RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.410_1 (952 letters) >gnl|CDD|31272 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]. Length = 1139 Score = 369 bits (949), Expect = e-102 Identities = 200/906 (22%), Positives = 344/906 (37%), Gaps = 82/906 (9%) Query: 68 LLSSFFLTQKFTPQKNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASL 127 L FF + K P L + ++ ++ + + ++ A L Sbjct: 279 LEKIFFQKKLKKKTKEAKLLAR----PPLHAEFEEIENRILLADELL---RLAPRLRALL 331 Query: 128 TLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQD 187 L + L Y+ K++ LDF+DLI LL + + ++ HILIDE QD Sbjct: 332 KLLEELIERYDAEKRQRNALDFDDLIHRLAKLLTSEG--EELAESLREQYPHILIDEFQD 389 Query: 188 TSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKR 247 T QW ++ L F G RTLF VGD KQSIY F GA+ L + Sbjct: 390 TDPQQWRILSRLFAGFKAGN------RTLFLVGDPKQSIYRFRGADIFTFLEAASSEKA- 442 Query: 248 ATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGT 307 F+ I L ++RST ++L V+ +F A D + +R G G+ Sbjct: 443 -------FARITLETNYRSTPELLNAVNALFKQAMFAYPGEIDYDP-VAELGARNGSPGS 494 Query: 308 VQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGK 367 V + +++ WT+ + + A + AR+IA + +I + + + Sbjct: 495 VNGEPLPALK----FWEEEDDWTAPENEEDEREIADLEARQIAAWLRELIEGEAVLDGER 550 Query: 368 KRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRF 427 I+A DI VLVR R + I R LK I V ++R L + L +DL+AL R Sbjct: 551 P--IRAGDIAVLVRSRNEAAAIE---RALKKAGIIPVYLSNRSSLFETLEAQDLLALLRA 605 Query: 428 ILSQEDDLSFVCMLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKY 487 IL+ EDDL +L+SPLF +EDD+ + E E ++E +++ A+ I +F+ V+ Sbjct: 606 ILNPEDDLPLAALLRSPLFGLTEDDLAALAQDEAEWEFLWENLRQLAD--IWRFRGVLAM 663 Query: 488 IHELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSSL 547 L A+ HD L + ++ + G ++L E L L E L Sbjct: 664 WRAL---AKITPLHDLIAERLLSTNLGERDL-TNGLHAQELLQELLTRALSYEHGLLRWL 719 Query: 548 QELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMH 607 + I+ +E R ++ + VRIMT+H +KGLE P+VFL S+ F+ + + Sbjct: 720 ERFIALIENNDEEQARRLESDRDLVRIMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLV 779 Query: 608 IMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIIC-- 665 D ++ + ++ E RLLYV +TRA +QLI+ Sbjct: 780 YY----DGLRFELFDDLKSYPTPESQANKELAEEEALAEELRLLYVALTRAKEQLILIGA 835 Query: 666 ----KHSNTSNEKKSNQR-------TWYDMVYDSFHNDERVKKIK--------LTNSINK 706 + S+ QR W ++ + + V + + + Sbjct: 836 PSKREKSSALAPLDLGQRVQVGGTQDWEGLLAIALKLSDPVLEEEALGAKESPQPPRADL 895 Query: 707 DEWIAYEWSTHHPENTPLEREETIKQLMDEQKIPKKLFSPIKNDINEPYILNPSTIDTKG 766 EW P + D ++ P + + + Sbjct: 896 LEWARVFRRLKEPLWRVTSFSSLQQGEQDAYPRLDARQEASVKELPRPLSESGTPHEFPK 955 Query: 767 KTNLESLLSD---NQTFN-------RGLIIHKLLQVIFTLPEHKRKNFITSYCTKNAKLW 816 + +LL N F+ G IH+LLQ + + ++ + Sbjct: 956 GKSFGTLLHSVLENLDFSAPVDAAEIGTAIHELLQHLPFEEDWEQ-ELAEWLEAMLSTPL 1014 Query: 817 PAKEYKNLLLSITRLLENPMMTTAMSCDSYSEVSVSGKINCPKKDIIISGRIDQISISQQ 876 E +L I +P + +S S+ ++ + ++ G ID + + Sbjct: 1015 EDAERAIILSQILAFFRDPELEFLFPINS-RPFSLLDPLSAGSERGLLQGIIDLLFRHEG 1073 Query: 877 NIFIFEYKTHHHVPQEIEHIPYTHIA------QLSIYEKILKDSYPNKSLVCLLIYVSEP 930 +I +YKT+ + P + QL +Y + L + L Sbjct: 1074 RYYILDYKTNRLGDDSAAYSPAEAMLKQRYDLQLQLYAEALHRILRKRVKDYALARHFGG 1133 Query: 931 KVFIIP 936 +++ Sbjct: 1134 VLYLFL 1139 >gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]. Length = 655 Score = 159 bits (403), Expect = 3e-39 Identities = 133/617 (21%), Positives = 224/617 (36%), Gaps = 126/617 (20%) Query: 62 IEERFSLLSSFFLTQKFTPQKNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFK 121 +++ +L+ + K ++ +E + + K L + Sbjct: 110 SDDQLALIKELLRRELNLDDKELLPREALRYISEAKNALL--SPLEASALLLAAIKSEAE 167 Query: 122 STLASLTLAKYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKR-DVSAWIRYKIDQEINHI 180 LA L Y+E + N LDF+DL++ LL++ +V ++ + +I Sbjct: 168 KKLAELY------EEYQELLRLNNALDFDDLLLLALRLLEENPEVLEALQARFR----YI 217 Query: 181 LIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLR- 239 L+DE QDT+ +Q+E+++ L + LF VGD+ QSIY F GA+P+ +L Sbjct: 218 LVDEFQDTNPLQYELLKLLAGN----------AANLFVVGDDDQSIYGFRGADPENILDF 267 Query: 240 EKRINQKRATNAGQKFSIIELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRS 299 EK +I+L ++RST +IL +KV I + Sbjct: 268 EKDFPAA---------KVIKLEQNYRSTPNILAAANKV-----------------IANNK 301 Query: 300 SRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSY-FDSLPQESSASILARRIAYTISNMIG 358 R + L ++ E + E AR IA I +I Sbjct: 302 KRQAK----TLR--------TEVEGSGEKVVLLLANDEEDE------ARWIASEIDALI- 342 Query: 359 TDTIFSNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAI 418 + + DI +L R + LI R Y+I + G F + I Sbjct: 343 --------EIGKVNYSDIAILYRTNAQSRLIEEALRAAGIPYRIVIGGTSFF---ERKEI 391 Query: 419 KDLMALGRFILSQEDDLSFVCMLKSPLFNFSEDDIFKICTQRHETETV-------YEYIQ 471 KDL+A R +L+ +DD +F+ +L P + + K+ E Sbjct: 392 KDLLAYLRLVLNPDDDAAFLRILNLPKRGIGDATLKKLLELARERNLSLLEALKALLSFI 451 Query: 472 KFANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDV--- 528 + + G++ + I EL + + +L A + + + Sbjct: 452 RLSERGLALLLDFAELIEELREAILLSTALELIRELLEALGYLEALLEAGSLVAAEDRLE 511 Query: 529 -LDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPV 587 L+E L+ R + SL+ +SEL + +V +MT+H AKGLE P Sbjct: 512 NLEELLDVLKRYAEPR-ESLRAFLSELSLLANDEEEEEPDEDGQVNLMTIHAAKGLEFPY 570 Query: 588 VFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEY 647 VFLV +F D+ P+ EE Sbjct: 571 VFLVGLEEGLFPAD---------RSLDEGDEPL------------------------EEE 597 Query: 648 NRLLYVGMTRASDQLII 664 RLLYV +TRA +L + Sbjct: 598 RRLLYVAITRAKKKLYL 614 >gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family. Length = 494 Score = 132 bits (335), Expect = 4e-31 Identities = 97/450 (21%), Positives = 160/450 (35%), Gaps = 92/450 (20%) Query: 82 KNIITQEINKKSPDLKEKLKKSQDEFIKIRDRF-----NTYKMFKSTLASLTLAKYLNAH 136 K I+ ++ L L + ++ K ++ + +T A++ Sbjct: 117 KEILKKDRLDLDSKLLRPLLELKELISKAKNELLSPEELQQASYAATPRDKLAAEFYQE- 175 Query: 137 YEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVI 196 Y+E K+N LDF+DL++ T +LL+ + + +IL+DE QDT+ IQ+E++ Sbjct: 176 YQERLKENNALDFDDLLLLTLELLRSDP---ELLEAYRERFKYILVDEFQDTNPIQYELL 232 Query: 197 RSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFS 256 + L LF VGD QSIY F GA+ + +L+ + K A Sbjct: 233 KLLA----------GGHPNLFLVGDPDQSIYGFRGADIENILKFE----KDFPAA----K 274 Query: 257 IIELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVS 316 +I L ++RST +IL +K+ I + ++R + + S Sbjct: 275 VITLEQNYRSTPEILNAANKL-----------------ISNNTARKEK-------RLLWS 310 Query: 317 QHDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDI 376 Q S + + A IA I + I DI Sbjct: 311 QKGSGEKVTVYEAETEQEE----------AEFIADEIKALH--------KSGAAIPFGDI 352 Query: 377 LVLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLS 436 VLVR + I LK ++G F D IKDL+AL R I + +DDL+ Sbjct: 353 AVLVRSNSQSRAI--EEALLKAGIPYKILGGLSFF--DRKEIKDLLALLRLIDNPKDDLA 408 Query: 437 FVCMLKSPLFNFSEDDI--------------FKICTQRHETETVYEYIQKFANCGISKFQ 482 + +L +P + FK Q E + + K Sbjct: 409 LLRILNTPKRGIGPTTLDKLRNLAKDRQISLFKALNQLLEK-----LNELLSARAYKKLL 463 Query: 483 HVIKYIHELIHIAQFCSPHDFFTLILGAKK 512 + I EL + +L Sbjct: 464 LFLALIEELEKLLLEILLEALLDEVLELLG 493 >gnl|CDD|145939 pfam03055, RPE65, Retinal pigment epithelial membrane protein. This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria. Length = 473 Score = 34.5 bits (80), Expect = 0.13 Identities = 10/31 (32%), Positives = 17/31 (54%) Query: 750 DINEPYILNPSTIDTKGKTNLESLLSDNQTF 780 + PY L+P T++T G+ + + L TF Sbjct: 132 EAGLPYRLDPETLETIGRYDFDGQLKPGPTF 162 >gnl|CDD|37319 KOG2108, KOG2108, KOG2108, 3'-5' DNA helicase [Replication, recombination and repair]. Length = 853 Score = 33.1 bits (75), Expect = 0.37 Identities = 32/125 (25%), Positives = 46/125 (36%), Gaps = 25/125 (20%) Query: 147 LDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVG 206 D L +N+ +L+ +I H+L+DE QD IQ E + V Sbjct: 207 EDSCTLAMNSLKVLQ--RPRVCSN-----KITHVLVDEFQDILKIQLEPL-------QVL 252 Query: 207 KNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRS 266 K + GD QSIY F G + + N+ AT A + F + RS Sbjct: 253 KI-----KAFAGTGDTDQSIYKFAGKWAEIRILYVTFNKFIATQAERLFP------NNRS 301 Query: 267 TADIL 271 I Sbjct: 302 CKTIH 306 Score = 32.7 bits (74), Expect = 0.55 Identities = 35/157 (22%), Positives = 58/157 (36%), Gaps = 37/157 (23%) Query: 568 NHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKS 627 V + T+H AKGLE V L + +VF S+++ +P + ++ + Sbjct: 671 KAENVILGTIHQAKGLEFDNVHLQNDFVKVF-----------GSVSNFERLPSFRVETYN 719 Query: 628 RNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTSNEKKSNQRTWYDMVYD 687 ++E+N LYV +TRA +LI+CK + K Q + Sbjct: 720 ----------------EDEWN-FLYVAVTRAKKRLIMCKSLHEILTLKGEQ--------E 754 Query: 688 SFHNDERVKKIKLTNSINKDE-WIAYEWSTHHPENTP 723 SF + LT +N + S N Sbjct: 755 SFSQAILTENKLLTGVVNCTVDRCSNAISVTTGLNMK 791 >gnl|CDD|37791 KOG2580, KOG2580, KOG2580, Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]. Length = 459 Score = 32.3 bits (73), Expect = 0.74 Identities = 24/78 (30%), Positives = 32/78 (41%), Gaps = 2/78 (2%) Query: 65 RFSLLSSFFLTQKFTPQKNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTL 124 R S LS F + KN QE KK D +L++S D K R ++ T + Sbjct: 61 RRSFLSEFSDNVRAELDKNKELQESIKKLKDRAGELEES-DALKKARTKYETAESET-QA 118 Query: 125 ASLTLAKYLNAHYEEAKK 142 +S L K L E K Sbjct: 119 SSEVLKKKLGELKETVKL 136 >gnl|CDD|33647 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]. Length = 1108 Score = 30.7 bits (69), Expect = 2.3 Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 6/95 (6%) Query: 861 DIIISGRIDQISISQQNIF--IFEYKTHHHVPQEIEHIPYTHIAQLSIYEKILKDSYPNK 918 +I++ GRID+I +++ + I +YK+ H + + Y QL Y +K + P Sbjct: 897 EILLRGRIDRIDQLEKDGYLGIVDYKSSAHQFD-LTDVYYGLSLQLMTYLDAIKQNAPED 955 Query: 919 SLV---CLLIYVSEPKVFIIPQNKLNKAFAEISTK 950 + L ++ EP++ + L+K E+ Sbjct: 956 DVKPGGALYFHMHEPEIKLNSDLGLDKIEQELKKS 990 >gnl|CDD|39451 KOG4250, KOG4250, KOG4250, TANK binding protein kinase TBK1 [Signal transduction mechanisms]. Length = 732 Score = 29.9 bits (67), Expect = 3.6 Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 1/67 (1%) Query: 540 EQNSYSSLQELISELEQYPPTIKRAHSANHNEVRI-MTVHTAKGLESPVVFLVDTGSQVF 598 N+ SL E IS+ P + GL+SP+ + D V Sbjct: 333 ADNTLHSLIERISKQTGIPEGKQELLFEGGLSHLEDSAQCIPDGLDSPLYLVSDQDKNVD 392 Query: 599 SHKHIKK 605 K +K+ Sbjct: 393 ERKILKR 399 >gnl|CDD|33753 COG3972, COG3972, Superfamily I DNA and RNA helicases [General function prediction only]. Length = 660 Score = 29.6 bits (66), Expect = 4.4 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 10/95 (10%) Query: 178 NHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRV 237 ++ILIDE QD ++ +T+D + L DE Q++ + P+ + Sbjct: 297 DYILIDESQDFPQSFIDLCFMVTKD----------KKRLVYAYDELQNLSNVKMRPPEEI 346 Query: 238 LREKRINQKRATNAGQKFSIIELPLSFRSTADILT 272 + R A + I L +R++ L Sbjct: 347 FGPDSDGEPRVNLARADRNDIVLKKCYRNSPKNLV 381 >gnl|CDD|38789 KOG3582, KOG3582, KOG3582, Mlx interactors and related transcription factors [Transcription]. Length = 856 Score = 29.3 bits (65), Expect = 5.0 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 3/78 (3%) Query: 664 ICKHSNTSNEKKSNQRTWYDMVYDSFHNDERVKKIKLTNSINKDEWIAYEWSTHHPENTP 723 H + +++ N + +D++ N + IK TNS + + + Y T E P Sbjct: 652 PITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVT-QQERVP 710 Query: 724 LEREETIKQLMDEQKIPK 741 ++ E L E Sbjct: 711 VQEEA--HSLRKEISELN 726 >gnl|CDD|32359 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]. Length = 1444 Score = 29.1 bits (65), Expect = 5.7 Identities = 31/151 (20%), Positives = 62/151 (41%), Gaps = 16/151 (10%) Query: 85 ITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEE---AK 141 IT E+ + +P+++E L+K + EFI + + AS + +LN +YE+ Sbjct: 477 ITDEMLENAPEIEEVLEKFR-EFIGDS-------ILVAHNASFDMG-FLNTNYEKYGLEP 527 Query: 142 KKNCVLDFEDLIINTNDLLKKRDVSAWI-RYKIDQEINHILIDEVQDTSLIQWEVIRSLT 200 N V+D +L N K + + ++ E +H + + T+ + + ++ L Sbjct: 528 LTNPVIDTLELARALNPEFKSHRLGTLCKKLGVELERHHRADYDAEATAKVFFVFLKDLK 587 Query: 201 EDFFVGKNTHSSPRTLFAVGDEKQSIYSFHG 231 E G S + D + + H Sbjct: 588 EK---GITNLSELNDKLSSEDLYKRLRPKHA 615 >gnl|CDD|88409 cd05014, SIS_Kpsf, KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.. Length = 128 Score = 28.9 bits (65), Expect = 7.1 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 9/80 (11%) Query: 344 ILARRIAYTISNMIGTDTIF------SNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLK 397 +AR+IA T+S+ GT F +G ++ D+++ + +T + L LK Sbjct: 13 HIARKIAATLSST-GTPAFFLHPTEALHGDLGMVTPGDVVIAISNSGETDELLNLLPHLK 71 Query: 398 ND--YKISVVGNDRFILTDH 415 I++ GN L Sbjct: 72 RRGAPIIAITGNPNSTLAKL 91 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.134 0.385 Gapped Lambda K H 0.267 0.0658 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 11,317,414 Number of extensions: 607063 Number of successful extensions: 1519 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1498 Number of HSP's successfully gapped: 32 Length of query: 952 Length of database: 6,263,737 Length adjustment: 103 Effective length of query: 849 Effective length of database: 4,038,010 Effective search space: 3428270490 Effective search space used: 3428270490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 62 (27.8 bits)