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= 0003.0014.p (620 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310559|ref|YP_003774651.1| TP-dependent DNA helicase RecG ... 887 0.0 gi|300312329|ref|YP_003776421.1| transcription-repair ATP-depend... 190 3e-49 >gi|300310559|ref|YP_003774651.1| TP-dependent DNA helicase RecG protein [Herbaspirillum seropedicae SmR1] Length = 722 Score = 887 bits (2292), Expect = 0.0, Method: Compositional matrix adjust. Identities = 459/579 (79%), Positives = 501/579 (86%), Gaps = 6/579 (1%) Query: 40 NKLAKLGLRSDMDLALHLPLRYEDETQVMSIHDASLRGTQVVQVEGVVSKSDVQFRPRRQ 99 NKLAKLGL +DMDL LHLPLRYEDET +MSI +AS+RG Q VQVEGVVS +VQFRPRRQ Sbjct: 49 NKLAKLGLHNDMDLVLHLPLRYEDETSLMSIAEASMRGLQTVQVEGVVSSCEVQFRPRRQ 108 Query: 100 LVVTITDDSGPLVMRFLNFYGSQATQLAEGVRVRVRGELRHGFFGAEMVHPAYKVVLEGA 159 L+VT+ DDSG L +RFLNFYGSQ Q+AEG R+RVRGELRHGFFGAEMVHP+YKVV EGA Sbjct: 109 LIVTVGDDSGQLTLRFLNFYGSQTKQMAEGTRLRVRGELRHGFFGAEMVHPSYKVVNEGA 168 Query: 160 PLPTALTPVYPAGEGLSQAYLRKAIGGALSRLDWRDTLPPAILAEHKLDGFEASVRQLHN 219 PLP LTPVYPAGEGLSQAYLRKAI A+SRLDW DTLPP++LA L FE SVR LHN Sbjct: 169 PLPDVLTPVYPAGEGLSQAYLRKAIANAMSRLDWSDTLPPSMLATLNLAAFEPSVRLLHN 228 Query: 220 PPTDVDEYALEERSHPAWIRMKFDELLAQQLSLKRAQAARRARNASALPTIGNISKAFIK 279 PP DVDE+AL E+SHPAWIRMKFDELLAQQLSLKRAQAARRA++A ALP G I++ + Sbjct: 229 PPPDVDEHALIEKSHPAWIRMKFDELLAQQLSLKRAQAARRAKSARALPVTGRITEELTR 288 Query: 280 QLPFKLTAAQQRVLEEIRHDLQESFPMQRLLQGDVGSGKTVVAAIAAAQAIDSGFQAVLM 339 LPF+LT AQQRVLEEIR DL++SFPMQRLLQGDVGSGKTVVAA+AAAQAIDSG QAVLM Sbjct: 289 LLPFQLTGAQQRVLEEIRADLRQSFPMQRLLQGDVGSGKTVVAALAAAQAIDSGCQAVLM 348 Query: 340 APTEILADQHFRKIAAWMEPLGVKVAWLTGSLKKKEKAAANALIESGEARLVIGTHALIQ 399 APTEILA+QHFRKIAAWMEPL V VAWL+GS KKKEK A A IESG ARLVIGTHALIQ Sbjct: 349 APTEILAEQHFRKIAAWMEPLDVGVAWLSGSQKKKEKTEALAHIESGAARLVIGTHALIQ 408 Query: 400 DNVQFRKLGLVIVDEQHRFGVGQRLALRNKARDDTAGDADIDAAPQTVPHQLMMSATPIP 459 D VQF LGLVIVDEQHRFGVGQRLALRNK+ + AD D+ VPHQLMMSATPIP Sbjct: 409 DTVQFENLGLVIVDEQHRFGVGQRLALRNKSFN----PADHDSP--AVPHQLMMSATPIP 462 Query: 460 RTLAMTYYADLEVSVIDELPPGRTPIVTRTIDQNRRDEVIARVHAAAQEGRQVYWVCPLI 519 RTLAMTYYADLEVSVIDELPPGR+PIVTR IDQNRRDEVI RVHAAA EG+Q+YWVCPLI Sbjct: 463 RTLAMTYYADLEVSVIDELPPGRSPIVTRVIDQNRRDEVIERVHAAALEGKQIYWVCPLI 522 Query: 520 EESEALQLQTATDTYSMLAEALPDLRIGLVHGRLKQAEKQDVMDAFSRGEIHVLVATTVI 579 EESEALQLQTATDT++ L+ ALPDL+IGLVHGR+K EKQ VM+ FSRG IH+LVATTVI Sbjct: 523 EESEALQLQTATDTHAALSAALPDLQIGLVHGRMKPVEKQMVMEGFSRGAIHLLVATTVI 582 Query: 580 EVGVDVPNASLMVIEHAERFGLSQLHQLRXGAQPGADAA 618 EVGVDVPNASLMVIEHAERFGLSQLHQLR G+ A+ Sbjct: 583 EVGVDVPNASLMVIEHAERFGLSQLHQLRGRVGRGSAAS 621 >gi|300312329|ref|YP_003776421.1| transcription-repair ATP-dependent coupling factor [Herbaspirillum seropedicae SmR1] Length = 1145 Score = 190 bits (483), Expect = 3e-49, Method: Compositional matrix adjust. Identities = 130/354 (36%), Positives = 187/354 (52%), Gaps = 29/354 (8%) Query: 258 ARRA-RNASALPTIGNISKAFIKQLPFKLTAAQQRVLEEIRHDLQESFPMQRLLQGDVGS 316 ARRA R A + +AF F+ TA Q + + D+ PM RL+ GDVG Sbjct: 575 ARRALRQGHAFQYSAHDYEAFADSFGFEETADQAAAINAVIKDMTGGKPMDRLICGDVGF 634 Query: 317 GKTVVAAIAAAQAIDSGFQAVLMAPTEILADQHFRKIAAWMEPLGVKVAWLTGSLKKKEK 376 GKT VA AA A+ G Q ++APT +LA+QH A VK+A L+ KE Sbjct: 635 GKTEVALRAAFVAVMGGKQVAILAPTTLLAEQHAATFADRFANWPVKIAELSRFRTGKEV 694 Query: 377 AAANALIESGEARLVIGTHALIQDNVQFRKLGLVIVDEQHRFGVGQRLALRNKARDDTAG 436 A + G +VIGTH L+ D V+F +LGLVI+DE+HRFGV Q+ AL++ Sbjct: 695 TQAIKGLGDGTIDIVIGTHKLLSDEVKFSRLGLVIIDEEHRFGVRQKEALKSLR------ 748 Query: 437 DADIDAAPQTVPHQLMMSATPIPRTLAMTYYADLEVSVIDELPPGRTPIVT--RTIDQNR 494 A++D L ++ATPIPRTL M + SVI P R I T R ++ Sbjct: 749 -AEVDV--------LTLTATPIPRTLGMALEGLRDFSVIATAPQKRLAIKTFVRAEQEST 799 Query: 495 RDEVIARVHAAAQEGRQVYWVCPLIEESEALQLQTATDTYSMLAEALPDLRIGLVHGRLK 554 E R + G QVY++ +E T + + L + LP+ RIG+ HG++ Sbjct: 800 IREACLR---ELKRGGQVYFLHNEVE--------TIANRKAALEQLLPEARIGVAHGQMH 848 Query: 555 QAEKQDVMDAFSRGEIHVLVATTVIEVGVDVPNASLMVIEHAERFGLSQLHQLR 608 + + + VM F ++L+ TT+IE G+DVP A+ +++ A++FGL+QLHQLR Sbjct: 849 ERDLEKVMRDFVAQRFNILLCTTIIETGIDVPTANTIIMHRADKFGLAQLHQLR 902 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 0.318 0.132 0.373 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: 1,623,447 Number of extensions: 62230 Number of successful extensions: 268 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 2 Length of query: 620 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 529 Effective length of database: 1,188,985 Effective search space: 628973065 Effective search space used: 628973065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 133 (55.8 bits)