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= 0030.0002.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|300313074|ref|YP_003777166.1| GGDEF domain-containing protein... 166 3e-42 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 153 4e-38 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 133 3e-32 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 123 4e-29 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 121 1e-28 >gi|300313074|ref|YP_003777166.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 738 Score = 166 bits (421), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 112/333 (33%), Positives = 165/333 (49%), Gaps = 15/333 (4%) Query: 67 ERSLEIDLLAR--SLTLVSDRLADPKVLQMLQLRKEAHNEYLWIGIGDLRGQVIHATDGI 124 ER ++I LL S+ D VL+ LQ R H Y WIG+ G V+ AT G+ Sbjct: 90 EREIDIRLLVSRPSIRQAQDPAHIRAVLEELQ-RNVPH--YAWIGMARPDGTVLAATKGL 146 Query: 125 LLGEKISMRPWFKAGLAGAYAGDVHEAVLLAKHLPQQKPNQPLRFIDFASPVYDRNGAVL 184 L G ++ RPWF+ G YA D H AVLL K LP Q + P RF+D + PV + G ++ Sbjct: 147 LEGMSVAERPWFQQGQQTEYAADYHPAVLLEKKLPPQ--SDPWRFVDLSMPVLNMQGQMI 204 Query: 185 GVLGAHASWDWVSDAVVKKIRDPQSDQQLEIFIVNSKGDILYPFEKVGATRLPDGQRPAE 244 GV+G H SW W + K + S +++ IV S G ++ + + T++ A Sbjct: 205 GVMGMHLSWGWAREIASKLLNPTSSRYDVDVLIVRSDGTVILGPKDMEETKIDTASFRAA 264 Query: 245 RFE------VSNWASEGQYLMSVVPVKSAMQLKLDWKIVVRQPAALAFEPVRQLRYKLIV 298 + + W +Y+ ++KL W ++VRQP +A E R L ++IV Sbjct: 265 QHSSAGGSLIETWPDGRRYVTGYARTGQGGEMKLKWTVIVRQPETVALEAFRDLERRVIV 324 Query: 299 LGLVAGLLMVMGAFYFARKLCKPIEALAEVAEQVLRRDRKVIFPDPRGAGSAELAQLCST 358 +G +AG ++V+ AF R+L PI AL+ EQ ++V P EL L S Sbjct: 325 VGALAGAVLVLLAFMLTRRLVAPINALSAALEQRAAGLQEVEI--PLVTSVRELQLLSSA 382 Query: 359 FHTMTESLLDREQKLRELNESLEHQVDVRTNEL 391 TM E +++R LNESLE +V RT+ L Sbjct: 383 LGTMVEREERYLREMRSLNESLEERVVERTSRL 415 Score = 102 bits (255), Expect = 6e-23, Method: Compositional matrix adjust. Identities = 60/168 (35%), Positives = 93/168 (55%), Gaps = 7/168 (4%) Query: 397 KLAELATEDPLTGLANRRYFEERLSAAFQQMKRTSHPYGVLMVDVDFFKKVNDTFGHEAG 456 ++ ELA D LT L NRR F +RL + +R + +D+D FK +ND +GHEAG Sbjct: 564 QMRELALTDVLTSLPNRRAFSDRLPEGMMRARRAHQLLALFFMDLDGFKGINDRYGHEAG 623 Query: 457 DKVLQKLAVLLSESLRNTDLVARYGGEEFVVLLAPVTSEEQAFIVADKIREIVAKAEFPS 516 D++L + A L S+R+ D VAR G+EFVV+L + S++ A +VA+KI + + + Sbjct: 624 DELLVEFARRLQASVRDVDTVARLAGDEFVVILENLQSQQDAIMVAEKILHAIREPFELT 683 Query: 517 VKSITISVGLAAASINDPTQDDAV------RRADGALYKAKEKGRNCV 558 ++ IS + A + P D + AD A+Y AK G+N + Sbjct: 684 HSTVHISSSIGVA-VYQPDLDGEIGPEELLSMADKAMYAAKRLGKNRI 730 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 153 bits (387), Expect = 4e-38, Method: Compositional matrix adjust. Identities = 107/292 (36%), Positives = 159/292 (54%), Gaps = 17/292 (5%) Query: 274 WKIVVRQPAALAFEPVRQLRYKLIVLGLVAGLLMVMGAFYFARKLCKPIEALAEVAEQVL 333 W + P+ R +R K+I +GLV + ++ + +R + P++ L ++ Sbjct: 284 WWVASITPSDRLNADTRSVRDKIIAIGLVCFAVSLLLSALISRSISVPLQRLVAAMKEAG 343 Query: 334 RRDRKVIFPDPRGAGSAELAQLCSTFHTMTESLLDREQKLRELNESLEHQVDVRTNELKL 393 D V G+ E+A L F+ M KL++ E LE QV +RT EL+ Sbjct: 344 SGDTTVRVEQH---GNDEIAVLSRKFNEMA-------GKLQQNREVLEEQVRLRTRELER 393 Query: 394 ANLKLAELATEDPLTGLANRRYFEERLSAAFQQMKRTSHPYGVLMVDVDFFKKVNDTFGH 453 AN KL L+ D LTG+ANRR F+E L+ ++ R+ +LM+DVD+FKK ND +GH Sbjct: 394 ANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGH 453 Query: 454 EAGDKVLQKLA-VLLSESLRNTDLVARYGGEEFVVLLAPVTSEEQAFIVADKIREIVAKA 512 AGD+ L+ +A VL S R TDLVARYGGEEF V++A + QA A+ I + + + Sbjct: 454 LAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDT-TQALQQAENICQAIFEL 512 Query: 513 EFPSVKS----ITISVGLAAASINDPTQ-DDAVRRADGALYKAKEKGRNCVI 559 + P S I+ S+G+A ++ T + VR AD ALY AK +GRN V+ Sbjct: 513 KLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVV 564 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 133 bits (335), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 92/271 (33%), Positives = 140/271 (51%), Gaps = 21/271 (7%) Query: 312 FYFARKLCKPIEALAEVAEQV----LRRDRKVIFPDPR-----------GAGSAELAQLC 356 + F R L +PI LA+ ++ + R + P R A+L + Sbjct: 92 YVFRRWLGQPITRLADFVRELDLNQMETPRSIHLPGRRRHELHFLADAINLMLAKLHRHT 151 Query: 357 STFHTMTESLLDREQKLRELNESLEHQVDVRTNELKLANLKLAELATEDPLTGLANRRYF 416 H + + L +Q L LN SLE ++ RT +L AN +L L+ D LTG+ANRR F Sbjct: 152 IHNHALYKELEQEKQSLSALNRSLELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSF 211 Query: 417 EERLSAAFQQMKRTSHPYGVLMVDVDFFKKVNDTFGHEAGDKVLQKLAVLLSESL-RNTD 475 +E L +++ R P + +DVD+FK ND +GH AGD VL+++A L +S+ R D Sbjct: 212 DETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGD 271 Query: 476 LVARYGGEEFVVLLAPVTSEEQAFI---VADKIREIVAKAEFPSVKSITISVGLAAASIN 532 VARYGGEEF ++ A + A + + D + + ++ ITIS G+A+ + Sbjct: 272 TVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPG 331 Query: 533 DPTQ--DDAVRRADGALYKAKEKGRNCVITA 561 P D ++ AD ALY+AK +GRN V+ A Sbjct: 332 QPGAGLDGLLQAADAALYRAKMEGRNRVVLA 362 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 123 bits (309), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 79/175 (45%), Positives = 104/175 (59%), Gaps = 8/175 (4%) Query: 394 ANLKLAELATEDPLTGLANRRYFEERLSAAFQQMKRT-SHPYGVLMVDVDFFKKVNDTFG 452 A +L +LA D LTGL NRR +E L A +Q+ +R+ + + L +DVD+FK+ NDT+G Sbjct: 319 AEKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLFIDVDYFKRYNDTYG 378 Query: 453 HEAGDKVLQKLAVLLSESL-RNTDLVARYGGEEFVVLLAPVTSEEQAFIVADKIREIVAK 511 HE GD VLQ +A +L E L R DL RYGGEEFVVLL T E A +A ++ E + Sbjct: 379 HEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQ-TDEHGALRMAQQLCEAIYN 437 Query: 512 AEFPSVKSI--TISVGLAAASIND-PTQ--DDAVRRADGALYKAKEKGRNCVITA 561 P S ISV + A++N P Q +D + AD ALY AK +GRN V A Sbjct: 438 RGIPHSGSPLGVISVSIGVATMNRAPHQRMEDVLNAADHALYIAKREGRNRVCVA 492 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 121 bits (304), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 73/180 (40%), Positives = 105/180 (58%), Gaps = 12/180 (6%) Query: 393 LANLKLAELATEDPLTGLANRRYFEERLSAAFQQMKRTSHPYGVLMVDVDFFKKVNDTFG 452 + N +L + DPLTG+ NRRY E+R+ + +R L +D+D FK+VND FG Sbjct: 191 INNERLKHIGLTDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFG 250 Query: 453 HEAGDKVLQKLAVLLSESLRNTDLVARYGGEEFVVLLAPVTSEEQAFIVADKIREIVAKA 512 H++GD VL+++A + + LR +D + R+GGEEFVVLL T E+ A I A++IR V Sbjct: 251 HQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARI-AERIRAGVCSR 309 Query: 513 EFPSVKS-----ITISVGLAAASINDPTQDDA------VRRADGALYKAKEKGRNCVITA 561 S IT S+G AA + D ++ A ++ AD ALY+AKE GRN V+ A Sbjct: 310 GVMIEGSRDPLKITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRVMLA 369 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 0.136 0.391 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: 1,614,769 Number of extensions: 64704 Number of successful extensions: 327 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 268 Number of HSP's successfully gapped: 40 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 (21.9 bits) S2: 133 (55.8 bits)