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= 0001.1781.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... 759 0.0 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 133 4e-32 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 127 2e-30 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 125 6e-30 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 124 3e-29 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 759 bits (1959), Expect = 0.0, Method: Compositional matrix adjust. Identities = 400/573 (69%), Positives = 481/573 (83%) Query: 1 MSLNRLFRLISIALLMLFLAFAIALVWTEWNTYRSGAKSVPGLHNLRLALLALERVSAER 60 MSLNRLFRLISIALL+LFLAFA++LVWTEWN+YR+GA SVP L RLAL+ALE++SAER Sbjct: 1 MSLNRLFRLISIALLLLFLAFAVSLVWTEWNSYRNGANSVPALRTFRLALVALEKLSAER 60 Query: 61 GSANAIMGASAQQAGDLQQKITRARNQTDAALAALHGVLEADARLRQSWAMDKVRTVEQG 120 G ANA MGASA Q + K+ AR +TDAALAAL L++ RLRQSW++DKV+TV+Q Sbjct: 61 GPANAFMGASASQREAVADKLKNARAETDAALAALRQALQSHPRLRQSWSLDKVKTVQQA 120 Query: 121 LGAARANVDHVARLAQQDRSDVLVLAAVANMVDLIPPMIRVVSELGNEVDRADPSLRDGL 180 L ARA +D + R + +R++V VL+AV MVD+IP MIRV SEL +EVD ADP LR+GL Sbjct: 121 LEPARAAIDRIGRQPEAERNNVYVLSAVGGMVDMIPLMIRVASELSSEVDHADPELREGL 180 Query: 181 AAVRATASLREYAGQVGSRFVAPLIAHRQLTKDEVIEIGSLYGRIELLRNILAAQMATYS 240 AA+RA ASLREYAGQVGSRF LIAHR+LT+DEVIEIG LYGRIELLR +L QMA+Y Sbjct: 181 AAIRAAASLREYAGQVGSRFTPALIAHRKLTQDEVIEIGRLYGRIELLRGLLNTQMASYV 240 Query: 241 NSPEFAAAQDRMDKEYFDGAFQFLDFLLQTGLNSGNYSVTPTDLLKFYVPQMASITDLRD 300 PEFA A + +DK+YFD FQFLDFLLQTG+ SG+Y +T DL +FYVPQM SITDLRD Sbjct: 241 QRPEFARALELVDKQYFDNGFQFLDFLLQTGVASGDYGLTSVDLFRFYVPQMKSITDLRD 300 Query: 301 LLLEDLMARAESHNLRARNLLVLVVSLTLIACLFFQLLMVLIRRRVLQPLVRATDLVSGL 360 LLL+D+M +AE HN RARN L+LV+++T++ACLFFQ+LMVLIRRRV+QPLV ATDLVSGL Sbjct: 301 LLLDDMMEQAERHNRRARNYLLLVIAVTVVACLFFQVLMVLIRRRVVQPLVLATDLVSGL 360 Query: 361 VEGKLEQDIPEARHQDEIGAMMRALRVLKHRMRERTSLAKEREALITQLQASSNTDFLTG 420 VEG+L+Q+IP+ R++DEI AMMRAL+VL+ RMRER SLA+EREALITQLQ SSNTDFLTG Sbjct: 361 VEGRLDQEIPQPRYEDEISAMMRALKVLRQRMRERNSLAREREALITQLQTSSNTDFLTG 420 Query: 421 VLNRRAFYSYAEQQLAVAQRYGRPLAVILFDIDHFKRINDSFGHQAGDAILVGAAQCVAQ 480 VLNRRAF+++ +QQ+ VA+RYGR LAV+LFDIDHFK+INDS+GHQAGDAIL G AQ V+Q Sbjct: 421 VLNRRAFFTHGQQQMTVAKRYGRELAVVLFDIDHFKQINDSYGHQAGDAILRGVAQSVSQ 480 Query: 481 LLRKVDVLARYGGEEFIILLPESGLEQAAAVAEKLRAALQERVFDIEAGQQIRLSASFGV 540 LLRKVDVLARYGGEEFIILLPES L QAAA +EKLRAAL F+I+ G++IR++ASFGV Sbjct: 481 LLRKVDVLARYGGEEFIILLPESSLLQAAAASEKLRAALAAGEFEIDGGRRIRVTASFGV 540 Query: 541 AGLDDHEALDRLTKRADLALYRAKRLGRNRVEL 573 A + L+ L K+AD+ALYRAK+LGRNRVEL Sbjct: 541 AAENGGPGLEHLIKQADIALYRAKKLGRNRVEL 573 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 133 bits (335), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 68/159 (42%), Positives = 101/159 (63%), Gaps = 1/159 (0%) Query: 416 DFLTGVLNRRAFYSYAEQQLAVAQRYGRPLAVILFDIDHFKRINDSFGHQAGDAILVGAA 475 D LTG LNRR ++++ A R PL V L D+D FKRIND+ GH GD +LV Sbjct: 367 DQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDDFKRINDTHGHATGDEVLVHMV 426 Query: 476 QCVAQLLRKVDVLARYGGEEFIILLPESGLEQAAAVAEKLRAALQERVFDIEAGQQIRLS 535 Q + + LRK+DV+AR+GGEEF++L+PE+ + A + +++ L +R+F + Q++ ++ Sbjct: 427 QVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQIITRVQRELTKRIF-MHESQRLLIT 485 Query: 536 ASFGVAGLDDHEALDRLTKRADLALYRAKRLGRNRVELA 574 S GVA E+ 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 = 127 bits (319), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 83/191 (43%), Positives = 115/191 (60%), Gaps = 5/191 (2%) Query: 387 VLKHRMRERTSLAKER-EALITQLQASSNTDFLTGVLNRRAFYSYAEQQLAVAQRYGRPL 445 V+ H + LA++R E L +L + TD LTG+ NR + ++ A RYG+ L Sbjct: 136 VISHVVITGRKLAEQRVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNL 195 Query: 446 AVILFDIDHFKRINDSFGHQAGDAILVGAAQCVAQLLRKVDVLARYGGEEFIILLPESGL 505 ++IL DIDHFK +ND+FGH GDA+LV A+ + +R D+ R+GGEEF+++LPE + Sbjct: 196 SLILLDIDHFKEVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDM 255 Query: 506 EQAAAVAEKLRAALQERVFDIEAGQQIRLSASFGVAGLDDHEALDRLTKRADLALYRAKR 565 E AA +AEKLR ++ F + G R + SFGVA L ADLALYRAK Sbjct: 256 EDAARMAEKLRLLIENYNF-VPVG---RRTCSFGVAAYQAGHDRTTLLTLADLALYRAKN 311 Query: 566 LGRNRVELAGD 576 GRNRVE+A + Sbjct: 312 TGRNRVEIAAN 322 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 125 bits (315), Expect = 6e-30, Method: Compositional matrix adjust. Identities = 102/286 (35%), Positives = 149/286 (52%), Gaps = 30/286 (10%) Query: 314 NLRARNLLVLVVSLTLIACLFFQLLMVLIRRRVLQPLVRATDLVSGLVE-GKLEQDIPEA 372 N R++ ++++ L+ LL LI R + PL R LV+ + E G + + Sbjct: 296 NADTRSVRDKIIAIGLVCFAVSLLLSALISRSISVPLQR---LVAAMKEAGSGDTTVRVE 352 Query: 373 RH-QDEIGAMMRALR-----------VLKHRMRERTSLAKEREALITQLQASSNTDFLTG 420 +H DEI + R VL+ ++R RT +E E +L+A S TD LTG Sbjct: 353 QHGNDEIAVLSRKFNEMAGKLQQNREVLEEQVRLRT---RELERANRKLEALSATDGLTG 409 Query: 421 VLNRRAFYSYAEQQLAVAQRYGRPLAVILFDIDHFKRINDSFGHQAGDAILVGAAQCVAQ 480 V NRR F ++ A R G+ LA+++ D+D+FK+ ND +GH AGD L + VA+ Sbjct: 410 VANRRRFDEALANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECL----RIVAR 465 Query: 481 LLRK-----VDVLARYGGEEFIILLPESGLEQAAAVAEKLRAALQERVFDIEAGQQIRLS 535 +L+K D++ARYGGEEF +++ E QA AE + A+ E +S Sbjct: 466 VLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAENICQAIFELKLPHADSPFGYIS 525 Query: 536 ASFGVAGL--DDHEALDRLTKRADLALYRAKRLGRNRVELAGDEVQ 579 AS GVA L D+H A +++ + AD ALY AK GRNRV L D Q Sbjct: 526 ASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVVLGSDATQ 571 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 124 bits (310), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 75/171 (43%), Positives = 102/171 (59%), Gaps = 9/171 (5%) Query: 415 TDFLTGVLNRRAFYSYAEQQLAVAQRYGRPLAVILFDIDHFKRINDSFGHQAGDAILVGA 474 TD LTGV NRR ++++A +QR L+ + DIDHFKR+ND FGHQ+GD +L Sbjct: 202 TDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQSGDDVLREV 261 Query: 475 AQCVAQLLRKVDVLARYGGEEFIILLPESGLEQAAAVAEKLRAALQERVFDIEAGQQ-IR 533 A + + LR D L R+GGEEF++LL + E AA +AE++RA + R IE + ++ Sbjct: 262 AARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVCSRGVMIEGSRDPLK 321 Query: 534 LSASFGVAGLDDH-------EALDRLTKRADLALYRAKRLGRNRVEL-AGD 576 ++AS G A L E + K AD ALY+AK GRNRV L AGD Sbjct: 322 ITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRVMLAAGD 372 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 0.374 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: 1,539,646 Number of extensions: 60372 Number of successful extensions: 341 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 289 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 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 133 (55.8 bits)