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= 0002.0237.p (656 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 ... 1040 0.0 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 254 1e-68 gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspi... 251 1e-67 gi|300312026|ref|YP_003776118.1| signal transduction protein con... 250 3e-67 gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies... 243 4e-65 >gi|300309883|ref|YP_003773975.1| GGDEF domain/EAL domain signal transduction protein [Herbaspirillum seropedicae SmR1] Length = 650 Score = 1040 bits (2689), Expect = 0.0, Method: Compositional matrix adjust. Identities = 510/647 (78%), Positives = 568/647 (87%) Query: 1 MSASSLMSMVRAYWRVGYDQPELLIAQYRAFSGKMPMMYLILLINSWALAQTYYPLAPHW 60 M SS MS +R YWRV +++P+L+IAQY+AFS KMPMMYLIL+INSWALA TY LAP W Sbjct: 1 MRLSSWMSSLRNYWRVDHERPQLVIAQYQAFSTKMPMMYLILIINSWALAYTYLDLAPLW 60 Query: 61 LSLYFPAMLTVLCVTRLIFWWRGRHVDPTPGMAAAALKRTNFLATPIALSFSLWSVMLFP 120 L LYFPA+L+VLC RL+FWWR RH+ PTP AA AL+RTN L PIALSFSLWS+MLFP Sbjct: 61 LGLYFPAVLSVLCSVRLLFWWRNRHLVPTPVAAAQALRRTNLLVAPIALSFSLWSIMLFP 120 Query: 121 YGDSYAQAHVAFYMGITVICCIFCLMYLRSAALSVALIVNGIFTVFFLNTHIPTFVAAAM 180 YG++YAQAHVAFYMGITVICCIFCLMYLRSAAL+ ALIVNGIFTVFFL+THIP FVAAA+ Sbjct: 121 YGNAYAQAHVAFYMGITVICCIFCLMYLRSAALTGALIVNGIFTVFFLSTHIPVFVAAAL 180 Query: 181 NVVLVTIGMLAIVNSHYNDFTRLIEAQVKTALLGNENLRLANLDSLTQIPNRRKFFAQLN 240 NVVLVTIGML IVNSHY DFTRL+EAQ++TA+L +ENL+LAN+DSLTQIPNRRKFFAQLN Sbjct: 181 NVVLVTIGMLVIVNSHYEDFTRLVEAQLRTAVLSDENLQLANVDSLTQIPNRRKFFAQLN 240 Query: 241 EICTRATGNGQRFAVAILDLDGFKAVNDLYGHTHGDQLLVEVGQRLTAVCLDERFHLARL 300 EIC RA G QRFAVAILDLDGFKAVNDLYGH+HGD+LL +VGQRL C D HLARL Sbjct: 241 EICARAHGAQQRFAVAILDLDGFKAVNDLYGHSHGDRLLEQVGQRLLTACRDPALHLARL 300 Query: 301 GGDEFSIIIDADLSNEVLSEFGDRICAALRRPFVLYKATVQIAASVGVATFPDMAVDASS 360 GGDEF++IID DLS+ L E G ++C LRR FVL KA VQIAASVGVATFPDMA DA++ Sbjct: 301 GGDEFALIIDRDLSDAALQEIGQQLCHTLRRAFVLDKAVVQIAASVGVATFPDMAADAAT 360 Query: 361 LYEHADYALYQGKRERRGTVTLFSEQDKAQIQRNANIEQALRLADFDRELSVFFQPIVRL 420 LYEHADYALYQGKRERRGTVTLFSE DKAQI+R +NIEQALRLADF+RELSVFFQPIVRL Sbjct: 361 LYEHADYALYQGKRERRGTVTLFSEHDKAQIRRKSNIEQALRLADFERELSVFFQPIVRL 420 Query: 421 DDCQPIAFEALARWHSAVKGSVAPMEFIPAAERMGIINQLSVILLKKALQAAASWPPSLR 480 DD Q IAFEALARWHS VKG+V+P+EFIPAAERMGIINQLSVILL+KAL AAASWP +R Sbjct: 421 DDGQVIAFEALARWHSTVKGAVSPVEFIPAAERMGIINQLSVILLRKALAAAASWPAQIR 480 Query: 481 LSFNLSANDINTSEGMAQIVQVIRSSGFNPARLDLEITETAVLQDLEKSRQLVTTLRQLG 540 LSFNLSANDIN+SEGMA+I+++IR SGF P+RLDLEITETA+LQDLEK+RQL+ +LRQLG Sbjct: 481 LSFNLSANDINSSEGMAEIIKLIRESGFCPSRLDLEITETALLQDLEKTRQLIHSLRQLG 540 Query: 541 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADIEHNAVSHKIVKSLLALTHDMQLAC 600 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADI +AVS KIVKSLLALT DM LAC Sbjct: 541 CGITLDDFGTGYASLSHLHALPLTRIKIDKSFVADIGQDAVSLKIVKSLLALTLDMDLAC 600 Query: 601 VVEGVETPAHLQSLRGLGAMYGQGYLFAVPLAADQVQPWLQSRQTAV 647 VVEG+ETP HL LR LGAMYGQGYL+A P+AAD V PWL R V Sbjct: 601 VVEGLETPQHLAVLRELGAMYGQGYLYARPMAADDVAPWLAQRAARV 647 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 254 bits (650), Expect = 1e-68, Method: Compositional matrix adjust. Identities = 161/432 (37%), Positives = 228/432 (52%), Gaps = 9/432 (2%) Query: 221 ANLDSLTQIPNRRKFFAQLNEICTRATGNGQRFAVAILDLDGFKAVNDLYGHTHGDQLLV 280 A D+LT +PNR L A G AVA +DLD FK +ND GH GD+LL Sbjct: 266 ATHDALTGLPNRNMLHEHLQRALRVARQKGALTAVAFVDLDQFKFINDSLGHQVGDELLK 325 Query: 281 EVGQRLTAVCLDERFHLARLGGDEFSIIIDADLSNEV-LSEFGDRICAALRRPFVLYKAT 339 V QRL A CL E +AR GGDEF +++ E ++E RI AA+ RP+ Sbjct: 326 TVAQRLQA-CLREADMVARQGGDEFVLVLQNQTEGEAGIAEVMQRILAAVARPWQAGDRE 384 Query: 340 VQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSEQDKAQIQRNANIEQ 399 Q+ AS+GV+ +P D SL +HAD A+Y+ K + R F+ +Q+ + Sbjct: 385 FQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQVSNRLEMLI 444 Query: 400 ALRLADFDRELSVFFQPIVRLDDCQPIAFEALARWHSAVKGSVAPMEFIPAAERMGIINQ 459 LR A E +++QP + L D + I EAL RW S +G V P FIP AE G+I Sbjct: 445 NLRRALDQDEFKLYYQPKLSLQDGRLIGAEALIRWESPQQGMVPPDRFIPFAEEAGLIVP 504 Query: 460 LSVILLKKALQAAASWP----PSLRLSFNLSANDINTSEGMAQIVQ-VIRSSGFNPARLD 514 + +L+ A + +W P + ++ NLS +N S + V V+ SG + L+ Sbjct: 505 IGEWVLRTACRQNQAWQQAGLPPIPVAVNLSPRQLNQS--LPDFVAGVLAQSGLAASWLE 562 Query: 515 LEITETAVLQDLEKSRQLVTTLRQLGCGITLDDFGTGYASLSHLHALPLTRIKIDKSFVA 574 LEITE V++D EKS + L++LG I++DDFGTGY+SLS+L P+ +KIDKSFV Sbjct: 563 LEITENVVMKDAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSFVR 622 Query: 575 DIEHNAVSHKIVKSLLALTHDMQLACVVEGVETPAHLQSLRGLGAMYGQGYLFAVPLAAD 634 DI +A S IVK++++L H + L + EGVE L+ QGY F P+ Sbjct: 623 DIVRDADSAAIVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACDEVQGYYFGKPMEVA 682 Query: 635 QVQPWLQSRQTA 646 W+ + A Sbjct: 683 VFTAWMSEQAQA 694 >gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 706 Score = 251 bits (642), Expect = 1e-67, Method: Compositional matrix adjust. Identities = 161/444 (36%), Positives = 252/444 (56%), Gaps = 10/444 (2%) Query: 207 QVKTALLGNEN---LRLANLDSLTQIPNRRKFFAQLNEICTRATGNGQRFAVAILDLDGF 263 QV ++G N L A D LT +PNR ++ A NG+ FAV +DLDGF Sbjct: 245 QVLKRIVGRTNDKLLHFATHDVLTGLPNRALLADRIQHAVEVARRNGKTFAVLFMDLDGF 304 Query: 264 KAVNDLYGHTHGDQLLVEVGQRLTAVCLDERFHLARLGGDEFSIIIDADLSNEVLSEFGD 323 KA+ND GH GD LLV V QR+ CL +AR+GGDEF +++ S +V+ + + Sbjct: 305 KAINDSLGHAVGDGLLVAVAQRIRQ-CLRGEDMVARIGGDEFVVVVGNLSSPDVVEQLSE 363 Query: 324 RICAALRRPFVLYKATVQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLF 383 I AALR+ F + AT+++ +S+G+A +P+ +L ++AD A+Y+ K+ R T F Sbjct: 364 NILAALRQDFQIDDATLRVTSSIGIAVYPNSGDSVDALMKNADAAMYEAKQSGRNTYRFF 423 Query: 384 SEQDKAQIQRNANIEQALRLADFDRELSVFFQPIVRLDDCQPIAFEALARWHSAVKGSVA 443 A R+ + QAL+ A +++ + FQP R + EAL RW G +A Sbjct: 424 EPAMHASAMRHLQVRQALQQAIDEQQFRLHFQPKYRGASKELTGLEALLRWTHPQLGEMA 483 Query: 444 PMEFIPAAERMGIINQLSVILLKKALQAAASWPPS----LRLSFNLSANDINTSEGMAQI 499 P EFIP AER G I + +L+ + A W + ++++ NLS + T + +A+I Sbjct: 484 PTEFIPIAERSGQILCIGDWVLQAVCEQIARWDAAGMKPVKVALNLSPLQMRT-DLVARI 542 Query: 500 VQVIRSSGFNPARLDLEITETAVLQDLEKSRQLVTTLRQLGCGITLDDFGTGYASLSHLH 559 V+++ ++G P RL EITETA ++D+E+S++++ L+ LG I +DDFGTGY+SL++L Sbjct: 543 VELVGAAGIAPQRLMFEITETAAMKDVERSQRVIGELQALGFDIAIDDFGTGYSSLAYLA 602 Query: 560 ALPLTRIKIDKSFVADIEHNAVSHK-IVKSLLALTHDMQLACVVEGVETPAHLQSLRGLG 618 +IKID+ F + ++ + S + IV +++AL H +Q+ V EGVET L+ L+ L Sbjct: 603 QFHCRQIKIDRFFTSRLDGDDHSGRAIVAAIIALAHALQMEVVAEGVETEGQLRELQLLH 662 Query: 619 AMYGQGYLFAVPLAADQVQPWLQS 642 QG+L P A V +Q+ Sbjct: 663 CDQVQGFLLGRPAEAPSVPGLVQA 686 >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 = 250 bits (638), Expect = 3e-67, Method: Compositional matrix adjust. Identities = 151/445 (33%), Positives = 240/445 (53%), Gaps = 17/445 (3%) Query: 215 NENLR-LANLDSLTQIPNRRKFFAQLNEICTRATGNGQRFAVAILDLDGFKAVNDLYGHT 273 +E +R LA+ D LT +PNR ++ T A AV ++DLD FK +ND +GH Sbjct: 663 DERIRHLAHYDELTGLPNRFLCTQHVSNAITHAEHRNGMVAVILMDLDRFKNINDTFGHE 722 Query: 274 HGDQLLVEVGQRLTAVCLDERFHLARLGGDEFSIIIDADLSNEV-LSEFGDRICAALRRP 332 G+ +L E+ QR L E LAR+GGDEF +++D D + V L E ++ R+P Sbjct: 723 TGEAVLQEIAQRFRN-SLRELDILARVGGDEFIVLVD-DFDDPVQLGEIAQKLLTEARKP 780 Query: 333 FVLYKATVQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSEQDKAQIQ 392 F++ ++ S+G+AT+P +A +L ++AD A+Y+ K + FS++ Sbjct: 781 FIIDGQEAMLSVSIGIATYPGDGDNAQTLIKNADIAMYRAKHHGKDDYRFFSDEINTNTV 840 Query: 393 RNANIEQALRLADFDRELSVFFQPIVRLDDCQPIAFEALARWHSAVKGSVAPMEFIPAAE 452 +E LR A E V +QP + L + + + EAL RW ++G + P EFI AE Sbjct: 841 ERIALEAELRRAIERAEFVVHYQPKIELAEGRIVGAEALVRWQHPLRGLLPPGEFITLAE 900 Query: 453 RMGIINQLSVILLKKALQAAASWPPSL----RLSFNLSANDINTSEGMAQIVQVIRSSGF 508 +I+Q+ +++L A + R+S NL+ + + I +V+ G Sbjct: 901 ETRLIDQIGLLVLDVACRDIGLMRQQQMTCGRISINLTGSQFGDERLLDDIKEVVDRHGT 960 Query: 509 NPARLDLEITETAVLQDLEKSRQLVTTLRQLGCGITLDDFGTGYASLSHLHALPLTRIKI 568 P+ L+ EITE+ V+ + E++ ++ +R G I++DDFGTGY+SL++L P+ +KI Sbjct: 961 PPSCLEFEITESMVMHNRERAIAIMDGIRAEGFTISIDDFGTGYSSLAYLKRFPVNTLKI 1020 Query: 569 DKSFVADIEHNAVSHKIVKSLLALTHDMQLACVVEGVETPAHLQSLRGLGAMYGQGYLFA 628 DKSF+ DI N S IV++++A++H + L V EGVET LQ+LR G+ QGY F+ Sbjct: 1021 DKSFINDIPDNPNSSAIVQAIIAMSHALNLKVVTEGVETEKQLQALREFGSDEYQGYYFS 1080 Query: 629 VP---------LAADQVQPWLQSRQ 644 P LA Q +P +RQ Sbjct: 1081 KPVPYAQFVQLLAGQQDRPQGLARQ 1105 >gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodiesterase A protein [Herbaspirillum seropedicae SmR1] Length = 1002 Score = 243 bits (619), Expect = 4e-65, Method: Compositional matrix adjust. Identities = 150/429 (34%), Positives = 221/429 (51%), Gaps = 10/429 (2%) Query: 219 RLANLDSLTQIPNRRKFFAQLNEICTRATGNGQRFAVAILDLDGFKAVNDLYGHTHGDQL 278 +LA DSLT +PNR Q + A N AV +DLD FK VND GH GD+L Sbjct: 556 QLAFYDSLTGLPNRSLLLVQAGQAIAAAERNCSTVAVMFIDLDRFKQVNDSLGHQAGDEL 615 Query: 279 LVEVGQRLTAVCLDERFHLARLGGDEFSIIIDADLSNEVLSEFGDRICAALRRPFVLYKA 338 L V RL + + RL GDEF +++ + L+E RI L P + Sbjct: 616 LRTVATRLQSQARRSDI-VGRLSGDEFVVVL-TQYDTQHLTEVVKRIQERLAMPCHINGT 673 Query: 339 TVQIAASVGVATFPDMAVDASSLYEHADYALYQGKRERRGTVTLFSEQDKAQIQRNANIE 398 + +AS+GVA FPD D +L AD A+YQ K RG + FSE+ + Q +E Sbjct: 674 PLNPSASIGVAIFPDNGNDIETLLHRADIAMYQAKAVNRGRFSFFSEEMNSMAQERLALE 733 Query: 399 QALRLADFDRELSVFFQPIVRLDDCQPIAFEALARWHSAVKGSVAPMEFIPAAERMGIIN 458 ALR A +L + FQP ++L D EALARWH G ++P FIP AE G+I Sbjct: 734 SALRDALRGGDLELNFQPQIKLHDQSLHGVEALARWHHPQLGQISPGRFIPIAEECGLIG 793 Query: 459 QLSVILLKKALQAAASWP------PSLRLSFNLSANDINTSEGMAQIVQVIRSSGFNPAR 512 +L L++A + W PS+ S NLSA + + + + ++R P+ Sbjct: 794 ELGKWALEEACFQLSDWRRRGIQVPSI--SVNLSATNFHDLDLPQFVTGLLRRYALEPSD 851 Query: 513 LDLEITETAVLQDLEKSRQLVTTLRQLGCGITLDDFGTGYASLSHLHALPLTRIKIDKSF 572 L LEITET ++ + Q + + LG + +DDFGTGY+SL +L LP++ +K+D+SF Sbjct: 852 LTLEITETVLMDTNPSTSQTIAAVHALGIPLAMDDFGTGYSSLGYLRKLPVSELKLDQSF 911 Query: 573 VADIEHNAVSHKIVKSLLALTHDMQLACVVEGVETPAHLQSLRGLGAMYGQGYLFAVPLA 632 V D+ + + +++ + ++L V EGVE L G QGYLF+ P++ Sbjct: 912 VRDMAKDPAVSALTNAVIRIGESLKLTVVAEGVEDAEQYALLISQGCDVAQGYLFSRPMS 971 Query: 633 ADQVQPWLQ 641 AD ++ W++ Sbjct: 972 ADALENWVR 980 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 0.409 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: 1,962,572 Number of extensions: 79962 Number of successful extensions: 422 Number of sequences better than 1.0e-08: 42 Number of HSP's gapped: 357 Number of HSP's successfully gapped: 42 Length of query: 656 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 565 Effective length of database: 1,188,985 Effective search space: 671776525 Effective search space used: 671776525 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)