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= 0002.0377.p (291 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309859|ref|YP_003773951.1| LysR family transcription regul... 427 e-121 gi|300312835|ref|YP_003776927.1| LysR family transcription regul... 97 1e-21 gi|300311165|ref|YP_003775257.1| transcription regulator protein... 88 7e-19 gi|300311145|ref|YP_003775237.1| transcription regulator protein... 82 4e-17 gi|300313217|ref|YP_003777309.1| LysR family transcription regul... 79 3e-16 >gi|300309859|ref|YP_003773951.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 297 Score = 427 bits (1098), Expect = e-121, Method: Compositional matrix adjust. Identities = 221/287 (77%), Positives = 248/287 (86%), Gaps = 8/287 (2%) Query: 1 MFNPVWLKTFTTVAASSSFSEAGRRLGLTQSSVSDHIRRLEDGSGRRLFVRDTHSLALTA 60 M NP+WL+TF+T A+S+SF+EAGR+LGLTQS+VSDHIRRLE+ GRRLFVRDTHSLALTA Sbjct: 16 MLNPIWLQTFSTAASSASFTEAGRQLGLTQSTVSDHIRRLEESLGRRLFVRDTHSLALTA 75 Query: 61 DGESLLVHARLILEAHARAEAQFTAPRLRGRVRFGAPDDLAMGPLPDMLAAFRNKHPEVE 120 DGESLLVHARLIL+AHARAEAQF+APRLRGRVRFG DDLAMGPLPDMLAAFR++HPEVE Sbjct: 76 DGESLLVHARLILQAHARAEAQFSAPRLRGRVRFGTSDDLAMGPLPDMLAAFRSQHPEVE 135 Query: 121 LEITIGLTGELYQRLDNGDLDLIVGKRRPGEQRGQAMFRVPLVWLARPETVVDLAQPLPL 180 LEITIGLT +LY LD G LDL+VGKRR GE RG +MF P+ WL RP+T+VDLA+PLPL Sbjct: 136 LEITIGLTSDLYASLDQGKLDLLVGKRRSGESRGHSMFSTPMQWLTRPDTLVDLAEPLPL 195 Query: 181 ILLPEPSVTRAAILATLGAAGRHWRIVCTSGSHAGCMAAARXPARARARGGLGLTVLPQH 240 ILLPEPS+TRAA L LG +G HWRIVCTSGSHAGCMAA ARGGLGL LPQH Sbjct: 196 ILLPEPSITRAATLQALGKSGHHWRIVCTSGSHAGCMAA--------ARGGLGLAALPQH 247 Query: 241 LASRELSLPVNHASLPVFPDVEYVALAAKRLSRPADTLFQILMASEL 287 LASR+L P+NHA+LP PDVEYVAL A+RLSRPADTL+QILMAS L Sbjct: 248 LASRDLVPPLNHAALPALPDVEYVALTARRLSRPADTLYQILMASRL 294 >gi|300312835|ref|YP_003776927.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 283 Score = 97.4 bits (241), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 90/283 (31%), Positives = 134/283 (47%), Gaps = 17/283 (6%) Query: 7 LKTFTTVAASSSFSEAGRRLGLTQSSVSDHIRRLEDGSGRRLFVRDTHSLALTADGESLL 66 L VA + +FS A + TQS+VS I+ LE G+ LF+R S+ T DGE LL Sbjct: 9 LAMIVAVADTGNFSRAAELVHRTQSAVSMQIKTLELALGKPLFLRKPRSVVPTQDGEVLL 68 Query: 67 VHARLILEAHARAEAQFTAPRLRGRVRFGAPDDLAMGPLPDMLAAFRNKHPEVELEITIG 126 +AR +L A A P + GRV G PDD A LP +L F +P+VE+++ +G Sbjct: 69 TYARRMLTLRDEAWAAVVRPDVTGRVVIGVPDDYASSLLPSILKKFSATYPKVEIQV-VG 127 Query: 127 L-TGELYQRLDNGDLDLIVGKRRPGEQRGQAMFRVPLVWLARPETVVDL--AQPLPLILL 183 L + L + +G +DL+ R G G+ + P+VW P + DL +PLP+ + Sbjct: 128 LPSSALAPMVKDGTVDLVCATRVKGIS-GEFIRFEPMVWATVP-SASDLWRERPLPIAVF 185 Query: 184 PEPSVTRAAILATLGAAGRHWRIVCTSGSHAGCMAAARXPARARARGGLGLTVLPQHLAS 243 SV R + +L A +R S S G ++ GL + L + Sbjct: 186 LPGSVARENAIRSLEKARIGYRTSYESPSLMGLLSM--------VEAGLAIAPLARCAVP 237 Query: 244 RELSLPVNHA-SLPVFPDVEYV-ALAAKRLSRPADTLFQILMA 284 +L ++HA LP +E V A + K P D L + +MA Sbjct: 238 PHFTL-LDHAHGLPDIAPLEVVLARSTKSKRPPCDFLAEKIMA 279 >gi|300311165|ref|YP_003775257.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 311 Score = 88.2 bits (217), Expect = 7e-19, Method: Compositional matrix adjust. Identities = 82/276 (29%), Positives = 120/276 (43%), Gaps = 23/276 (8%) Query: 3 NPVWLKTFTTVAASSSFSEAGRRLGLTQSSVSDHIRRLEDGSGRRLFVRDTHSLALTADG 62 N +L+TF +A +F RL TQ++VS I LE G RLF R +ALTADG Sbjct: 2 NIRFLETFVWLARLRNFRLTAERLHTTQAAVSSRIASLEQDFGVRLFDRSAREVALTADG 61 Query: 63 ESLLVHA-RLILEAHARAEAQFTAPRLRGRVRFGAPDDLAMGPLPDMLAAFRNKHPEVEL 121 LVHA R++ E G +R G + + PD L P +++ Sbjct: 62 SKALVHAERMVKLMREMKEDMSDREVYAGVIRIGVIESIVHSWFPDFLGRLHKTFPRLQI 121 Query: 122 EITIGLTGELYQRLDNGDLDLIV-GKRRPGEQRGQ-AMFRVPLVWLARPE--------TV 171 EI T L+++ G+LDL++ + G Q A+ P+ W+ P+ ++ Sbjct: 122 EIVSDTTIHLHEQFSKGNLDLVLQAEAVIGPQVSNLALCEFPMRWVGSPKLDIGSETLSL 181 Query: 172 VDLAQPLPLILLPEPSVTRAAILATLGAAGRHWRIVCTSGSHAGCMAAARXPARARARGG 231 DLA P+I S A I + R R + H C+A+ R A G Sbjct: 182 ADLA-AFPIISFARNSGPHAVIERLFSDSQRSERTL-----HINCIASVATMIRL-ATDG 234 Query: 232 LGLTVLPQHLASRELSLPVNHASLPVF-PDVEYVAL 266 G+T +P + REL N SL + D E+ AL Sbjct: 235 FGITAVPPAIIQREL----NEESLHLLRVDTEFPAL 266 >gi|300311145|ref|YP_003775237.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 281 Score = 82.4 bits (202), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 64/207 (30%), Positives = 96/207 (46%), Gaps = 6/207 (2%) Query: 7 LKTFTTVAASSSFSEAGRRLGLTQSSVSDHIRRLEDGSGRRLFVRDTHSLALTADGESLL 66 ++ F A SF+ A L TQS+VS +++LE GRRL R + L+A+G+ L Sbjct: 10 VQAFVLAADLHSFTRAAEALESTQSAVSLKLKKLEQRLGRRLLERTPRQVRLSAEGQQFL 69 Query: 67 VHARLILEAHARAEAQFTAPRLRGRVRF--GAPDDLAMGPLPDMLAAFRNKHPEVELEIT 124 AR +L AH RA Q +G VRF G D +A LP LA P V +E+ Sbjct: 70 PAARELLAAHERALEQLD----QGPVRFSVGISDHVAGASLPRALAQVHALDPGVVVEVR 125 Query: 125 IGLTGELYQRLDNGDLDLIVGKRRPGEQRGQAMFRVPLVWLARPETVVDLAQPLPLILLP 184 + + +L + G+LD ++ +R P ++ G+ + + W A P+ L + Sbjct: 126 VASSHDLMPLYERGELDAVIVRREPQDRGGKLVMEERIGWFAHPDAQCWAGGALRVATFS 185 Query: 185 EPSVTRAAILATLGAAGRHWRIVCTSG 211 + R L L AAG W V G Sbjct: 186 QACRIRELSLRRLDAAGIAWVEVFVGG 212 >gi|300313217|ref|YP_003777309.1| LysR family transcription regulator [Herbaspirillum seropedicae SmR1] Length = 296 Score = 79.3 bits (194), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 51/135 (37%), Positives = 69/135 (51%) Query: 7 LKTFTTVAASSSFSEAGRRLGLTQSSVSDHIRRLEDGSGRRLFVRDTHSLALTADGESLL 66 L+ F TV A + A RL QS+V+ I++LE G LFVRD + LTA GE+LL Sbjct: 15 LEIFRTVVAEGGVTRAAERLNRVQSNVTTRIKQLEQSMGVPLFVRDRRRMVLTAAGEALL 74 Query: 67 VHARLILEAHARAEAQFTAPRLRGRVRFGAPDDLAMGPLPDMLAAFRNKHPEVELEITIG 126 +A IL+ A RGR+R G+ + A LP LA F + PEV LE++ Sbjct: 75 DYAERILDLAQEARQAVAPQSPRGRLRIGSMESAAASRLPGPLAEFHQRWPEVRLELSTA 134 Query: 127 LTGELYQRLDNGDLD 141 T L ++ LD Sbjct: 135 PTDVLMAQVRACKLD 149 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 0.136 0.403 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: 918,795 Number of extensions: 39464 Number of successful extensions: 271 Number of sequences better than 1.0e-08: 52 Number of HSP's gapped: 267 Number of HSP's successfully gapped: 52 Length of query: 291 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 207 Effective length of database: 1,222,130 Effective search space: 252980910 Effective search space used: 252980910 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: 130 (54.7 bits)