ss_pred EECCCCCCCCHH---HHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCC--CCCCCCCCCCCCCHHHHHHHH
Q ss_conf 972685346887---984230121699999998288677785574213888606866--554345654558988899999
Q gi|254780823|r 916 TDYKTGDNPKKE---TAQKLIDPQLSLEAAALKAGSFSQIDCRKVANLFYIRLKQKF--KIDCITNDKKKYSADELSEKS 990 (1040)
Q Consensus 916 vDYKTG~~p~~~---~~~~~~~~QL~lY~~~~~~~~~~~~~~~~~~~~~y~~l~~~~--~~~~~~~~~~~~~~~~~~~~~ 990 (1040)
||||||+.++.. +...++.+||++|++++++. .+..+....|+.+..+. ..............++..+++
T Consensus 157 iDyKTg~~~~~~~~~~~~~~~~~Ql~lY~~~l~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (265)
T 3h4r_A 157 MDVKTTADIQRFKTAYYDYRYHVQDAFYSDGYEAQ-----FGVQPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEY 231 (265)
T ss_dssp EEEEEESCHHHHHHHHHHHTTTHHHHHHHHHHHHH-----HSSCCEEEEEEEESSCBTTBCCEEEEECCHHHHHHHHHHH
T ss_pred EEEEECCCHHHHHHCCCCCCHHHHHHHHHHHHHHH-----CCCCCCEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf 89830267776532012337799999999999984-----2999863999998335677622799968999999999999
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 999999999984889885555451015668986544
Q gi|254780823|r 991 LKNLIEIVTLLQNGEQPFISHLRLSEKSNIQSEYDH 1026 (1040)
Q Consensus 991 ~~~l~~~~~~~~~~~~~f~~~~~~~~~~~~~~~y~~ 1026 (1040)
.+.+..+...+.++..| +......|.||+|+.
T Consensus 232 ~~~~~~~~~~~~~~~~~----~~~~~~~C~~C~~k~ 263 (265)
T 3h4r_A 232 HRNLRTLSDCLNTDEWP----AIKTLSLPRWAKEYA 263 (265)
T ss_dssp HHHHHHHHHHHHTCCCC----CCCCCCCCTTCTTCC
T ss_pred HHHHHHHHHHHHCCCCC----CCCCCCCCCCCCCCC
T ss_conf 99999999999669799----986467884511000
|
| >3l0a_A (A:) Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale} | Back alignment and structure |
|---|
| >1w36_C (C:808-1035) RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} | Back alignment and structure |
|---|
| >1w36_B (B:444-587,B:727-885) RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} | Back alignment and structure |
|---|
| >1w36_C (C:371-446,C:653-739,C:781-807) RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} | Back alignment and structure |
|---|
| >3dmn_A (A:) Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, structural genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum} | Back alignment and structure |
|---|
| >1w36_D (D:361-595) RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} | Back alignment and structure |
|---|
| >1uaa_A (A:278-376,A:544-673) REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} | Back alignment and structure |
|---|
| >1pjr_A (A:287-385,A:549-724) PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} | Back alignment and structure |
|---|
| >1w36_B (B:886-964,B:1014-1180) RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} | Back alignment and structure |
|---|
| >2is6_A (A:284-381,A:547-680) DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A {Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A* | Back alignment and structure |
|---|
| >1uaa_A (A:1-102,A:185-277) REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} | Back alignment and structure |
|---|