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= 0002.0304.p (756 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph... 939 0.0 gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alph... 284 2e-77 >gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 942 Score = 939 bits (2426), Expect = 0.0, Method: Compositional matrix adjust. Identities = 491/748 (65%), Positives = 577/748 (77%), Gaps = 22/748 (2%) Query: 1 LFCLSNFTFLEGASHAEELAVRAIQLGYAALAVTDECSLAGVVRAYTQTKDR-------E 53 L+C SNF+FL+GASHA EL RAI L Y ALA+TDEC+LAGVVRAY K++ + Sbjct: 11 LYCRSNFSFLQGASHAHELVQRAIALDYRALAITDECTLAGVVRAYAAWKEQFDKGRTQD 70 Query: 54 IKLIIGAHFRIDWSPEQPP-----MTLIALAQNREGYGNLSELITLGRTRADKGDYRLGI 108 KLIIG+ FR ++P +TL+ALA+NREGYGNLSELITL RTRA KG Y L Sbjct: 71 FKLIIGSCFRFTGLEDEPAHPLAALTLVALARNREGYGNLSELITLARTRAAKGSYLLHP 130 Query: 109 DDFSAPQASHAHLRGLPDCLLILAPHYPADAEILEQQTRWLKQTFPQRAWLGLTQLYRPL 168 +D S P + +HLR LPDC LIL P YPAD E L+ Q RW P R+W+G+T+LYRPL Sbjct: 131 EDLSGPPPALSHLRALPDCQLILVPDYPADEETLDAQLRWFAPLAPGRSWVGITRLYRPL 190 Query: 169 DARHRGVLQATADRHGLCIAALGQVNMHVRSRKPLQDTLTAIRLGKAVGDCGYDLAPNAE 228 D HR L+A RHGL +AA+G V MH RSRK LQD +TAIRLG+ V +CG+ LAPNAE Sbjct: 191 DDLHRAALEAATRRHGLPLAAVGDVQMHQRSRKYLQDVVTAIRLGQPVQECGHALAPNAE 250 Query: 229 QHLRSRLRLANIFPAAALQETLHIAALCTFKLSDLRYEYPEELVPDGQTPAAYLRQEVYL 288 QHLRSR+RL + A L +TL IAA C F L++LRYEYP+ELVP G + A YLRQ+ Sbjct: 251 QHLRSRVRLGMVHTPATLAQTLAIAADCRFSLAELRYEYPDELVPLGMSAADYLRQQTLA 310 Query: 289 GAYLRYPGGIPQKVIDQIEHELTMINDMAYEPYFLTVYDIVRFARDQGILRQGRGSAANS 348 GA RYP G+P V +QIE EL +I YE YFLTVYD+V+FAR +GIL QGRGSAANS Sbjct: 311 GAAKRYPQGLPGGVREQIEAELALIAQKEYEAYFLTVYDLVQFARSRGILCQGRGSAANS 370 Query: 349 VVCYCLGVTEVDPTCSVMLFERFISKERGEPPDIDVDFEHQRREEVIQYIYRKYGRMRAA 408 VCYCLGVTEVDPT + +LF RFIS++R EPPDIDVDFEHQRREEVIQ+IYRKYGR RAA Sbjct: 371 AVCYCLGVTEVDPTSTRLLFARFISEKREEPPDIDVDFEHQRREEVIQHIYRKYGRRRAA 430 Query: 409 IAAAVHTYRPRGVLRDVGKALGVDASIVDKVAKSHQWFDNRYNMLERFAECGLDPASPIA 468 +AAAVH+YRPRG LR+VGKALGVDA+IVD VAKS WFD+R +L RFAE GLDP P Sbjct: 431 LAAAVHSYRPRGALREVGKALGVDAAIVDAVAKSQHWFDSREELLARFAEAGLDPELPQI 490 Query: 469 HQWAILAQQLLNFPRHLSQHSGGFVIARDKLSRLVPIENAAMPDRSVIQWDKDDLESLGL 528 WA + +LL FPRHLSQH+GGFVIAR +LSRLVPI+NAAMP+R VI+WDKDDLESL L Sbjct: 491 GLWASITGKLLRFPRHLSQHTGGFVIARGQLSRLVPIQNAAMPERCVIEWDKDDLESLKL 550 Query: 529 LKVDVLALGMLSALRRALELVGKRRGVPFTMQ--DIPREDPVTYDMICKADTIGVFQIES 586 LKVDVLALGML+ALRR LELV RRG+P MQ IPREDP T++MICKADTIGVFQIES Sbjct: 551 LKVDVLALGMLTALRRTLELVSLRRGLPEVMQMHAIPREDPATFEMICKADTIGVFQIES 610 Query: 587 RAQMSMLPRLKPRRFYDLVVQVAIVRPGPIQGGMVHPFLRRRE-GREPET--YPKEI--- 640 RAQMSMLPR++PR YDLVVQVAIVRPGPIQGGMVHP+LRRRE RE + YP Sbjct: 611 RAQMSMLPRMQPRTQYDLVVQVAIVRPGPIQGGMVHPYLRRRELVREGGSFDYPDNTSKS 670 Query: 641 --LRQALERTRGVPIFQEQVMQIAVLAAGFTPGEADGLRRAMAAWKRKGGMEKYETKLIN 698 +++ LERT G+PIFQEQVM +A+ AAG++P EAD LRR+MAAWKRKGGM + +L+ Sbjct: 671 GKIKKVLERTLGIPIFQEQVMDVAIEAAGYSPSEADDLRRSMAAWKRKGGMGPHYERLVL 730 Query: 699 GMLERGYEKTFAEAIFRQIQGFGEYGFP 726 GM + GY + FAE+IF+QI+GFGEYGFP Sbjct: 731 GMTDNGYSREFAESIFKQIEGFGEYGFP 758 >gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 1152 Score = 284 bits (727), Expect = 2e-77, Method: Compositional matrix adjust. Identities = 220/753 (29%), Positives = 358/753 (47%), Gaps = 43/753 (5%) Query: 5 SNFTFLEGASHAEELAVRAIQLGYAALAVTDECSLAGVVRAYTQTKDREIKLIIGAHFRI 64 S ++ ++G +++ A + G AALAVTD +L +VR Y + + + +K I G I Sbjct: 13 SEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGKGVKPIAGCDLWI 72 Query: 65 -DWSPEQPPMTLIALAQNREGYGNLSELIT---LGRTRADKGDYRLGIDDFSAPQASHAH 120 + + + P L+ L +NR GY L E+++ L + + R+ D Q Sbjct: 73 TNDADREKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEWLDALRHQEGGNG 132 Query: 121 LRGLPDCLLILAPHYPADAEILEQQT---RWLKQTFPQRAWLGLT---QLYRPLDARHRG 174 L L + + + + + RW + FP +L L Q + R Sbjct: 133 LIALSGAAMGDIGQAIDNGNLAQAEACARRW-AEIFPGAFYLELQRAGQANMEVQVRQSV 191 Query: 175 VLQATADRHGLCIAALGQVNMHVRSRKPLQDTLTAIRLGKAVGDCGYDLAPNAEQHLRSR 234 L A + GL A + + T I G+ + + N +Q+ +S+ Sbjct: 192 ALGA---KLGLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFNEQQYFKSQ 248 Query: 235 LRLANIFPA--AALQETLHIAALCTFKLSDLRYEYPEELVPDGQTPAAYLRQEVYLGAYL 292 + +F A+ T+ IA C L + + P+ PDG T +L + G + Sbjct: 249 AEMVELFADLPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVAQTKAGLEV 308 Query: 293 RYPGGIPQKVIDQ---------IEHELTMINDMAYEPYFLTVYDIVRFARDQGI-LRQGR 342 R P + + +E E I M + YFL V D +++A++ G+ + GR Sbjct: 309 RLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNNGVPVGPGR 368 Query: 343 GSAANSVVCYCLGVTEVDPTCSVMLFERFISKERGEPPDIDVDFEHQRREEVIQYIYRKY 402 GS A S+V YCL +T++DP +LFERF++ ER PD D+DF + R+ VIQY+ +Y Sbjct: 369 GSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRVIQYVKDRY 428 Query: 403 GRMRAAIAAAVHTYRPRGVLRDVGKALGVDASIVDKVAKSHQWFDNRYNML------ERF 456 G+ + A T +G +RDVG+ L + + D ++K + + L E Sbjct: 429 GKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLADAIEEEPL 488 Query: 457 AECGLDPASPIAHQWAILAQQLLNFPRHLSQHSGGFVIARDKLSRLVPIENAAMPDRSVI 516 + L+ + Q LAQQ+ R++ H+GG +IA KL+ P+ V Sbjct: 489 LKERLENEEEV-KQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQGGDSGVVS 547 Query: 517 QWDKDDLESLGLLKVDVLALGMLSALRRALELVGKRRGVP----FTMQDIPREDPVTYDM 572 Q+DKDD+E++GL+K D L L L+ L RA+ + R P F + +P +D +Y++ Sbjct: 548 QYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYI--RMLDPAMADFDLAKLPLDDRPSYEL 605 Query: 573 ICKADTIGVFQIESRAQMSMLPRLKPRRFYDLVVQVAIVRPGPIQGGMVHPFLRRREGRE 632 + KA T+ VFQ+ESR ML +P RF D++ VA+ RPGP+ ++ F +R+ G E Sbjct: 606 LTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMD--LIPDFCKRKHG-E 662 Query: 633 PETYPKEILRQALERTRGVPIFQEQVMQIAVLAAGFTPGEADGLRRAMAAWKRKGGMEKY 692 YP L T G+ ++QEQVMQ+A + G++ G AD LRRAM K+ M K+ Sbjct: 663 AFDYPDPRTEGILSETYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGK-KKAEEMAKH 721 Query: 693 ETKLINGMLERGYEKTFAEAIFRQIQGFGEYGF 725 G + G ++ A+ IF ++ F YGF Sbjct: 722 RELFREGAAKNGLDQAKADEIFDLMEKFAGYGF 754 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 0.323 0.139 0.422 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: 2,518,033 Number of extensions: 111918 Number of successful extensions: 293 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 285 Number of HSP's successfully gapped: 2 Length of query: 756 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 664 Effective length of database: 1,184,250 Effective search space: 786342000 Effective search space used: 786342000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 134 (56.2 bits)