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= 0028.0088.p (581 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 788 0.0 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 136 6e-33 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 129 6e-31 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 126 5e-30 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 114 2e-26 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 788 bits (2036), Expect = 0.0, Method: Compositional matrix adjust. Identities = 416/573 (72%), Positives = 491/573 (85%) Query: 1 MSLNRLFRLISVALLALFLAFAVALVWTEWNTYRSGANSVPALRKLRLALLAMEKISAER 60 MSLNRLFRLIS+ALL LFLAFAV+LVWTEWN+YR+GANSVPALR RLAL+A+EK+SAER Sbjct: 1 MSLNRLFRLISIALLLLFLAFAVSLVWTEWNSYRNGANSVPALRTFRLALVALEKLSAER 60 Query: 61 GPANAVMGAGASLPPELQARLATARAQSDAALSQLRAALEADARLRQSWAMDKVRLVQQG 120 GPANA MGA AS + +L ARA++DAAL+ LR AL++ RLRQSW++DKV+ VQQ Sbjct: 61 GPANAFMGASASQREAVADKLKNARAETDAALAALRQALQSHPRLRQSWSLDKVKTVQQA 120 Query: 121 LGPARANVDRVARLAPQDRSDVLVVSAVSSMVDLMPLMVRVVSDLSNEADRADPLLRDGL 180 L PARA +DR+ R +R++V V+SAV MVD++PLM+RV S+LS+E D ADP LR+GL Sbjct: 121 LEPARAAIDRIGRQPEAERNNVYVLSAVGGMVDMIPLMIRVASELSSEVDHADPELREGL 180 Query: 181 SAVRAVASLREYAGQVGSRFVAPLIAHRQLTQDEVIEIGRLYGRIELLRNFIAGQLGSYS 240 +A+RA ASLREYAGQVGSRF LIAHR+LTQDEVIEIGRLYGRIELLR + Q+ SY Sbjct: 181 AAIRAAASLREYAGQVGSRFTPALIAHRKLTQDEVIEIGRLYGRIELLRGLLNTQMASYV 240 Query: 241 RAPEFAAALERVEKEYFDSGFQFLDFLLQIGLKSGDFGVTPTDLFKFYVPSMASITDLRD 300 + PEFA ALE V+K+YFD+GFQFLDFLLQ G+ SGD+G+T DLF+FYVP M SITDLRD Sbjct: 241 QRPEFARALELVDKQYFDNGFQFLDFLLQTGVASGDYGLTSVDLFRFYVPQMKSITDLRD 300 Query: 301 LLLDDLLEQAERHNTRARNLLILVVSLTLVACLFFQMLVVLIGRRVVRPLVQATDLVSGL 360 LLLDD++EQAERHN RARN L+LV+++T+VACLFFQ+L+VLI RRVV+PLV ATDLVSGL Sbjct: 301 LLLDDMMEQAERHNRRARNYLLLVIAVTVVACLFFQVLMVLIRRRVVQPLVLATDLVSGL 360 Query: 361 VDGKLEQEIPEARHQDEIGAMMRALRVLKQRMRERNSLAKEREALITQLQTSSNTDFLTG 420 V+G+L+QEIP+ R++DEI AMMRAL+VL+QRMRERNSLA+EREALITQLQTSSNTDFLTG Sbjct: 361 VEGRLDQEIPQPRYEDEISAMMRALKVLRQRMRERNSLAREREALITQLQTSSNTDFLTG 420 Query: 421 VLNRRAFYTHADQQLGVAQRYRRAVSVVLFDIDHFKRINDSYGHQAGDAILIGVSQCVAQ 480 VLNRRAF+TH QQ+ VA+RY R ++VVLFDIDHFK+INDSYGHQAGDAIL GV+Q V+Q Sbjct: 421 VLNRRAFFTHGQQQMTVAKRYGRELAVVLFDIDHFKQINDSYGHQAGDAILRGVAQSVSQ 480 Query: 481 LLRKVDVLARYGGEEFIILLPESDLAQAAAVADKLRAALEERVFETEGDRRINVTASFGV 540 LLRKVDVLARYGGEEFIILLPES L QAAA ++KLRAAL FE +G RRI VTASFGV Sbjct: 481 LLRKVDVLARYGGEEFIILLPESSLLQAAAASEKLRAALAAGEFEIDGGRRIRVTASFGV 540 Query: 541 ATLAGGEALDKLTKRADIALYRAKRLGRNRVEL 573 A GG L+ L K+ADIALYRAK+LGRNRVEL Sbjct: 541 AAENGGPGLEHLIKQADIALYRAKKLGRNRVEL 573 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 136 bits (342), Expect = 6e-33, Method: Compositional matrix adjust. Identities = 69/159 (43%), Positives = 102/159 (64%), Gaps = 1/159 (0%) Query: 416 DFLTGVLNRRAFYTHADQQLGVAQRYRRAVSVVLFDIDHFKRINDSYGHQAGDAILIGVS 475 D LTG LNRR D+++ A R + V L D+D FKRIND++GH GD +L+ + Sbjct: 367 DQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDDFKRINDTHGHATGDEVLVHMV 426 Query: 476 QCVAQLLRKVDVLARYGGEEFIILLPESDLAQAAAVADKLRAALEERVFETEGDRRINVT 535 Q + + LRK+DV+AR+GGEEF++L+PE+ A + +++ L +R+F E +R+ +T Sbjct: 427 QVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQIITRVQRELTKRIFMHES-QRLLIT 485 Query: 536 ASFGVATLAGGEALDKLTKRADIALYRAKRLGRNRVELA 574 S GVA GE+ L KRAD+ALY+AK G+NR+ A Sbjct: 486 FSAGVAVYHPGESQADLLKRADVALYKAKNAGKNRIVFA 524 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 129 bits (324), Expect = 6e-31, Method: Compositional matrix adjust. Identities = 78/181 (43%), Positives = 111/181 (61%), Gaps = 5/181 (2%) Query: 397 SLAKER-EALITQLQTSSNTDFLTGVLNRRAFYTHADQQLGVAQRYRRAVSVVLFDIDHF 455 LA++R E L +L + TD LTG+ NR D ++ A RY + +S++L DIDHF Sbjct: 146 KLAEQRVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHF 205 Query: 456 KRINDSYGHQAGDAILIGVSQCVAQLLRKVDVLARYGGEEFIILLPESDLAQAAAVADKL 515 K +ND++GH GDA+L+ +++ + +R D+ R+GGEEF+++LPE D+ AA +A+KL Sbjct: 206 KEVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKL 265 Query: 516 RAALEERVFETEGDRRINVTASFGVATLAGGEALDKLTKRADIALYRAKRLGRNRVELAG 575 R +E F G R T SFGVA G L AD+ALYRAK GRNRVE+A Sbjct: 266 RLLIENYNFVPVGRR----TCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRVEIAA 321 Query: 576 D 576 + Sbjct: 322 N 322 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 126 bits (316), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 75/171 (43%), Positives = 101/171 (59%), Gaps = 9/171 (5%) Query: 415 TDFLTGVLNRRAFYTHADQQLGVAQRYRRAVSVVLFDIDHFKRINDSYGHQAGDAILIGV 474 TD LTGV NRR +++ +QR R A+S + DIDHFKR+ND +GHQ+GD +L V Sbjct: 202 TDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQSGDDVLREV 261 Query: 475 SQCVAQLLRKVDVLARYGGEEFIILLPESDLAQAAAVADKLRAALEERVFETEGDRR-IN 533 + + + LR D L R+GGEEF++LL + AA +A+++RA + R EG R + Sbjct: 262 AARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVCSRGVMIEGSRDPLK 321 Query: 534 VTASFGVATLA-------GGEALDKLTKRADIALYRAKRLGRNRVEL-AGD 576 +TAS G A L E + K AD ALY+AK GRNRV L AGD Sbjct: 322 ITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRVMLAAGD 372 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 114 bits (285), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 16/280 (5%) Query: 310 AERHNTRARNLLILVVSLTLVACLFFQMLVVLIGRRVVRPLVQATDLVSGLVD-GKLEQE 368 ++R N R++ ++++ LV +L LI R + PL + LV+ + + G + Sbjct: 292 SDRLNADTRSVRDKIIAIGLVCFAVSLLLSALISRSISVPLQR---LVAAMKEAGSGDTT 348 Query: 369 IPEARH-QDEIGAMMRALRVLKQRMRERNSLAKEREALIT--------QLQTSSNTDFLT 419 + +H DEI + R + ++++ + +E+ L T +L+ S TD LT Sbjct: 349 VRVEQHGNDEIAVLSRKFNEMAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLT 408 Query: 420 GVLNRRAFYTHADQQLGVAQRYRRAVSVVLFDIDHFKRINDSYGHQAGDAILIGVSQCVA 479 GV NRR F ++ A R +++++++ D+D+FK+ ND YGH AGD L V++ + Sbjct: 409 GVANRRRFDEALANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQ 468 Query: 480 QLLRK-VDVLARYGGEEFIILLPESDLAQAAAVADKLRAALEERVFETEGDRRINVTASF 538 + R+ D++ARYGGEEF +++ E D QA A+ + A+ E ++AS Sbjct: 469 KSSRRATDLVARYGGEEFSVIIAECDTTQALQQAENICQAIFELKLPHADSPFGYISASI 528 Query: 539 GVATLAGGE--ALDKLTKRADIALYRAKRLGRNRVELAGD 576 GVA L E A +++ + AD ALY AK GRNRV L D Sbjct: 529 GVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVVLGSD 568 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 0.375 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: 1,502,977 Number of extensions: 57124 Number of successful extensions: 345 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 296 Number of HSP's successfully gapped: 39 Length of query: 581 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 491 Effective length of database: 1,193,720 Effective search space: 586116520 Effective search space used: 586116520 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: 133 (55.8 bits)