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= 0028.0020.p (452 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309604|ref|YP_003773696.1| diguanylate cyclase [Herbaspiri... 471 e-134 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 169 5e-43 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 160 2e-40 gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspi... 157 1e-39 gi|300313408|ref|YP_003777500.1| branched-chain amino acid ABC t... 153 3e-38 >gi|300309604|ref|YP_003773696.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 696 Score = 471 bits (1212), Expect = e-134, Method: Compositional matrix adjust. Identities = 236/294 (80%), Positives = 258/294 (87%) Query: 8 GATLARLGGDEFVILYPLTAHAEPPEHVAQRLIAAMRQPFARLAHRHIGLSLGIYLSRGD 67 GATLARLGGDEFVILY L A AE PE +A+RLI +RQPFARLAHRHIGLSLGI LS D Sbjct: 344 GATLARLGGDEFVILYALDAQAELPELLARRLIEVVRQPFARLAHRHIGLSLGITLSDRD 403 Query: 68 DINEMLVCSDAAMYEAKRRGRNQYQVFNAALDAHLQMKRDVERDLAQALADGELQVWFQP 127 DI+EMLVCSDAAMY+AKRRGRNQ+ VFN L+AHLQMKRDVERDLA ALA EL VWFQP Sbjct: 404 DIDEMLVCSDAAMYQAKRRGRNQFCVFNETLNAHLQMKRDVERDLAGALARRELAVWFQP 463 Query: 128 IVCEDGRALDGFEALVRWTHRRHGPIAPPDLIEIAALAGLSEELLRFIMGEVAHMIQFMR 187 IV DG+ LDGFEAL+RW H +HG IA PDLIEIAALAGLSEELLRFI+ EVA MI F++ Sbjct: 464 IVQHDGQTLDGFEALLRWQHGKHGAIAAPDLIEIAALAGLSEELLRFILEEVAGMIAFLQ 523 Query: 188 DNGRSDLRVSMNISPREMERIIIEDLVVGTLKRQNLPAQMLEIEITEETALDLQAATQTL 247 +GRSDLR+SMNISPREMER+++++LVV LK LPA+MLEIEITEETALDLQAATQTL Sbjct: 524 SSGRSDLRISMNISPREMERLVVDELVVSMLKAHRLPARMLEIEITEETALDLQAATQTL 583 Query: 248 TALALQGVSIAIDDFGVGYSSLGFLRQLHVSRVKIDRSFVTGLADQTENQALVS 301 ALALQGV IAIDDFGVGYSSLGFLRQ+ VSRVKIDRSFVTGLADQTENQALVS Sbjct: 584 VALALQGVRIAIDDFGVGYSSLGFLRQMQVSRVKIDRSFVTGLADQTENQALVS 637 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 169 bits (427), Expect = 5e-43, Method: Compositional matrix adjust. Identities = 113/296 (38%), Positives = 169/296 (57%), Gaps = 5/296 (1%) Query: 10 TLARLGGDEFVILYPLTAHAEPPEHVAQRLIAAMRQPFARLAHR-HIGLSLGI--YLSRG 66 T+ARLGGDEFVIL L E VA++L+ A+ QPF H + S+GI Y G Sbjct: 340 TVARLGGDEFVILVDLNT-PEDAMGVAEKLVEAVNQPFKVDQHELRVSASVGIAIYPEDG 398 Query: 67 DDINEMLVCSDAAMYEAKRRGRNQYQVFNAALDAHLQMKRDVERDLAQALADGELQVWFQ 126 +++++ +DAAMY KR GRN Y F +++A+ Q + +DL AL G+ ++ +Q Sbjct: 399 ATRHDLVINADAAMYHTKRSGRNGYHFFEPSMNANAQQQLQWLQDLRVALERGQFRLVYQ 458 Query: 127 PIVCEDGRALDGFEALVRWTHRRHGPIAPPDLIEIAALAGLSEELLRFIMGEVAHMIQFM 186 P + G EAL+RW H HG +AP I +A +GL + +++ E ++ Sbjct: 459 PKFSLPAGPVLGAEALLRWEHPVHGLVAPDQFIGLAERSGLILPIGAWVLDEACRQMREW 518 Query: 187 RDNGRSDLRVSMNISPREMERIIIEDLVVGTLKRQNLPAQMLEIEITEETAL-DLQAATQ 245 G D +S+N+S + + ++V TL+R LP L +E+TE TA+ D +A+ Q Sbjct: 519 FALGYVDWTMSVNLSALQFADPHLLEVVRTTLERHQLPPPCLTLEVTESTAMHDTEASLQ 578 Query: 246 TLTALALQGVSIAIDDFGVGYSSLGFLRQLHVSRVKIDRSFVTGLADQTENQALVS 301 TL +A GV I+IDDFG GYSSL +L++L + +KIDR FV L E+ A+VS Sbjct: 579 TLRQIADLGVEISIDDFGTGYSSLLYLKRLPANELKIDRGFVRELRQDGEDAAIVS 634 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 160 bits (405), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 103/298 (34%), Positives = 167/298 (56%), Gaps = 10/298 (3%) Query: 11 LARLGGDEFVILYPLTAHAEPP-EHVAQRLIAAMRQPFARLAHRHIGLSLGIYLSR---- 65 +AR GGDEFV++ E V QR++AA+ +P+ + R ++ I +SR Sbjct: 341 VARQGGDEFVLVLQNQTEGEAGIAEVMQRILAAVARPW-QAGDREFQVTASIGVSRYPAD 399 Query: 66 GDDINEMLVCSDAAMYEAKRRGRNQYQVFNAALDAHLQMKRDVERDLAQALADGELQVWF 125 G D+ +L +D+AMY AK +GRN +Q F +D+ + + ++ +L +AL E ++++ Sbjct: 400 GKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQVSNRLEMLINLRRALDQDEFKLYY 459 Query: 126 QP-IVCEDGRALDGFEALVRWTHRRHGPIAPPDLIEIAALAGLSEELLRFIMGEVAHMIQ 184 QP + +DGR L G EAL+RW + G + P I A AGL + +++ Q Sbjct: 460 QPKLSLQDGR-LIGAEALIRWESPQQGMVPPDRFIPFAEEAGLIVPIGEWVLRTACRQNQ 518 Query: 185 FMRDNGRSDLRVSMNISPREMERIIIEDLVVGTLKRQNLPAQMLEIEITEETAL-DLQAA 243 + G + V++N+SPR++ + + D V G L + L A LE+EITE + D + + Sbjct: 519 AWQQAGLPPIPVAVNLSPRQLNQ-SLPDFVAGVLAQSGLAASWLELEITENVVMKDAEKS 577 Query: 244 TQTLTALALQGVSIAIDDFGVGYSSLGFLRQLHVSRVKIDRSFVTGLADQTENQALVS 301 TL AL G+ I++DDFG GYSSL +LR+ V +KID+SFV + ++ A+V Sbjct: 578 VATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSFVRDIVRDADSAAIVK 635 >gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 706 Score = 157 bits (398), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 99/284 (34%), Positives = 159/284 (55%), Gaps = 5/284 (1%) Query: 11 LARLGGDEFVILYPLTAHAEPPEHVAQRLIAAMRQPFA-RLAHRHIGLSLGI--YLSRGD 67 +AR+GGDEFV++ + + E +++ ++AA+RQ F A + S+GI Y + GD Sbjct: 337 VARIGGDEFVVVVGNLSSPDVVEQLSENILAALRQDFQIDDATLRVTSSIGIAVYPNSGD 396 Query: 68 DINEMLVCSDAAMYEAKRRGRNQYQVFNAALDAHLQMKRDVERDLAQALADGELQVWFQP 127 ++ ++ +DAAMYEAK+ GRN Y+ F A+ A V + L QA+ + + ++ FQP Sbjct: 397 SVDALMKNADAAMYEAKQSGRNTYRFFEPAMHASAMRHLQVRQALQQAIDEQQFRLHFQP 456 Query: 128 IVCEDGRALDGFEALVRWTHRRHGPIAPPDLIEIAALAGLSEELLRFIMGEVAHMIQFMR 187 + L G EAL+RWTH + G +AP + I IA +G + +++ V I Sbjct: 457 KYRGASKELTGLEALLRWTHPQLGEMAPTEFIPIAERSGQILCIGDWVLQAVCEQIARWD 516 Query: 188 DNGRSDLRVSMNISPREMERIIIEDLVVGTLKRQNLPAQMLEIEITEETAL-DLQAATQT 246 G ++V++N+SP +M ++ +V + + Q L EITE A+ D++ + + Sbjct: 517 AAGMKPVKVALNLSPLQMRTDLVAR-IVELVGAAGIAPQRLMFEITETAAMKDVERSQRV 575 Query: 247 LTALALQGVSIAIDDFGVGYSSLGFLRQLHVSRVKIDRSFVTGL 290 + L G IAIDDFG GYSSL +L Q H ++KIDR F + L Sbjct: 576 IGELQALGFDIAIDDFGTGYSSLAYLAQFHCRQIKIDRFFTSRL 619 >gi|300313408|ref|YP_003777500.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 381 Score = 153 bits (386), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 75/81 (92%), Positives = 77/81 (95%) Query: 317 SLAIAKDMVARGYQRIAFIGYSNAYGEGWYEEFKKAAGLKKLELVANERFAPNDTSATAQ 376 SLAIA+DMVARGYQRIAFIGYSNAYGEGWYEEFKKAAGLKKLELVANERFAP D+S TAQ Sbjct: 142 SLAIARDMVARGYQRIAFIGYSNAYGEGWYEEFKKAAGLKKLELVANERFAPTDSSTTAQ 201 Query: 377 ALKLVAAKPDAILIAASGNSA 397 ALKLVAAKPDAILIAASG A Sbjct: 202 ALKLVAAKPDAILIAASGTPA 222 Score = 108 bits (270), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 52/66 (78%), Positives = 55/66 (83%) Query: 387 AILIAASGNSAYPXEFRAALRDALEATKEVTGVHGVYNMSATDHLGLDQRASVMVKIVDG 446 AI +A G EFRAALRD LEATKEVTGVHGVY MS+TDHLGLDQRA+VMVKIVDG Sbjct: 316 AIPVALKGAKPGTPEFRAALRDVLEATKEVTGVHGVYTMSSTDHLGLDQRAAVMVKIVDG 375 Query: 447 AWQYQP 452 AWQYQP Sbjct: 376 AWQYQP 381 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 0.135 0.390 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: 1,300,112 Number of extensions: 50607 Number of successful extensions: 269 Number of sequences better than 1.0e-08: 20 Number of HSP's gapped: 235 Number of HSP's successfully gapped: 22 Length of query: 452 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 364 Effective length of database: 1,203,190 Effective search space: 437961160 Effective search space used: 437961160 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: 132 (55.5 bits)