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= 0036.0062.p (240 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313032|ref|YP_003777124.1| GGDEF domain-containing protein... 487 e-139 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 115 2e-27 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 107 1e-24 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 103 9e-24 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 101 6e-23 >gi|300313032|ref|YP_003777124.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 240 Score = 487 bits (1254), Expect = e-139, Method: Compositional matrix adjust. Identities = 240/240 (100%), Positives = 240/240 (100%) Query: 1 MSKVDLFEQEALALQRANDVLAMAAPDPSAYRTALQELVQHYGQLMRQSRRLISRSDRTE 60 MSKVDLFEQEALALQRANDVLAMAAPDPSAYRTALQELVQHYGQLMRQSRRLISRSDRTE Sbjct: 1 MSKVDLFEQEALALQRANDVLAMAAPDPSAYRTALQELVQHYGQLMRQSRRLISRSDRTE 60 Query: 61 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSPMSLVVLDIDFFKR 120 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSPMSLVVLDIDFFKR Sbjct: 61 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSPMSLVVLDIDFFKR 120 Query: 121 INDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQ 180 INDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQ Sbjct: 121 INDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQ 180 Query: 181 AIAGERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVESEETVTG 240 AIAGERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVESEETVTG Sbjct: 181 AIAGERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVESEETVTG 240 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 115 bits (289), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 72/180 (40%), Positives = 98/180 (54%), Gaps = 7/180 (3%) Query: 61 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSP-----MSLVVLDI 115 RE N L + L +L + D LTG LNR A F Q + + +++V+ DI Sbjct: 393 RERNSLAREREALITQLQTSSNTDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVVLFDI 452 Query: 116 DFFKRINDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLA 175 D FK+IND +GH GDA++R + + + V V+ R GGEEF ILLP +L A + Sbjct: 453 DHFKQINDSYGHQAGDAILRGVAQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAAAS 512 Query: 176 GRIRQAIAGERFGCLPAR--PVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVE 233 ++R A+A F R VT+SFGVA G E +AD ALY+AK+ GRNRVE Sbjct: 513 EKLRAALAAGEFEIDGGRRIRVTASFGVAAENGGPGLEHLIKQADIALYRAKKLGRNRVE 572 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 107 bits (266), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 70/170 (41%), Positives = 97/170 (57%), Gaps = 7/170 (4%) Query: 69 RLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSP-----MSLVVLDIDFFKRIND 123 R+++L+++L A D LTG NR + E + ++ +SL++LDID FK +ND Sbjct: 151 RVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHFKEVND 210 Query: 124 EFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQAIA 183 FGH TGDAV+ + LR V + GR GGEEF ++LP +E A +A ++R I Sbjct: 211 NFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLRLLI- 269 Query: 184 GERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVE 233 E + +P T SFGVA AG D AD ALY+AK +GRNRVE Sbjct: 270 -ENYNFVPVGRRTCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRVE 318 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 103 bits (258), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 66/181 (36%), Positives = 99/181 (54%), Gaps = 9/181 (4%) Query: 61 RELNQLNARLQQLSDEL---DYKARHDNLTGALNRGAVFER-----AHQVLQKSPMSLVV 112 +E+ + R+Q L +L R D LTG+LNR + E + + + +P+ + + Sbjct: 341 QEVEKAEERIQTLEQQLLQMGELVREDQLTGSLNRRGMDESLDREITNALRRDTPLCVAL 400 Query: 113 LDIDFFKRINDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAV 172 LD+D FKRIND GH TGD V+ +V +R T+ + VI R GGEEF +L+P A + AV Sbjct: 401 LDLDDFKRINDTHGHATGDEVLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDAV 460 Query: 173 VLAGRIRQAIAGERFGCLPAR-PVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNR 231 + R+++ + F R +T S GVA G RAD ALY+AK +G+NR Sbjct: 461 QIITRVQRELTKRIFMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKNAGKNR 520 Query: 232 V 232 + Sbjct: 521 I 521 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 101 bits (251), Expect = 6e-23, Method: Compositional matrix adjust. Identities = 65/174 (37%), Positives = 95/174 (54%), Gaps = 15/174 (8%) Query: 74 SDELDYKARHDNLTGALNRGAVFERAHQVL-----QKSPMSLVVLDIDFFKRINDEFGHP 128 ++ L + D LTG NR + +R + + +S +S + +DID FKR+ND+FGH Sbjct: 193 NERLKHIGLTDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQ 252 Query: 129 TGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQAIAGERF- 187 +GD V+RE+ AR++ + +GR GGEEF +LL E A +A RIR + Sbjct: 253 SGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVCSRGVM 312 Query: 188 --GCLPARPVTSSFGVAWAT------AGSDFEQAYAR-ADQALYQAKRSGRNRV 232 G +T+S G A T ++ +QA + ADQALYQAK +GRNRV Sbjct: 313 IEGSRDPLKITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRV 366 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 0.134 0.375 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: 684,417 Number of extensions: 25814 Number of successful extensions: 214 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 159 Number of HSP's successfully gapped: 39 Length of query: 240 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 157 Effective length of database: 1,226,865 Effective search space: 192617805 Effective search space used: 192617805 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: 129 (54.3 bits)