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= 0005.0239.p (307 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311453|ref|YP_003775545.1| signal transduction containing ... 539 e-155 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 312 3e-86 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 293 9e-81 gi|300312026|ref|YP_003776118.1| signal transduction protein con... 291 4e-80 gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [... 255 3e-69 >gi|300311453|ref|YP_003775545.1| signal transduction containing PAS/GGDEF/EAL domains protein [Herbaspirillum seropedicae SmR1] Length = 683 Score = 539 bits (1389), Expect = e-155, Method: Compositional matrix adjust. Identities = 267/304 (87%), Positives = 283/304 (93%) Query: 1 MYPQDATDTETLLRLADIAMYRAKQGGENNEGGYAYYSEEMNRNTLDLLRIETGLLHAFE 60 +YP++ATDTETLLRLADIAMYRAKQGGENNEGGYA YSEEMNRNTLDLLRIETGLLHAFE Sbjct: 371 LYPENATDTETLLRLADIAMYRAKQGGENNEGGYACYSEEMNRNTLDLLRIETGLLHAFE 430 Query: 61 YNELLLYYQPKIDFAQGHITGAEALVRWQHPERGLLAPGDFIPIAEETGLIVQLSDWVLE 120 YNELLLYYQPK+D ITGAEALVRWQHPERGLL PG+FIPIAEETGLIVQLSDWVL+ Sbjct: 431 YNELLLYYQPKVDMQTLAITGAEALVRWQHPERGLLLPGEFIPIAEETGLIVQLSDWVLD 490 Query: 121 AACAQARQWKEAGLEPIRIAINVTAREFTRSLPDRVRAALSRHQLTGEWLELEITESMLM 180 A C QAR WK+AGL PIRIA+NVTAREFTRSLPDRV AAL RH L+GEWLELEITESMLM Sbjct: 491 AVCRQARAWKDAGLPPIRIALNVTAREFTRSLPDRVGAALERHMLSGEWLELEITESMLM 550 Query: 181 HSTDRVISIMEKICLLGVTISLDDFGTGYSSLSYLKRFPINTLKIDRSFTTGIPDDTNDC 240 HSTDRVISIMEKIC LG+T+SLDDFGTGYSSLSYLKRFPINTLKIDRSFT GIPDDTNDC Sbjct: 551 HSTDRVISIMEKICGLGITVSLDDFGTGYSSLSYLKRFPINTLKIDRSFTMGIPDDTNDC 610 Query: 241 AIASAIIGIAKQLRHKVIAEGVENMEQFNFLKEAGCNELQGYLFSRPVPAADFHLMLTEG 300 AIASAIIGIAKQLRHKVIAEGVE+ +QFNFL+EAGCNELQGY+FSRPVPA DFH ML EG Sbjct: 611 AIASAIIGIAKQLRHKVIAEGVEDEKQFNFLREAGCNELQGYIFSRPVPAPDFHAMLLEG 670 Query: 301 RKFS 304 RK + Sbjct: 671 RKLA 674 >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 = 312 bits (799), Expect = 3e-86, Method: Compositional matrix adjust. Identities = 151/301 (50%), Positives = 205/301 (68%), Gaps = 4/301 (1%) Query: 2 YPQDATDTETLLRLADIAMYRAKQGGENNEGGYAYYSEEMNRNTLDLLRIETGLLHAFEY 61 YP D TD ETL++ ADIAMYR KQ G NN + +Y+ MN L+ LRIE L +A ++ Sbjct: 648 YPNDGTDGETLIKHADIAMYRGKQTGRNN---FQFYTPAMNEQALERLRIEGDLRNALDH 704 Query: 62 NELLLYYQPKIDFAQGHITGAEALVRWQHPERGLLAPGDFIPIAEETGLIVQLSDWVLEA 121 E LL+YQPK+D A G + G+EAL+RWQHP+ G+++P FI +AEETGLI+ + WVL A Sbjct: 705 GEFLLHYQPKVDLASGRVIGSEALIRWQHPQLGMVSPARFIGLAEETGLILPIGAWVLRA 764 Query: 122 ACAQARQWKEAGLEPIRIAINVTAREF-TRSLPDRVRAALSRHQLTGEWLELEITESMLM 180 AC Q RQW+ G I +++N++ +F + L + L L E LELE+TES++M Sbjct: 765 ACTQCRQWQLGGYADISVSVNLSVGQFLQKDLVSSIADVLEDTGLPPESLELELTESLMM 824 Query: 181 HSTDRVISIMEKICLLGVTISLDDFGTGYSSLSYLKRFPINTLKIDRSFTTGIPDDTNDC 240 + I I+ + LGV +S+DDFGTGYSSL+YLKRFPI+ LKIDRSF I D +D Sbjct: 825 TDVEHAIGILAGLKKLGVRLSIDDFGTGYSSLAYLKRFPIDVLKIDRSFVRDITIDADDA 884 Query: 241 AIASAIIGIAKQLRHKVIAEGVENMEQFNFLKEAGCNELQGYLFSRPVPAADFHLMLTEG 300 AI ++II +A+ L+ +VIAEGVE EQ ++L+ GC+E+QGYLFS PVPA F +L + Sbjct: 885 AITASIISLARHLKLRVIAEGVETDEQLDYLRHYGCDEIQGYLFSPPVPADKFEQILRQD 944 Query: 301 R 301 R Sbjct: 945 R 945 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 293 bits (751), Expect = 9e-81, Method: Compositional matrix adjust. Identities = 141/298 (47%), Positives = 197/298 (66%), Gaps = 3/298 (1%) Query: 2 YPQDATDTETLLRLADIAMYRAKQGGENNEGGYAYYSEEMNRNTLDLLRIETGLLHAFEY 61 YP D D E+LL+ AD AMYRAK+ G NN +A + + N L++L L A + Sbjct: 396 YPADGKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQVSNRLEML---INLRRALDQ 452 Query: 62 NELLLYYQPKIDFAQGHITGAEALVRWQHPERGLLAPGDFIPIAEETGLIVQLSDWVLEA 121 +E LYYQPK+ G + GAEAL+RW+ P++G++ P FIP AEE GLIV + +WVL Sbjct: 453 DEFKLYYQPKLSLQDGRLIGAEALIRWESPQQGMVPPDRFIPFAEEAGLIVPIGEWVLRT 512 Query: 122 ACAQARQWKEAGLEPIRIAINVTAREFTRSLPDRVRAALSRHQLTGEWLELEITESMLMH 181 AC Q + W++AGL PI +A+N++ R+ +SLPD V L++ L WLELEITE+++M Sbjct: 513 ACRQNQAWQQAGLPPIPVAVNLSPRQLNQSLPDFVAGVLAQSGLAASWLELEITENVVMK 572 Query: 182 STDRVISIMEKICLLGVTISLDDFGTGYSSLSYLKRFPINTLKIDRSFTTGIPDDTNDCA 241 ++ ++ + + LG+ IS+DDFGTGYSSLSYL+RFP++ LKID+SF I D + A Sbjct: 573 DAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSFVRDIVRDADSAA 632 Query: 242 IASAIIGIAKQLRHKVIAEGVENMEQFNFLKEAGCNELQGYLFSRPVPAADFHLMLTE 299 I AII +A L +VIAEGVE+ EQ FLKE C+E+QGY F +P+ A F ++E Sbjct: 633 IVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACDEVQGYYFGKPMEVAVFTAWMSE 690 >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 = 291 bits (746), Expect = 4e-80, Method: Compositional matrix adjust. Identities = 149/297 (50%), Positives = 200/297 (67%), Gaps = 4/297 (1%) Query: 2 YPQDATDTETLLRLADIAMYRAKQGGENNEGGYAYYSEEMNRNTLDLLRIETGLLHAFEY 61 YP D + +TL++ ADIAMYRAK G+++ Y ++S+E+N NT++ + +E L A E Sbjct: 799 YPGDGDNAQTLIKNADIAMYRAKHHGKDD---YRFFSDEINTNTVERIALEAELRRAIER 855 Query: 62 NELLLYYQPKIDFAQGHITGAEALVRWQHPERGLLAPGDFIPIAEETGLIVQLSDWVLEA 121 E +++YQPKI+ A+G I GAEALVRWQHP RGLL PG+FI +AEET LI Q+ VL+ Sbjct: 856 AEFVVHYQPKIELAEGRIVGAEALVRWQHPLRGLLPPGEFITLAEETRLIDQIGLLVLDV 915 Query: 122 ACAQARQWKEAGLEPIRIAINVTAREF-TRSLPDRVRAALSRHQLTGEWLELEITESMLM 180 AC ++ + RI+IN+T +F L D ++ + RH LE EITESM+M Sbjct: 916 ACRDIGLMRQQQMTCGRISINLTGSQFGDERLLDDIKEVVDRHGTPPSCLEFEITESMVM 975 Query: 181 HSTDRVISIMEKICLLGVTISLDDFGTGYSSLSYLKRFPINTLKIDRSFTTGIPDDTNDC 240 H+ +R I+IM+ I G TIS+DDFGTGYSSL+YLKRFP+NTLKID+SF IPD+ N Sbjct: 976 HNRERAIAIMDGIRAEGFTISIDDFGTGYSSLAYLKRFPVNTLKIDKSFINDIPDNPNSS 1035 Query: 241 AIASAIIGIAKQLRHKVIAEGVENMEQFNFLKEAGCNELQGYLFSRPVPAADFHLML 297 AI AII ++ L KV+ EGVE +Q L+E G +E QGY FS+PVP A F +L Sbjct: 1036 AIVQAIIAMSHALNLKVVTEGVETEKQLQALREFGSDEYQGYYFSKPVPYAQFVQLL 1092 >gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 1036 Score = 255 bits (652), Expect = 3e-69, Method: Compositional matrix adjust. Identities = 141/306 (46%), Positives = 190/306 (62%), Gaps = 11/306 (3%) Query: 6 ATDTETLLRLADIAMYRAKQGGENNEGGYAYYSEEMNRNTLDLLRIETGLLHAFEYNELL 65 A + L++ AD+AMY+AK+ G N ++ M L+ +E GL A + N+LL Sbjct: 737 AASVDELMKQADLAMYKAKETGRN---ALRFFDPAMQTAVLERATLEAGLRKAIDGNQLL 793 Query: 66 LYYQPKIDFAQGHITGAEALVRWQHPERGLLAPGDFIPIAEETGLIVQLSDWVLEAACAQ 125 L+YQP++ G +TGAE LVRWQHP+RG++ PGDFIP+AEETGLI+ L +WVLE AC Q Sbjct: 794 LHYQPQV-VEGGRVTGAEVLVRWQHPQRGMVPPGDFIPLAEETGLILSLGNWVLETACRQ 852 Query: 126 ARQWK-EAGLEPIRIAINVTAREFTRSLPDRVRAALSRHQLTG---EWLELEITESMLMH 181 W + + + IA+NV+A + PD V+ L + TG L+LE+TES+L+ Sbjct: 853 LATWAAQPQMADLSIAVNVSAPQLRE--PDFVQTVLDTIERTGANPRRLKLELTESLLVD 910 Query: 182 STDRVISIMEKICLLGVTISLDDFGTGYSSLSYLKRFPINTLKIDRSFTTGIPDDTNDCA 241 + + +I M + GV SLDDFGTGYSSLSYLKR P+N LKID+SF + D ND + Sbjct: 911 NVEDIIQKMFALKAYGVEFSLDDFGTGYSSLSYLKRLPLNQLKIDQSFVRDVLIDPNDAS 970 Query: 242 IASAIIGIAKQLRHKVIAEGVENMEQFNFLKEAGCNELQGYLFSRPVPAADFHLMLTE-G 300 IA I+ +A+ L VIAEGVE Q +FL +AGC+ QGY F RPV F E Sbjct: 971 IAKTIVNLAQSLGLGVIAEGVETDAQRSFLADAGCHAYQGYFFCRPVTVEAFEKFAQEFD 1030 Query: 301 RKFSAA 306 +FSAA Sbjct: 1031 PQFSAA 1036 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 0.320 0.136 0.402 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: 897,764 Number of extensions: 35262 Number of successful extensions: 160 Number of sequences better than 1.0e-08: 18 Number of HSP's gapped: 131 Number of HSP's successfully gapped: 18 Length of query: 307 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 222 Effective length of database: 1,217,395 Effective search space: 270261690 Effective search space used: 270261690 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: 130 (54.7 bits)