RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764515|ref|YP_003065608.2| SNF2 related [Candidatus Liberibacter asiaticus str. psy62] (458 letters) >gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]. Length = 866 Score = 93.7 bits (231), Expect = 9e-20 Identities = 94/523 (17%), Positives = 179/523 (34%), Gaps = 77/523 (14%) Query: 2 NLAPHQTKIVDWILD-----HKRCAIWASMGSGKTVSVLTALSYIHLWGE---KSVLVIA 53 L P+Q + V+W+ + + MG GKTV + L + + L++ Sbjct: 338 ELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVV 397 Query: 54 PLRVAQSVWTSEVQRWSNFSHMNISVI---TGTVKQRTKVLKTPAVLYVINFE----NLG 106 P + S W E ++++ + + + K+R + + VI F+ Sbjct: 398 PASLL-SNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYE 456 Query: 107 WLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166 L + L I D ++ R++ +++ A ++ ++LTGTP N L Sbjct: 457 LLRRFLVDHGGLKKIEWDRVVLDEAHRIK-NDQSSEGKALQFLKALNRLDLTGTPLENRL 515 Query: 167 IDLWGQIWFLDKGKRLGRVFQSFVARWFNTTQIGSHIGAV--RYTAKETAQKEIEAQLSD 224 +LW + LG F F + Q IG + R E +K + + Sbjct: 516 GELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSPFILR 575 Query: 225 CCLSLDIADYQNIDKPILITKKVPLPQPVMKQY--------------------------- 257 D+ + + I + L + + Y Sbjct: 576 -RTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRI 634 Query: 258 ---------HKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEK 308 + C+ E + + L + Y ++ + + Sbjct: 635 GDSELNILALLTRLRQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKL 694 Query: 309 IKALEVI----IEKANAAPIIVAYHFNSDLARLQK---------AFPQGRTLDKDPC-TI 354 E++ +E+ + +++ F L L+ G T K I Sbjct: 695 QALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELI 754 Query: 355 QEWNEGKIPLLF-AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAG 413 +N + +F + G GLNL + ++ F WW+ Q I+R R Q Sbjct: 755 DRFNADEEEKVFLLSLKAGGLGLNLTG-ADTVILFDPWWNPAVELQAIDRA--HRIGQ-- 809 Query: 414 FKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLLLNALKKETI 456 KR V VY LI + TI+E +L+ K + D L++A ++ + Sbjct: 810 -KRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAEGEKEL 851 >gnl|CDD|36218 KOG1000, KOG1000, KOG1000, Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]. Length = 689 Score = 76.2 bits (187), Expect = 2e-14 Identities = 98/468 (20%), Positives = 166/468 (35%), Gaps = 78/468 (16%) Query: 2 NLAPHQTKIVDWILDHK-RCAIWASMGSGKTVSVLT-ALSYIHLWGEKSVLVIAPLRVAQ 59 L P Q + V + L+ R + MG GKT+ L A Y W +L++ P V Sbjct: 198 RLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEW---PLLIVCPASVRF 254 Query: 60 SVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFA 119 + W + R+ H V + T + ++++E L L LK + Sbjct: 255 T-WAKALNRFLPSIHPIFVVDKS--SDPLPDVCTSNTVAIVSYEQLSLLHDILK-KEKYR 310 Query: 120 TIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKG 179 ++ DES LK + ++ +K A L K A + I L+GTP+ + +L+ QI +D Sbjct: 311 VVIFDESHMLKDSKTKR-TKAATDLLKVA---KHVILLSGTPAVSRPSELYTQIRAVD-- 364 Query: 180 KRLGRVFQSFVARWFNTTQI--------GSHIGAVRYTAKETA-----QKEIEAQLSD-- 224 L F F R+ + Q+ +++ + + + ++ QL Sbjct: 365 HTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLPPKR 424 Query: 225 -----CCLSLDIADYQNIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSA 279 A ++ K KV M++ H+ Y A Sbjct: 425 REVVYVSGGRIDARMDDLVKAAADYTKV----NSMERKHESLLLFYSLTGIAKAAAV--- 477 Query: 280 SKTVKCLQLANGAVYYDEEKHWKEV---HDEKIKALEVIIEKANAAPIIVAYHFNSDLAR 336 C + D V H + ++V + K I R Sbjct: 478 -----CEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSI-----------R 521 Query: 337 LQ-KAFPQGRTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWD-- 393 + RTL + Q E ++ +L + G GL L + VF L W+ Sbjct: 522 IDGSTPSHRRTLLCQ--SFQTSEEVRVAVLSI--TAAGVGLTLTAASVV-VFAELHWNPG 576 Query: 394 -LEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVLQRLRTK 440 L + + RIG +VFV YL+A+ T D+ + L+ K Sbjct: 577 VLLQAEDRAHRIGQK--------SSVFVQYLVAKGTADDYMWPMLQQK 616 >gnl|CDD|143942 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). Length = 295 Score = 67.3 bits (165), Expect = 8e-12 Identities = 72/300 (24%), Positives = 123/300 (41%), Gaps = 53/300 (17%) Query: 6 HQTKIVDWILD----HKRCAIWASMGSGKTVSVLTALSYIHLWGEKS--VLVIAPLRVAQ 59 +Q + V+W++ + MG GKT+ ++ L+Y+ + LV+ PL Sbjct: 1 YQLEGVNWLISLYNNGLGGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLD 60 Query: 60 SVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLY-----VINFENLGWLVQELKG 114 + W +E ++W +NI V G R+++L+ + ++E + EL Sbjct: 61 N-WLNEFEKW--APDLNIVVYYGDGDSRSELLRNVLRTGKFDVLITSYEYIRRDKDELHK 117 Query: 115 T-WPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQI 173 W + +++DE ++K+ + SK + AL ++ + LTGTP N L +LW + Sbjct: 118 ANWRY--VILDEGHRIKNAK----SKLSLALKS--LKTNNRLLLTGTPIQNNLAELWSLL 169 Query: 174 WFLDKGKRLGRVFQSF--VARWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDI 231 FL G F SF +WF + + T +K EA L I Sbjct: 170 NFLRPGI-----FGSFKEFDKWFVNPILNGG------CSDAT-EKLEEAGL------KLI 211 Query: 232 ADYQNIDKPILI--TKKV---PLPQPVMKQYH----KFQRELYCD-LQGENIEAFNSASK 281 I KP L+ KK LP K Q+ELY L ++++ N + Sbjct: 212 NRLHKILKPFLLRRLKKDVEKSLPPKTEYVLFCNLSKLQKELYKKFLTSKDVKFINDGNG 271 >gnl|CDD|35606 KOG0385, KOG0385, KOG0385, Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]. Length = 971 Score = 58.1 bits (140), Expect = 4e-09 Identities = 58/296 (19%), Positives = 121/296 (40%), Gaps = 46/296 (15%) Query: 3 LAPHQTKIVDWILDHKRCAIWA----SMGSGKTVSVLTALSYIH--LWGEKSVLVIAPLR 56 L +Q + ++W++ I MG GKT+ ++ L Y+ LVIAP Sbjct: 168 LRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKS 227 Query: 57 VAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLK-----TPAVLYVINFENLGWLVQE 111 + W +E +R++ +N+ V G ++R + + + + ++E + + Sbjct: 228 TLDN-WMNEFKRFT--PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYE-IAIKDKS 283 Query: 112 LKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWG 171 + + +V+DE+ ++K+ + SK ++ L + ++++ + LTGTP N L +LW Sbjct: 284 FLKKFNWRYLVIDEAHRIKN----EKSKLSKILRE--FKTDNRLLLTGTPLQNNLHELWA 337 Query: 172 QIWFLDKGKRLGRVFQSF--VARWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSL 229 + FL L +F S WF+ T + + L L Sbjct: 338 LLNFL-----LPDIFNSAEDFDSWFDFTNC---------EGDQELVSRLHKVLRPFLLRR 383 Query: 230 DIADYQ-NIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSASKTVK 284 +D + ++ + V + Q++ Y + ++++A N K K Sbjct: 384 IKSDVEKSLPPKKELIIYVGMSSM--------QKKWYKAILMKDLDALNGEGKGEK 431 Score = 33.8 bits (77), Expect = 0.10 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 12/79 (15%) Query: 373 GHGLNLQYGGNILVFFSLW---WDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTI 429 G G+NL ++++ S W DL+ RIG + V VY LI +NT+ Sbjct: 551 GLGINLTAADTVILYDSDWNPQVDLQA-MDRAHRIGQKKP--------VVVYRLITENTV 601 Query: 430 DELVLQRLRTKSTIQDLLL 448 +E +++R K + L++ Sbjct: 602 EEKIVERAAAKLRLDKLVI 620 >gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.. Length = 144 Score = 54.7 bits (131), Expect = 5e-08 Identities = 25/148 (16%), Positives = 54/148 (36%), Gaps = 8/148 (5%) Query: 18 KRCAIWASMGSGKT-VSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMN 76 + + A GSGKT ++L L + VLV+AP R + +E + + Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTREL-ANQVAERLKELFGEGIK 59 Query: 77 ISVITGTV---KQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKLKSFR 133 + + G +Q + ++ L L + +++DE+ +L + Sbjct: 60 VGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN-- 117 Query: 134 LRQGSKTARALAKPAWESERFIELTGTP 161 + + + + + L+ TP Sbjct: 118 -QGFGLLGLKILLKLPKDRQVLLLSATP 144 >gnl|CDD|35608 KOG0387, KOG0387, KOG0387, Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription, Replication, recombination and repair]. Length = 923 Score = 51.9 bits (124), Expect = 4e-07 Identities = 47/199 (23%), Positives = 81/199 (40%), Gaps = 31/199 (15%) Query: 3 LAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYIHLWG--EKSVLVIAPLR 56 L P+Q + V W+ + I MG GKT+ +++ L+ +H G K L++ P Sbjct: 206 LFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPAT 265 Query: 57 VAQSVWTSEVQRWSNFSHMNISVITGTV-------------KQRTKVLKTPAVLYVINFE 103 + W E Q W + I TG+ K + + T + + ++ Sbjct: 266 IIHQ-WMKEFQTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYD 324 Query: 104 NLGWLVQELKG-TWPFATIVVDESTKLKSFRLRQGSKTARALA-KPAWESERFIELTGTP 161 +L G W + ++DE ++++ + +LA K R I L+GTP Sbjct: 325 GFRIQGDDLLGILWDYV--ILDEGHRIRN------PNSKISLACKKIRTVHRII-LSGTP 375 Query: 162 SPNGLIDLWGQIWFLDKGK 180 N L +LW F+ GK Sbjct: 376 IQNNLTELWSLFDFVFPGK 394 Score = 32.7 bits (74), Expect = 0.22 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 7/87 (8%) Query: 351 PCTIQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQ 409 + +NE + I + G GLNL G N ++ F W+ Q ER Sbjct: 587 QKLVDRFNEDESIFVFLLTTRVGGLGLNLT-GANRVIIFDPDWNPSTDNQARERA----- 640 Query: 410 RQAGFKRAVFVYYLIAQNTIDELVLQR 436 + G K+ V VY L+ TI+E + R Sbjct: 641 WRIGQKKDVVVYRLMTAGTIEEKIYHR 667 >gnl|CDD|35605 KOG0384, KOG0384, KOG0384, Chromodomain-helicase DNA-binding protein [Transcription]. Length = 1373 Score = 49.6 bits (118), Expect = 2e-06 Identities = 51/170 (30%), Positives = 76/170 (44%), Gaps = 28/170 (16%) Query: 26 MGSGKTVSVLTALSYIHLWGEK--SVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITG- 82 MG GKTV +T LSY+ + LV+ PL + W E + W++ MN+ V G Sbjct: 398 MGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITA-WEREFETWTD---MNVIVYHGN 453 Query: 83 ------------TVKQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKLK 130 TK LK A+L +E + EL P+ ++VDE+ +LK Sbjct: 454 LESRQLIRQYEFYHSSNTKKLKFNALL--TTYEIVLKDKAEL-SKIPWRYLLVDEAHRLK 510 Query: 131 SFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGK 180 + SK +L ++ + +TGTP N L +LW + FL GK Sbjct: 511 N----DESKLYESLN--QFKMNHRLLITGTPLQNSLKELWSLLHFLMPGK 554 >gnl|CDD|35607 KOG0386, KOG0386, KOG0386, Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics, Transcription]. Length = 1157 Score = 47.7 bits (113), Expect = 7e-06 Identities = 47/182 (25%), Positives = 83/182 (45%), Gaps = 28/182 (15%) Query: 26 MGSGKTVSVLTALSYI--HLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGT 83 MG GKT+ ++ ++Y+ H + L+I PL W+SE +W+ + GT Sbjct: 422 MGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTL-VNWSSEFPKWA--PSVQKIQYKGT 478 Query: 84 VKQRTKVLKTPAVL----YVINFENLGW---LVQELKGTWPFATIVVDESTKLKSFRLRQ 136 +QR+ + K + +E + L+ ++ W + +++DE ++K+ Sbjct: 479 PQQRSGLTKQQRHGKFNVLLTTYEYIIKDKALLSKIS--WKY--MIIDEGHRMKN----A 530 Query: 137 GSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSFVA--RWF 194 K L + ++R + LTGTP N L +LW + FL L +F S A +WF Sbjct: 531 ICKLTDTL-NTHYRAQRRLLLTGTPLQNNLPELWALLNFL-----LPNIFNSCKAFEQWF 584 Query: 195 NT 196 N Sbjct: 585 NQ 586 >gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 167 Score = 47.2 bits (113), Expect = 9e-06 Identities = 35/134 (26%), Positives = 58/134 (43%), Gaps = 21/134 (15%) Query: 5 PHQTKIVDWILDHKRCAIWASMGSGKT-VSVLTALSYI-HLWGEKSVLVIAPLR--VAQS 60 P Q + + IL+ K + A GSGKT +L AL + LV+AP R Q Sbjct: 2 PIQAEAIPAILEGKDVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQI 61 Query: 61 VWTSEVQRWSNFSHMNISVITGTV---KQRTKVLKTPAVLYV------INFENLGWLVQE 111 E+++ + + ++++ G +Q K+ K P +L E G L++ Sbjct: 62 Y--EELKKLGKYLGLKVALLYGGDSPKEQLRKLKKGPDILVGTPGRLLDLLERGGLLLKN 119 Query: 112 LKGTWPFATIVVDE 125 LK +V+DE Sbjct: 120 LK------LLVLDE 127 >gnl|CDD|35611 KOG0390, KOG0390, KOG0390, DNA repair protein, SNF2 family [Replication, recombination and repair]. Length = 776 Score = 46.2 bits (109), Expect = 2e-05 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%) Query: 358 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 417 E + + G GLNL G + L+ F W+ QQ + R + G K+ Sbjct: 644 PESPSFVFLLSSKAGGEGLNL-IGASRLILFDPDWNPAVDQQAMARA-----WRDGQKKP 697 Query: 418 VFVYYLIAQNTIDELVLQRLRTKSTI 443 V++Y L+A TI+E + QR K + Sbjct: 698 VYIYRLLATGTIEEKIYQRQTHKEGL 723 >gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]. Length = 1567 Score = 42.4 bits (99), Expect = 2e-04 Identities = 55/210 (26%), Positives = 92/210 (43%), Gaps = 37/210 (17%) Query: 20 CAIWASMGSGKTVSVLTALSYIHL---WGEKSVLVIAPLRVAQSVWTSEVQRW----SNF 72 C + MG GKT+ V+T L + L G K+ LV+ PL A + W +E ++W + Sbjct: 699 CILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLNTALN-WMNEFEKWMEGLEDD 757 Query: 73 SHMNISVITGTVK---QRTKVLK---TPAVLYVINFENLGWLVQE-----LKGTWPFAT- 120 + +S + TVK +R+ +L+ + +I ++ L Q K F Sbjct: 758 EKLEVSEL-ATVKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKA 816 Query: 121 --------IVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQ 172 +V DE LK+ + S ++A+ ++R I LTGTP N L++ Sbjct: 817 LVDPGPDFVVCDEGHILKN----EKSAVSKAMNS--IRTKRRIILTGTPLQNNLMEYHCM 870 Query: 173 IWFLDKGKRLGRVFQSFVARWFNTTQIGSH 202 + F+ + LG + F R+ N Q G Sbjct: 871 VNFVKEN-LLG-SIKEFRNRFVNPIQNGQC 898 Score = 34.0 bits (77), Expect = 0.079 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%) Query: 375 GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVL 434 G+NL N ++ F W+ Q I R+ + G + V++Y IAQ T++E + Sbjct: 1231 GINL-VAANRVIIFDASWNPSYDTQSIFRV-----YRFGQTKPVYIYRFIAQGTMEEKIY 1284 Query: 435 QRLRTK 440 +R TK Sbjct: 1285 KRQVTK 1290 >gnl|CDD|35612 KOG0391, KOG0391, KOG0391, SNF2 family DNA-dependent ATPase [General function prediction only]. Length = 1958 Score = 42.4 bits (99), Expect = 3e-04 Identities = 50/190 (26%), Positives = 88/190 (46%), Gaps = 29/190 (15%) Query: 2 NLAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYI----HLWGEKSVLVIA 53 L +Q +DW+ + I A MG GKT+ ++ L+++ WG L++ Sbjct: 615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPH--LIVV 672 Query: 54 PLRVAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLK---TPAVLYVINFENLGWLVQ 110 P V + W E++RW + I G+ K+R + + P +V + + Q Sbjct: 673 PTSVILN-WEMELKRWC--PGLKILTYYGSHKERKEKRQGWAKPNAFHVC-ITSYKLVFQ 728 Query: 111 ELKG----TWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166 +L W + +V+DE+ +K+F+ + R A + S+R + LTGTP N L Sbjct: 729 DLTAFKRKRWQY--LVLDEAQNIKNFKSQ------RWQALLNFNSQRRLLLTGTPLQNSL 780 Query: 167 IDLWGQIWFL 176 ++LW + FL Sbjct: 781 MELWSLMHFL 790 >gnl|CDD|35613 KOG0392, KOG0392, KOG0392, SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]. Length = 1549 Score = 41.9 bits (98), Expect = 4e-04 Identities = 79/345 (22%), Positives = 131/345 (37%), Gaps = 68/345 (19%) Query: 26 MGSGKTVSVLT--ALSYIHLWGE------KSVLVIAPLRVAQSVWTSEVQRWSNFSHMNI 77 MG GKT+ + A + E L++ P + W SEV+++ F + Sbjct: 1003 MGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPSTLTGH-WKSEVKKFFPFLKVLQ 1061 Query: 78 SVITGTVKQRTKVLKTPAVLYVINFENLGWLVQEL-KGTWPFATIVVDESTKLKSFRLRQ 136 V ++ + A + V +++ + V L K W + V+DE +K+ + + Sbjct: 1062 YVGPPAERRELRDQYKNANIIVTSYDVVRNDVDYLIKIDWNY--CVLDEGHVIKNSKTK- 1118 Query: 137 GSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLG--RVFQSFVARWF 194 K + R I L+GTP N +++LW FL G LG + FQS Sbjct: 1119 ----LTKAVKQLRANHRLI-LSGTPIQNNVLELWSLFDFLMPG-FLGTEKQFQS------ 1166 Query: 195 NTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDIADYQNIDKPILITKKVPLPQPVM 254 + G I A R +++ KE EA + L+L+ Q + P L+ + L + V+ Sbjct: 1167 ---RFGKPILASRDP--KSSSKEQEAGV----LALEALHKQVL--PFLLRR---LKEDVL 1212 Query: 255 KQY-HKFQRELYCDL---QGENIEAFNSASKTVKCLQLANGAVYYDEEK----------- 299 K K ++ YC+L Q + F +K Q+ G +K Sbjct: 1213 KDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLR 1272 Query: 300 ----HWKEVHDEKIKALEVIIEKANAAPIIVAYHFNSDLARLQKA 340 H V L I+ HFNS L +Q + Sbjct: 1273 KLCNHPALVLTPVHPDLAAIVSH--------LAHFNSSLHDIQHS 1309 Score = 39.6 bits (92), Expect = 0.002 Identities = 36/144 (25%), Positives = 64/144 (44%), Gaps = 15/144 (10%) Query: 308 KIKALEVIIEKANAAPIIVAYHFNSDLARLQKAFPQGRTLDKDPCTIQEWNEGK-IPLLF 366 ++K++ ++EK + Y + RL + P G ++ +NE I +L Sbjct: 1348 QLKSMLDLVEKD----LFKKYMPSVTYMRLDGSVPPGDRQK----IVERFNEDPTIDVLL 1399 Query: 367 AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQ 426 G GLNL G + +VF W+ Q ++R + G KR V VY LI + Sbjct: 1400 LTTHVGGLGLNLT-GADTVVFVEHDWNPMRDLQAMDR-----AHRIGQKRVVNVYRLITR 1453 Query: 427 NTIDELVLQRLRTKSTIQDLLLNA 450 T++E V+ + K + + ++N Sbjct: 1454 GTLEEKVMGLQKFKMNVANTVINQ 1477 >gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. Length = 103 Score = 38.4 bits (90), Expect = 0.004 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%) Query: 1 MNLAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAP 54 + L P+Q + + +L+ KR I + GSGKT+ L L G+K VL + P Sbjct: 2 LELRPYQIEAIRNLLEKKRGLIVMATGSGKTL-TAAKLIARLLKGKKKVLFLVP 54 >gnl|CDD|31397 COG1204, COG1204, Superfamily II helicase [General function prediction only]. Length = 766 Score = 37.7 bits (87), Expect = 0.007 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 5/97 (5%) Query: 3 LAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVW 62 P Q + +L + I A GSGKT+ L A+ L G V+ I PL+ ++ Sbjct: 33 FNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLK---ALA 89 Query: 63 TSEVQRWSNFSHMNISV--ITGTVKQRTKVLKTPAVL 97 + + +S + I V TG + L V+ Sbjct: 90 EEKYEEFSRLEELGIRVGISTGDYDLDDERLARYDVI 126 >gnl|CDD|39640 KOG4439, KOG4439, KOG4439, RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription, Replication, recombination and repair]. Length = 901 Score = 37.0 bits (85), Expect = 0.010 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%) Query: 358 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 417 G +L + A G GLNL G N L+ L W+ QQ +RI + G K+ Sbjct: 796 KGGARVMLLSLTAG-GVGLNL-IGANHLILVDLHWNPALEQQACDRI-----YRMGQKKD 848 Query: 418 VFVYYLIAQNTIDELVLQRLRTKSTIQDLLL 448 VF++ L+ + T+++ V K + +L Sbjct: 849 VFIHRLMCKGTVEQRVKSLQDKKLDLAKGVL 879 >gnl|CDD|35610 KOG0389, KOG0389, KOG0389, SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]. Length = 941 Score = 36.5 bits (84), Expect = 0.017 Identities = 46/190 (24%), Positives = 73/190 (38%), Gaps = 28/190 (14%) Query: 3 LAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYIHLWGEKSV-LVIAPLRV 57 L +Q V+W+L K I A MG GKT+ V+ L+Y+ G LV+ P Sbjct: 400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSST 459 Query: 58 AQSVWTSEVQRW-----------SNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLG 106 ++ W E +W S + K VL T L + ++ Sbjct: 460 LEN-WLREFAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRS 518 Query: 107 WLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166 +L F ++ DE LK+ + S+ + L + + LTGTP N L Sbjct: 519 FLKN-----QKFNYVIYDEGHMLKN----RTSERYKHLMSIN--ANFRLLLTGTPLQNNL 567 Query: 167 IDLWGQIWFL 176 +L + F+ Sbjct: 568 KELISLLAFV 577 Score = 28.8 bits (64), Expect = 3.2 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 7/88 (7%) Query: 354 IQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQA 412 I E+N K I + + G G+NL N ++ + D + ++ R + Sbjct: 820 IDEFNTDKDIFVFLLSTKAGGFGINLT-CANTVIIHDI--DFNPY---DDKQAEDRCHRV 873 Query: 413 GFKRAVFVYYLIAQNTIDELVLQRLRTK 440 G + V VY LI ++TI+E +L+ +TK Sbjct: 874 GQTKPVTVYRLITKSTIEEGILRLAKTK 901 >gnl|CDD|36219 KOG1001, KOG1001, KOG1001, Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription, Replication, recombination and repair]. Length = 674 Score = 36.1 bits (83), Expect = 0.022 Identities = 32/197 (16%), Positives = 65/197 (32%), Gaps = 28/197 (14%) Query: 257 YHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVY----YDEEKHWKEVHDEKIKAL 312 H F E ++I+ +A + L + + KI A Sbjct: 472 GHDFCVECLK----KSIQQSENAPCPLCRNVLKEKKLLSANPLPSIINDLLPESSKIYAF 527 Query: 313 EVIIE--KANAAP-IIVAYHFNSDLARLQ----------KAFPQGRTLDKDPCTIQEWNE 359 I++ + + P I++ LA + + + + ++ Sbjct: 528 LKILQAKEMSEQPKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPC 587 Query: 360 GKIPLLFAHPASCGH-GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAV 418 + G GLNL ++L+ WW+ +Q I+R Q + V Sbjct: 588 DPLVTALLMSLKAGKVGLNLTAASHVLLM-DPWWNPAVEEQAIDRAHRIGQT-----KPV 641 Query: 419 FVYYLIAQNTIDELVLQ 435 V I ++T++E +L+ Sbjct: 642 KVSRFIIKDTVEERILK 658 Score = 33.4 bits (76), Expect = 0.15 Identities = 39/178 (21%), Positives = 67/178 (37%), Gaps = 33/178 (18%) Query: 16 DHKRCAIWA-SMGSGKTVSVLTALSYIHLWGE--------KSVLVIAPLRVAQSVWTSEV 66 R I A MG GKTV + + L + K+ L++ P + W +E+ Sbjct: 150 QSLRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSLLTQ-WKTEL 208 Query: 67 QRWSNFSHMNISVITGTVKQRTK------VLKTPAVLYVINFENLGWLVQELKGTWPFAT 120 ++ + ++I V G K +++ VL T +L + WL Sbjct: 209 EKVTEEDKLSIYVYHGRTKDKSELNSYDVVLTTYDILKNSPLVKIKWL------------ 256 Query: 121 IVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDK 178 +V + + Q K L +++ LTGTP N L +L+ FL+ Sbjct: 257 RIVLDEAHTIKNKDTQIFKAVCQL-----DAKYRWCLTGTPIQNNLDELYSLFKFLEI 309 >gnl|CDD|28960 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process. Length = 131 Score = 35.7 bits (82), Expect = 0.030 Identities = 25/137 (18%), Positives = 57/137 (41%), Gaps = 21/137 (15%) Query: 298 EKHWKEVHDEKIKALEVIIEKANAAP--IIVAYHFNSDLARLQKAFP-----------QG 344 +++ V DEK++AL ++++ +++ L L + G Sbjct: 3 KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62 Query: 345 RTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERI 404 +++ ++++ EG+I +L A G++L ++++ + L W + Q I R Sbjct: 63 SQEEREE-VLKDFREGEIVVLVATDVI-ARGIDLP-NVSVVINYDLPWSPSSYLQRIGRA 119 Query: 405 GVTRQRQAGFKRAVFVY 421 G +AG K + Sbjct: 120 G-----RAGQKGTAILL 131 >gnl|CDD|144016 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78 Score = 35.2 bits (82), Expect = 0.044 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%) Query: 353 TIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIG 405 ++++ GK +L A G G++L N+++ + L W+ + Q I R G Sbjct: 25 ILEDFRNGKSKVLVA-TDVAGRGIDLP-DVNVVINYDLPWNPASYIQRIGRAG 75 >gnl|CDD|35609 KOG0388, KOG0388, KOG0388, SNF2 family DNA-dependent ATPase [Replication, recombination and repair]. Length = 1185 Score = 34.7 bits (79), Expect = 0.052 Identities = 39/170 (22%), Positives = 75/170 (44%), Gaps = 35/170 (20%) Query: 26 MGSGKTVSVLTALSYI----HLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVIT 81 MG GKTV ++ L+++ ++WG LV+ P + W E+ R+ + Sbjct: 595 MGLGKTVQSISVLAHLAETHNIWG--PFLVVTPASTLHN-WAQEISRF--LPSFKVLPYW 649 Query: 82 GTVKQRTKVLKTPAVLYVINFENLGWLV---------------QELKGTWPFATIVVDES 126 G+ +R K+L+ + N + V Q++K W + +++DE+ Sbjct: 650 GSPSER-KILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKVK--WQY--MILDEA 704 Query: 127 TKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFL 176 +KS S ++R +++ + LTGTP N + +LW + F+ Sbjct: 705 QAIKS------SSSSRWKTLLSFKCRNRLLLTGTPIQNSMQELWALLHFI 748 >gnl|CDD|36234 KOG1016, KOG1016, KOG1016, Predicted DNA helicase, DEAD-box superfamily [General function prediction only]. Length = 1387 Score = 34.3 bits (78), Expect = 0.066 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%) Query: 20 CAIWASMGSGKTVSVLTALS-YIHLWGEKSVLVIAPLRVAQSVWTSEVQRW 69 C + SMG GKT+ V++ ++ K+VLVI P+ Q+ W SE W Sbjct: 285 CILAHSMGLGKTLQVISFSDIFLRHTKAKTVLVIVPINTLQN-WLSEFNMW 334 >gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]. Length = 442 Score = 33.5 bits (76), Expect = 0.12 Identities = 33/165 (20%), Positives = 62/165 (37%), Gaps = 20/165 (12%) Query: 1 MNLAPHQTKIVD----WILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLR 56 L P+Q + +D +R I G+GKTV A++ + ++S LV+ P + Sbjct: 35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL----KRSTLVLVPTK 90 Query: 57 VAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLGWLVQELKGTW 116 W ++++ + I + G K+ T A + + L + Sbjct: 91 ELLDQWAEALKKFLLLND-EIGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNE--- 146 Query: 117 PFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTP 161 F I+ DE L + + R + + + + LT TP Sbjct: 147 -FGLIIFDEVHHL-------PAPSYRRILELLSAAYPRLGLTATP 183 >gnl|CDD|36339 KOG1123, KOG1123, KOG1123, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription, Replication, recombination and repair]. Length = 776 Score = 33.4 bits (76), Expect = 0.12 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 4/63 (6%) Query: 27 GSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGTVKQ 86 G+GKT+ +TA I +KS LV+ V+ W + ++WS I T K+ Sbjct: 330 GAGKTLVGVTAACTI----KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQICRFTSDAKE 385 Query: 87 RTK 89 R Sbjct: 386 RFP 388 >gnl|CDD|30859 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]. Length = 513 Score = 32.8 bits (74), Expect = 0.21 Identities = 29/127 (22%), Positives = 53/127 (41%), Gaps = 21/127 (16%) Query: 5 PHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK---SVLVIAPLRVAQS 60 P Q + IL + A G+GKT + +L L I E+ S L++AP R Sbjct: 54 PIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAV 113 Query: 61 VWTSEVQRWS-NFSHMNISVITG--TVKQRTKVLK--------TPAVL------YVINFE 103 E+++ N + ++V+ G +++++ + LK TP L ++ Sbjct: 114 QIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLS 173 Query: 104 NLGWLVQ 110 + LV Sbjct: 174 GVETLVL 180 >gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction only]. Length = 814 Score = 32.1 bits (73), Expect = 0.31 Identities = 30/140 (21%), Positives = 54/140 (38%), Gaps = 22/140 (15%) Query: 3 LAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK------SVLVIAPL 55 L P Q + I + I A GSGKT + L ++ + G+ L I+PL Sbjct: 23 LTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPL 82 Query: 56 RVAQSVWTSEVQRWSNFSHMNISVITGTV--KQRTKVLKTPAVLYVINFENLGWLVQELK 113 + + ++ + ++V G ++ K+LK P + + E+L L+ Sbjct: 83 KALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILL---- 138 Query: 114 GTWPFA--------TIVVDE 125 P ++VDE Sbjct: 139 -NSPKFRELLRDVRYVIVDE 157 >gnl|CDD|33166 COG3358, COG3358, Uncharacterized conserved protein [Function unknown]. Length = 262 Score = 30.0 bits (67), Expect = 1.5 Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 6/79 (7%) Query: 148 AWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSFVARWFN--TTQIGSHIGA 205 AW R E S G L W + F S RW+ +G+H+ Sbjct: 18 AWHFSRNKEAI---SRTGATSLSATEWISATTLKDAHTFPSLPGRWYKRGGGVVGAHLP- 73 Query: 206 VRYTAKETAQKEIEAQLSD 224 +T TAQ+ A Sbjct: 74 PPFTTTGTAQRRRGALFRA 92 >gnl|CDD|31398 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]. Length = 851 Score = 29.6 bits (66), Expect = 1.8 Identities = 35/159 (22%), Positives = 60/159 (37%), Gaps = 31/159 (19%) Query: 2 NLAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSV-LVIAPLRVAQS 60 L HQ + I + + + GSGKT S L + L + L++ P + Sbjct: 70 RLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTN---A 126 Query: 61 VWTSEVQRWSNFSH-----MNISVITGTVKQRTK----------VLKTPAVLYVI---NF 102 + + +R + TG + +L P +L+ + N Sbjct: 127 LANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNH 186 Query: 103 ENLGWLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTA 141 + WL++ LK +VVDE L ++R QGS+ A Sbjct: 187 DAWLWLLRNLK------YLVVDE---LHTYRGVQGSEVA 216 >gnl|CDD|33957 COG4232, COG4232, Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]. Length = 569 Score = 29.5 bits (66), Expect = 1.8 Identities = 21/108 (19%), Positives = 34/108 (31%), Gaps = 9/108 (8%) Query: 144 LAKPAWESERFIELTGTPSPNGLIDLWGQIWFL---DKGKRLGRVFQS-----FVARWFN 195 LA W R + G + GL+ L W KR VF + Sbjct: 373 LATAIWLLWRVLPEVGALALWGLLLLAFGAWLFGRWLAAKRGPWVFALVLILALLGALVG 432 Query: 196 TTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDIADYQNIDKPILI 243 + + A+ + E +S LD A + KP+++ Sbjct: 433 VQPLQAKAFLNPEAAQSVSHGEFWQPISPLAE-LDQALAEAKAKPVML 479 >gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA processing and modification]. Length = 519 Score = 29.6 bits (66), Expect = 1.9 Identities = 27/131 (20%), Positives = 49/131 (37%), Gaps = 24/131 (18%) Query: 3 LAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK-------SVLVIAP 54 P Q + L + A GSGKT++ +L A+ +++ K VLV+AP Sbjct: 114 PTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAP 173 Query: 55 LRVAQSVWTSEVQRWSNFSHMNISVITGTVKQRTK----------VLKTPAVLY------ 98 R +E + + + + + G + + V+ TP L Sbjct: 174 TRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEG 233 Query: 99 VINFENLGWLV 109 +N + +LV Sbjct: 234 SLNLSRVTYLV 244 >gnl|CDD|39131 KOG3928, KOG3928, KOG3928, Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]. Length = 461 Score = 29.2 bits (65), Expect = 2.6 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 5/66 (7%) Query: 6 HQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSE 65 ++VD + KR + G+GK++ AL+ + +I + A+ WT+ Sbjct: 168 LYKRLVDPMHPVKRFVLDGEPGTGKSI----ALAQAVHYAADQKWLILHIPYAEL-WTNG 222 Query: 66 VQRWSN 71 + +S Sbjct: 223 RKDYSY 228 >gnl|CDD|35551 KOG0330, KOG0330, KOG0330, ATP-dependent RNA helicase [RNA processing and modification]. Length = 476 Score = 28.8 bits (64), Expect = 3.4 Identities = 31/141 (21%), Positives = 54/141 (38%), Gaps = 18/141 (12%) Query: 1 MNLAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEKS---VLVIAPLR 56 Q++ + L + A GSGKT + L L L E LV+ P R Sbjct: 82 KKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQ--RLLQEPKLFFALVLTPTR 139 Query: 57 VAQSVWTSEVQRWSNFSHMNISVITG---TVKQRTKVLKTPAVLYVINFENLGWLVQELK 113 + + + + ++V+ G + Q ++ K P +L G L L+ Sbjct: 140 ELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVA----TPGRLWDHLE 195 Query: 114 GTWPFAT-----IVVDESTKL 129 T F+ +V+DE+ +L Sbjct: 196 NTKGFSLEQLKFLVLDEADRL 216 >gnl|CDD|145508 pfam02399, Herpes_ori_bp, Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication. Length = 829 Score = 28.5 bits (64), Expect = 3.6 Identities = 12/29 (41%), Positives = 17/29 (58%) Query: 24 ASMGSGKTVSVLTALSYIHLWGEKSVLVI 52 A MGSGKT +++ L + SVLV+ Sbjct: 56 APMGSGKTTALIEWLRAALDSPDTSVLVV 84 >gnl|CDD|35519 KOG0298, KOG0298, KOG0298, DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]. Length = 1394 Score = 28.4 bits (63), Expect = 3.7 Identities = 12/47 (25%), Positives = 20/47 (42%) Query: 401 IERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLL 447 E + R + G KR FV+ I T++E +L + +K Sbjct: 1300 DEAQAIGRVHRIGQKRPTFVHRFIVNETVEENILSLITSKEETLTKS 1346 >gnl|CDD|33398 COG3598, RepA, RecA-family ATPase [DNA replication, recombination, and repair]. Length = 402 Score = 28.1 bits (62), Expect = 5.0 Identities = 18/93 (19%), Positives = 32/93 (34%), Gaps = 8/93 (8%) Query: 179 GKRLGRVFQSFVA----RWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCC--LSLDIA 232 GK ++ F G V Y + E +++I +L + L A Sbjct: 101 GKTTLLLYLCIALAAGKNLFGNKVKEP--GKVLYVSLELYREDILERLEPVRARMGLSPA 158 Query: 233 DYQNIDKPILITKKVPLPQPVMKQYHKFQRELY 265 D +N+D + K Y +F++ L Sbjct: 159 DVRNMDLTDVSGAADESDVLSPKLYRRFEKILE 191 >gnl|CDD|30596 COG0247, GlpC, Fe-S oxidoreductase [Energy production and conversion]. Length = 388 Score = 28.0 bits (61), Expect = 5.1 Identities = 22/105 (20%), Positives = 33/105 (31%), Gaps = 13/105 (12%) Query: 256 QYHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEKIKALEVI 315 Y E L +NIEAF + + A Y +K + E+ E+ + + Sbjct: 193 AYRSGFLERAKKLAKKNIEAFKKLIEGGDPIVTVCPACYGALKKEYPELLGERALKVVDL 252 Query: 316 IE-------------KANAAPIIVAYHFNSDLARLQKAFPQGRTL 347 +E IV YH L R + R L Sbjct: 253 VELLAELLREGKLKLLPKLKGKIVTYHDPCHLRRGGGVVDEPREL 297 >gnl|CDD|35900 KOG0681, KOG0681, KOG0681, Actin-related protein - Arp5p [Cytoskeleton]. Length = 645 Score = 27.7 bits (61), Expect = 7.9 Identities = 10/34 (29%), Positives = 16/34 (47%) Query: 232 ADYQNIDKPILITKKVPLPQPVMKQYHKFQRELY 265 D Q ID PI++T+ + P + + E Y Sbjct: 110 VDGQGIDHPIILTEALANPVYSRSEMVELLFETY 143 >gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA processing and modification]. Length = 673 Score = 27.7 bits (61), Expect = 7.9 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%) Query: 298 EKHWKEV-HDEKIKALEVIIEKANAAPIIV 326 E+ + V DEK K L I+E PII+ Sbjct: 493 EQKVEMVSEDEKRKKLIEILESNFDPPIII 522 >gnl|CDD|147517 pfam05373, Pro_3_hydrox_C, L-proline 3-hydroxylase, C-terminal. Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain. Length = 101 Score = 27.1 bits (60), Expect = 9.3 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 3/43 (6%) Query: 295 YDEEKHWKEVHDEKIKALEVIIEKANAAPIIV---AYHFNSDL 334 DE K + + E+I A II +AN I+ HF + Sbjct: 19 VDERKPFTDETKERILAFSGIISEANFRDIVFILSKLHFTYKV 61 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 0.321 0.135 0.416 Gapped Lambda K H 0.267 0.0630 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,622,220 Number of extensions: 294740 Number of successful extensions: 735 Number of sequences better than 10.0: 1 Number of HSP's gapped: 723 Number of HSP's successfully gapped: 52 Length of query: 458 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 361 Effective length of database: 4,167,664 Effective search space: 1504526704 Effective search space used: 1504526704 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 (21.9 bits) S2: 59 (26.7 bits)