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= 0002.0367.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... 318 2e-88 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 110 1e-25 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 103 9e-24 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 103 1e-23 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 = 318 bits (816), Expect = 2e-88, Method: Compositional matrix adjust. Identities = 168/233 (72%), Positives = 191/233 (81%) Query: 1 MSDIDLFEAETAVLANANDVLANDVVSANEYRVALKELVQGYGQLMRESRRLIARSDRTE 60 MS +DLFE E L ANDVLA + YR AL+ELVQ YGQLMR+SRRLI+RSDRTE Sbjct: 1 MSKVDLFEQEALALQRANDVLAMAAPDPSAYRTALQELVQHYGQLMRQSRRLISRSDRTE 60 Query: 61 RELNLLNSRLKQLSDELDYKARHDNLTGALNRGAVFDLAHRFLQDSSLSLIVLDIDFFKR 120 RELN LN+RL+QLSDELDYKARHDNLTGALNRGAVF+ AH+ LQ S +SL+VLDIDFFKR Sbjct: 61 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSPMSLVVLDIDFFKR 120 Query: 121 INDEFGHPAGDAVIRELVNRLRKSLDGKGEIGRVGGEEFTVLLRNASLDEAVQLAEKVRL 180 INDEFGHP GDAVIRELV RLR ++DG G IGRVGGEEFT+LL +L+ AV LA ++R Sbjct: 121 INDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQ 180 Query: 181 TIAGELFSGLPSRPVTASFGVSWSKAGSDFENAYARADAALYKAKHGGRNRVE 233 IAGE F LP+RPVT+SFGV+W+ AGSDFE AYARAD ALY+AK GRNRVE Sbjct: 181 AIAGERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVE 233 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 110 bits (275), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 74/183 (40%), Positives = 104/183 (56%), Gaps = 13/183 (7%) Query: 61 RELNLLNSRLKQLSDELDYKARHDNLTGALNRGAVFD-------LAHRFLQDSSLSLIVL 113 RE N L + L +L + D LTG LNR A F +A R+ ++ L++++ Sbjct: 393 RERNSLAREREALITQLQTSSNTDFLTGVLNRRAFFTHGQQQMTVAKRYGRE--LAVVLF 450 Query: 114 DIDFFKRINDEFGHPAGDAVIRELVNRLRKSLDGKGEIGRVGGEEFTVLLRNASLDEAVQ 173 DID FK+IND +GH AGDA++R + + + L + R GGEEF +LL +SL +A Sbjct: 451 DIDHFKQINDSYGHQAGDAILRGVAQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAA 510 Query: 174 LAEKVRLTIAG---ELFSGLPSRPVTASFGVSWSKAGSDFENAYARADAALYKAKHGGRN 230 +EK+R +A E+ G R VTASFGV+ G E+ +AD ALY+AK GRN Sbjct: 511 ASEKLRAALAAGEFEIDGGRRIR-VTASFGVAAENGGPGLEHLIKQADIALYRAKKLGRN 569 Query: 231 RVE 233 RVE Sbjct: 570 RVE 572 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 103 bits (258), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 72/176 (40%), Positives = 103/176 (58%), Gaps = 11/176 (6%) Query: 65 LLNSRLKQLSDELDYKARHDNLTGALNRGAV-------FDLAHRFLQDSSLSLIVLDIDF 117 L R+++L+++L A D LTG NR + + A R+ +LSLI+LDID Sbjct: 147 LAEQRVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRY--GKNLSLILLDIDH 204 Query: 118 FKRINDEFGHPAGDAVIRELVNRLRKSLDGKGEIGRVGGEEFTVLLRNASLDEAVQLAEK 177 FK +ND FGH GDAV+ + LR ++ GR GGEEF ++L +++A ++AEK Sbjct: 205 FKEVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEK 264 Query: 178 VRLTIAGELFSGLPSRPVTASFGVSWSKAGSDFENAYARADAALYKAKHGGRNRVE 233 +RL I E ++ +P T SFGV+ +AG D AD ALY+AK+ GRNRVE Sbjct: 265 LRLLI--ENYNFVPVGRRTCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRVE 318 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 103 bits (258), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 65/188 (34%), Positives = 101/188 (53%), Gaps = 10/188 (5%) Query: 57 DRTERELNLLNSRLKQLSDELDYKARHDNLTGALNRGAV-----FDLAHRFLQDSSLSLI 111 ++ E + L +L Q+ + + R D LTG+LNR + ++ + +D+ L + Sbjct: 344 EKAEERIQTLEQQLLQMGELV----REDQLTGSLNRRGMDESLDREITNALRRDTPLCVA 399 Query: 112 VLDIDFFKRINDEFGHPAGDAVIRELVNRLRKSLDGKGEIGRVGGEEFTVLLRNASLDEA 171 +LD+D FKRIND GH GD V+ +V +R++L I R GGEEF VL+ + +A Sbjct: 400 LLDLDDFKRINDTHGHATGDEVLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDA 459 Query: 172 VQLAEKVRLTIAGELFSGLPSR-PVTASFGVSWSKAGSDFENAYARADAALYKAKHGGRN 230 VQ+ +V+ + +F R +T S GV+ G + RAD ALYKAK+ G+N Sbjct: 460 VQIITRVQRELTKRIFMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKNAGKN 519 Query: 231 RVERDAPP 238 R+ PP Sbjct: 520 RIVFADPP 527 >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 = 66/166 (39%), Positives = 98/166 (59%), Gaps = 19/166 (11%) Query: 84 DNLTGALNRGAVF-----DLAHRFLQDSSLSLIVLDIDFFKRINDEFGHPAGDAVIRELV 138 D LTG NR + ++A S+LS + +DID FKR+ND+FGH +GD V+RE+ Sbjct: 203 DPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQSGDDVLREVA 262 Query: 139 NRLRKSLDGKGEIGRVGGEEFTVLLRNASLDEAVQLAEKVRLTIA--GELFSGLPSR--- 193 R++K L +GR GGEEF VLL +A+ ++A ++AE++R + G + G SR Sbjct: 263 ARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVCSRGVMIEG--SRDPL 320 Query: 194 PVTASFGVSW------SKAGSDFENAYAR-ADAALYKAKHGGRNRV 232 +TAS G + S+ ++ + A + AD ALY+AK GRNRV Sbjct: 321 KITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRV 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 0.318 0.135 0.373 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: 637,175 Number of extensions: 24431 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 140 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 129 (54.3 bits)