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= 0027.0108.p (278 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 358 e-100 gi|300313030|ref|YP_003777122.1| two component response regulato... 105 3e-24 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 84 1e-17 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 83 2e-17 gi|300312843|ref|YP_003776935.1| response regulator containing a... 81 8e-17 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 358 bits (919), Expect = e-100, Method: Compositional matrix adjust. Identities = 172/220 (78%), Positives = 197/220 (89%) Query: 20 LPPADYKIMVLLVDDQAMVGEAIRRALLTESDIDFHFCPRAEDALGIAEKTQPTVILQDL 79 LP +YKIMVLLVDDQ MVGEAIRRAL E IDFHFC RAE+AL +AE+T+PTVILQDL Sbjct: 15 LPADEYKIMVLLVDDQPMVGEAIRRALANEPHIDFHFCTRAEEALTVAERTRPTVILQDL 74 Query: 80 VMPGVDGLTLVKQYRSNPLTMDIPIIVLSSKEDALVKRDAFATGVNDYMVKLPDTIELIA 139 VMPGVDG+TLV+QYR++ + +++PIIVLSS++DA+VKRDAFA G NDYMVKLPD IEL+A Sbjct: 75 VMPGVDGMTLVRQYRASAVLVNVPIIVLSSRDDAVVKRDAFAGGANDYMVKLPDVIELVA 134 Query: 140 RIRYHSRSYNNLLQRDAAYRALRESQQQLQKSNFELQRLTNTDGLTSIANRRYFDDYLNA 199 RIRYHSRSY NLLQRDAAY ALRESQQQLQKSNFELQRLTNTDGLT IANRRYFDDYL A Sbjct: 135 RIRYHSRSYINLLQRDAAYSALRESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGA 194 Query: 200 EWKRAKRVQQEISLLLIDVDNFKLYNDNYGHVAGNSXLRR 239 EW+RA+R +++LLLIDVD FKLYNDNYGHVAG++ LR+ Sbjct: 195 EWRRARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVLRQ 234 >gi|300313030|ref|YP_003777122.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 105 bits (263), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 79/233 (33%), Positives = 114/233 (48%), Gaps = 24/233 (10%) Query: 29 VLLVDDQAMVGEAIRRALLTESDIDFHFCPRAEDALGIAEKTQPTVILQDLVMPGVDGLT 88 +LL DDQ + + ALL + D + A+ ++E+ P +IL D+ MPG++G Sbjct: 18 ILLCDDQP-INIRLVNALL-KGDYEIFMATSGLQAIELSERVTPDLILMDVNMPGLNGYD 75 Query: 89 LVKQYRSNPLTMDIPIIVLSSKEDALVKRDAFATGVNDYMVKLPDTIELIARIRYHSRSY 148 + + N LT+ IP+I L+ + + AF G D++ K + L AR+ H Sbjct: 76 TCARLKQNTLTLGIPVIFLTGLKSEEDEVKAFEVGGVDFISKPINGTVLKARVLTHL--- 132 Query: 149 NNLLQRDAAYRALRESQQQLQKSNFELQRLTNTDGLTSIANRRYFDDYLNAEWKRAKRVQ 208 +LQ S+F L + TD LT + NRR FD L +W+ KR Sbjct: 133 ----------------TLKLQ-SDFYLN-IAVTDSLTGLFNRRKFDSELAEKWELCKRSG 174 Query: 209 QEISLLLIDVDNFKLYNDNYGHVAGNSXLRRRRVRGHPAGHRCRRC-ARCGRE 260 Q +SLLLID+D+FK YND+YGH AG+ L HR C AR G E Sbjct: 175 QAMSLLLIDIDHFKQYNDHYGHQAGDHCLAEVAHTIRSNFHRSYDCVARYGGE 227 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 84.0 bits (206), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 44/99 (44%), Positives = 65/99 (65%), Gaps = 5/99 (5%) Query: 145 SRSYNNLLQRDAAYRALRESQ-----QQLQKSNFELQRLTNTDGLTSIANRRYFDDYLNA 199 SR +N + + R + E Q ++L+++N +L+ L+ TDGLT +ANRR FD+ L Sbjct: 363 SRKFNEMAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDEALAN 422 Query: 200 EWKRAKRVQQEISLLLIDVDNFKLYNDNYGHVAGNSXLR 238 E +RA R Q ++LL++DVD FK YND YGH+AG+ LR Sbjct: 423 EMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECLR 461 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 83.2 bits (204), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 57/149 (38%), Positives = 79/149 (53%), Gaps = 19/149 (12%) Query: 131 LPDTIEL-IARIRYHSRS----YNNLLQRDAAYRALR--------ESQQQLQKSNFELQR 177 L D I L +A++ H+ Y L Q + AL E + L ++N +L+ Sbjct: 136 LADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIAERTRDLAQANEQLRS 195 Query: 178 LTNTDGLTSIANRRYFDDYLNAEWKRAKRVQQEISLLLIDVDNFKLYNDNYGHVAGNSXL 237 L+ TDGLT IANRR FD+ L EW+R+ R + L IDVD FK YND+YGH+AG++ L Sbjct: 196 LSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVL 255 Query: 238 RRRRVRGHPAGHRCRRCARCGREITRDGG 266 R+ A + AR G + R GG Sbjct: 256 RQ------VAQTLRQSIARVGDTVARYGG 278 >gi|300312843|ref|YP_003776935.1| response regulator containing a CheY-like receiver and a GGDEF domains protein [Herbaspirillum seropedicae SmR1] Length = 525 Score = 81.3 bits (199), Expect = 8e-17, Method: Compositional matrix adjust. Identities = 50/141 (35%), Positives = 77/141 (54%), Gaps = 15/141 (10%) Query: 104 IIVLSSKEDALV--KRDAFATGVNDYMVKLPDTI---ELIARIRYHSRSYNNLLQRDAAY 158 ++V ++E+AL K+ F G ++ + L+ +I R+ + LQ Sbjct: 277 LVVTLAREEALADWKQQTFVYGAAVLLLLAIIGVFGWRLVGQIELRLRAEDRALQ----- 331 Query: 159 RALRESQQQLQKSNFELQRLTNTDGLTSIANRRYFDDYLNAEWKRAKRVQQEISLLLIDV 218 + +LQ +N L+ L + DGLT +ANRR+ D L E+KRA+R ++L++IDV Sbjct: 332 -----AMGELQMANHRLEMLAHQDGLTGLANRRHLDTMLETEFKRAERSGAALALIMIDV 386 Query: 219 DNFKLYNDNYGHVAGNSXLRR 239 D FK YND YGH AG+ LRR Sbjct: 387 DFFKQYNDLYGHQAGDECLRR 407 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 0.137 0.400 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: 801,962 Number of extensions: 29610 Number of successful extensions: 215 Number of sequences better than 1.0e-08: 22 Number of HSP's gapped: 243 Number of HSP's successfully gapped: 22 Length of query: 278 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 194 Effective length of database: 1,222,130 Effective search space: 237093220 Effective search space used: 237093220 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 (21.9 bits) S2: 130 (54.7 bits)