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= 0099.0004.p (315 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|EAI89171.1| unknown [environmental sequence] 70 6e-11 ref|NP_388706.1| similar to transcriptional regulator (AraC/XylS... 69 2e-10 ref|NP_745577.1| transcriptional regulator, AraC family [Pseudom... 66 1e-09 ref|ZP_00088831.1| COG2207: AraC-type DNA-binding domain-contain... 65 3e-09 ref|NP_746593.1| transcriptional regulator, AraC family [Pseudom... 64 7e-09 >gb|EAI89171.1| unknown [environmental sequence] Length = 314 Score = 70.1 bits (170), Expect = 6e-11, Method: Compositional matrix adjust. Identities = 69/270 (25%), Positives = 118/270 (43%), Gaps = 14/270 (5%) Query: 51 KVIDFHKHAEFEFHFIPRGRGKVILSGQQYSLSEGMLYLTGPGVIHYQEADA--GEAMD- 107 + I +H H EFE H I RGK + S G L L GP + H +D GE ++ Sbjct: 22 RTIRWHFHPEFELHLIVATRGKYFVGDHIGSFGPGHLVLLGPNLPHNWVSDMAEGETVER 81 Query: 108 -ELCLHVDITAKERKGVDPW-EAAEAEETMVKLRALPVVPAYDYHRAMYCFLEAYEACDG 165 L + D A R+ +D + E +A+ + + R A F E A Sbjct: 82 RNLVIQFD-PAFVRRCMDAFPECRDAQALLDEARRGVGFDAATSAAIAPLFDELLAARGM 140 Query: 166 KLLGYYTSIKQLVISILLKTIRAYDSGDNRAEAPVRNMAAYRYEYAVQYMEANHKTPVTL 225 + + + +I + + +T+ A + D P R +A+ Y+ N + + Sbjct: 141 RRIALFMTILERLCGAAERTLLASPAYDQADVTPTR------LSHALSYIGKNLASELRE 194 Query: 226 DNVAEKLHISSRQLQRIFKQVQPERPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFT 285 ++A+ S R F + Q PF + + +R+++ C+ L + +SI I +GF Sbjct: 195 SDLAQLTGQSVSAFSRAFHR-QTGMPFVQYVNRLRIESACQMLLADDASITDICFQAGFN 253 Query: 286 NANYLHAVFRKRLGMTPAAFRALRQQSNSK 315 N + + FR GM P+ FRAL Q+ N++ Sbjct: 254 NVSNFNRQFRAVKGMAPSEFRAL-QRLNAR 282 >ref|NP_388706.1| similar to transcriptional regulator (AraC/XylS family) [Bacillus subtilis] sp|P54722|YFIF_BACSU Putative HTH-type transcriptional regulator yfiF pir||A69803 transcription regulator AraC/XylS family homolog yfiF - Bacillus subtilis dbj|BAA09110.1| unknown [Bacillus subtilis] emb|CAB12654.1| yfiF [Bacillus subtilis subsp. subtilis str. 168] Length = 314 Score = 68.6 bits (166), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 61/267 (22%), Positives = 121/267 (45%), Gaps = 25/267 (9%) Query: 55 FHKHAEFEFHFIPRGRGKVILSGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVD 114 HKH+ +E ++ RG G + + Y L E ++L+ P +H +++ G +V Sbjct: 43 LHKHSFYEICYVVRGEGYYLEGDRTYPLREQTIFLSKPEHLHQIKSETG----LFLFYVA 98 Query: 115 ITAKERKGVDPWEAAEAEETMVKLRALPVV---------PAYDYHRAMYCFLEAYEACDG 165 E + +AE + M +++ P + P + M + A D Sbjct: 99 FELSEDQS-----SAEWIKVMEEVKQSPFITMQLKDGEPPGLLWKTLMLQAAQPVNAFDK 153 Query: 166 KLLGYYTSIKQLVISILLKTIRAYDSGDNRAEAPVRNMAAYRYEYAVQYMEANHKTPVTL 225 ++L + + +I L++T Y + + + P+ +A E + +++ N P+ L Sbjct: 154 EILSH---LSHALILSLIQTFLPY-AQRPKQKQPIHTSSALLTEVKL-HIKDNLSQPLKL 208 Query: 226 DNVAEKLHISSRQLQRIFKQVQPERPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFT 285 +VA HIS R L R+F + +S ++ ++ L+ SI++IA++ GF+ Sbjct: 209 TDVASHFHISGRHLSRLFA-AELGVSYSEFVQNEKINKAAELLKSTNLSIKEIAEEIGFS 267 Query: 286 NANYLHAVFRKRLGMTPAAFRALRQQS 312 +Y VF ++G +P FR+L + S Sbjct: 268 -VHYFTRVFSAKIGSSPGLFRSLYKDS 293 >ref|NP_745577.1| transcriptional regulator, AraC family [Pseudomonas putida KT2440] gb|AAN69041.1| transcriptional regulator, AraC family [Pseudomonas putida KT2440] Length = 282 Score = 65.9 bits (159), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 66/257 (25%), Positives = 106/257 (41%), Gaps = 38/257 (14%) Query: 56 HKHAEFEFHFIPRGRGKVILSGQQYSLSEGMLYLTGPGVIHYQEADAGEAMDELCLHVDI 115 H H F I GR I S Q + G L PGV+H AGE L L VD Sbjct: 32 HSHESFSIGVITGGRSTYINSDQCVEVGAGTTVLMNPGVVHTCNPVAGEPWSYLMLFVD- 90 Query: 116 TAKERKGVDPWEAAEA--EETMVKLRALPVVPAYDYHRAMYCFLEAYEA----CDGKLLG 169 PW A T R+ PV+ Y R + F + ++A + +L Sbjct: 91 --------QPWLQAVGFTLPTQTWSRS-PVL----YRRLLQAFADLFDARLPDREARLAA 137 Query: 170 YYTSIKQLVISILLKTIRAYDSGDNRAEAPVRNMAAYRYEYAVQYMEANHKTPVTLDNVA 229 + + ++ G N +E N R + A ++ A+ P++L+++ Sbjct: 138 LFHELPGML-------------GGNASEGGEGNP---RLDAAAAFIRAHRSDPLSLEDIC 181 Query: 230 EKLHISSRQLQRIFKQVQPERPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANY 289 +S L R F+Q P +L++ R+Q + RA SI ++AQ++GF + + Sbjct: 182 GACGLSRSYLIRAFRQRFGLTPHGYLLDQ-RVQ-LARAQLRQGRSIAEVAQEAGFADQAH 239 Query: 290 LHAVFRKRLGMTPAAFR 306 L F++ L TP +R Sbjct: 240 LQRAFKQHLAATPGHYR 256 >ref|ZP_00088831.1| COG2207: AraC-type DNA-binding domain-containing proteins [Azotobacter vinelandii] Length = 314 Score = 64.7 bits (156), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 66/272 (24%), Positives = 108/272 (39%), Gaps = 21/272 (7%) Query: 47 FPAGKVIDFHKHAEFEFHFIPRGRGKVILSGQQYSLSEGMLYLTGPG-----VIHYQEAD 101 FP ++ +H H E+E H I GKV + + G L LTGP + H +E D Sbjct: 46 FP-DPLVCWHYHKEYELHLITHSSGKVFVGDYIGNFYPGNLILTGPNLPHNWISHTEEQD 104 Query: 102 AGEAMDELCLHVDITAKERKGVDPWEAAEAEETMVKLRALPVVPAYDYHRAMYCFLEAYE 161 D + + D + + V P E E + + + R D + ++ Sbjct: 105 IYPERDMVVVFTDDMIQTARNVLP-EFTELDTLLQRARFGIEFQGNDTIGEAHRLMQKIA 163 Query: 162 ACDG-KLLGYYTSIKQLVISI----LLKTIRAYDSGDNRAEAPVRNMAAYRYEYAVQYME 216 G + L ++ SI L+ LL + G R + R AV Y+ Sbjct: 164 TSSGLECLAHFLSIMSLLAKADRYQLLSSEHYLSIGGERNQQ--------RVNQAVNYIF 215 Query: 217 ANHKTPVTLDNVAEKLHISSRQLQRIFKQVQPERPFSRILEEIRLQAVCRALEENLSSIE 276 ++ ++L+ VAE+L + R F+Q R F + +R+ C L + I Sbjct: 216 DHYHENLSLEEVAEELGMQPTYFSRFFRQATGRR-FVEFVNSLRITRACDLLAHSDLPIT 274 Query: 277 QIAQDSGFTNANYLHAVFRKRLGMTPAAFRAL 308 I + GFTN + + F MTP+ +R L Sbjct: 275 NICFEVGFTNISNFNRHFMALKAMTPSDYRKL 306 >ref|NP_746593.1| transcriptional regulator, AraC family [Pseudomonas putida KT2440] gb|AAN70057.1| transcriptional regulator, AraC family [Pseudomonas putida KT2440] Length = 326 Score = 63.5 bits (153), Expect = 7e-09, Method: Compositional matrix adjust. Identities = 42/125 (33%), Positives = 63/125 (50%), Gaps = 4/125 (3%) Query: 192 GDNRAEAPVRNMAAY---RYEYAVQYMEANHKTPVTLDNVAEKLHISSRQLQRIFKQVQP 248 G R P++N + AV MEAN + P+T D +A+ + +S RQL+RIFKQ Sbjct: 191 GGERQRIPLQNRLGSSHPKLTQAVLLMEANIEEPLTTDEIAQHVCVSRRQLERIFKQYLN 250 Query: 249 ERPFSRILEEIRLQAVCRALEENLSSIEQIAQDSGFTNANYLHAVFRKRLGMTPAAFRAL 308 P S+ E+RL + L + SI QI GF++ + + +R G TP R Sbjct: 251 RVP-SQYYLELRLNKARQMLMQTSKSIIQIGLSCGFSSGPHFSSAYRNFFGATPREDRNQ 309 Query: 309 RQQSN 313 R+ S+ Sbjct: 310 RRSSS 314 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 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: 2715099 Number of Hits to DB: 451,544,006 Number of extensions: 17786269 Number of successful extensions: 40962 Number of sequences better than 1.0e-05: 99 Number of HSP's gapped: 41519 Number of HSP's successfully gapped: 99 Length of query: 315 Length of database: 757,237,578 Length adjustment: 125 Effective length of query: 190 Effective length of database: 417,850,203 Effective search space: 79391538570 Effective search space used: 79391538570 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 (21.9 bits) S2: 126 (53.1 bits)