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= 0001.0839.p (283 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310378|ref|YP_003774470.1| transcription regulator protein... 541 e-155 gi|300310493|ref|YP_003774585.1| transcription regulator protein... 71 1e-13 gi|300313290|ref|YP_003777382.1| IclR family transcription regul... 69 4e-13 gi|300311600|ref|YP_003775692.1| transcription regulator protein... 64 1e-11 gi|300313062|ref|YP_003777154.1| IclR family transcription regul... 62 8e-11 >gi|300310378|ref|YP_003774470.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 541 bits (1395), Expect = e-155, Method: Compositional matrix adjust. Identities = 266/283 (93%), Positives = 273/283 (96%), Gaps = 1/283 (0%) Query: 1 MPRTRKINPADAPALQTAAEHEDEQGGAKTRYAAPALDKGLDILELLSRSEQMLTLNQIS 60 MPRTRKINP DA +QTAA +D G KTRYAAPALDKGLDILELLSRSEQMLTLNQIS Sbjct: 1 MPRTRKINPDDAATVQTAAAEDDSSSG-KTRYAAPALDKGLDILELLSRSEQMLTLNQIS 59 Query: 61 RQLGRSVNEIFRMVVTLEQRGYLIADNDHYRLSLKLFELAHHHQPIRSLVSTALPHMREL 120 RQLGRSVNEIFRMVVTLEQRGYLIADNDHYRLSLKLFELAHHHQPIRSLVSTALPHMREL Sbjct: 60 RQLGRSVNEIFRMVVTLEQRGYLIADNDHYRLSLKLFELAHHHQPIRSLVSTALPHMREL 119 Query: 121 AQRSMQSTHLTVYEAGRVIVVAQVDSPERWAFGLKVGALVSLTDTASGHVLLAFRDEAER 180 A R++QSTHLTVYEAGRVIVVAQVDSPERWAFGLKVGALVSLTDTASGHVLLAFRDEAER Sbjct: 120 ASRAVQSTHLTVYEAGRVIVVAQVDSPERWAFGLKVGALVSLTDTASGHVLLAFRDEAER 179 Query: 181 ASMLAAHVRMDGEQEIETAQLMRQIEETRKRGHSRMESRQIRGVVNLSYPVMGANNRMLA 240 A+MLAAHVRMDGEQEIETAQLMRQIE+TRKRGHSRMESRQIRGVVNLSYPVMGANNRMLA Sbjct: 180 AAMLAAHVRMDGEQEIETAQLMRQIEDTRKRGHSRMESRQIRGVVNLSYPVMGANNRMLA 239 Query: 241 ALNVPYIERIDKKVNPSLDEVQGIVQEVSARLSRLMGDSSFGS 283 ALNVPYIERIDKKVNPSLDEVQGIVQE+SARLSRLMGDSSFGS Sbjct: 240 ALNVPYIERIDKKVNPSLDEVQGIVQEISARLSRLMGDSSFGS 282 >gi|300310493|ref|YP_003774585.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 263 Score = 70.9 bits (172), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 59/237 (24%), Positives = 115/237 (48%), Gaps = 22/237 (9%) Query: 36 ALDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLI--ADNDHYRLS 93 +L+KGL +L + + +TL ++ G S + RMV TLE GY+ Y+L+ Sbjct: 16 SLEKGLAVLRAFNAQHRTMTLGDVASATGISKSSAQRMVHTLETLGYICKHPKTRRYQLT 75 Query: 94 LKLFELAHHHQPIRSLVSTALPHMRELAQRSMQSTHLTVYEAGRVIVVAQVDSPERWAFG 153 K+ E+ +++ LV A P + ELA + ++ +LT G ++ VA+ + + Sbjct: 76 PKVMEVGYNYLAADILVDVANPFLSELANITGETVNLTEPYDGEMVYVARFVASKFIPIH 135 Query: 154 LKVGALVSLTDTASGHVLLAFRDEAERASMLAA--------HVRMDGEQEIETAQLMRQI 205 + +G+ + + TASG L+ + E ++L + H R D E +M+ + Sbjct: 136 MPIGSRIPMYCTASGRAYLSALEPEEAQAILESSERTVHTPHTRTDVE------DIMQLL 189 Query: 206 EETRKRGHSRMESRQIRGVVNLSYPVMGANNRMLAALNV--PY----IERIDKKVNP 256 +R+RG + G ++++ PV + + +A+++V P +E +KK+ P Sbjct: 190 AASRERGFASNREELFLGDMSIASPVFNSERKPVASVHVVAPTSRWSVEEAEKKLGP 246 >gi|300313290|ref|YP_003777382.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 68.9 bits (167), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 55/211 (26%), Positives = 107/211 (50%), Gaps = 2/211 (0%) Query: 36 ALDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLIADNDHYRLSLK 95 +L +GL ++ S S + LT+ QIS++ G + R + TL+Q GY +D +++ L K Sbjct: 18 SLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYADSDVNNFSLRPK 77 Query: 96 LFELAHHHQPIRSLVSTALPHMRELAQRSMQSTHLTVYEAGRVIVVAQVDSPERWAFGLK 155 + L + + L +A P++ +++ +S L V + V+ VA+ + + L Sbjct: 78 ILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDHEVLYVARSAASRVMSVALN 137 Query: 156 VGALVSLTDTASGHVLLAFRDEAE-RASMLAAHVRMDGEQEIETAQLMRQI-EETRKRGH 213 G+ + T+ G +LA E + +A +R E+ + + + +R I R G+ Sbjct: 138 TGSRLPAYCTSLGRAMLAHLPEDQLKAYFDKVKLRALTEKTVVSQKRLRDILAGVRANGY 197 Query: 214 SRMESRQIRGVVNLSYPVMGANNRMLAALNV 244 + ++ G+ +++ PV GA+ +LAALNV Sbjct: 198 AVIDEELEVGLRSIAVPVRGASGNVLAALNV 228 >gi|300311600|ref|YP_003775692.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 292 Score = 63.9 bits (154), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 57/206 (27%), Positives = 102/206 (49%), Gaps = 9/206 (4%) Query: 37 LDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLI--ADNDHYRLSL 94 +D+ L +L ++R+ + ++ QI+ + + V+ ++R + +L++ G L ++ + Sbjct: 57 VDRVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGP 116 Query: 95 KLFELAHHHQPIRSLVSTALPHMRELAQRSMQSTHLTVYEAGRVIVVA--QVDSPERWAF 152 +LA +LVS + + L QRS +S L V G+++ +A + D P R +F Sbjct: 117 TGVQLAWGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSF 176 Query: 153 GLKVGALVSLTDTASGHVLLAFRDEAERASMLAAHVRMDGEQEIETAQLMRQIEETRKRG 212 G L AS LLAF + +L + G++ E A L Q+EE R+RG Sbjct: 177 --TKGRAHPLLKGASAKSLLAFMPRKLQQKLLTDQL---GDKPEELAALETQLEEIRRRG 231 Query: 213 HSRMESRQIRGVVNLSYPVMGANNRM 238 + ES GV +S P+M +N R+ Sbjct: 232 YCISESEVDLGVWGVSVPIMTSNGRL 257 >gi|300313062|ref|YP_003777154.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 61.6 bits (148), Expect = 8e-11, Method: Compositional matrix adjust. Identities = 47/216 (21%), Positives = 100/216 (46%), Gaps = 12/216 (5%) Query: 36 ALDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLIADNDHYRLSLK 95 L KG D++ L+ ++++ ++G + + R ++TL G +D + L + Sbjct: 19 GLMKGFDVITAFDSDSPQLSASEVAERVGLTRSAARRYLLTLVHTGMAASDGKKFWLMPR 78 Query: 96 LFELAHHHQPIRSLVSTALPHMRELAQRSMQSTHLTVYEAGRVIVVAQVDSPERWAFGLK 155 L L + + +P ++ L Q+ +ST+ ++ + ++ V +V + + G + Sbjct: 79 LLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVYVTRVTAAQLVNAGFE 138 Query: 156 VGALVSLTDTASGHVLLAFRDEAERASMLA-------AHVRMDGEQEIETAQLMRQIEET 208 G + T +G VLL R++AE + L H+ M + A L ++I Sbjct: 139 PGTRLPAYTTTAGRVLLGMREDAEIQAYLERVNLIPHTHMAM-----TDKAALFQEILTM 193 Query: 209 RKRGHSRMESRQIRGVVNLSYPVMGANNRMLAALNV 244 R++G+ E++ G+ ++ V N R++ AL+V Sbjct: 194 RRQGYGITENQFEMGMRGIAIAVKNRNGRVIGALSV 229 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 0.131 0.360 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: 802,167 Number of extensions: 29884 Number of successful extensions: 122 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 116 Number of HSP's successfully gapped: 8 Length of query: 283 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 199 Effective length of database: 1,222,130 Effective search space: 243203870 Effective search space used: 243203870 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: 130 (54.7 bits)