BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0002.0060.p (759 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309775|ref|YP_003773867.1| ATP-dependent DNA helicase [Her... 1555 0.0 gi|300313605|ref|YP_003777697.1| ATP-dependent DNA helicase rep ... 318 1e-87 gi|300312090|ref|YP_003776182.1| ATP-dependent DNA helicase [Her... 196 6e-51 gi|300310196|ref|YP_003774288.1| ATP-dependent DNA helicase [Her... 66 1e-11 >gi|300309775|ref|YP_003773867.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 759 Score = 1555 bits (4026), Expect = 0.0, Method: Compositional matrix adjust. Identities = 748/759 (98%), Positives = 754/759 (99%) Query: 1 MQNLLHNLNEEQLAAVTLPAQSALILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTF 60 MQNLL NLNEEQLAAVTLPAQSALILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTF Sbjct: 1 MQNLLLNLNEEQLAAVTLPAQSALILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTF 60 Query: 61 TNKAAKEMTARLSGMLPINTRGMWIGTFHGLCNRLLRAHHKDAGLPQTFQILDTQDQLSA 120 TNKAAKEMTARLSGMLPINTRGMWIGTFHGLCNRLLRAHHKDAGLPQTFQILDTQDQLSA Sbjct: 61 TNKAAKEMTARLSGMLPINTRGMWIGTFHGLCNRLLRAHHKDAGLPQTFQILDTQDQLSA 120 Query: 121 IKRLLKQMNVDDEKYPPRNLMYFINSAKDQGLRAKDVDAYDDYNRKFVELYELYDQQCQR 180 IKRLLKQMNVDDEKYPPRNLMYFINSAKDQGLRAKDVDAYDDYNRKFVELYELYDQQCQR Sbjct: 121 IKRLLKQMNVDDEKYPPRNLMYFINSAKDQGLRAKDVDAYDDYNRKFVELYELYDQQCQR 180 Query: 181 EGVVDFAELLLRTYELLSRNQPLREHYQGRFRHILVDEFQDTNDLQYKWLKIMAGQHGAV 240 EGVVDFAELLLRTYELLSRNQPLREHYQ RFRHILVDEFQDTNDLQYKWLK+MAGQH AV Sbjct: 181 EGVVDFAELLLRTYELLSRNQPLREHYQSRFRHILVDEFQDTNDLQYKWLKLMAGQHNAV 240 Query: 241 FAVGDDDQSIYAFRGANVGNMSAFEQEFHVENLIKLEQNYRSHGHILDTANELIANNSKR 300 FAVGDDDQSIYAFRGANVGNM AFEQEFHV+NLIKLEQNYRSHGHILDTANELIANNSKR Sbjct: 241 FAVGDDDQSIYAFRGANVGNMQAFEQEFHVQNLIKLEQNYRSHGHILDTANELIANNSKR 300 Query: 301 LGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEGWARSEIAILYRSNAQSRVL 360 LGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEGWARSEIAILYRSNAQSRVL Sbjct: 301 LGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEGWARSEIAILYRSNAQSRVL 360 Query: 361 EHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHNDSAFLRVVNFPTRGIGAKAM 420 EHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHNDSAFLRVVNFPTRGIGAKAM Sbjct: 361 EHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHNDSAFLRVVNFPTRGIGAKAM 420 Query: 421 ESLQDAARQYGCSLYAAVPYVAGKAGSSLNAFIKLIEGARFETQHLPLPEMVKVVLDLSG 480 ESLQDAARQYGCSLYAAVPYVAGKAGSSLNAF+KLIEGARFETQHLPLPEMVKVVLDLSG Sbjct: 421 ESLQDAARQYGCSLYAAVPYVAGKAGSSLNAFVKLIEGARFETQHLPLPEMVKVVLDLSG 480 Query: 481 LMTHYRNEKEGADRIENLEQLVSAATLFVSEEGYGLDAPAFLGPQAQASAGTAITTADGV 540 LMTHYRNEKEGADRIENLEQLVSAATLFVSEEGYGLDAPAFLGPQAQA+AG AITTADGV Sbjct: 481 LMTHYRNEKEGADRIENLEQLVSAATLFVSEEGYGLDAPAFLGPQAQATAGAAITTADGV 540 Query: 541 EVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQDALQLMTVHSAKGLEFDAVFITGM 600 EVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQDALQLMTVHSAKGLEFDAVFITGM Sbjct: 541 EVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQDALQLMTVHSAKGLEFDAVFITGM 600 Query: 601 EEGLFPHENSAKEEGGVEEERRLMYVAITRARKRLFMTFSQTRMLHGQTRYNMRSRFFDE 660 EEGLFPHENSAKEEGGVEEERRLMYVAITRARKRLFMTFSQTRMLHGQTRYNMRSRFFDE Sbjct: 601 EEGLFPHENSAKEEGGVEEERRLMYVAITRARKRLFMTFSQTRMLHGQTRYNMRSRFFDE 660 Query: 661 MPEQSIKWLSPKIAQHHWFANPKSAWDEVPEAGNNRIAQNFSRQTDSGWRIGQNVSHAKF 720 MPEQSIKWLSPKIAQHHWFANPKSAWDEVPEAGNN+IAQ+FSRQTDSGWRIGQNVSHAKF Sbjct: 661 MPEQSIKWLSPKIAQHHWFANPKSAWDEVPEAGNNKIAQSFSRQTDSGWRIGQNVSHAKF 720 Query: 721 GEGVIVNIEGGGGAARAQINFGKFGMKLLDLSVAKLEKI 759 GEGVIVNIEGGGGAARAQINFGKFGMKLLDLSVAKLEKI Sbjct: 721 GEGVIVNIEGGGGAARAQINFGKFGMKLLDLSVAKLEKI 759 >gi|300313605|ref|YP_003777697.1| ATP-dependent DNA helicase rep [Herbaspirillum seropedicae SmR1] Length = 690 Score = 318 bits (814), Expect = 1e-87, Method: Compositional matrix adjust. Identities = 244/702 (34%), Positives = 362/702 (51%), Gaps = 56/702 (7%) Query: 8 LNEEQLAAVTLPAQSALILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTFTNKAAKE 67 LN+ Q AV A L+LAGAGSGKTRV+T +IA LI+ I A+TFTNKAA E Sbjct: 8 LNKPQSEAVHYMAGPCLVLAGAGSGKTRVITQKIAHLIENCGYESRNIAALTFTNKAALE 67 Query: 68 MTARLSGML--PINTRGMWIGTFHGLCNRLLRAHHKDAGLPQTFQILDTQDQLSAIKRLL 125 M R++ +L P + + + TFH L ++LR + GL F I+D+ D S L+ Sbjct: 68 MQERIAKLLKDPKQAKHLTVSTFHSLGVKILRQESQHLGLKDRFSIMDSDDCFS----LV 123 Query: 126 KQMNVDDEKYPPRNLMYFI----NSAKDQGLRAKDVDAYDDYNRKFVELYELYDQQCQRE 181 +++ V +K R + I N D L K+ D+ + +Y Y + Sbjct: 124 QELAVTTDKAIIRGVQNSISLWKNGLVDPDLAEKNARTEDEA--QAARIYRSYVATLKAY 181 Query: 182 GVVDFAELLLRTYELLSRNQPLREHYQGRFRHILVDEFQDTNDLQYKWLKIMA---GQHG 238 VDF +L+ EL N+ +R+ +Q + R++L+DE+QDTN QY+ +K++ G+ Sbjct: 182 QAVDFDDLIRLPVELFRSNEEVRDRWQRKLRYLLIDEYQDTNTCQYELVKLLVTGIGKKP 241 Query: 239 AVFAVGDDDQSIYAFRGANVGNMSAFEQEFHVENLIKLEQNYRSHGHILDTANELIANNS 298 AVGDDDQ+IYA+RGA + N+ +F +LIKLEQNYRS IL AN +I+NN Sbjct: 242 MFTAVGDDDQAIYAWRGATIENLKLLGVDFPNLHLIKLEQNYRSSTRILQAANAVISNNP 301 Query: 299 KRLGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEGWAR-SEIAILYRSNAQS 357 K K L ++ G G+ + V + EA I + E A+ ++ AILYR N Q+ Sbjct: 302 KLFDKTLWSEHGLGDPITVMAMDDEEAEADQIAITLSAHRFERRAKFADYAILYRGNHQA 361 Query: 358 RVLEHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHNDSAFLRVVNFPTRGIGA 417 R+LE +L IPY + GGQ +F+RAEIK IAYL+L+ N +D AF+R V P RG+G Sbjct: 362 RILEKSLRRERIPYVMSGGQSYFDRAEIKDIIAYLRLIANQDDDPAFIRAVTTPRRGVGQ 421 Query: 418 KAMESLQDAARQYGCSLYAAVPYVAGKAGSSLNAFIKLIEGARFETQHLPLPEMVKVVLD 477 +E L A Q+ CSL+ AV Y G +E + Q LPL + + Sbjct: 422 ATLEVLGTLAGQWQCSLFEAV-YKGG------------LEDKLTDRQLLPLRKFCDFINA 468 Query: 478 LSGLMTHYRNEKEGADRIENLEQLVSAATLFVSEEGYGLDAPAFLGPQAQASAGTAIT-- 535 L T G + + L+ ++ A ++ E Y D +F AQA + Sbjct: 469 LESRATRPGPSGSGENAGKVLDDMMEA----INYEFYLYD--SFEERAAQARWQNVVDFI 522 Query: 536 -----TADGVEVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQDALQLMTVHSAKGL 590 A G + + + ++ + A +S LE D + QDA+++ T+H++KGL Sbjct: 523 NWLKERACGGRDGEGEEKNLLEITQMVALMSM--LEGRDEE----QDAVRMSTLHASKGL 576 Query: 591 EFDAVFITGMEEGLFPHENSA-----KEEGGVEEERRLMYVAITRARKRLFMTFSQTRML 645 EF VF+ G+EEG+ PH+ + VEEERRLMYV ITRA++ L +++ + R Sbjct: 577 EFPHVFLVGVEEGILPHKGDPDTPPEEAAARVEEERRLMYVGITRAQRSLHLSWCKRRKR 636 Query: 646 HGQTRYNMRSRFFDEM---PEQSIKWLSPKIAQHHWFANPKS 684 + SRF EM +++ S KI AN K+ Sbjct: 637 AKEVIECQISRFVKEMRLDEGEAVPQESEKITPQARLANLKA 678 >gi|300312090|ref|YP_003776182.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 707 Score = 196 bits (498), Expect = 6e-51, Method: Compositional matrix adjust. Identities = 204/727 (28%), Positives = 315/727 (43%), Gaps = 103/727 (14%) Query: 8 LNEEQLAAVT-----LPAQSA--LILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTF 60 LN +Q AV P+Q LI+AGAGSGKT L R+A L+ G P IL ++F Sbjct: 26 LNAQQREAVEHGGKLPPSQQPPLLIVAGAGSGKTNTLAHRVARLVLEG-ADPQRILLLSF 84 Query: 61 TNKAAKEMTARLSGMLPINTRGM----------WIGTFHGLCNRLLRAHHKDAGLPQTFQ 110 + +AA +M R+ G + G+ W GTFH + RLLR + K GL + F Sbjct: 85 SRRAAADMGRRV-GQVIAQVLGLAASDTPPQLHWSGTFHAIGARLLREYAKVIGLEEDFT 143 Query: 111 ILDTQDQLSAIKRLLKQMNVD--DEKYPPRNLMYFI-----NSAKDQG-LRAKDVDAYDD 162 I D D + L M + ++++P + I N+ +D G + + + Sbjct: 144 IQDRGDSEDLMGLLRHDMGLSATEKRFPLKATCLAIYSRAVNTRQDLGEVLQQHFPWCCE 203 Query: 163 YNRKFVELYELYDQQCQREGVVDFAELLLRTYELLSRNQPLREHYQGRFRHILVDEFQDT 222 + R EL+ Y + + V+D+ +LLL ++L Q + + RF H+LVDE+QDT Sbjct: 204 WERPLGELFGRYVDAKEEQHVLDYDDLLLFWADMLGDAQ-IAQSVGQRFDHVLVDEYQDT 262 Query: 223 NDLQYKWLKIMAGQHGAVFAVGDDDQSIYAFRGANVGNMSAFEQEF-HVENLIKLEQNYR 281 N LQ + L+ M V AVGDD Q+IY+FRGA V N+ F F L+ LEQNYR Sbjct: 263 NRLQAEILQRMKPDGAGVTAVGDDAQAIYSFRGATVRNILDFPGLFTQPVRLLTLEQNYR 322 Query: 282 SHGHILDTANELIANNSKRLGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEG 341 S IL +N +IA+ +R K+L +D ++ ++ + ++A+W+ ++ EG Sbjct: 323 STQPILHASNAVIADAPERHVKHLWSDKPSSQKPQLVVIPDEAEQARWVANRILAHREEG 382 Query: 342 WARSEIAILYRSNAQSRVLEHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHND 401 A+L+R+ S LE L IP+ +GG +F E IK +A L+L N Sbjct: 383 LTLKSQAVLFRTATHSAALELELARRNIPFVKFGGLKFLESGHIKDLLALLRLAHNPSGR 442 Query: 402 SAFLRVVNFPTRGIG-AKAMESLQDAARQYGCSLYAAVPYVAGKAGSSLNAFIKLIEGAR 460 A LR + G+G A A + L A + AF R Sbjct: 443 MAGLRALQL-IPGVGPATARKVLDLMAAAADPADALLNFGAPANIALQWQAFADTYALMR 501 Query: 461 FETQHLPLPEMVKVVLDLSGLMTHYRNEKEGADRIENLEQLVSAATLFVSEEGY----GL 516 + P + L L Y + + R ++EQL A + S E + L Sbjct: 502 RASASWPTDILAARDWYLPQLQERYDDAQA---RAADIEQLAVLANGYASREKFLTELTL 558 Query: 517 DAPAFLGPQAQASAGTAITTADGVEVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQ 576 D P A + G + D D +L+ +++ + Q Sbjct: 559 DPP------------EASSDFSGPPLRDED------------YLTLSTIHSAKGQ----- 589 Query: 577 DALQLMTVHSAKGLEFDAVFITGMEEGLFPHENSAKEEGGVEEERRLMYVAITRARKRLF 636 + +VH I + +G P + + E + EERRL+YVA+TRAR+ L Sbjct: 590 ---EWRSVH-----------ILNVVDGCIPSDLATGSEAEIAEERRLLYVAMTRARQYLH 635 Query: 637 MTFSQTRMLHGQTRY------NMRSRFFDEMPEQSIKWLSPKIAQHH----WF-ANPKSA 685 + Q + QT +RSRF ++P++ H WF A A Sbjct: 636 LVVPQRFYITQQTPQGDRHVNGIRSRF-----------ITPRMLPHFEDSLWFSAETNGA 684 Query: 686 WDEVPEA 692 +PE+ Sbjct: 685 RTPMPES 691 >gi|300310196|ref|YP_003774288.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 1158 Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 45/130 (34%), Positives = 65/130 (50%), Gaps = 13/130 (10%) Query: 174 YDQQCQREGVVDFAELLLRTYELLSRNQP----LREHYQGRFRHILVDEFQDTNDLQY-- 227 Y + + V+DFA+L + Y LL RN+ L+ R++HIL+DEFQDTN LQ+ Sbjct: 387 YQEVKAEQRVLDFADLEWQAYRLL-RNEASAAYLQTRLDARYKHILLDEFQDTNPLQWCI 445 Query: 228 --KWLKIMAGQ--HGAVFAVGDDDQSIYAFRGANVGNMSAFEQEFHVEN--LIKLEQNYR 281 WL G +VF VGD QSIY FR A A + + +++ Q R Sbjct: 446 VRCWLDAYGGDAAQPSVFVVGDPKQSIYRFRRAEPRVFVAAREMLRAQGAAILRANQTRR 505 Query: 282 SHGHILDTAN 291 + ++D N Sbjct: 506 NATAVVDVLN 515 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.319 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 2,179,191 Number of extensions: 88663 Number of successful extensions: 295 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 286 Number of HSP's successfully gapped: 5 Length of query: 759 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 666 Effective length of database: 1,179,515 Effective search space: 785556990 Effective search space used: 785556990 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 (21.8 bits) S2: 134 (56.2 bits)