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= 0013.0041.p (269 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 278 3e-76 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 123 2e-29 gi|300312843|ref|YP_003776935.1| response regulator containing a... 107 1e-24 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 101 5e-23 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 91 1e-19 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 278 bits (711), Expect = 3e-76, Method: Compositional matrix adjust. Identities = 137/232 (59%), Positives = 180/232 (77%), Gaps = 1/232 (0%) Query: 3 IARSVAEN-SGNFVSYRDGDNREQLAAFAPVPRTSWMVVNVTPLNALNAEVRSIRNKIIL 61 I S+A+ +F++Y D AA A +P TSW V ++TP + LNA+ RS+R+KII Sbjct: 249 ITESLAQGRDSDFIAYVGADKTPYYAAIARLPHTSWWVASITPSDRLNADTRSVRDKIIA 308 Query: 62 IGVLCFILALVLSFIIARSISLPLKQLVGVMKATRTGNYLIRMDYEGKDEITELSQRFND 121 IG++CF ++L+LS +I+RSIS+PL++LV MK +G+ +R++ G DEI LS++FN+ Sbjct: 309 IGLVCFAVSLLLSALISRSISVPLQRLVAAMKEAGSGDTTVRVEQHGNDEIAVLSRKFNE 368 Query: 122 MASKVHQHNERLEELVAERTRELEQANRQLEALSATDSLTGIANRRRFDEALSGELRRAV 181 MA K+ Q+ E LEE V RTRELE+ANR+LEALSATD LTG+ANRRRFDEAL+ E+RRAV Sbjct: 369 MAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAV 428 Query: 182 RSQKPLALMMLDVDYFKNYNDRYGHLAGDDCLRTIARVMRASSRRATDLAAR 233 RS + LAL+MLDVDYFK YNDRYGHLAGD+CLR +ARV++ SSRRATDL AR Sbjct: 429 RSGQSLALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVAR 480 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 123 bits (308), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 80/206 (38%), Positives = 105/206 (50%), Gaps = 37/206 (17%) Query: 57 NKIILIGVLCFILALVLSFIIARSISLPLKQLVGV--------MKATRTGNYLIRMDYEG 108 N +I VL FI ++ R + P+ +L M+ R+ I + Sbjct: 78 NSVIKTLVLWFIFL----YVFRRWLGQPITRLADFVRELDLNQMETPRS----IHLPGRR 129 Query: 109 KDEITELSQRFNDMASKVHQH---------------------NERLEELVAERTRELEQA 147 + E+ L+ N M +K+H+H N LE +AERTR+L QA Sbjct: 130 RHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIAERTRDLAQA 189 Query: 148 NRQLEALSATDSLTGIANRRRFDEALSGELRRAVRSQKPLALMMLDVDYFKNYNDRYGHL 207 N QL +LS TD LTGIANRR FDE L E RR++R PL L +DVD+FK YND YGHL Sbjct: 190 NEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHL 249 Query: 208 AGDDCLRTIARVMRASSRRATDLAAR 233 AGD LR +A+ +R S R D AR Sbjct: 250 AGDAVLRQVAQTLRQSIARVGDTVAR 275 >gi|300312843|ref|YP_003776935.1| response regulator containing a CheY-like receiver and a GGDEF domains protein [Herbaspirillum seropedicae SmR1] Length = 525 Score = 107 bits (266), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 54/102 (52%), Positives = 68/102 (66%) Query: 132 RLEELVAERTRELEQANRQLEALSATDSLTGIANRRRFDEALSGELRRAVRSQKPLALMM 191 R E+ + EL+ AN +LE L+ D LTG+ANRR D L E +RA RS LAL+M Sbjct: 324 RAEDRALQAMGELQMANHRLEMLAHQDGLTGLANRRHLDTMLETEFKRAERSGAALALIM 383 Query: 192 LDVDYFKNYNDRYGHLAGDDCLRTIARVMRASSRRATDLAAR 233 +DVD+FK YND YGH AGD+CLR +A V++ RR DLAAR Sbjct: 384 IDVDFFKQYNDLYGHQAGDECLRRVAGVLKERQRRPGDLAAR 425 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 101 bits (252), Expect = 5e-23, Method: Compositional matrix adjust. Identities = 49/95 (51%), Positives = 68/95 (71%) Query: 139 ERTRELEQANRQLEALSATDSLTGIANRRRFDEALSGELRRAVRSQKPLALMMLDVDYFK 198 E ++L+++N +L+ L+ TD LTGIANRR FD+ L E RRA R LAL+++DVD+FK Sbjct: 158 ESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFK 217 Query: 199 NYNDRYGHLAGDDCLRTIARVMRASSRRATDLAAR 233 YND YGH+AGD LR +A + +S +R DL+AR Sbjct: 218 LYNDNYGHVAGDAVLRQVAEALDSSIQRPADLSAR 252 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 48/91 (52%), Positives = 62/91 (68%), Gaps = 1/91 (1%) Query: 143 ELEQANRQLEALSATDSLTGIANRRRFDEALSGELRRAVRSQKPLALMMLDVDYFKNYND 202 E +A ++LE + TD+LTGI NRR FD L E R +R+ +PL+L+M+DVDYFK YND Sbjct: 190 EARRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNARPLSLLMVDVDYFKQYND 249 Query: 203 RYGHLAGDDCLRTIARVMRASSRRATDLAAR 233 YGH AGD L + RV+R S RA+D AR Sbjct: 250 TYGHPAGDALLTQLGRVLR-SPLRASDFLAR 279 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 0.324 0.135 0.382 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: 642,212 Number of extensions: 23739 Number of successful extensions: 244 Number of sequences better than 1.0e-08: 32 Number of HSP's gapped: 239 Number of HSP's successfully gapped: 32 Length of query: 269 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 185 Effective length of database: 1,222,130 Effective search space: 226094050 Effective search space used: 226094050 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: 130 (54.7 bits)