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= 0001.2785.p (706 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312090|ref|YP_003776182.1| ATP-dependent DNA helicase [Her... 1195 0.0 gi|300309775|ref|YP_003773867.1| ATP-dependent DNA helicase [Her... 199 5e-52 gi|300313605|ref|YP_003777697.1| ATP-dependent DNA helicase rep ... 194 2e-50 gi|300310196|ref|YP_003774288.1| ATP-dependent DNA helicase [Her... 57 6e-09 >gi|300312090|ref|YP_003776182.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 707 Score = 1195 bits (3092), Expect = 0.0, Method: Compositional matrix adjust. Identities = 592/706 (83%), Positives = 634/706 (89%), Gaps = 1/706 (0%) Query: 1 MSPDFVQDAPDTRSAAAAQHDPFARLNPQQRAAVEHGSQLPPAQQAPLLIVAGAGTGKTN 60 M P+ +QDAPDT S + DPFARLN QQR AVEHG +LPP+QQ PLLIVAGAG+GKTN Sbjct: 1 MPPELIQDAPDTTSLPDRESDPFARLNAQQREAVEHGGKLPPSQQPPLLIVAGAGSGKTN 60 Query: 61 TLAHRVARLILDGADPQRILLLSFSRRAAADLGRRVGQVIAEVLGLAPGATPPQLPWSGT 120 TLAHRVARL+L+GADPQRILLLSFSRRAAAD+GRRVGQVIA+VLGLA TPPQL WSGT Sbjct: 61 TLAHRVARLVLEGADPQRILLLSFSRRAAADMGRRVGQVIAQVLGLAASDTPPQLHWSGT 120 Query: 121 FHAIGARLLRDYAAVISLEENFTIQDRGDSEDLLGLLRHELGLSATEQRFPLKATCLSIY 180 FHAIGARLLR+YA VI LEE+FTIQDRGDSEDL+GLLRH++GLSATE+RFPLKATCL+IY Sbjct: 121 FHAIGARLLREYAKVIGLEEDFTIQDRGDSEDLMGLLRHDMGLSATEKRFPLKATCLAIY 180 Query: 181 SRVVNTRQDLGQVLASHFPWCREWERQLGELFSQYVQAKENQHVLDYDDLLLFWAEMLSD 240 SR VNTRQDLG+VL HFPWC EWER LGELF +YV AKE QHVLDYDDLLLFWA+ML D Sbjct: 181 SRAVNTRQDLGEVLQQHFPWCCEWERPLGELFGRYVDAKEEQHVLDYDDLLLFWADMLGD 240 Query: 241 TQIAQSVGARFDHVLVDEYQDTNRLQAEILQRIKPDGGGVTAVGDDAQSIYSFRGATVRN 300 QIAQSVG RFDHVLVDEYQDTNRLQAEILQR+KPDG GVTAVGDDAQ+IYSFRGATVRN Sbjct: 241 AQIAQSVGQRFDHVLVDEYQDTNRLQAEILQRMKPDGAGVTAVGDDAQAIYSFRGATVRN 300 Query: 301 ILDFPSLFAQPARLLTLEQNYRSTQAILQASNAVIADAPERHFKNLWSDKISSHKPQLVV 360 ILDFP LF QP RLLTLEQNYRSTQ IL ASNAVIADAPERH K+LWSDK SS KPQLVV Sbjct: 301 ILDFPGLFTQPVRLLTLEQNYRSTQPILHASNAVIADAPERHVKHLWSDKPSSQKPQLVV 360 Query: 361 IPDEAEQARWVANRILAHREEGLTLKSQAVLFRTATHSAALELELVRRNIPFVKFGGLKF 420 IPDEAEQARWVANRILAHREEGLTLKSQAVLFRTATHSAALELEL RRNIPFVKFGGLKF Sbjct: 361 IPDEAEQARWVANRILAHREEGLTLKSQAVLFRTATHSAALELELARRNIPFVKFGGLKF 420 Query: 421 LESTHIKDLLALLRLAHNPSARMAGFRVLQLIPGVGPATAKKVLDRMAAASDPTQALQDF 480 LES HIKDLLALLRLAHNPS RMAG R LQLIPGVGPATA+KVLD MAAA+DP AL +F Sbjct: 421 LESGHIKDLLALLRLAHNPSGRMAGLRALQLIPGVGPATARKVLDLMAAAADPADALLNF 480 Query: 481 QPPASIALQWRDFAQAYAFM-RGTTTWPADLQAARDWYLPLLEQRYEDADARLLDIEQLV 539 PA+IALQW+ FA YA M R + +WP D+ AARDWYLP L++RY+DA AR DIEQL Sbjct: 481 GAPANIALQWQAFADTYALMRRASASWPTDILAARDWYLPQLQERYDDAQARAADIEQLA 540 Query: 540 ALAQGYASREKLLTELTLDPPEASSDFSGVPYRDEDYLTLSTIHSAKGQEWRSVHVLNVV 599 LA GYASREK LTELTLDPPEASSDFSG P RDEDYLTLSTIHSAKGQEWRSVH+LNVV Sbjct: 541 VLANGYASREKFLTELTLDPPEASSDFSGPPLRDEDYLTLSTIHSAKGQEWRSVHILNVV 600 Query: 600 DGCIPSDLATGSEVEIAEERRLLYVAMTRAKEYLHLVVPQRFYLTQQTAQGERHVNGIRS 659 DGCIPSDLATGSE EIAEERRLLYVAMTRA++YLHLVVPQRFY+TQQT QG+RHVNGIRS Sbjct: 601 DGCIPSDLATGSEAEIAEERRLLYVAMTRARQYLHLVVPQRFYITQQTPQGDRHVNGIRS 660 Query: 660 RFITPRMLPHFEDSLWLSAETNGARTPMPESVRMLIRQRARNAWSK 705 RFITPRMLPHFEDSLW SAETNGARTPMPESVRML+RQRAR +W+K Sbjct: 661 RFITPRMLPHFEDSLWFSAETNGARTPMPESVRMLVRQRARQSWNK 706 >gi|300309775|ref|YP_003773867.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 759 Score = 199 bits (507), Expect = 5e-52, Method: Compositional matrix adjust. Identities = 200/674 (29%), Positives = 310/674 (45%), Gaps = 87/674 (12%) Query: 42 PAQQAPLLIVAGAGTGKTNTLAHRVARLILDG-ADPQRILLLSFSRRAAADLGRRVGQVI 100 PAQ A LI+AGAG+GKT L R+A LI G P IL ++F+ +AA ++ R+ Sbjct: 19 PAQSA--LILAGAGSGKTRVLTTRIAWLIQTGQVSPSGILAVTFTNKAAKEMTARLS--- 73 Query: 101 AEVLGLAPGATPPQLPWSGTFHAIGARLLRDYAAVISLEENFTIQDRGDSEDLLGLLRHE 160 G+ P T W GTFH + RLLR + L + F I D ++D L ++ Sbjct: 74 ----GMLPINTRGM--WIGTFHGLCNRLLRAHHKDAGLPQTFQILD---TQDQLSAIKRL 124 Query: 161 LG-LSATEQRFPLKATCLSIYSRVVNTRQDLGQVLASHFPWCREWERQLGELFSQYVQAK 219 L ++ ++++P + +N+ +D G + A ++ R+ EL+ Y Q Sbjct: 125 LKQMNVDDEKYPPRNLMY-----FINSAKDQG-LRAKDVDAYDDYNRKFVELYELYDQQC 178 Query: 220 ENQHVLDYDDLLLFWAEMLSDTQ-IAQSVGARFDHVLVDEYQDTNRLQAEILQRIKPDGG 278 + + V+D+ +LLL E+LS Q + + +RF H+LVDE+QDTN LQ + L+ + Sbjct: 179 QREGVVDFAELLLRTYELLSRNQPLREHYQSRFRHILVDEFQDTNDLQYKWLKLMAGQHN 238 Query: 279 GVTAVGDDAQSIYSFRGATVRNILDFPSLFAQPARLLTLEQNYRSTQAILQASNAVIADA 338 V AVGDD QSIY+FRGA V N+ F F L+ LEQNYRS IL +N +IA+ Sbjct: 239 AVFAVGDDDQSIYAFRGANVGNMQAFEQEF-HVQNLIKLEQNYRSHGHILDTANELIANN 297 Query: 339 PERHFKNLWSDKISSHKPQLVVIPDEAEQARWVANRILAHREEGLTLKSQAVLFRTATHS 398 +R KNL +D + ++ + ++A+W+ ++ EG A+L+R+ S Sbjct: 298 SKRLGKNLRTDAGHGEQVRVYEATSDLQEAQWIIEQVKDLIAEGWARSEIAILYRSNAQS 357 Query: 399 AALELELVRRNIPFVKFGGLKFLESTHIKDLLALLRLAHNPSARMAGFRVLQL-IPGVGP 457 LE L IP+ +GG +F E IK +A L+L N A RV+ G+G Sbjct: 358 RVLEHALFSSAIPYRVYGGQRFFERAEIKHAIAYLQLMDNLHNDSAFLRVVNFPTRGIGA 417 Query: 458 ATAKKVLDRMAAASDPTQALQDFQP----PASIALQ-WRDFAQAYAFMRGTTTWPADLQA 512 + + D AA +L P A +L + + F P ++ Sbjct: 418 KAMESLQD---AARQYGCSLYAAVPYVAGKAGSSLNAFVKLIEGARFETQHLPLPEMVKV 474 Query: 513 ARDWYLPLLEQRYEDADA-RLLDIEQLVALAQGYASREKLLTELTLDPP----------- 560 D + R E A R+ ++EQLV+ A + S E LD P Sbjct: 475 VLDLSGLMTHYRNEKEGADRIENLEQLVSAATLFVSEEG----YGLDAPAFLGPQAQATA 530 Query: 561 -EASSDFSGVPYRDED------------YLTLSTIHS-------------------AKGQ 588 A + GV D D +L+ +++ + AKG Sbjct: 531 GAAITTADGVEVLDADAPLVTIMSPLSAFLSHASLEAGDNQAQAGQDALQLMTVHSAKGL 590 Query: 589 EWRSVHVLNVVDGCIPSDLATGSEVEIAEERRLLYVAMTRAKEYLHLVVPQRFYLTQQTA 648 E+ +V + + +G P + + E + EERRL+YVA+TRA++ L + Q L QT Sbjct: 591 EFDAVFITGMEEGLFPHENSAKEEGGVEEERRLMYVAITRARKRLFMTFSQTRMLHGQTR 650 Query: 649 QGERHVNGIRSRFI 662 +RSRF Sbjct: 651 Y------NMRSRFF 658 >gi|300313605|ref|YP_003777697.1| ATP-dependent DNA helicase rep [Herbaspirillum seropedicae SmR1] Length = 690 Score = 194 bits (494), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 197/668 (29%), Positives = 319/668 (47%), Gaps = 87/668 (13%) Query: 22 PFARLNPQQRAAVEHGSQLPPAQQAPLLIVAGAGTGKTNTLAHRVARLILD-GADPQRIL 80 P LN Q AV + + P L++AGAG+GKT + ++A LI + G + + I Sbjct: 4 PSFGLNKPQSEAVHYMA-------GPCLVLAGAGSGKTRVITQKIAHLIENCGYESRNIA 56 Query: 81 LLSFSRRAAADLGRRVGQVIAEVLGLAPGATPPQLPW--SGTFHAIGARLLRDYAAVISL 138 L+F+ +AA ++ R+ +++ + P Q TFH++G ++LR + + L Sbjct: 57 ALTFTNKAALEMQERIAKLLKD---------PKQAKHLTVSTFHSLGVKILRQESQHLGL 107 Query: 139 EENFTIQDRGDSEDLLGLLRHELGLSATEQRFPLKATCLSIYSRVVNTRQDLGQVLASHF 198 ++ F+I D S+D L++ EL ++ + +S++ + DL + A Sbjct: 108 KDRFSIMD---SDDCFSLVQ-ELAVTTDKAIIRGVQNSISLWKNGL-VDPDLAEKNAR-- 160 Query: 199 PWCREWERQLGELFSQYVQAKENQHVLDYDDLLLFWAEML-SDTQIAQSVGARFDHVLVD 257 E E Q ++ YV + +D+DDL+ E+ S+ ++ + ++L+D Sbjct: 161 ---TEDEAQAARIYRSYVATLKAYQAVDFDDLIRLPVELFRSNEEVRDRWQRKLRYLLID 217 Query: 258 EYQDTNRLQAEILQRIKPDGGG---VTAVGDDAQSIYSFRGATVRNI----LDFPSLFAQ 310 EYQDTN Q E+++ + G TAVGDD Q+IY++RGAT+ N+ +DFP+L Sbjct: 218 EYQDTNTCQYELVKLLVTGIGKKPMFTAVGDDDQAIYAWRGATIENLKLLGVDFPNL--- 274 Query: 311 PARLLTLEQNYRSTQAILQASNAVIADAPERHFKNLWSDKISSHKPQLVVIPDEAEQARW 370 L+ LEQNYRS+ ILQA+NAVI++ P+ K LWS+ ++ + DE +A Sbjct: 275 --HLIKLEQNYRSSTRILQAANAVISNNPKLFDKTLWSEHGLGDPITVMAMDDEEAEADQ 332 Query: 371 VANRILAHR-EEGLTLKSQAVLFRTATHSAALELELVRRNIPFVKFGGLKFLESTHIKDL 429 +A + AHR E A+L+R + LE L R IP+V GG + + IKD+ Sbjct: 333 IAITLSAHRFERRAKFADYAILYRGNHQARILEKSLRRERIPYVMSGGQSYFDRAEIKDI 392 Query: 430 LALLRLAHNPSARMAGFRVLQLIP--GVGPATAKKVLDRMAAASDPT-------QALQDF 480 +A LRL N A R + P GVG AT +VL +A + L+D Sbjct: 393 IAYLRLIANQDDDPAFIRAVT-TPRRGVGQATL-EVLGTLAGQWQCSLFEAVYKGGLEDK 450 Query: 481 QPPASIALQWRDFAQAYAFMRGTTTWPA-------------DLQAARDWYLPLLEQRYED 527 + L R F + T P D+ A ++ L + E Sbjct: 451 LTDRQL-LPLRKFCDFINALESRATRPGPSGSGENAGKVLDDMMEAINYEFYLYDSFEER 509 Query: 528 -ADARLLDIEQLVALAQGYAS-------REKLLTELTLDPPEASSDFSGVPYRDE--DYL 577 A AR ++ + + A EK L E+T + + S + RDE D + Sbjct: 510 AAQARWQNVVDFINWLKERACGGRDGEGEEKNLLEIT----QMVALMSMLEGRDEEQDAV 565 Query: 578 TLSTIHSAKGQEWRSVHVLNVVDGCIP--SDLAT---GSEVEIAEERRLLYVAMTRAKEY 632 +ST+H++KG E+ V ++ V +G +P D T + + EERRL+YV +TRA+ Sbjct: 566 RMSTLHASKGLEFPHVFLVGVEEGILPHKGDPDTPPEEAAARVEEERRLMYVGITRAQRS 625 Query: 633 LHLVVPQR 640 LHL +R Sbjct: 626 LHLSWCKR 633 >gi|300310196|ref|YP_003774288.1| ATP-dependent DNA helicase [Herbaspirillum seropedicae SmR1] Length = 1158 Score = 56.6 bits (135), Expect = 6e-09, Method: Compositional matrix adjust. Identities = 45/129 (34%), Positives = 62/129 (48%), Gaps = 11/129 (8%) Query: 215 YVQAKENQHVLDYDDLLLFWAEML----SDTQIAQSVGARFDHVLVDEYQDTNRLQAEIL 270 Y + K Q VLD+ DL +L S + + AR+ H+L+DE+QDTN LQ I+ Sbjct: 387 YQEVKAEQRVLDFADLEWQAYRLLRNEASAAYLQTRLDARYKHILLDEFQDTNPLQWCIV 446 Query: 271 QRIKPDGGG------VTAVGDDAQSIYSFRGATVRNILDFPSLF-AQPARLLTLEQNYRS 323 + GG V VGD QSIY FR A R + + AQ A +L Q R+ Sbjct: 447 RCWLDAYGGDAAQPSVFVVGDPKQSIYRFRRAEPRVFVAAREMLRAQGAAILRANQTRRN 506 Query: 324 TQAILQASN 332 A++ N Sbjct: 507 ATAVVDVLN 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 0.320 0.134 0.395 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: 2,168,974 Number of extensions: 89796 Number of successful extensions: 338 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 324 Number of HSP's successfully gapped: 5 Length of query: 706 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 614 Effective length of database: 1,184,250 Effective search space: 727129500 Effective search space used: 727129500 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)