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= 0005.0001.p (241 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309921|ref|YP_003774013.1| LysR family transcription regul... 113 1e-26 gi|300313769|ref|YP_003777861.1| transcription regulator protein... 108 4e-25 gi|300310278|ref|YP_003774370.1| transcription regulator protein... 107 7e-25 gi|300311233|ref|YP_003775325.1| LysR family transcription regul... 102 4e-23 gi|300311929|ref|YP_003776021.1| LysR family transcription regul... 91 7e-20 >gi|300309921|ref|YP_003774013.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 113 bits (283), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 63/160 (39%), Positives = 97/160 (60%) Query: 11 FCHVAKAGSLSKAAKALSLSRSALSHRIKAIEGRLGCQLLMRTTRRVGLTEAGYRLAEHA 70 F VA GS KAA+AL +S++A+S + +E RLG +L+ RTTRR+ LTEAG E Sbjct: 10 FIAVADLGSFVKAAEALGISKAAVSRTVLELEARLGSRLMQRTTRRLSLTEAGALYLERC 69 Query: 71 DRMADILKDANMLAHGLNEDTAGLVRISAPLTLGSVWLKPLLMSYMQANPRVQVDLRFSE 130 ++ L++A+ L + GL+RI+APLT G + L PL +++ +P + +D+ S+ Sbjct: 70 KQIVAALEEADDLLSSGSAKPTGLLRINAPLTFGVLHLAPLWPMFLERHPEISLDITLSD 129 Query: 131 QAVDITSDPVDLAIRVASTLPDDVVAKKLFGISWRLCASP 170 + VDI + D+AIR+A +V +KL S +CASP Sbjct: 130 RIVDIIDEGYDMAIRIARLSDSTLVHRKLTSTSLHVCASP 169 >gi|300313769|ref|YP_003777861.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 318 Score = 108 bits (270), Expect = 4e-25, Method: Compositional matrix adjust. Identities = 63/168 (37%), Positives = 97/168 (57%), Gaps = 1/168 (0%) Query: 4 DANSLIIFCHVAKAGSLSKAAKALSLSRSALSHRIKAIEGRLGCQLLMRTTRRVGLTEAG 63 D N L +F V GS S AA+AL+ +S +S R+ +E RLG +LL R+TR V +TE G Sbjct: 3 DLNDLALFAAVVVHGSFSAAARALNTPKSRVSRRVAELEQRLGVRLLQRSTRVVRVTEVG 62 Query: 64 YRLAEHADRMADILKDANMLAHGLNEDTAGLVRISAPLTLGSVWLKPLLMSYMQANPRVQ 123 H + M + + A + AG +R+S+P+ + V+L PLL ++ A+P V+ Sbjct: 63 SAFFTHCEAMTNAARAAVEVTEHAGARPAGRLRVSSPMGVAHVFLAPLLARFLCAHPDVR 122 Query: 124 VDLRFSEQAVDITSDPVDLAIRVASTLPDDVVAKKLFGISWR-LCASP 170 ++L S + VD+ + D+A+RV STL D + + FG S + L ASP Sbjct: 123 LELELSNRRVDVIGEGFDVAMRVRSTLEDSSLVVRTFGTSQQVLAASP 170 >gi|300310278|ref|YP_003774370.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 107 bits (268), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 58/163 (35%), Positives = 99/163 (60%), Gaps = 2/163 (1%) Query: 8 LIIFCHVAKAGSLSKAAKALSLSRSALSHRIKAIEGRLGCQLLMRTTRRVGLTEAGYRLA 67 ++IF V + G+ SKAA+ L L+ S++S I A+E LG LL RTTR++ LTEAG+ Sbjct: 12 MVIFSRVVELGAFSKAARELGLTSSSVSQHISALEAMLGTTLLHRTTRKLSLTEAGHSFY 71 Query: 68 EHADRMADILKDANMLAHGLNEDTAGLVRISAPLTLGSVWLKPLLMSYMQANPRVQVDLR 127 + R+ D+ +A L L+++ G +RI+A + S +L P L +++A+P++++++ Sbjct: 72 ANCSRIVDLASEARQLTESLHKELLGELRIAASSFMASEYLVPALDDFIRAHPKLRINID 131 Query: 128 FSEQAVDITSDPVDLAIRVASTLPDDVVAKKLFGISWRLCASP 170 ++ +D+ VDLA+RV T ++ V L + LCASP Sbjct: 132 VNDHNIDLMDKSVDLALRVGKTSSENDV--YLASLPAVLCASP 172 >gi|300311233|ref|YP_003775325.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 315 Score = 102 bits (253), Expect = 4e-23, Method: Compositional matrix adjust. Identities = 55/165 (33%), Positives = 92/165 (55%) Query: 6 NSLIIFCHVAKAGSLSKAAKALSLSRSALSHRIKAIEGRLGCQLLMRTTRRVGLTEAGYR 65 N + +F V + GS S+AA+ L + SA+S I +E LG QLL RTTR++ L+E+G Sbjct: 11 NEMAVFAKVVETGSFSEAARQLGATPSAISRAIARLEKALGTQLLQRTTRKLRLSESGQD 70 Query: 66 LAEHADRMADILKDANMLAHGLNEDTAGLVRISAPLTLGSVWLKPLLMSYMQANPRVQVD 125 + M + + ++ + + G VR+S P +G + P + ++ A+P+V V Sbjct: 71 IHARCRDMLNAAQAVLAVSGAFDAEPQGQVRVSVPKAVGHALVHPHVPDFLAAHPKVDVL 130 Query: 126 LRFSEQAVDITSDPVDLAIRVASTLPDDVVAKKLFGISWRLCASP 170 LR ++ +D+ D VDLAIR+ P ++ ++L I LCA+P Sbjct: 131 LRLEDRYMDLIDDEVDLAIRITDHPPPGLMGRRLMRIDHLLCATP 175 >gi|300311929|ref|YP_003776021.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 91.3 bits (225), Expect = 7e-20, Method: Compositional matrix adjust. Identities = 55/170 (32%), Positives = 89/170 (52%) Query: 6 NSLIIFCHVAKAGSLSKAAKALSLSRSALSHRIKAIEGRLGCQLLMRTTRRVGLTEAGYR 65 S+ +FC A+ GS + AA+AL L+ +++S I +E RLG +L RTTR++ LT G Sbjct: 10 GSIELFCKAAELGSFTAAAEALGLTPASVSRSISRLESRLGVRLFARTTRQIRLTREGEL 69 Query: 66 LAEHADRMADILKDANMLAHGLNEDTAGLVRISAPLTLGSVWLKPLLMSYMQANPRVQVD 125 + + + + DA + G + +GL+RIS L PLL + QA P+++V+ Sbjct: 70 YRDQCQQALEQIADAERILTGQQKVPSGLLRISVGTPYAHYRLLPLLPRFQQAYPQIEVE 129 Query: 126 LRFSEQAVDITSDPVDLAIRVASTLPDDVVAKKLFGISWRLCASPDLAGR 175 L + + VD + DLAIR+ ++A L + L A+P R Sbjct: 130 LSIANRVVDFVEEGYDLAIRLGVPPDSRLIAHTLEEATLGLFAAPAYLAR 179 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 0.322 0.133 0.383 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: 570,738 Number of extensions: 20013 Number of successful extensions: 138 Number of sequences better than 1.0e-08: 47 Number of HSP's gapped: 132 Number of HSP's successfully gapped: 47 Length of query: 241 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 158 Effective length of database: 1,226,865 Effective search space: 193844670 Effective search space used: 193844670 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 (22.0 bits) S2: 129 (54.3 bits)