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= 0001.0247.p (672 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... 994 0.0 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 258 1e-69 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 243 4e-65 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 236 3e-63 gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspi... 234 2e-62 >gi|300309604|ref|YP_003773696.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 696 Score = 994 bits (2569), Expect = 0.0, Method: Compositional matrix adjust. Identities = 511/666 (76%), Positives = 580/666 (87%), Gaps = 11/666 (1%) Query: 8 HVPVQDAG-NAP----SMMKLIRADQLMALRKTVLLSMPVNMLLGLISTFVAWRADKLPI 62 H P G AP S+ +LIRADQL ALR+TVLLS+PVNM+LG I TFVAWRA L I Sbjct: 33 HTPTPQTGVQAPAAQLSLQQLIRADQLAALRQTVLLSIPVNMVLGAICTFVAWRAGHLAI 92 Query: 63 ALLWLACSGVVNVLRVLACRIPVERLAALLPWLGQGQQPDARVDPVTELNLRLHWMLALL 122 ALLWLACSG+VN+LR+LACR+PV+R+AAL+ Q+ A V +LNLR+HWMLAL Sbjct: 93 ALLWLACSGMVNLLRILACRLPVQRVAALV------QRIAAPGAGVIDLNLRVHWMLALC 146 Query: 123 SGIVWAGVPLLCEGYTTPETLFYLTCVCGITAGAVTHGFAFARIPICFITPPLLSIIVCL 182 SG+VWAGV LLC GYT P TLFYLTCVCGITAGAVTHGFA+ARIPI FITPPLL+II L Sbjct: 147 SGLVWAGVALLCAGYTAPGTLFYLTCVCGITAGAVTHGFAYARIPIAFITPPLLAIIASL 206 Query: 183 AGIQTDSTRLALAAAVLLYLAALIRGSKVSEGLVSHASALKNQATAANQALELAHQDLHR 242 ++ D+TR+ALAAAVLLYL ALIRGSKVSEGLVSHASALKN+AT A+QALE+AH+DLH+ Sbjct: 207 VLVEPDTTRVALAAAVLLYLGALIRGSKVSEGLVSHASALKNEATTASQALEVAHRDLHQ 266 Query: 243 FAQRMQYQAEHDLLTGLLGRAGFMEVAPRMVARQEHALCMMFLDLDGFKVINDAYGHEAG 302 FA+RM+YQAEHDLLTGLLGRAGFM A M AR+E LCMMFLDLDGFKVINDAYGH+AG Sbjct: 267 FAERMRYQAEHDLLTGLLGRAGFMAAAQAMAARREEVLCMMFLDLDGFKVINDAYGHDAG 326 Query: 303 DQVLIEVARRLHDCIPAEATLARLGGDEFVVLYALAPNAELPEHLARRLIDAVRQPFARL 362 DQVL+EVARRL C+PA ATLARLGGDEFV+LYAL AELPE LARRLI+ VRQPFARL Sbjct: 327 DQVLVEVARRLQGCLPAGATLARLGGDEFVILYALDAQAELPELLARRLIEVVRQPFARL 386 Query: 363 AHRHIGLSLGITVTRSEDINEMLVCSDAAMYEAKRRGRNQFCLFNDSLNAHLQMKRDVER 422 AHRHIGLSLGIT++ +DI+EMLVCSDAAMY+AKRRGRNQFC+FN++LNAHLQMKRDVER Sbjct: 387 AHRHIGLSLGITLSDRDDIDEMLVCSDAAMYQAKRRGRNQFCVFNETLNAHLQMKRDVER 446 Query: 423 DLAHALTQRQLEVWFQPIVHHDGRTLDGFEALLRWHHPRHGDIAAPELIGIAALAGLSEE 482 DLA AL +R+L VWFQPIV HDG+TLDGFEALLRW H +HG IAAP+LI IAALAGLSEE Sbjct: 447 DLAGALARRELAVWFQPIVQHDGQTLDGFEALLRWQHGKHGAIAAPDLIEIAALAGLSEE 506 Query: 483 LLRFIIGEVAEMIRFLQASTRSDLRVSMNISPREMERLCIEELVMATLKTYRVPAQMLEI 542 LLRFI+ EVA MI FLQ+S RSDLR+SMNISPREMERL ++ELV++ LK +R+PA+MLEI Sbjct: 507 LLRFILEEVAGMIAFLQSSGRSDLRISMNISPREMERLVVDELVVSMLKAHRLPARMLEI 566 Query: 543 EITEETALDLQAATQTLVSLSMQGVSIAIDDFGVGYSSLGFLRQMRVSRVKIDRSFVTGL 602 EITEETALDLQAATQTLV+L++QGV IAIDDFGVGYSSLGFLRQM+VSRVKIDRSFVTGL Sbjct: 567 EITEETALDLQAATQTLVALALQGVRIAIDDFGVGYSSLGFLRQMQVSRVKIDRSFVTGL 626 Query: 603 AGQTENQALVAAMLQLSGSLGFQVVAEGVESEQDLHTLQAMGCHAMQGYYFSPPMPARQA 662 A QTENQALV+A+LQL+GS GFQVVAEGVES +DL TLQAM CHAMQGYYF+PPMPA QA Sbjct: 627 ADQTENQALVSAVLQLAGSFGFQVVAEGVESAEDLQTLQAMHCHAMQGYYFAPPMPAAQA 686 Query: 663 CEMVKA 668 ++A Sbjct: 687 RARIEA 692 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 258 bits (658), Expect = 1e-69, Method: Compositional matrix adjust. Identities = 179/525 (34%), Positives = 281/525 (53%), Gaps = 45/525 (8%) Query: 162 AFARIPICF-----ITPPLLSIIVCLAGIQTDSTRLALAAAVLLYLAALIRGSKVSEGLV 216 +F+R IC + P L++++ + + LAA + L +++ L Sbjct: 200 SFSRDSICLSAREGVAPGWLAVLIIV---------VTLAALTIALLTSVLDAR-----LE 245 Query: 217 SHASALKNQATAANQALE--LAHQDLHRFAQRMQYQAEHDLLTGLLGRAGFMEVAPRMVA 274 S + L AAN+ L + H L R R + D L + +A A Sbjct: 246 SRTAKLARSLAAANEELTQMVLHDQLTRLPNRTLLE---DRLNQAINKA----------A 292 Query: 275 RQEHALCMMFLDLDGFKVINDAYGHEAGDQVLIEVARRLHDCIPAEATLARLGGDEFVVL 334 R++ +MF+DLDGFK IND+ GH GD++L+EVA+RL A T+ARLGGDEFV+L Sbjct: 293 REQGHFALMFMDLDGFKAINDSLGHHVGDRLLVEVAQRLTSSSRANDTVARLGGDEFVIL 352 Query: 335 YALAPNAELPEH---LARRLIDAVRQPFARLAHR-HIGLSLGITVTRSEDI--NEMLVCS 388 L PE +A +L++AV QPF H + S+GI + + +++++ + Sbjct: 353 VDL----NTPEDAMGVAEKLVEAVNQPFKVDQHELRVSASVGIAIYPEDGATRHDLVINA 408 Query: 389 DAAMYEAKRRGRNQFCLFNDSLNAHLQMKRDVERDLAHALTQRQLEVWFQPIVHHDGRTL 448 DAAMY KR GRN + F S+NA+ Q + +DL AL + Q + +QP + Sbjct: 409 DAAMYHTKRSGRNGYHFFEPSMNANAQQQLQWLQDLRVALERGQFRLVYQPKFSLPAGPV 468 Query: 449 DGFEALLRWHHPRHGDIAAPELIGIAALAGLSEELLRFIIGEVAEMIRFLQASTRSDLRV 508 G EALLRW HP HG +A + IG+A +GL + +++ E +R A D + Sbjct: 469 LGAEALLRWEHPVHGLVAPDQFIGLAERSGLILPIGAWVLDEACRQMREWFALGYVDWTM 528 Query: 509 SMNISPREMERLCIEELVMATLKTYRVPAQMLEIEITEETAL-DLQAATQTLVSLSMQGV 567 S+N+S + + E+V TL+ +++P L +E+TE TA+ D +A+ QTL ++ GV Sbjct: 529 SVNLSALQFADPHLLEVVRTTLERHQLPPPCLTLEVTESTAMHDTEASLQTLRQIADLGV 588 Query: 568 SIAIDDFGVGYSSLGFLRQMRVSRVKIDRSFVTGLAGQTENQALVAAMLQLSGSLGFQVV 627 I+IDDFG GYSSL +L+++ + +KIDR FV L E+ A+V+A++ L +L ++V Sbjct: 589 EISIDDFGTGYSSLLYLKRLPANELKIDRGFVRELRQDGEDAAIVSAIVALGRTLNLRIV 648 Query: 628 AEGVESEQDLHTLQAMGCHAMQGYYFSPPMPARQACEMVKAQGRS 672 AEGVE+ + L A GC A+QGY PM + ++ + +S Sbjct: 649 AEGVETVEQQDFLTAAGCDALQGYLMGRPMTPELFLQTMRERHKS 693 >gi|300314042|ref|YP_003778134.1| signal transduction protein containing a membrane domain, an EAL and a GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 948 Score = 243 bits (620), Expect = 4e-65, Method: Compositional matrix adjust. Identities = 145/435 (33%), Positives = 240/435 (55%), Gaps = 7/435 (1%) Query: 240 LHRFAQRMQYQAEHDLLTGLLGRAGF---MEVAPRMVARQEHALCMMFLDLDGFKVINDA 296 + R+ +++QA D LTGL+ R +E A + RQ+ AL ++F+DLD FK +ND Sbjct: 508 MKRYEAELEFQASRDTLTGLINRHMLRHHLEQAIGVAERQKQALWVVFVDLDRFKFVNDT 567 Query: 297 YGHEAGDQVLIEVARRLHDCIPAEATLARLGGDEFVVLYALAPNAELPEHLARRLIDAVR 356 GH+AGD +L VA RL + T+ARLGGDEF+++ L +R++DAV Sbjct: 568 LGHKAGDTLLRTVAGRLRAAVREADTVARLGGDEFIMILPEQDELTLDTRSLQRIMDAVA 627 Query: 357 QPFARLAHR-HIGLSLGITVTRSE--DINEMLVCSDAAMYEAKRRGRNQFCLFNDSLNAH 413 P H + S+G+ ++ D ++ +D AMY K+ GRN F + ++N Sbjct: 628 APVTLGGHTLFMTCSVGVACYPNDGTDGETLIKHADIAMYRGKQTGRNNFQFYTPAMNEQ 687 Query: 414 LQMKRDVERDLAHALTQRQLEVWFQPIVHHDGRTLDGFEALLRWHHPRHGDIAAPELIGI 473 + +E DL +AL + + +QP V + G EAL+RW HP+ G ++ IG+ Sbjct: 688 ALERLRIEGDLRNALDHGEFLLHYQPKVDLASGRVIGSEALIRWQHPQLGMVSPARFIGL 747 Query: 474 AALAGLSEELLRFIIGEVAEMIRFLQASTRSDLRVSMNISPREMERLCIEELVMATLKTY 533 A GL + +++ R Q +D+ VS+N+S + + + + L+ Sbjct: 748 AEETGLILPIGAWVLRAACTQCRQWQLGGYADISVSVNLSVGQFLQKDLVSSIADVLEDT 807 Query: 534 RVPAQMLEIEITEETAL-DLQAATQTLVSLSMQGVSIAIDDFGVGYSSLGFLRQMRVSRV 592 +P + LE+E+TE + D++ A L L GV ++IDDFG GYSSL +L++ + + Sbjct: 808 GLPPESLELELTESLMMTDVEHAIGILAGLKKLGVRLSIDDFGTGYSSLAYLKRFPIDVL 867 Query: 593 KIDRSFVTGLAGQTENQALVAAMLQLSGSLGFQVVAEGVESEQDLHTLQAMGCHAMQGYY 652 KIDRSFV + ++ A+ A+++ L+ L +V+AEGVE+++ L L+ GC +QGY Sbjct: 868 KIDRSFVRDITIDADDAAITASIISLARHLKLRVIAEGVETDEQLDYLRHYGCDEIQGYL 927 Query: 653 FSPPMPARQACEMVK 667 FSPP+PA + ++++ Sbjct: 928 FSPPVPADKFEQILR 942 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 236 bits (603), Expect = 3e-63, Method: Compositional matrix adjust. Identities = 149/421 (35%), Positives = 237/421 (56%), Gaps = 13/421 (3%) Query: 247 MQYQAEHDLLTGLLGRAGFMEVAPRM--VARQEHAL-CMMFLDLDGFKVINDAYGHEAGD 303 M++QA HD LTGL R E R VARQ+ AL + F+DLD FK IND+ GH+ GD Sbjct: 262 MRHQATHDALTGLPNRNMLHEHLQRALRVARQKGALTAVAFVDLDQFKFINDSLGHQVGD 321 Query: 304 QVLIEVARRLHDCIPAEATLARLGGDEFVVLYALAPNAELP-EHLARRLIDAVRQPFARL 362 ++L VA+RL C+ +AR GGDEFV++ E + +R++ AV +P+ + Sbjct: 322 ELLKTVAQRLQACLREADMVARQGGDEFVLVLQNQTEGEAGIAEVMQRILAAVARPW-QA 380 Query: 363 AHRHIGLSLGITVTR----SEDINEMLVCSDAAMYEAKRRGRNQFCLFNDSLNAHLQMKR 418 R ++ I V+R +D+ +L +D+AMY AK +GRN F F +++ + + Sbjct: 381 GDREFQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQVSNRL 440 Query: 419 DVERDLAHALTQRQLEVWFQPIVH-HDGRTLDGFEALLRWHHPRHGDIAAPELIGIAALA 477 ++ +L AL Q + ++++QP + DGR + G EAL+RW P+ G + I A A Sbjct: 441 EMLINLRRALDQDEFKLYYQPKLSLQDGRLI-GAEALIRWESPQQGMVPPDRFIPFAEEA 499 Query: 478 GLSEELLRFIIGEVAEMIRFLQASTRSDLRVSMNISPREMERLCIEELVMATLKTYRVPA 537 GL + +++ + Q + + V++N+SPR++ + + + V L + A Sbjct: 500 GLIVPIGEWVLRTACRQNQAWQQAGLPPIPVAVNLSPRQLNQ-SLPDFVAGVLAQSGLAA 558 Query: 538 QMLEIEITEETAL-DLQAATQTLVSLSMQGVSIAIDDFGVGYSSLGFLRQMRVSRVKIDR 596 LE+EITE + D + + TL +L G+ I++DDFG GYSSL +LR+ V +KID+ Sbjct: 559 SWLELEITENVVMKDAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDK 618 Query: 597 SFVTGLAGQTENQALVAAMLQLSGSLGFQVVAEGVESEQDLHTLQAMGCHAMQGYYFSPP 656 SFV + ++ A+V A++ L+ L +V+AEGVE E+ L+ C +QGYYF P Sbjct: 619 SFVRDIVRDADSAAIVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACDEVQGYYFGKP 678 Query: 657 M 657 M Sbjct: 679 M 679 >gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 706 Score = 234 bits (596), Expect = 2e-62, Method: Compositional matrix adjust. Identities = 154/435 (35%), Positives = 242/435 (55%), Gaps = 9/435 (2%) Query: 242 RFAQRMQYQAEHDLLTGLLGRAGF---MEVAPRMVARQEHALCMMFLDLDGFKVINDAYG 298 R ++ + A HD+LTGL RA ++ A + R ++F+DLDGFK IND+ G Sbjct: 253 RTNDKLLHFATHDVLTGLPNRALLADRIQHAVEVARRNGKTFAVLFMDLDGFKAINDSLG 312 Query: 299 HEAGDQVLIEVARRLHDCIPAEATLARLGGDEFVVLYALAPNAELPEHLARRLIDAVRQP 358 H GD +L+ VA+R+ C+ E +AR+GGDEFVV+ + ++ E L+ ++ A+RQ Sbjct: 313 HAVGDGLLVAVAQRIRQCLRGEDMVARIGGDEFVVVVGNLSSPDVVEQLSENILAALRQD 372 Query: 359 FA-RLAHRHIGLSLGITV--TRSEDINEMLVCSDAAMYEAKRRGRNQFCLFNDSLNAHLQ 415 F A + S+GI V + ++ ++ +DAAMYEAK+ GRN + F +++A Sbjct: 373 FQIDDATLRVTSSIGIAVYPNSGDSVDALMKNADAAMYEAKQSGRNTYRFFEPAMHASAM 432 Query: 416 MKRDVERDLAHALTQRQLEVWFQPIVHHDGRTLDGFEALLRWHHPRHGDIAAPELIGIAA 475 V + L A+ ++Q + FQP + L G EALLRW HP+ G++A E I IA Sbjct: 433 RHLQVRQALQQAIDEQQFRLHFQPKYRGASKELTGLEALLRWTHPQLGEMAPTEFIPIAE 492 Query: 476 LAGLSEELLRFIIGEVAEMIRFLQASTRSDLRVSMNISPREMERLCIEELVMATLKTYRV 535 +G + +++ V E I A+ ++V++N+SP +M + +V + + Sbjct: 493 RSGQILCIGDWVLQAVCEQIARWDAAGMKPVKVALNLSPLQMRTDLVARIV-ELVGAAGI 551 Query: 536 PAQMLEIEITEETAL-DLQAATQTLVSLSMQGVSIAIDDFGVGYSSLGFLRQMRVSRVKI 594 Q L EITE A+ D++ + + + L G IAIDDFG GYSSL +L Q ++KI Sbjct: 552 APQRLMFEITETAAMKDVERSQRVIGELQALGFDIAIDDFGTGYSSLAYLAQFHCRQIKI 611 Query: 595 DRSFVTGLAGQTEN-QALVAAMLQLSGSLGFQVVAEGVESEQDLHTLQAMGCHAMQGYYF 653 DR F + L G + +A+VAA++ L+ +L +VVAEGVE+E L LQ + C +QG+ Sbjct: 612 DRFFTSRLDGDDHSGRAIVAAIIALAHALQMEVVAEGVETEGQLRELQLLHCDQVQGFLL 671 Query: 654 SPPMPARQACEMVKA 668 P A +V+A Sbjct: 672 GRPAEAPSVPGLVQA 686 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 0.325 0.137 0.404 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: 2,048,751 Number of extensions: 85995 Number of successful extensions: 522 Number of sequences better than 1.0e-08: 45 Number of HSP's gapped: 433 Number of HSP's successfully gapped: 45 Length of query: 672 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 580 Effective length of database: 1,184,250 Effective search space: 686865000 Effective search space used: 686865000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 134 (56.2 bits)