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= 0104.0006.p (1185 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310121|ref|YP_003774213.1| type III secretion HrcV transme... 1139 0.0 gi|300311342|ref|YP_003775434.1| flagellar biosynthesis FlhA tra... 287 4e-78 >gi|300310121|ref|YP_003774213.1| type III secretion HrcV transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 1139 bits (2947), Expect = 0.0, Method: Compositional matrix adjust. Identities = 577/683 (84%), Positives = 635/683 (92%), Gaps = 4/683 (0%) Query: 27 RMMGLVLVLNKLAARMAKRAELLAAALVIGIVFMLVLPMPVWLLDILIAFSLCISGLIVV 86 + MG+V++LNK A ++ KRAELLAAALVIGIVFMLVLPMP+WLLDILIA SLC SGLIVV Sbjct: 2 KAMGIVMLLNKFAIQLGKRAELLAAALVIGIVFMLVLPMPIWLLDILIAMSLCASGLIVV 61 Query: 87 VAMYMAGPTAFSTFPAVLLLTTLFRLAISVSTTRLILLEADAGHIVETFGNFVVGGNLVV 146 VAMYMAGPTAFSTFPAVLLLTTLFRLAISVSTTRLILLEADAGHIVETFGNFVVGGNLVV Sbjct: 62 VAMYMAGPTAFSTFPAVLLLTTLFRLAISVSTTRLILLEADAGHIVETFGNFVVGGNLVV 121 Query: 147 GLVIFLILTVVQFIVITKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILTAEEAKAKR 206 GLVIFLILTVVQFIVITKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILT EEAKAKR Sbjct: 122 GLVIFLILTVVQFIVITKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILTPEEAKAKR 181 Query: 207 SLL-PESQLHGAMDGAMKFVKGDAIAGLCIVAINLIGGISIGIIQRNMDAAEAMRVYSIL 265 + L ESQLHGAMDGAMKFVKGDAIAG+CIVAINLIGGISIGIIQR MDA +AM+VYSIL Sbjct: 182 AHLGQESQLHGAMDGAMKFVKGDAIAGICIVAINLIGGISIGIIQRGMDAGQAMQVYSIL 241 Query: 266 SIGDALIAQIPALLISLGAGIITTRVTNDDEGEGEEKSNVGRDIVAQLFAEPKALLTAAG 325 SIGDALIAQIPALLISLGAGIITTRV++D+E EGE +N+GRDIV +LF EPKALLTAAG Sbjct: 242 SIGDALIAQIPALLISLGAGIITTRVSDDNE-EGE--TNIGRDIVGELFGEPKALLTAAG 298 Query: 326 IMLLFGLIPGMPTGVFITLSLALFVSGVVGLLKPLADAEIQRENEELERKNAGIVDLTNF 385 IMLLFGLIPGMPT +F+ L++ L V+GVVG+LKPLADAE+ RE+EELERKNAGIVDLT+F Sbjct: 299 IMLLFGLIPGMPTVIFVALAVGLCVAGVVGMLKPLADAEMARESEELERKNAGIVDLTSF 358 Query: 386 SATTPFILRMPEALRATPQAEMIRNAVRVMRNGMLERRGIPDLKPIEFEFSETMPDNRVH 445 +ATTPFILRM E++R +AE+IR AVR+MRN MLERRGIPDLKPI+FEFS +P+ RV Sbjct: 359 AATTPFILRMNESMRGKAEAEVIRTAVRIMRNAMLERRGIPDLKPIDFEFSSMVPEGRVF 418 Query: 446 FLMAEVPLVDNEIMIGWGATRETLDRVTELGFQAVERNISGSRRRRVWLRLDDEARLTEH 505 F+M+EVPLVD EIM+GW ATRE+L+RV ELGFQ ERNI GSRRRRVW++ +D +L E Sbjct: 419 FMMSEVPLVDAEIMLGWSATRESLERVQELGFQGFERNIPGSRRRRVWVKTEDPEKLAEA 478 Query: 506 GVMVQRWETVFAADIEVELLRNCQMFVGVNEVIRFTRWAERRYPELGKEVLKSVTLPRLT 565 G++ + WE VFA+DIEVE+LRNCQMFVGVNEVIRFTRWAERRYPELGKEV+K+VTLPRLT Sbjct: 479 GLLAESWEKVFASDIEVEMLRNCQMFVGVNEVIRFTRWAERRYPELGKEVVKTVTLPRLT 538 Query: 566 EVVQRLTKEGVSLRNARLLLETTLDWAPKERDPDVIADYVRLAFKRQLCFEAARDGLIEV 625 EVVQRLT+EGVSLRNARLLLETTLDWAPKERDPDVIADYVRLAFKRQLCFEA+R+GLIEV Sbjct: 539 EVVQRLTREGVSLRNARLLLETTLDWAPKERDPDVIADYVRLAFKRQLCFEASREGLIEV 598 Query: 626 ILLSPELEDQLRNAMRQTSQGSYLDIDSELEQMLLDKLNDLSTNVCTPITPPVLVTAADI 685 ILLSPELEDQLRNAMRQTSQGSYLDIDSELEQM+LD+LN+LSTNV TPI PPVLVTAADI Sbjct: 599 ILLSPELEDQLRNAMRQTSQGSYLDIDSELEQMILDRLNELSTNVSTPIVPPVLVTAADI 658 Query: 686 RRSVRKLIEEEFFPVPVFAFSQL 708 RRSVRKLIEEEFFPVPVFAFS+L Sbjct: 659 RRSVRKLIEEEFFPVPVFAFSEL 681 >gi|300311342|ref|YP_003775434.1| flagellar biosynthesis FlhA transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 705 Score = 287 bits (734), Expect = 4e-78, Method: Compositional matrix adjust. Identities = 139/308 (45%), Positives = 224/308 (72%), Gaps = 15/308 (4%) Query: 44 KRAELLAA-ALVIGIVFMLVLPMPVWLLDILIAFSLCISGLIVVVAMYMAGPTAFSTFPA 102 K A +AA L++ ++ M+VLP+P ++LD+L +F++ +S ++++ A+Y P F FPA Sbjct: 17 KNARAMAAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLMTALYTVKPLDFIAFPA 76 Query: 103 VLLLTTLFRLAISVSTTRLILLEAD-----AGHIVETFGNFVVGGNLVVGLVIFLILTVV 157 VLL++T+ RL+++V++TR++L E AG ++E FG+F++GGN VG+V+F+ILT++ Sbjct: 77 VLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGIVVFVILTII 136 Query: 158 QFIVITKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILTAEEAKAKR-SLLPESQLHG 216 F+V+TKG+ R++EV ARF+LDAMPGKQM+ID+DL AG++ EA+A+R + ES+ +G Sbjct: 137 NFMVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPEARARRKEVAQESEFYG 196 Query: 217 AMDGAMKFVKGDAIAGLCIVAINLIGGISIGIIQRNMDAAEAMRVYSILSIGDALIAQIP 276 AMDGA K+V+GDA+AG+ + +N++GG+ +G++Q ++ A++ Y++L+IGD L+AQIP Sbjct: 197 AMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALKNYTLLAIGDGLVAQIP 256 Query: 277 ALLISLGAGIITTRVTNDDEGEGEEKSNVGRDIVAQLFAEPKALLTAAGIMLLFGLIPGM 336 +L+IS AG++ +RV ND +VG ++ QLFA+P+ L A I+ GLIPGM Sbjct: 257 SLIISTAAGVVVSRVAND--------QDVGGQLINQLFAKPEVLYITAVIIGGMGLIPGM 308 Query: 337 PTGVFITL 344 P FI L Sbjct: 309 PHIAFILL 316 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 0.137 0.402 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: 3,240,006 Number of extensions: 126497 Number of successful extensions: 429 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 424 Number of HSP's successfully gapped: 2 Length of query: 1185 Length of database: 1,619,870 Length adjustment: 96 Effective length of query: 1089 Effective length of database: 1,165,310 Effective search space: 1269022590 Effective search space used: 1269022590 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 (22.0 bits) S2: 136 (57.0 bits)