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= 0001.0529.p (653 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309883|ref|YP_003773975.1| GGDEF domain/EAL domain signal ... 1004 0.0 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 263 3e-71 gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspi... 246 3e-66 gi|300312026|ref|YP_003776118.1| signal transduction protein con... 246 5e-66 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 239 7e-64 >gi|300309883|ref|YP_003773975.1| GGDEF domain/EAL domain signal transduction protein [Herbaspirillum seropedicae SmR1] Length = 650 Score = 1004 bits (2597), Expect = 0.0, Method: Compositional matrix adjust. Identities = 489/643 (76%), Positives = 560/643 (87%) Query: 1 MAPSALMSMVRRYWRVNVDQPELLIAQYRAFAGKMPMMYLILLINTWGLAYTYLGLVPLW 60 M S+ MS +R YWRV+ ++P+L+IAQY+AF+ KMPMMYLIL+IN+W LAYTYL L PLW Sbjct: 1 MRLSSWMSSLRNYWRVDHERPQLVIAQYQAFSTKMPMMYLILIINSWALAYTYLDLAPLW 60 Query: 61 LGLYFPVLLTVLCVIRISFWWRGRHVDPTPGMAAAALKRTNLLAPPIALSFSLWSVLLFP 120 LGLYFP +L+VLC +R+ FWWR RH+ PTP AA AL+RTNLL PIALSFSLWS++LFP Sbjct: 61 LGLYFPAVLSVLCSVRLLFWWRNRHLVPTPVAAAQALRRTNLLVAPIALSFSLWSIMLFP 120 Query: 121 YGDSYAQAHVAFYMGITVICCIFCLMYLRSAALSVALIVNGIFTLFFLATHIPTFVAAAM 180 YG++YAQAHVAFYMGITVICCIFCLMYLRSAAL+ ALIVNGIFT+FFL+THIP FVAAA+ Sbjct: 121 YGNAYAQAHVAFYMGITVICCIFCLMYLRSAALTGALIVNGIFTVFFLSTHIPVFVAAAL 180 Query: 181 NVVLVTLGMLAIVNSHYNDFRRLIDAQVKTTLLGNENLRLANLDSLTQIPNRRKFFAQLD 240 NVVLVT+GML IVNSHY DF RL++AQ++T +L +ENL+LAN+DSLTQIPNRRKFFAQL+ Sbjct: 181 NVVLVTIGMLVIVNSHYEDFTRLVEAQLRTAVLSDENLQLANVDSLTQIPNRRKFFAQLN 240 Query: 241 QICSRATANGQRFAVAILDLDGFKAVNDLYGHTHGDQLLVEVGQRLSALCGEEYLHLARL 300 +IC+RA QRFAVAILDLDGFKAVNDLYGH+HGD+LL +VGQRL C + LHLARL Sbjct: 241 EICARAHGAQQRFAVAILDLDGFKAVNDLYGHSHGDRLLEQVGQRLLTACRDPALHLARL 300 Query: 301 GGDEFAIIIDAGQSDDVLQQFGARICDALRRPFVLYKATVQIAASVGVATFPDMAVDASS 360 GGDEFA+IID SD LQ+ G ++C LRR FVL KA VQIAASVGVATFPDMA DA++ Sbjct: 301 GGDEFALIIDRDLSDAALQEIGQQLCHTLRRAFVLDKAVVQIAASVGVATFPDMAADAAT 360 Query: 361 LYEHADYALYQGKRERRGTVTLFSAQDKAQIQRNANVEQALRRADFERELSVVFQPIVRL 420 LYEHADYALYQGKRERRGTVTLFS DKAQI+R +N+EQALR ADFERELSV FQPIVRL Sbjct: 361 LYEHADYALYQGKRERRGTVTLFSEHDKAQIRRKSNIEQALRLADFERELSVFFQPIVRL 420 Query: 421 DDCQPVAFEALARWHSATKGVVAPMEFIPAAERMGIINQLSVTLLKKALQAAATWPPDMR 480 DD Q +AFEALARWHS KG V+P+EFIPAAERMGIINQLSV LL+KAL AAA+WP +R Sbjct: 421 DDGQVIAFEALARWHSTVKGAVSPVEFIPAAERMGIINQLSVILLRKALAAAASWPAQIR 480 Query: 481 LSFNLSANDINTSEGMSEIVKVITGSGFCASRLDLEITETAVLQDLGKSRQLVTSLRQLG 540 LSFNLSANDIN+SEGM+EI+K+I SGFC SRLDLEITETA+LQDL K+RQL+ SLRQLG Sbjct: 481 LSFNLSANDINSSEGMAEIIKLIRESGFCPSRLDLEITETALLQDLEKTRQLIHSLRQLG 540 Query: 541 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADIEHDAVSHKIIKSLLALSHDMQLAC 600 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADI DAVS KI+KSLLAL+ DM LAC Sbjct: 541 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADIGQDAVSLKIVKSLLALTLDMDLAC 600 Query: 601 VVEGVETPQHLQSLRELGAVYGQGYLFSVPLAADQVQSWLEHQ 643 VVEG+ETPQHL LRELGA+YGQGYL++ P+AAD V WL + Sbjct: 601 VVEGLETPQHLAVLRELGAMYGQGYLYARPMAADDVAPWLAQR 643 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 263 bits (673), Expect = 3e-71, Method: Compositional matrix adjust. Identities = 161/433 (37%), Positives = 236/433 (54%), Gaps = 9/433 (2%) Query: 221 ANLDSLTQIPNRRKFFAQLDQICSRATANGQRFAVAILDLDGFKAVNDLYGHTHGDQLLV 280 A D+LT +PNR L + A G AVA +DLD FK +ND GH GD+LL Sbjct: 266 ATHDALTGLPNRNMLHEHLQRALRVARQKGALTAVAFVDLDQFKFINDSLGHQVGDELLK 325 Query: 281 EVGQRLSALCGEEYLHLARLGGDEFAIII-DAGQSDDVLQQFGARICDALRRPFVLYKAT 339 V QRL A C E +AR GGDEF +++ + + + + + RI A+ RP+ Sbjct: 326 TVAQRLQA-CLREADMVARQGGDEFVLVLQNQTEGEAGIAEVMQRILAAVARPWQAGDRE 384 Query: 340 VQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSAQDKAQIQRNANVEQ 399 Q+ AS+GV+ +P D SL +HAD A+Y+ K + R F+ +Q+ + Sbjct: 385 FQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQVSNRLEMLI 444 Query: 400 ALRRADFERELSVVFQPIVRLDDCQPVAFEALARWHSATKGVVAPMEFIPAAERMGIINQ 459 LRRA + E + +QP + L D + + EAL RW S +G+V P FIP AE G+I Sbjct: 445 NLRRALDQDEFKLYYQPKLSLQDGRLIGAEALIRWESPQQGMVPPDRFIPFAEEAGLIVP 504 Query: 460 LSVTLLKKALQAAATWP----PDMRLSFNLSANDINTSEGMSEIVK-VITGSGFCASRLD 514 + +L+ A + W P + ++ NLS +N S + + V V+ SG AS L+ Sbjct: 505 IGEWVLRTACRQNQAWQQAGLPPIPVAVNLSPRQLNQS--LPDFVAGVLAQSGLAASWLE 562 Query: 515 LEITETAVLQDLGKSRQLVTSLRQLGCGITLDDFGTGYASLSHLHALPLTRIKIDKSFVA 574 LEITE V++D KS + +L++LG I++DDFGTGY+SLS+L P+ +KIDKSFV Sbjct: 563 LEITENVVMKDAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSFVR 622 Query: 575 DIEHDAVSHKIIKSLLALSHDMQLACVVEGVETPQHLQSLRELGAVYGQGYLFSVPLAAD 634 DI DA S I+K++++L+H + L + EGVE + L+E QGY F P+ Sbjct: 623 DIVRDADSAAIVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACDEVQGYYFGKPMEVA 682 Query: 635 QVQSWLEHQTQCG 647 +W+ Q Q G Sbjct: 683 VFTAWMSEQAQAG 695 >gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 706 Score = 246 bits (629), Expect = 3e-66, Method: Compositional matrix adjust. Identities = 161/439 (36%), Positives = 247/439 (56%), Gaps = 12/439 (2%) Query: 207 QVKTTLLGNEN---LRLANLDSLTQIPNRRKFFAQLDQICSRATANGQRFAVAILDLDGF 263 QV ++G N L A D LT +PNR ++ A NG+ FAV +DLDGF Sbjct: 245 QVLKRIVGRTNDKLLHFATHDVLTGLPNRALLADRIQHAVEVARRNGKTFAVLFMDLDGF 304 Query: 264 KAVNDLYGHTHGDQLLVEVGQRL-SALCGEEYLHLARLGGDEFAIIIDAGQSDDVLQQFG 322 KA+ND GH GD LLV V QR+ L GE+ + AR+GGDEF +++ S DV++Q Sbjct: 305 KAINDSLGHAVGDGLLVAVAQRIRQCLRGEDMV--ARIGGDEFVVVVGNLSSPDVVEQLS 362 Query: 323 ARICDALRRPFVLYKATVQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTL 382 I ALR+ F + AT+++ +S+G+A +P+ +L ++AD A+Y+ K+ R T Sbjct: 363 ENILAALRQDFQIDDATLRVTSSIGIAVYPNSGDSVDALMKNADAAMYEAKQSGRNTYRF 422 Query: 383 FSAQDKAQIQRNANVEQALRRADFERELSVVFQPIVRLDDCQPVAFEALARWHSATKGVV 442 F A R+ V QAL++A E++ + FQP R + EAL RW G + Sbjct: 423 FEPAMHASAMRHLQVRQALQQAIDEQQFRLHFQPKYRGASKELTGLEALLRWTHPQLGEM 482 Query: 443 APMEFIPAAERMGIINQLSVTLLKKALQAAATWP----PDMRLSFNLSANDINTSEGMSE 498 AP EFIP AER G I + +L+ + A W ++++ NLS + T + ++ Sbjct: 483 APTEFIPIAERSGQILCIGDWVLQAVCEQIARWDAAGMKPVKVALNLSPLQMRT-DLVAR 541 Query: 499 IVKVITGSGFCASRLDLEITETAVLQDLGKSRQLVTSLRQLGCGITLDDFGTGYASLSHL 558 IV+++ +G RL EITETA ++D+ +S++++ L+ LG I +DDFGTGY+SL++L Sbjct: 542 IVELVGAAGIAPQRLMFEITETAAMKDVERSQRVIGELQALGFDIAIDDFGTGYSSLAYL 601 Query: 559 HALPLTRIKIDKSFVADIEHDAVSHK-IIKSLLALSHDMQLACVVEGVETPQHLQSLREL 617 +IKID+ F + ++ D S + I+ +++AL+H +Q+ V EGVET L+ L+ L Sbjct: 602 AQFHCRQIKIDRFFTSRLDGDDHSGRAIVAAIIALAHALQMEVVAEGVETEGQLRELQLL 661 Query: 618 GAVYGQGYLFSVPLAADQV 636 QG+L P A V Sbjct: 662 HCDQVQGFLLGRPAEAPSV 680 >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 = 246 bits (627), Expect = 5e-66, Method: Compositional matrix adjust. Identities = 142/422 (33%), Positives = 229/422 (54%), Gaps = 6/422 (1%) Query: 215 NENLR-LANLDSLTQIPNRRKFFAQLDQICSRATANGQRFAVAILDLDGFKAVNDLYGHT 273 +E +R LA+ D LT +PNR + + A AV ++DLD FK +ND +GH Sbjct: 663 DERIRHLAHYDELTGLPNRFLCTQHVSNAITHAEHRNGMVAVILMDLDRFKNINDTFGHE 722 Query: 274 HGDQLLVEVGQRLSALCGEEYLHLARLGGDEFAIIIDAGQSDDVLQQFGARICDALRRPF 333 G+ +L E+ QR E + LAR+GGDEF +++D L + ++ R+PF Sbjct: 723 TGEAVLQEIAQRFRNSLRELDI-LARVGGDEFIVLVDDFDDPVQLGEIAQKLLTEARKPF 781 Query: 334 VLYKATVQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSAQDKAQIQR 393 ++ ++ S+G+AT+P +A +L ++AD A+Y+ K + FS + Sbjct: 782 IIDGQEAMLSVSIGIATYPGDGDNAQTLIKNADIAMYRAKHHGKDDYRFFSDEINTNTVE 841 Query: 394 NANVEQALRRADFERELSVVFQPIVRLDDCQPVAFEALARWHSATKGVVAPMEFIPAAER 453 +E LRRA E V +QP + L + + V EAL RW +G++ P EFI AE Sbjct: 842 RIALEAELRRAIERAEFVVHYQPKIELAEGRIVGAEALVRWQHPLRGLLPPGEFITLAEE 901 Query: 454 MGIINQLSVTLLKKALQAAATWPPDM----RLSFNLSANDINTSEGMSEIVKVITGSGFC 509 +I+Q+ + +L A + R+S NL+ + + +I +V+ G Sbjct: 902 TRLIDQIGLLVLDVACRDIGLMRQQQMTCGRISINLTGSQFGDERLLDDIKEVVDRHGTP 961 Query: 510 ASRLDLEITETAVLQDLGKSRQLVTSLRQLGCGITLDDFGTGYASLSHLHALPLTRIKID 569 S L+ EITE+ V+ + ++ ++ +R G I++DDFGTGY+SL++L P+ +KID Sbjct: 962 PSCLEFEITESMVMHNRERAIAIMDGIRAEGFTISIDDFGTGYSSLAYLKRFPVNTLKID 1021 Query: 570 KSFVADIEHDAVSHKIIKSLLALSHDMQLACVVEGVETPQHLQSLRELGAVYGQGYLFSV 629 KSF+ DI + S I+++++A+SH + L V EGVET + LQ+LRE G+ QGY FS Sbjct: 1022 KSFINDIPDNPNSSAIVQAIIAMSHALNLKVVTEGVETEKQLQALREFGSDEYQGYYFSK 1081 Query: 630 PL 631 P+ Sbjct: 1082 PV 1083 >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 = 239 bits (609), Expect = 7e-64, Method: Compositional matrix adjust. Identities = 151/426 (35%), Positives = 221/426 (51%), Gaps = 5/426 (1%) Query: 221 ANLDSLTQIPNRRKFFAQLDQICSRATANGQRFAVAILDLDGFKAVNDLYGHTHGDQLLV 280 A+ D+LT + NR L+Q A Q V +DLD FK VND GH GD LL Sbjct: 519 ASRDTLTGLINRHMLRHHLEQAIGVAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLR 578 Query: 281 EVGQRLSALCGEEYLHLARLGGDEFAIIIDAGQSDDVLQQFGARICDALRRPFVLYKATV 340 V RL A E +ARLGGDEF +I+ + + RI DA+ P L T+ Sbjct: 579 TVAGRLRAAV-READTVARLGGDEFIMILPEQDELTLDTRSLQRIMDAVAAPVTLGGHTL 637 Query: 341 QIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSAQDKAQIQRNANVEQA 400 + SVGVA +P+ D +L +HAD A+Y+GK+ R ++ Q +E Sbjct: 638 FMTCSVGVACYPNDGTDGETLIKHADIAMYRGKQTGRNNFQFYTPAMNEQALERLRIEGD 697 Query: 401 LRRADFERELSVVFQPIVRLDDCQPVAFEALARWHSATKGVVAPMEFIPAAERMGIINQL 460 LR A E + +QP V L + + EAL RW G+V+P FI AE G+I + Sbjct: 698 LRNALDHGEFLLHYQPKVDLASGRVIGSEALIRWQHPQLGMVSPARFIGLAEETGLILPI 757 Query: 461 SVTLLKKALQAAATWP----PDMRLSFNLSANDINTSEGMSEIVKVITGSGFCASRLDLE 516 +L+ A W D+ +S NLS + +S I V+ +G L+LE Sbjct: 758 GAWVLRAACTQCRQWQLGGYADISVSVNLSVGQFLQKDLVSSIADVLEDTGLPPESLELE 817 Query: 517 ITETAVLQDLGKSRQLVTSLRQLGCGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADI 576 +TE+ ++ D+ + ++ L++LG +++DDFGTGY+SL++L P+ +KID+SFV DI Sbjct: 818 LTESLMMTDVEHAIGILAGLKKLGVRLSIDDFGTGYSSLAYLKRFPIDVLKIDRSFVRDI 877 Query: 577 EHDAVSHKIIKSLLALSHDMQLACVVEGVETPQHLQSLRELGAVYGQGYLFSVPLAADQV 636 DA I S+++L+ ++L + EGVET + L LR G QGYLFS P+ AD+ Sbjct: 878 TIDADDAAITASIISLARHLKLRVIAEGVETDEQLDYLRHYGCDEIQGYLFSPPVPADKF 937 Query: 637 QSWLEH 642 + L Sbjct: 938 EQILRQ 943 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 0.326 0.138 0.414 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: 1,949,646 Number of extensions: 79549 Number of successful extensions: 415 Number of sequences better than 1.0e-08: 44 Number of HSP's gapped: 345 Number of HSP's successfully gapped: 44 Length of query: 653 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 562 Effective length of database: 1,188,985 Effective search space: 668209570 Effective search space used: 668209570 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)