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= 0001.0012.p (797 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane... 1602 0.0 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 348 1e-96 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 325 6e-90 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 324 2e-89 gi|300312026|ref|YP_003776118.1| signal transduction protein con... 310 2e-85 >gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 797 Score = 1602 bits (4147), Expect = 0.0, Method: Compositional matrix adjust. Identities = 796/797 (99%), Positives = 797/797 (100%) Query: 1 VVRLYRLESKIVALFITLLVVVQLAGFVAIRTAIDRNARASISEELAVGERVFARQLDQN 60 +VRLYRLESKIVALFITLLVVVQLAGFVAIRTAIDRNARASISEELAVGERVFARQLDQN Sbjct: 1 MVRLYRLESKIVALFITLLVVVQLAGFVAIRTAIDRNARASISEELAVGERVFARQLDQN 60 Query: 61 AQKLTQGARLLASDFGFRQAIGTDDRETIASVLSNHGARIGASMAMLIGNDGQIRASTVE 120 AQKLTQGARLLASDFGFRQAIGTDDRETIASVLSNHGARIGASMAMLIGNDGQIRASTVE Sbjct: 61 AQKLTQGARLLASDFGFRQAIGTDDRETIASVLSNHGARIGASMAMLIGNDGQIRASTVE 120 Query: 121 YPDTDLQRSSLELVRKAGNGNGASENAVVGDRLFQIVAVPIKAPVTIAWVVMGFPIDHQL 180 YPDTDLQRSSLELVRKAGNGNGASENAVVGDRLFQIVAVPIKAPVTIAWVVMGFPIDHQL Sbjct: 121 YPDTDLQRSSLELVRKAGNGNGASENAVVGDRLFQIVAVPIKAPVTIAWVVMGFPIDHQL 180 Query: 181 VSDMRELSSLQVSILVSQRGGVGWNADVSTLTAPAASMLLKEVGQPAMRAGGLIDLQIDG 240 VSDMRELSSLQVSILVSQRGGVGWNADVSTLTAPAASMLLKEVGQPAMRAGGLIDLQIDG Sbjct: 181 VSDMRELSSLQVSILVSQRGGVGWNADVSTLTAPAASMLLKEVGQPAMRAGGLIDLQIDG 240 Query: 241 NQYRARLLPLAQASNGQQAVAVLQRSVSEAVEPYQRLQLILLSITVLGVLGAAVASAVLA 300 NQYRARLLPLAQASNGQQAVAVLQRSVSEAVEPYQRLQLILLSITVLGVLGAAVASAVLA Sbjct: 241 NQYRARLLPLAQASNGQQAVAVLQRSVSEAVEPYQRLQLILLSITVLGVLGAAVASAVLA 300 Query: 301 RRITSPLRDLADVAKRLGEGDYSEGLFIRRQDEIGRLGNAFETMRLEIASRELKISRLAY 360 RRITSPLRDLADVAKRLGEGDYSEGLFIRRQDEIGRLGNAFETMRLEIASRELKISRLAY Sbjct: 301 RRITSPLRDLADVAKRLGEGDYSEGLFIRRQDEIGRLGNAFETMRLEIASRELKISRLAY 360 Query: 361 QDQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVNDVLGHSFGDDLLRQ 420 QDQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVNDVLGHSFGDDLLRQ Sbjct: 361 QDQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVNDVLGHSFGDDLLRQ 420 Query: 421 VALRLSAQLLHPGAKLSRLGGDEFAILLPGVDQEGAVEQALQILRALEQPLSLHQQTVDL 480 VALRLSAQLLHPGAKLSRLGGDEFAILLPGVDQEGAVEQALQILRALEQPLSLHQQTVDL Sbjct: 421 VALRLSAQLLHPGAKLSRLGGDEFAILLPGVDQEGAVEQALQILRALEQPLSLHQQTVDL 480 Query: 481 GAGIGISGYPAHGQSSDVLLSHAEVAMYIAKRKGSGLVIYDPAIDQSSQESLSLLSELRR 540 GAGIGISGYPAHGQSSDVLLSHAEVAMYIAKRKGSGLVIYDPAIDQSSQESLSLLSELRR Sbjct: 481 GAGIGISGYPAHGQSSDVLLSHAEVAMYIAKRKGSGLVIYDPAIDQSSQESLSLLSELRR 540 Query: 541 ALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIPFAETTGFIRMLTLW 600 ALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIPFAETTGFIRMLTLW Sbjct: 541 ALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIPFAETTGFIRMLTLW 600 Query: 601 MMEQVARLSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQRHRLQPAALCLEITES 660 MMEQVARLSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQRHRLQPAALCLEITES Sbjct: 601 MMEQVARLSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQRHRLQPAALCLEITES 660 Query: 661 AIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQDQ 720 AIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQDQ Sbjct: 661 AIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQDQ 720 Query: 721 DDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGYFMGKPMPVQHFLAWR 780 DDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGYFMGKPMPVQHFLAWR Sbjct: 721 DDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGYFMGKPMPVQHFLAWR 780 Query: 781 EQWRAPDMLDQSENMAV 797 EQWRAPDMLDQSENMAV Sbjct: 781 EQWRAPDMLDQSENMAV 797 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 348 bits (893), Expect = 1e-96, Method: Compositional matrix adjust. Identities = 197/454 (43%), Positives = 273/454 (60%), Gaps = 9/454 (1%) Query: 332 DEIGRLGNAFETMR--LEIASRELKISRLAYQDQLTGLPNRVQFADLLRDAIAEAARTPG 389 DE G+L T+ E + E ++ A D LTGLPNR + L+ A+ AR G Sbjct: 237 DEAGKLSCYEGTVEAITERKAHEAEMRHQATHDALTGLPNRNMLHEHLQRAL-RVARQKG 295 Query: 390 AACYILMMDLDRFQQVNDVLGHSFGDDLLRQVALRLSAQLLHPGAKLSRLGGDEFAILLP 449 A + +DLD+F+ +ND LGH GD+LL+ VA RL A L ++R GGDEF ++L Sbjct: 296 ALTAVAFVDLDQFKFINDSLGHQVGDELLKTVAQRLQA-CLREADMVARQGGDEFVLVLQ 354 Query: 450 G-VDQEGAVEQALQ-ILRALEQPLSLHQQTVDLGAGIGISGYPAHGQSSDVLLSHAEVAM 507 + E + + +Q IL A+ +P + + A IG+S YPA G+ + LL HA+ AM Sbjct: 355 NQTEGEAGIAEVMQRILAAVARPWQAGDREFQVTASIGVSRYPADGKDVESLLKHADSAM 414 Query: 508 YIAKRKG-SGLVIYDPAIDQSSQESLSLLSELRRALERDEFMLYLQPKLELCSGQVVGAE 566 Y AK +G + + P +D L +L LRRAL++DEF LY QPKL L G+++GAE Sbjct: 415 YRAKEQGRNNFQFFAPWMDSQVSNRLEMLINLRRALDQDEFKLYYQPKLSLQDGRLIGAE 474 Query: 567 ALVRWIHPEKGFIGPDNFIPFAETTGFIRMLTLWMMEQVARLSEQLQQQGVQ-LKFSVNL 625 AL+RW P++G + PD FIPFAE G I + W++ R ++ QQ G+ + +VNL Sbjct: 475 ALIRWESPQQGMVPPDRFIPFAEEAGLIVPIGEWVLRTACRQNQAWQQAGLPPIPVAVNL 534 Query: 626 STRDLLDQELPTAFAAILQRHRLQPAALCLEITESAIMDDPARAQNTLERLSNMGFALSI 685 S R L +Q LP A +L + L + L LEITE+ +M D ++ TL L +G +S+ Sbjct: 535 SPRQL-NQSLPDFVAGVLAQSGLAASWLELEITENVVMKDAEKSVATLHALKRLGLQISV 593 Query: 686 DDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQDQDDAKIVRSTVDLGHNLGLRVVAEGV 745 DDFGTGYSSL+YL+R PVD LKIDKSFV + +D D A IV++ + L H L LRV+AEGV Sbjct: 594 DDFGTGYSSLSYLRRFPVDALKIDKSFVRDIVRDADSAAIVKAIISLAHILNLRVIAEGV 653 Query: 746 ESEEVWFLLRQMGCDQGQGYFMGKPMPVQHFLAW 779 E EE L++ CD+ QGY+ GKPM V F AW Sbjct: 654 EDEEQHAFLKENACDEVQGYYFGKPMEVAVFTAW 687 >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 = 325 bits (834), Expect = 6e-90, Method: Compositional matrix adjust. Identities = 189/452 (41%), Positives = 265/452 (58%), Gaps = 9/452 (1%) Query: 331 QDEIGRLGNAFETMRLEIASRELKISRLAYQ---DQLTGLPNRVQFADLLRDAIAEAART 387 +DE G + + F +I S + + L +Q D LTGL NR L AI A R Sbjct: 489 RDESGEVTH-FVAALYDITSMKRYEAELEFQASRDTLTGLINRHMLRHHLEQAIGVAERQ 547 Query: 388 PGAACYILMMDLDRFQQVNDVLGHSFGDDLLRQVALRLSAQLLHPGAKLSRLGGDEFAIL 447 A +++ +DLDRF+ VND LGH GD LLR VA RL A + ++RLGGDEF ++ Sbjct: 548 K-QALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRAAV-READTVARLGGDEFIMI 605 Query: 448 LPGVDQEGAVEQALQ-ILRALEQPLSLHQQTVDLGAGIGISGYPAHGQSSDVLLSHAEVA 506 LP D+ ++LQ I+ A+ P++L T+ + +G++ YP G + L+ HA++A Sbjct: 606 LPEQDELTLDTRSLQRIMDAVAAPVTLGGHTLFMTCSVGVACYPNDGTDGETLIKHADIA 665 Query: 507 MYIAKRKG-SGLVIYDPAIDQSSQESLSLLSELRRALERDEFMLYLQPKLELCSGQVVGA 565 MY K+ G + Y PA+++ + E L + +LR AL+ EF+L+ QPK++L SG+V+G+ Sbjct: 666 MYRGKQTGRNNFQFYTPAMNEQALERLRIEGDLRNALDHGEFLLHYQPKVDLASGRVIGS 725 Query: 566 EALVRWIHPEKGFIGPDNFIPFAETTGFIRMLTLWMMEQVARLSEQLQQQG-VQLKFSVN 624 EAL+RW HP+ G + P FI AE TG I + W++ Q Q G + SVN Sbjct: 726 EALIRWQHPQLGMVSPARFIGLAEETGLILPIGAWVLRAACTQCRQWQLGGYADISVSVN 785 Query: 625 LSTRDLLDQELPTAFAAILQRHRLQPAALCLEITESAIMDDPARAQNTLERLSNMGFALS 684 LS L ++L ++ A +L+ L P +L LE+TES +M D A L L +G LS Sbjct: 786 LSVGQFLQKDLVSSIADVLEDTGLPPESLELELTESLMMTDVEHAIGILAGLKKLGVRLS 845 Query: 685 IDDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQDQDDAKIVRSTVDLGHNLGLRVVAEG 744 IDDFGTGYSSLAYLKR P+D LKID+SFV + D DDA I S + L +L LRV+AEG Sbjct: 846 IDDFGTGYSSLAYLKRFPIDVLKIDRSFVRDITIDADDAAITASIISLARHLKLRVIAEG 905 Query: 745 VESEEVWFLLRQMGCDQGQGYFMGKPMPVQHF 776 VE++E LR GCD+ QGY P+P F Sbjct: 906 VETDEQLDYLRHYGCDEIQGYLFSPPVPADKF 937 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 324 bits (831), Expect = 2e-89, Method: Compositional matrix adjust. Identities = 186/432 (43%), Positives = 260/432 (60%), Gaps = 4/432 (0%) Query: 348 IASRELKISRLAYQDQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVND 407 +A+ +++++ DQLT LPNR D L AI +AAR G ++ MDLD F+ +ND Sbjct: 255 LAAANEELTQMVLHDQLTRLPNRTLLEDRLNQAINKAAREQGHFA-LMFMDLDGFKAIND 313 Query: 408 VLGHSFGDDLLRQVALRLSAQLLHPGAKLSRLGGDEFAILLPGVDQEGAVEQALQILRAL 467 LGH GD LL +VA RL++ ++RLGGDEF IL+ E A+ A +++ A+ Sbjct: 314 SLGHHVGDRLLVEVAQRLTSSS-RANDTVARLGGDEFVILVDLNTPEDAMGVAEKLVEAV 372 Query: 468 EQPLSLHQQTVDLGAGIGISGYPAHGQSSDVLLSHAEVAMYIAKRKG-SGLVIYDPAIDQ 526 QP + Q + + A +GI+ YP G + L+ +A+ AMY KR G +G ++P+++ Sbjct: 373 NQPFKVDQHELRVSASVGIAIYPEDGATRHDLVINADAAMYHTKRSGRNGYHFFEPSMNA 432 Query: 527 SSQESLSLLSELRRALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIP 586 ++Q+ L L +LR ALER +F L QPK L +G V+GAEAL+RW HP G + PD FI Sbjct: 433 NAQQQLQWLQDLRVALERGQFRLVYQPKFSLPAGPVLGAEALLRWEHPVHGLVAPDQFIG 492 Query: 587 FAETTGFIRMLTLWMMEQVAR-LSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQR 645 AE +G I + W++++ R + E V SVNLS D L L+R Sbjct: 493 LAERSGLILPIGAWVLDEACRQMREWFALGYVDWTMSVNLSALQFADPHLLEVVRTTLER 552 Query: 646 HRLQPAALCLEITESAIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDE 705 H+L P L LE+TES M D + TL +++++G +SIDDFGTGYSSL YLKRLP +E Sbjct: 553 HQLPPPCLTLEVTESTAMHDTEASLQTLRQIADLGVEISIDDFGTGYSSLLYLKRLPANE 612 Query: 706 LKIDKSFVMKMAQDQDDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGY 765 LKID+ FV ++ QD +DA IV + V LG L LR+VAEGVE+ E L GCD QGY Sbjct: 613 LKIDRGFVRELRQDGEDAAIVSAIVALGRTLNLRIVAEGVETVEQQDFLTAAGCDALQGY 672 Query: 766 FMGKPMPVQHFL 777 MG+PM + FL Sbjct: 673 LMGRPMTPELFL 684 >gi|300312026|ref|YP_003776118.1| signal transduction protein containing a membrane domain, an EAL and a GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 1106 Score = 310 bits (795), Expect = 2e-85, Method: Compositional matrix adjust. Identities = 173/429 (40%), Positives = 251/429 (58%), Gaps = 9/429 (2%) Query: 354 KISRLAYQDQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVNDVLGHSF 413 +I LA+ D+LTGLPNR + +AI A G ILM DLDRF+ +ND GH Sbjct: 665 RIRHLAHYDELTGLPNRFLCTQHVSNAITHAEHRNGMVAVILM-DLDRFKNINDTFGHET 723 Query: 414 GDDLLRQVALRLSAQLLHPGAKLSRLGGDEFAILLPGVD---QEGAVEQALQILRALEQP 470 G+ +L+++A R L L+R+GGDEF +L+ D Q G + Q L L +P Sbjct: 724 GEAVLQEIAQRFRNSLRELDI-LARVGGDEFIVLVDDFDDPVQLGEIAQKL--LTEARKP 780 Query: 471 LSLHQQTVDLGAGIGISGYPAHGQSSDVLLSHAEVAMYIAKRKGSG-LVIYDPAIDQSSQ 529 + Q L IGI+ YP G ++ L+ +A++AMY AK G + I+ ++ Sbjct: 781 FIIDGQEAMLSVSIGIATYPGDGDNAQTLIKNADIAMYRAKHHGKDDYRFFSDEINTNTV 840 Query: 530 ESLSLLSELRRALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIPFAE 589 E ++L +ELRRA+ER EF+++ QPK+EL G++VGAEALVRW HP +G + P FI AE Sbjct: 841 ERIALEAELRRAIERAEFVVHYQPKIELAEGRIVGAEALVRWQHPLRGLLPPGEFITLAE 900 Query: 590 TTGFIRMLTLWMMEQVAR-LSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQRHRL 648 T I + L +++ R + QQQ + S+NL+ D+ L ++ RH Sbjct: 901 ETRLIDQIGLLVLDVACRDIGLMRQQQMTCGRISINLTGSQFGDERLLDDIKEVVDRHGT 960 Query: 649 QPAALCLEITESAIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDELKI 708 P+ L EITES +M + RA ++ + GF +SIDDFGTGYSSLAYLKR PV+ LKI Sbjct: 961 PPSCLEFEITESMVMHNRERAIAIMDGIRAEGFTISIDDFGTGYSSLAYLKRFPVNTLKI 1020 Query: 709 DKSFVMKMAQDQDDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGYFMG 768 DKSF+ + + + + IV++ + + H L L+VV EGVE+E+ LR+ G D+ QGY+ Sbjct: 1021 DKSFINDIPDNPNSSAIVQAIIAMSHALNLKVVTEGVETEKQLQALREFGSDEYQGYYFS 1080 Query: 769 KPMPVQHFL 777 KP+P F+ Sbjct: 1081 KPVPYAQFV 1089 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 0.382 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: 2,335,755 Number of extensions: 95732 Number of successful extensions: 551 Number of sequences better than 1.0e-08: 45 Number of HSP's gapped: 459 Number of HSP's successfully gapped: 45 Length of query: 797 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 704 Effective length of database: 1,179,515 Effective search space: 830378560 Effective search space used: 830378560 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 (21.8 bits) S2: 134 (56.2 bits)