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= 0020.0084.p (684 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... 1160 0.0 gi|300310121|ref|YP_003774213.1| type III secretion HrcV transme... 295 9e-81 >gi|300311342|ref|YP_003775434.1| flagellar biosynthesis FlhA transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 705 Score = 1160 bits (3002), Expect = 0.0, Method: Compositional matrix adjust. Identities = 587/699 (83%), Positives = 634/699 (90%), Gaps = 16/699 (2%) Query: 1 MKLPAWVPIKHAKALTAPILIVMMLAMMVLPLPAFALDILFSFNISLSVIVLLTALYTVK 60 MK+PAWVP+K+A+A+ APILIVMMLAMMVLPLPAF LD+LFSFNISLSVIVL+TALYTVK Sbjct: 8 MKIPAWVPVKNARAMAAPILIVMMLAMMVLPLPAFMLDLLFSFNISLSVIVLMTALYTVK 67 Query: 61 PLDFVAFPAVLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGI 120 PLDF+AFPAVLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGI Sbjct: 68 PLDFIAFPAVLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGI 127 Query: 121 VVFIILTIINFTVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGMIGEPEARARRKE 180 VVF+ILTIINF VVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAG+IGEPEARARRKE Sbjct: 128 VVFVILTIINFMVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGLIGEPEARARRKE 187 Query: 181 VAQEAEFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDMALKNYTLLAI 240 VAQE+EFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFD ALKNYTLLAI Sbjct: 188 VAQESEFYGAMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDAALKNYTLLAI 247 Query: 241 GDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAKAEVLYLTAIIIGGMGMIPG 300 GDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAK EVLY+TA+IIGGMG+IPG Sbjct: 248 GDGLVAQIPSLIISTAAGVVVSRVANDQDVGGQLINQLFAKPEVLYITAVIIGGMGLIPG 307 Query: 301 MPHIAFIIIAALLAAAGYSVNKRKEQAGA--------IAELPAPVTTPQ-------XDIL 345 MPHIAFI++AA + Y+++KR E+A A PQ D++ Sbjct: 308 MPHIAFILLAAAMGGGAYAISKRVEKAKTEAAASQAQAAAGGGAAAAPQESEEATWNDVM 367 Query: 346 PVDTLGLEVGYRLIPLVDKGQGGELLRRIKGIRKKFAQEVGFLSPPVHIRDNLELKPSAY 405 PVDTLGLEVGYRLIPLVDKGQGGELL+RIKGIRKKFAQEVGFLSPP+HIRDNLELKPSAY Sbjct: 368 PVDTLGLEVGYRLIPLVDKGQGGELLKRIKGIRKKFAQEVGFLSPPIHIRDNLELKPSAY 427 Query: 406 RIALKGVEIGKGEATFGQFLAINPGMVTGPLPGLMTTDPAFGLPAVWIESNMREMAQTMG 465 RI LKGVE+G GEA GQ+LAINPGMVTGPLPG+MTTDPAFGLPAVWI++ +RE A TMG Sbjct: 428 RITLKGVEVGNGEAHAGQYLAINPGMVTGPLPGMMTTDPAFGLPAVWIDNGLREQASTMG 487 Query: 466 YTVVDTGTVIATHLNHLITVHAAELLGRQEVQQLLDHIGKDAPKLVEDLVPKALPLGTVQ 525 YTVVD GTV+ATHLNHLIT HAAELLGRQEVQ LLDH+ KDAPKLVEDLVPK LPLG++Q Sbjct: 488 YTVVDAGTVVATHLNHLITTHAAELLGRQEVQSLLDHLAKDAPKLVEDLVPKMLPLGSLQ 547 Query: 526 KVLQNLLIEGVHIRDMRTIIETLAEHAPRVQEPNELTAIVRIALGRAIVQQIFPTESELS 585 KVLQNLLIEGVHIRDMRTIIETLAEHA R+Q+P +LTAIVRIALGRAIVQQ+FP ESEL Sbjct: 548 KVLQNLLIEGVHIRDMRTIIETLAEHAARIQDPTDLTAIVRIALGRAIVQQMFPGESELP 607 Query: 586 VMTLDNKLERLLMQAMQASGPEGGGIEPGLADTLITQTENAARHQEQLGLTPVLLVPGPL 645 VM LD+KLERLLMQA+QASG E GGIEPGLAD+L+ TE AA+ QEQ+G +PVLLV PL Sbjct: 608 VMALDSKLERLLMQALQASG-ESGGIEPGLADSLVQHTEIAAQRQEQMGYSPVLLVGAPL 666 Query: 646 RALLARFLRRAMPQLRVLSHAEVPDSKTIKVTSLVGGQA 684 R LLARFLRRAMPQLRVLSHAEVP+SKTIKVTSLVGGQA Sbjct: 667 RTLLARFLRRAMPQLRVLSHAEVPESKTIKVTSLVGGQA 705 >gi|300310121|ref|YP_003774213.1| type III secretion HrcV transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 295 bits (754), Expect = 9e-81, Method: Compositional matrix adjust. Identities = 216/700 (30%), Positives = 368/700 (52%), Gaps = 64/700 (9%) Query: 10 KHAKALTAPILIVMMLAMMVLPLPAFALDILFSFNISLSVIVLLTALYTVKPLDFVAFPA 69 K A+ L A L++ ++ M+VLP+P + LDIL + ++ S ++++ A+Y P F FPA Sbjct: 19 KRAELLAAA-LVIGIVFMLVLPMPIWLLDILIAMSLCASGLIVVVAMYMAGPTAFSTFPA 77 Query: 70 VLLVSTMLRLSLNVASTRVVLTEGHTGPDAAGKVIEAFGHFLIGGNYTVGIVVFIILTII 129 VLL++T+ RL+++V++TR++L E AG ++E FG+F++GGN VG+V+F+ILT++ Sbjct: 78 VLLLTTLFRLAISVSTTRLILLEAD-----AGHIVETFGNFVVGGNLVVGLVIFLILTVV 132 Query: 130 NFTVVTKGAGRIAEVGARFTLDAMPGKQMAIDADLNAGMIGEPEARARRKEVAQEAEFYG 189 F V+TKG+ R++EV ARF+LDAMPGKQM+ID+DL AG++ EA+A+R + QE++ +G Sbjct: 133 QFIVITKGSERVSEVSARFSLDAMPGKQMSIDSDLRAGILTPEEAKAKRAHLGQESQLHG 192 Query: 190 AMDGASKYVRGDAVAGIIVTVVNIVGGLVVGMVQHDLAFDMALKNYTLLAIGDGLVAQIP 249 AMDGA K+V+GDA+AGI + +N++GG+ +G++Q + A++ Y++L+IGD L+AQIP Sbjct: 193 AMDGAMKFVKGDAIAGICIVAINLIGGISIGIIQRGMDAGQAMQVYSILSIGDALIAQIP 252 Query: 250 SLIISTAAGVVVSRVANDQD-----VGGQLINQLFAKAEVLYLTAIIIGGMGMIPGMPHI 304 +L+IS AG++ +RV++D + +G ++ +LF + + L A I+ G+IPGMP + Sbjct: 253 ALLISLGAGIITTRVSDDNEEGETNIGRDIVGELFGEPKALLTAAGIMLLFGLIPGMPTV 312 Query: 305 AFIIIAALLAAAGY---------------SVNKRKEQAGAIAELPAPVTTPQXDILPVDT 349 F+ +A L AG S ++ AG + TTP + Sbjct: 313 IFVALAVGLCVAGVVGMLKPLADAEMARESEELERKNAGIVDLTSFAATTPFILRMNESM 372 Query: 350 LGLEVGYRLIPLVDKGQGGELLRR----IKGIRKKFAQ-----EVGFLSPPVHIRD-NLE 399 G + V + L RR +K I +F+ V F+ V + D + Sbjct: 373 RGKAEAEVIRTAVRIMRNAMLERRGIPDLKPIDFEFSSMVPEGRVFFMMSEVPLVDAEIM 432 Query: 400 LKPSAYRIALKGV-EIGKGEATFGQFLAINPGMVTGPLPGLMTTDPAFGLPAVWIESNMR 458 L SA R +L+ V E+G G P VW+++ Sbjct: 433 LGWSATRESLERVQELG--------------------FQGFERNIPGSRRRRVWVKTEDP 472 Query: 459 EMAQTMGYTVVDTGTVIATHLNHLITVHAAELLGRQEVQQLLDHIGKDAPKLVEDLVPKA 518 E G V A+ + + + +G EV + + P+L +++V K Sbjct: 473 EKLAEAGLLAESWEKVFASDIEVEMLRNCQMFVGVNEVIRFTRWAERRYPELGKEVV-KT 531 Query: 519 LPLGTVQKVLQNLLIEGVHIRDMRTIIETLAEHAPRVQEPNELTAIVRIALGRAIVQQIF 578 + L + +V+Q L EGV +R+ R ++ET + AP+ ++P+ + VR+A R Q F Sbjct: 532 VTLPRLTEVVQRLTREGVSLRNARLLLETTLDWAPKERDPDVIADYVRLAFKR---QLCF 588 Query: 579 PTESE--LSVMTLDNKLERLLMQAM-QASGPEGGGIEPGLADTLITQTENAARHQEQLGL 635 E + V+ L +LE L AM Q S I+ L ++ + + + + Sbjct: 589 EASREGLIEVILLSPELEDQLRNAMRQTSQGSYLDIDSELEQMILDRLNELSTNVSTPIV 648 Query: 636 TPVLLVPGPLRALLARFLRRAMPQLRVLSHAEVPDSKTIK 675 PVL+ +R + + + + V + +E+ +K Sbjct: 649 PPVLVTAADIRRSVRKLIEEEFFPVPVFAFSELTQHAKVK 688 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 0.322 0.139 0.392 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: 1,843,477 Number of extensions: 72806 Number of successful extensions: 266 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 263 Number of HSP's successfully gapped: 3 Length of query: 684 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 592 Effective length of database: 1,184,250 Effective search space: 701076000 Effective search space used: 701076000 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 (21.9 bits) S2: 134 (56.2 bits)