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= 0001.1965.p (561 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311427|ref|YP_003775519.1| signal transduction histidine k... 889 0.0 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 114 2e-26 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 113 3e-26 gi|300312093|ref|YP_003776185.1| hypothetical protein Hsero_2782... 112 8e-26 gi|300311453|ref|YP_003775545.1| signal transduction containing ... 107 3e-24 >gi|300311427|ref|YP_003775519.1| signal transduction histidine kinase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 889 bits (2296), Expect = 0.0, Method: Compositional matrix adjust. Identities = 444/561 (79%), Positives = 491/561 (87%), Gaps = 1/561 (0%) Query: 1 MVCLVLTIGWFLYRAGDDATEVLARNALTEVMGRVSQAIDRQTQGARETLNVIAPRPVPP 60 MVCLVLTIGWFLYRAGDDATEVLARNALTE++GRVSQAIDRQT GARE+LNV+AP V Sbjct: 1 MVCLVLTIGWFLYRAGDDATEVLARNALTELIGRVSQAIDRQTMGARESLNVVAPPAVRT 60 Query: 61 VEVGQAPALLPFPKSRKELEDRLWLANSLFDEPSYVYFGGVDGSFLGIKQEQPNVFMYSV 120 GQ PA+LPFP KELE+RLWLAN +F++PSYVYFGG DGSFLGIKQE+ + F YSV Sbjct: 61 AAPGQPPAMLPFPVHSKELEERLWLANLMFEDPSYVYFGGADGSFLGIKQEEGSQFTYSV 120 Query: 121 REPGQKNYVYYLRGPGTEMKLVAVQDYEPRKRPWYEQAVKQGHETWSPVYIDYRVKNIVG 180 REP KNYVY LRGPGT M+LVA Q+YEPRKRPWY QAV++G ETWS VY DYR K++ G Sbjct: 121 REPDGKNYVYQLRGPGTPMELVAAQEYEPRKRPWYVQAVQRGRETWSSVYADYRQKHL-G 179 Query: 181 INLSKPIFDADGTLLGVANSSIGLQQLGALLRQVPQSTHGVAFVTELQGDMIATSLNEPI 240 INLSKPIFDADG LLGVANSSIGL +L LLR +P HGVAFVTEL GDMIA S+NEP+ Sbjct: 180 INLSKPIFDADGKLLGVANSSIGLLRLTTLLRALPLGAHGVAFVTELNGDMIADSVNEPL 239 Query: 241 YQAGEQGSEPMRLNAGRSTSPLVQQAFEEVQSYLATHQAVPDRLVLLGARSQGSKIEVAF 300 +Q +Q + RLNA +S+SPLV+QA+EEV+ YLA A +L+LL +R++G KIEVAF Sbjct: 240 HQIRDQDPDLRRLNASQSSSPLVRQAYEEVRRYLARQPAQSGKLMLLSSRTEGGKIEVAF 299 Query: 301 RLHRDPAGLEWLAISAAPRSDFLGSVTSGVYQTLILGLLAVGLSFVIGLLLLRWVLRDIR 360 RLH D AGL+WLAISAAPRSDFLGSVTSGVYQTL+LGL+AV L+FVIG LLLRWVLRDIR Sbjct: 300 RLHHDAAGLDWLAISAAPRSDFLGSVTSGVYQTLMLGLMAVCLTFVIGFLLLRWVLRDIR 359 Query: 361 KLTLAAKSIGNGSPFPTLNIDRNDEIGQLAQSFVEMERNLRTDRLTNVLNRDSLIAQIDF 420 +LT AAKSIGNGSPFP LNI+RNDEIGQLAQSFVEMERNLRTDRLTNVLNRDSLIAQIDF Sbjct: 360 RLTQAAKSIGNGSPFPDLNINRNDEIGQLAQSFVEMERNLRTDRLTNVLNRDSLIAQIDF 419 Query: 421 RRRNSSQAVPLHFALLFIDLDRFKAVNDEYGHDEGDKVLITIAERLQHSLRHDDSVARFG 480 RR N PLHF LLFIDLDRFKAVNDEYGHDEGDKVL+TIA+RLQH+LRHDDSVARFG Sbjct: 420 RRSNCVDGSPLHFGLLFIDLDRFKAVNDEYGHDEGDKVLVTIAQRLQHTLRHDDSVARFG 479 Query: 481 GDEFVVYLHGVTEVEVARSIGDKIRHAVNKPIAGRDGQQYTVDASVGVSLYPDDGLDVET 540 GDEFVVYLHGV+++EVARSI DKIRHAVNKPI GR+GQQY VDASVGVSLYPDDGLDVET Sbjct: 480 GDEFVVYLHGVSDMEVARSIADKIRHAVNKPIPGREGQQYVVDASVGVSLYPDDGLDVET 539 Query: 541 LLRVADSRMFDQKRLHRILSV 561 LLRVADSRMFDQKRLHRILSV Sbjct: 540 LLRVADSRMFDQKRLHRILSV 560 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 114 bits (286), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 77/208 (37%), Positives = 118/208 (56%), Gaps = 9/208 (4%) Query: 354 WVLRDIRKLTLAAKSIGNGSPFPTLNIDRNDEIGQLAQSFV----EMERNLRTDRLTNVL 409 W+ I +TLAA +I + L+ +LA+S E+ + + D+LT + Sbjct: 218 WLAVLIIVVTLAALTIALLTS--VLDARLESRTAKLARSLAAANEELTQMVLHDQLTRLP 275 Query: 410 NRDSLIAQIDFRRRNSSQAVPLHFALLFIDLDRFKAVNDEYGHDEGDKVLITIAERLQHS 469 NR L +++ + N + HFAL+F+DLD FKA+ND GH GD++L+ +A+RL S Sbjct: 276 NRTLLEDRLN-QAINKAAREQGHFALMFMDLDGFKAINDSLGHHVGDRLLVEVAQRLTSS 334 Query: 470 LRHDDSVARFGGDEFVVYLHGVTEVEVARSIGDKIRHAVNKPIAGRDGQQYTVDASVGVS 529 R +D+VAR GGDEFV+ L + E A + +K+ AVN+P D + V ASVG++ Sbjct: 335 SRANDTVARLGGDEFVI-LVDLNTPEDAMGVAEKLVEAVNQPFK-VDQHELRVSASVGIA 392 Query: 530 LYPDDGLDVETLLRVADSRMFDQKRLHR 557 +YP+DG L+ AD+ M+ KR R Sbjct: 393 IYPEDGATRHDLVINADAAMYHTKRSGR 420 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 113 bits (283), Expect = 3e-26, Method: Compositional matrix adjust. Identities = 72/164 (43%), Positives = 95/164 (57%), Gaps = 3/164 (1%) Query: 395 EMERNLRTDRLTNVLNRDSLIAQIDFRRRNSSQAVPLHFALLFIDLDRFKAVNDEYGHDE 454 EM D LT + NR+ L + R + Q L A+ F+DLD+FK +ND GH Sbjct: 261 EMRHQATHDALTGLPNRNMLHEHLQRALRVARQKGALT-AVAFVDLDQFKFINDSLGHQV 319 Query: 455 GDKVLITIAERLQHSLRHDDSVARFGGDEFVVYLHGVTEVEVA-RSIGDKIRHAVNKPIA 513 GD++L T+A+RLQ LR D VAR GGDEFV+ L TE E + +I AV +P Sbjct: 320 GDELLKTVAQRLQACLREADMVARQGGDEFVLVLQNQTEGEAGIAEVMQRILAAVARPWQ 379 Query: 514 GRDGQQYTVDASVGVSLYPDDGLDVETLLRVADSRMFDQKRLHR 557 D +++ V AS+GVS YP DG DVE+LL+ ADS M+ K R Sbjct: 380 AGD-REFQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQGR 422 >gi|300312093|ref|YP_003776185.1| hypothetical protein Hsero_2782 [Herbaspirillum seropedicae SmR1] Length = 601 Score = 112 bits (280), Expect = 8e-26, Method: Compositional matrix adjust. Identities = 76/223 (34%), Positives = 112/223 (50%), Gaps = 35/223 (15%) Query: 354 WVLRDIRKLTLAAKSIGNGS-PFPTLNIDRNDEIGQLAQSF-----------VEMERNLR 401 W R +R+ A + G P L +DR DE+GQL +F E++ Sbjct: 352 WFFRPLRRAAALADRMTRGELPLSPLPVDRRDEVGQLTMAFNGLLARLKLHQAELQHQAH 411 Query: 402 TDRLTNVLNRDSLIAQID------FRRRNSSQAVPLHFALLFIDLDRFKAVNDEYGHDEG 455 D LT + NR L ++ R RN LLF+DLD FK +ND GH G Sbjct: 412 HDVLTGLPNRMMLAERMQAALTHACRERNG-------VGLLFLDLDGFKPINDTLGHKAG 464 Query: 456 DKVLITIAERLQHSLRHDDSVARFGGDEFVVYLHGVTEVEV-----ARSIGDKIRHAVNK 510 D+VL I RL+ RH D++AR GGDEFV+ VT++ + A+++ +K V++ Sbjct: 465 DQVLQEITRRLRQVARHGDTLARVGGDEFVLL---VTDLRLPFEQGAQALAEKCIKTVSE 521 Query: 511 PIAGRDGQQYTVDASVGVSLYPDDGLDVETLLRVADSRMFDQK 553 PI D +QY + SVG+++ D D ++LL+ AD M+ K Sbjct: 522 PIC-LDQRQYRLGVSVGIAVC-DGSCDADSLLQAADQAMYAAK 562 >gi|300311453|ref|YP_003775545.1| signal transduction containing PAS/GGDEF/EAL domains protein [Herbaspirillum seropedicae SmR1] Length = 683 Score = 107 bits (267), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 63/152 (41%), Positives = 89/152 (58%), Gaps = 3/152 (1%) Query: 403 DRLTNVLNRDSLIAQIDFRRRNSSQAVPLHFALLFIDLDRFKAVNDEYGHDEGDKVLITI 462 D LT + NR L +D + ++ LH ++FIDL+RFK +ND GH GD +L+ + Sbjct: 247 DALTGLPNRTLLTRTVD-QALEEARHENLHGCVMFIDLNRFKPINDTLGHVAGDMLLVEV 305 Query: 463 AERLQHSLRHDDSVARFGGDEFVVYLHGVTEVEVARSIGDKIRHAVNKPIAGRDGQQYTV 522 A RL+ +LR D VAR G DEF V L G+ + A + K+ + P DG + V Sbjct: 306 AMRLRRALREQDVVARLGADEFAVALFGIDKDSPA-YVAQKLLALFDDPFF-IDGHELRV 363 Query: 523 DASVGVSLYPDDGLDVETLLRVADSRMFDQKR 554 AS+GVSLYP++ D ETLLR+AD M+ K+ Sbjct: 364 GASIGVSLYPENATDTETLLRLADIAMYRAKQ 395 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 0.320 0.138 0.400 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: 1,805,929 Number of extensions: 80282 Number of successful extensions: 381 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 348 Number of HSP's successfully gapped: 39 Length of query: 561 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 471 Effective length of database: 1,193,720 Effective search space: 562242120 Effective search space used: 562242120 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: 133 (55.8 bits)