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= 0001.1886.p (702 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311342|ref|YP_003775434.1| flagellar biosynthesis FlhA tra... 1301 0.0 gi|300310121|ref|YP_003774213.1| type III secretion HrcV transme... 275 8e-75 >gi|300311342|ref|YP_003775434.1| flagellar biosynthesis FlhA transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 705 Score = 1301 bits (3368), Expect = 0.0, Method: Compositional matrix adjust. Identities = 671/705 (95%), Positives = 685/705 (97%), Gaps = 3/705 (0%) Query: 1 MATKLNTMKIPAWVPVKSGRALAAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLM 60 MATKLNTMKIPAWVPVK+ RA+AAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLM Sbjct: 1 MATKLNTMKIPAWVPVKNARAMAAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLM 60 Query: 61 TALYTVKPLDFIAFPAVLLVSTMLRLSLNVASTRIVLTEGHTGPDAAGKVIEAFGHFLIG 120 TALYTVKPLDFIAFPAVLLVSTMLRLSLNVASTR+VLTEGHTGPDAAGKVIEAFGHFLIG Sbjct: 61 TALYTVKPLDFIAFPAVLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIG 120 Query: 121 GNYTVGIVVFVILTIINFMVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPE 180 GNYTVGIVVFVILTIINFMVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPE Sbjct: 121 GNYTVGIVVFVILTIINFMVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPE 180 Query: 181 ARARRKEVAQESEFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALK 240 ARARRKEVAQESEFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALK Sbjct: 181 ARARRKEVAQESEFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALK 240 Query: 241 NYTLLAIGDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAKPEVLYITAVIIG 300 NYTLLAIGDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAKPEVLYITAVIIG Sbjct: 241 NYTLLAIGDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAKPEVLYITAVIIG 300 Query: 301 GMGLIPGMPHIAFILLAAAMGGGAYAIGKRVEKTKAEAAAAAPQATASAAA---PAEGEE 357 GMGLIPGMPHIAFILLAAAMGGGAYAI KRVEK K EAAA+ QA A A P E EE Sbjct: 301 GMGLIPGMPHIAFILLAAAMGGGAYAISKRVEKAKTEAAASQAQAAAGGGAAAAPQESEE 360 Query: 358 ATWSDVMPVDTLGLEVGYRLIPLVDKGQGGELLKRIKGIRKKFAQEVGFLSPPIHIRDNL 417 ATW+DVMPVDTLGLEVGYRLIPLVDKGQGGELLKRIKGIRKKFAQEVGFLSPPIHIRDNL Sbjct: 361 ATWNDVMPVDTLGLEVGYRLIPLVDKGQGGELLKRIKGIRKKFAQEVGFLSPPIHIRDNL 420 Query: 418 ELKPSAYRITLKGVEVGNGEAHAGQYLAINPGMVTGPLPGMMTSDPAFGLPAVWIDNSLR 477 ELKPSAYRITLKGVEVGNGEAHAGQYLAINPGMVTGPLPGMMT+DPAFGLPAVWIDN LR Sbjct: 421 ELKPSAYRITLKGVEVGNGEAHAGQYLAINPGMVTGPLPGMMTTDPAFGLPAVWIDNGLR 480 Query: 478 EQASTMGYTVVDAGTVVATHLNHLITTHAAELLGRQEVQSLLDHLGKEAPKLVEDLVPKM 537 EQASTMGYTVVDAGTVVATHLNHLITTHAAELLGRQEVQSLLDHL K+APKLVEDLVPKM Sbjct: 481 EQASTMGYTVVDAGTVVATHLNHLITTHAAELLGRQEVQSLLDHLAKDAPKLVEDLVPKM 540 Query: 538 LPLGTLQKVLQNLLAEGVHIRDMRTIIETLAEHAARIQDPTDLTAIVRIALGRAIVQQIF 597 LPLG+LQKVLQNLL EGVHIRDMRTIIETLAEHAARIQDPTDLTAIVRIALGRAIVQQ+F Sbjct: 541 LPLGSLQKVLQNLLIEGVHIRDMRTIIETLAEHAARIQDPTDLTAIVRIALGRAIVQQMF 600 Query: 598 PGESELAVMALDSKLERLLMQALQASGDSGGIEPGLADSLVQQTEMAAQRQEQMGFAPVL 657 PGESEL VMALDSKLERLLMQALQASG+SGGIEPGLADSLVQ TE+AAQRQEQMG++PVL Sbjct: 601 PGESELPVMALDSKLERLLMQALQASGESGGIEPGLADSLVQHTEIAAQRQEQMGYSPVL 660 Query: 658 LVGAPLRTLLARFLRRALPQLRVLSHAEVPESKTIKVTSLVGGQA 702 LVGAPLRTLLARFLRRA+PQLRVLSHAEVPESKTIKVTSLVGGQA Sbjct: 661 LVGAPLRTLLARFLRRAMPQLRVLSHAEVPESKTIKVTSLVGGQA 705 >gi|300310121|ref|YP_003774213.1| type III secretion HrcV transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 275 bits (703), Expect = 8e-75, Method: Compositional matrix adjust. Identities = 134/304 (44%), Positives = 222/304 (73%), Gaps = 10/304 (3%) Query: 22 LAAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLMTALYTVKPLDFIAFPAVLLVS 81 L A L++ ++ M+VLP+P ++LD+L + ++ S ++++ A+Y P F FPAVLL++ Sbjct: 23 LLAAALVIGIVFMLVLPMPIWLLDILIAMSLCASGLIVVVAMYMAGPTAFSTFPAVLLLT 82 Query: 82 TMLRLSLNVASTRIVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGIVVFVILTIINFMVV 141 T+ RL+++V++TR++L E AG ++E FG+F++GGN VG+V+F+ILT++ F+V+ Sbjct: 83 TLFRLAISVSTTRLILLEAD-----AGHIVETFGNFVVGGNLVVGLVIFLILTVVQFIVI 137 Query: 142 TKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPEARARRKEVAQESEFYGAMDGA 201 TKG+ R++EV ARF+LDAMPGKQM+ID+DL AG++ EA+A+R + QES+ +GAMDGA Sbjct: 138 TKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILTPEEAKAKRAHLGQESQLHGAMDGA 197 Query: 202 SKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALKNYTLLAIGDGLVAQIPSLIIS 261 K+V+GDA+AGI + +N++GG+ +G++Q + A++ Y++L+IGD L+AQIP+L+IS Sbjct: 198 MKFVKGDAIAGICIVAINLIGGISIGIIQRGMDAGQAMQVYSILSIGDALIAQIPALLIS 257 Query: 262 TAAGVVVSRVANDQD-----VGGQLINQLFAKPEVLYITAVIIGGMGLIPGMPHIAFILL 316 AG++ +RV++D + +G ++ +LF +P+ L A I+ GLIPGMP + F+ L Sbjct: 258 LGAGIITTRVSDDNEEGETNIGRDIVGELFGEPKALLTAAGIMLLFGLIPGMPTVIFVAL 317 Query: 317 AAAM 320 A + Sbjct: 318 AVGL 321 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 0.321 0.137 0.384 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: 1,793,102 Number of extensions: 69788 Number of successful extensions: 273 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 271 Number of HSP's successfully gapped: 3 Length of query: 702 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 610 Effective length of database: 1,184,250 Effective search space: 722392500 Effective search space used: 722392500 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)