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= 0011.0253.p (466 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 749 0.0 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 181 1e-46 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 166 3e-42 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 161 1e-40 gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspi... 159 7e-40 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 749 bits (1933), Expect = 0.0, Method: Compositional matrix adjust. Identities = 365/369 (98%), Positives = 366/369 (99%) Query: 98 MALGNIIDNSGAQVHIEEDGSQSAVRSGFLNAATSHRFPILYRDEHGGMHDIGSWTVYSS 157 MALGNIID+SGAQVHIEEDGSQSAVR GFLNAATSHRFPILYRDEHG MHDIGSWTVYSS Sbjct: 1 MALGNIIDSSGAQVHIEEDGSQSAVRPGFLNAATSHRFPILYRDEHGVMHDIGSWTVYSS 60 Query: 158 RHVVIGKVAYGFTLILINSVIKTLVLWFIFLYVFRRWLGQPITRLADFVRELDLNQMETP 217 RHVVIGKVAYGFTLILINSVIKTLVLWFIFLYVFRRWLGQPITRLADFVRELDLNQMETP Sbjct: 61 RHVVIGKVAYGFTLILINSVIKTLVLWFIFLYVFRRWLGQPITRLADFVRELDLNQMETP 120 Query: 218 RSIHLPGRRRHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIA 277 RSIHLPGRRRHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIA Sbjct: 121 RSIHLPGRRRHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIA 180 Query: 278 ERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFK 337 ERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFK Sbjct: 181 ERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFK 240 Query: 338 PYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRM 397 PYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRM Sbjct: 241 PYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRM 300 Query: 398 CDAVHALAIAHAGSAMGRITISAGVASCNPGQPGASLDGLLQAADAALYRAKMEGRNRVV 457 CDAVHALAIAHAGSAMGRITISAGVASCNPGQPGA LDGLLQAADAALYRAKMEGRNRVV Sbjct: 301 CDAVHALAIAHAGSAMGRITISAGVASCNPGQPGAGLDGLLQAADAALYRAKMEGRNRVV 360 Query: 458 LATELIVSP 466 LATELIVSP Sbjct: 361 LATELIVSP 369 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 181 bits (458), Expect = 1e-46, Method: Compositional matrix adjust. Identities = 95/190 (50%), Positives = 124/190 (65%), Gaps = 1/190 (0%) Query: 272 LELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFI 331 LE ++ RTR+L +AN +L +LS TDGLTG+ANRR FDE L E RR++R G L L + Sbjct: 380 LEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLML 439 Query: 332 DVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGA 391 DVD+FK YND YGHLAGD LR VA+ L++S R D VARYGGEEF++I A+ D Sbjct: 440 DVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQAL 499 Query: 392 DMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGASLDGLLQAADAALYRAKME 451 +C A+ L + HA S G I+ S GVA P + A + +++ AD ALY AK + Sbjct: 500 QQAENICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTAP-EQMVRIADQALYHAKYQ 558 Query: 452 GRNRVVLATE 461 GRNRVVL ++ Sbjct: 559 GRNRVVLGSD 568 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 166 bits (421), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 103/226 (45%), Positives = 136/226 (60%), Gaps = 15/226 (6%) Query: 233 LADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIAERTRDLAQANEQLRS 292 L D I L+ A++ H+ Y L Q + SAL E + L ++N +L+ Sbjct: 126 LPDVIELV-ARIRYHSRS----YINLLQRDAAYSALR--------ESQQQLQKSNFELQR 172 Query: 293 LSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVL 352 L+ TDGLTGIANRR FD+ L EWRR+ R G L L IDVD+FK YND+YGH+AGDAVL Sbjct: 173 LTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVL 232 Query: 353 RQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHALAIAHAGSA 412 RQVA+ L SI R D AR+GGEEFA+I T + +++C V +L + H GS+ Sbjct: 233 RQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVESLQVPHEGSS 292 Query: 413 MGR-ITISAGVASCNPGQPGASLDGLLQAADAALYRAKMEGRNRVV 457 + +T+S G A+ P Q L L++AAD LY AK +GRNRVV Sbjct: 293 VSAWLTVSVGAATLVP-QEQQELRELIEAADRRLYLAKQQGRNRVV 337 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 161 bits (407), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 85/175 (48%), Positives = 110/175 (62%), Gaps = 2/175 (1%) Query: 286 ANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTP-LMLAFIDVDWFKPYNDHYG 344 A +QL L+ TDGLTG+ NRRS DE L W+RS R T FIDVD+FK YND YG Sbjct: 319 AEKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLFIDVDYFKRYNDTYG 378 Query: 345 HLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHAL 404 H GD VL+ VA LR+ + R D RYGGEEF ++ TD M +++C+A++ Sbjct: 379 HEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCEAIYNR 438 Query: 405 AIAHAGSAMGRITISAGVASCNPGQPGASLDGLLQAADAALYRAKMEGRNRVVLA 459 I H+GS +G I++S GVA+ N P ++ +L AAD ALY AK EGRNRV +A Sbjct: 439 GIPHSGSPLGVISVSIGVATMNRA-PHQRMEDVLNAADHALYIAKREGRNRVCVA 492 >gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 515 Score = 159 bits (401), Expect = 7e-40, Method: Compositional matrix adjust. Identities = 87/191 (45%), Positives = 114/191 (59%), Gaps = 2/191 (1%) Query: 272 LELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRH-GTPLMLAF 330 L L + + R A QL +L+ TDGLT + NRR+ DE L+ W R R+ G + F Sbjct: 325 LLLHVRQELRRRVTAERQLEALARTDGLTDLLNRRALDEALQATWERCQRNLGASFSVLF 384 Query: 331 IDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAG 390 IDVD+FK YND YGH GD VL++VA TL + R D RYGGEEF ++ TD Q Sbjct: 385 IDVDYFKAYNDTYGHKLGDTVLKEVAATLTARLPRHTDCAGRYGGEEFVVLLEQTDLQGA 444 Query: 391 ADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGASLDGLLQAADAALYRAKM 450 M +R+CDAV IAH S + +TIS GVA+ ++ +L AADAALYRAK Sbjct: 445 QMMAQRLCDAVRERHIAHTSSPLAVVTISVGVATLERDHH-RRVEDVLNAADAALYRAKQ 503 Query: 451 EGRNRVVLATE 461 GR+RV L+++ Sbjct: 504 AGRDRVHLSSQ 514 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 0.136 0.398 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: 1,395,094 Number of extensions: 57284 Number of successful extensions: 326 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 264 Number of HSP's successfully gapped: 39 Length of query: 466 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 377 Effective length of database: 1,198,455 Effective search space: 451817535 Effective search space used: 451817535 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: 132 (55.5 bits)