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= 0016.0006.p (238 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 482 e-137 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 127 1e-30 gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies... 98 7e-22 gi|300312514|ref|YP_003776606.1| GGDEF domain-containing protein... 93 2e-20 gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein... 90 1e-19 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 482 bits (1241), Expect = e-137, Method: Compositional matrix adjust. Identities = 236/238 (99%), Positives = 236/238 (99%) Query: 1 MTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERA 60 MTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERA Sbjct: 87 MTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERA 146 Query: 61 LLKDLAAMVEQELTAVRMATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQ 120 LLKDLAAMVEQELTAVRMATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQ Sbjct: 147 LLKDLAAMVEQELTAVRMATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQ 206 Query: 121 FKQINDRFGHAEGDAALVDFAALLSSSFRESDVIGRLGGDEFAVFLTNADLAESDTVLAH 180 FKQINDRFGHAEGDAALVDFAALLSSSFRESDVI RLGGDEFAVFLTNADLAESDTVLAH Sbjct: 207 FKQINDRFGHAEGDAALVDFAALLSSSFRESDVIARLGGDEFAVFLTNADLAESDTVLAH 266 Query: 181 FAQSVREFNVLRPRPYALAYSVGVVQYDAARHADLAALQHSADALMYERKKARRAQAG 238 FAQSVREFNVLRPRPYALAYSVGVVQYDAARHADLAALQHSADALMYERKK RRAQAG Sbjct: 267 FAQSVREFNVLRPRPYALAYSVGVVQYDAARHADLAALQHSADALMYERKKTRRAQAG 324 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 127 bits (318), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 81/240 (33%), Positives = 109/240 (45%), Gaps = 10/240 (4%) Query: 1 MTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERA 60 +T + D D RF + G P +RFYA P+ S +G GTLC++D R A +R Sbjct: 117 LTEISDLQADQRFCDSALANGNPRVRFYAAVPLVSSNGDIFGTLCVMDREARVLTAAQRD 176 Query: 61 LLKDLAAMVEQELTAVR-------MATIDELTGISNRRGFDALARHALANSRRMDWPACM 113 L +E +L A R D LTGI NRR FD R R P + Sbjct: 177 AFLKLGRQLEGQLEARRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNARPLSL 236 Query: 114 LYFDLDQFKQINDRFGHAEGDAALVDFAALLSSSFRESDVIGRLGGDEFAVFLTNADLAE 173 L D+D FKQ ND +GH GDA L +L S R SD + R GGDEF++ L + D Sbjct: 237 LMVDVDYFKQYNDTYGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPDTDEIG 296 Query: 174 SDTVLAHFAQSVREFNVLRPRPYALAYSVGVVQYDAARHADLAALQHSADALMYERKKAR 233 + V +V + + + S+G + D +AL +AD MY RK R Sbjct: 297 ALQVAERIKAAVEQAHW---EHCDIEISLGAATVTPSEMCDFSALLQAADQAMYRRKHGR 353 >gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodiesterase A protein [Herbaspirillum seropedicae SmR1] Length = 1002 Score = 97.8 bits (242), Expect = 7e-22, Method: Compositional matrix adjust. Identities = 76/242 (31%), Positives = 108/242 (44%), Gaps = 8/242 (3%) Query: 2 TIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERAL 61 I D DP ++ + +R PIKS SG +GT P A L Sbjct: 474 VISEDIQTDPHWNDYKHLALPHGLRACWSTPIKSASGQVIGTFGFYYRHPGQPSAFHHLL 533 Query: 62 LK---DLAAM-VEQELTAVR---MATIDELTGISNRRGFDALARHALANSRRMDWPACML 114 ++ L A+ +E+E R +A D LTG+ NR A A+A + R ++ Sbjct: 534 VEAGLHLCALAIEREDARARIHQLAFYDSLTGLPNRSLLLVQAGQAIAAAERNCSTVAVM 593 Query: 115 YFDLDQFKQINDRFGHAEGDAALVDFAALLSSSFRESDVIGRLGGDEFAVFLTNADLAES 174 + DLD+FKQ+ND GH GD L A L S R SD++GRL GDEF V LT D Sbjct: 594 FIDLDRFKQVNDSLGHQAGDELLRTVATRLQSQARRSDIVGRLSGDEFVVVLTQYDTQHL 653 Query: 175 DTVLAHFAQSVREFNVLRPRPYALAYSVGVVQYDAARHADLAALQHSADALMYERKKARR 234 V+ + + + P + S+GV + + D+ L H AD MY+ K R Sbjct: 654 TEVVKRIQERLAMPCHINGTPLNPSASIGVAIFPDNGN-DIETLLHRADIAMYQAKAVNR 712 Query: 235 AQ 236 + Sbjct: 713 GR 714 >gi|300312514|ref|YP_003776606.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 93.2 bits (230), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 58/153 (37%), Positives = 86/153 (56%), Gaps = 8/153 (5%) Query: 82 DELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQFKQINDRFGHAEGDAALVDFA 141 D LTGI NRR F L + D AC L D+D FK+IND FGHA GD AL+ A Sbjct: 195 DPLTGIDNRRRFMQQLPIILQAGQPSD--ACFLMIDIDNFKKINDDFGHASGDEALILTA 252 Query: 142 ALLSSSFRESDVIGRLGGDEFAVFLTNADLAESDTVLAHFAQSVREFNVLRPRPYALAYS 201 + S+ E +GR+GG+EF + L+ LA ++ V A Q VR+ ++ RP L S Sbjct: 253 RAMQSALSEG-ALGRMGGEEFGIALSGGGLAHAEQVAAKLLQEVRQIHI-HARP--LTVS 308 Query: 202 VGVVQYDAARHADLAALQHSADALMYERKKARR 234 +G+ + A H+ ++ + +AD +Y+ K+A + Sbjct: 309 IGIAR--ATDHSSVSKVLSAADQALYQAKRAGK 339 >gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 384 Score = 90.1 bits (222), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 62/165 (37%), Positives = 87/165 (52%), Gaps = 11/165 (6%) Query: 77 RMATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQFKQINDRFGHAEGDAA 136 ++A D LTG+ NRR A A +A + + P +L D+D FKQ+ND GHA GD Sbjct: 217 QLAARDPLTGLLNRRALQARAPALIAQASQAH-PGALLLIDIDNFKQVNDLHGHAAGDKL 275 Query: 137 LVDFAALLSSSFRESDVIGRLGGDEFAVFLTNADLAESDTVLAHFAQSVREFNVLRPR-- 194 L + LL + + RLGGDEFA+ L + A+ +AH + +R+ V + Sbjct: 276 LEALSTLLREVLPDDALAARLGGDEFAILLPDGRQAQ----VAHIGEQLRQAFVHVTQTA 331 Query: 195 ---PYALAYSVGVVQYDAARHADLAALQHSADALMYERKKARRAQ 236 P A++ SVGV + A DLA L ADA +YE K+A R Q Sbjct: 332 VATPEAVSLSVGVSLFSTAA-LDLAGLMARADAALYEAKRAGRNQ 375 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 0.323 0.136 0.395 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: 711,475 Number of extensions: 28149 Number of successful extensions: 168 Number of sequences better than 1.0e-08: 44 Number of HSP's gapped: 139 Number of HSP's successfully gapped: 44 Length of query: 238 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 156 Effective length of database: 1,231,600 Effective search space: 192129600 Effective search space used: 192129600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 129 (54.3 bits)