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= 0405.0002.p (401 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 ref|ZP_00098917.1| COG1940: Transcriptional regulator/sugar kina... 181 4e-44 ref|NP_347569.1| Transcriptional regulator of NagC/XylR family (... 128 2e-28 ref|NP_463709.1| similar to xylose repressor [Listeria monocytog... 126 9e-28 ref|NP_469562.1| similar to xylose repressor [Listeria innocua] ... 122 1e-26 ref|NP_623501.1| Transcriptional regulator [Thermoanaerobacter t... 117 6e-25 >ref|ZP_00098917.1| COG1940: Transcriptional regulator/sugar kinase [Desulfitobacterium hafniense] Length = 406 Score = 181 bits (458), Expect = 4e-44, Method: Compositional matrix adjust. Identities = 107/358 (29%), Positives = 178/358 (49%), Gaps = 7/358 (1%) Query: 23 KGTVSKQTLLEESGLTVSTLTRIXXXXXXXXXXXEVGFGESTGGRRPTLYETNPAYGYVF 82 KG ++K L + +GL ++TL R+ GESTGGR+P +Y+ NP YV Sbjct: 29 KGGMTKSQLAKVAGLKLTTLNRMMLPLEKADLILPTETGESTGGRKPVIYDVNPRRYYVI 88 Query: 83 GLEISRTFSRXXXXXXXXXXXDEYSWPMDEQATPERLIESVHAQVLRMLEQASIDISQVI 142 G++ISR +S+ ++ + MD ++P+ + + + R++E+ VI Sbjct: 89 GIDISRLYSQVVLTNLKMELIEKDRFDMDRNSSPQATLNRILDWIGRVMEKRGH--GYVI 146 Query: 143 GLGIGAVGPLDRKEGMILQPAGFAAPGWSQVPVKERLEQLLDVPVCLDNGANTALLGEYW 202 G+GIG VGPLDR+ G+IL P F A GW +P+K +E+ +PV +DNGAN A+L E Sbjct: 147 GVGIGTVGPLDRQSGIILNPENFEAQGWENIPLKAIVEERTGLPVIIDNGANGAVLAETR 206 Query: 203 AGGDRRQHQLLYLHAGIGLRSAIMNEGRILYGVIDTEGAVGQMIIEXXXXXXXXXXXXXX 262 G + ++YL+ G+G+R+ +++ G ++ + D + M+I+ Sbjct: 207 YGSGKGMKSVIYLNCGVGIRTGVISSGTLVRTINDADDTFAHMVID--VNGKPCHCGNQG 264 Query: 263 AWESYVSIRTLEMQAREEWKRGRPTLLRELAGRPEDIEFAHLVEALQAGDSVVNGIFGQA 322 E Y SI + EE +G+ + A RP + + L + D++ + A Sbjct: 265 CVERYSSIYAIMEALAEEMPQGKDRRNHK-ADRP--VSYLELCREAEENDTIARQVLQNA 321 Query: 323 AAYCGIGLANLINILHPEEVILGGPLFSAADFFYREATRTALEKTYYRGQYKVRFTQG 380 A G GLAN I +L+P V+L GPL + FY A + + + F++G Sbjct: 322 AVRMGTGLANFIQLLNPGLVVLSGPLILHSQLFYEVCVEAAKRRRPWDKGGHLVFSRG 379 >ref|NP_347569.1| Transcriptional regulator of NagC/XylR family (xylose repressor) [Clostridium acetobutylicum] pir||B97015 transcription regulator of NagC/XylR family (xylose repressor) [imported] - Clostridium acetobutylicum gb|AAK78909.1| Transcriptional regulator of NagC/XylR family (xylose repressor) [Clostridium acetobutylicum] Length = 375 Score = 128 bits (322), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 86/357 (24%), Positives = 167/357 (46%), Gaps = 23/357 (6%) Query: 10 NSRTKEMYLSVRKKGTVSKQTLLEESGLTVSTLTRIXXXXXXXXXXXEVGFGESTGGRRP 69 + R+K ++ ++KKG ++K+ +L+ + ++TL R+ E G +S GGR+P Sbjct: 6 DDRSKRIFDLLQKKGAMTKKEILKNIDMKLTTLNRLMRPLEDERLIVEYGIEDSAGGRKP 65 Query: 70 TLYETNPAYGYVFGLEISRTFSRXXXXXXXXXXXDEYSWPMDEQATPERLIESVHAQVLR 129 +Y N Y+ G++ISR F E + + +++ + + + + Sbjct: 66 IMYNVNLCGFYIIGIDISREFINIVFTNIKLELFYEDRINLKGILSEKKIADKIINCINK 125 Query: 130 MLEQASIDISQVIGLGIGAVGPLDRKEGMILQPAGFAAPGWSQVPVKERLEQLLDVPVCL 189 ++ + +D+ + G+G+ +L A F G+++ +K LE+ L V + Sbjct: 126 VVGELRLDVLTLFGVGVS-----------VLNVASFKCSGYTK--LKSELERELSSRVII 172 Query: 190 DNGANTALLGEYWAGGDRRQHQLLYLHAGIGLRSAIMNEGRILYGVIDTEGAVGQMIIEX 249 +NGAN+A L EY G +RR + Y + +RS ++ G++L + + E A M+I Sbjct: 173 ENGANSAALAEYLYGFNRRISNMAYFNCTEIIRSGVVLSGQVLRTINNKEDAFSNMLI-- 230 Query: 250 XXXXXXXXXXXXXAWESYVSIRTLEMQAREEWKRGRPTLLRELAGRPEDIEFAHLVEALQ 309 +YVS ++ + K GR T++++ +I+ L A+ Sbjct: 231 -----INNKNKFDFLGNYVSESSIINNFCSKVKSGRKTIIKK---NLREIKLLDLENAIN 282 Query: 310 AGDSVVNGIFGQAAAYCGIGLANLINILHPEEVILGGPLFSAADFFYREATRTALEK 366 GDS+ + +A GI LAN I +L + ++LGG L + + FY T+ ++ Sbjct: 283 KGDSLSKEVILNSAVIFGIALANYIQVLGLKAIVLGGSLIANSKTFYDVLTKIVFDR 339 >ref|NP_463709.1| similar to xylose repressor [Listeria monocytogenes EGD-e] pir||AC1097 xylose repressor homolog lmo0178 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAC98393.1| lmo0178 [Listeria monocytogenes] Length = 404 Score = 126 bits (316), Expect = 9e-28, Method: Compositional matrix adjust. Identities = 95/384 (24%), Positives = 163/384 (42%), Gaps = 21/384 (5%) Query: 20 VRKKGTVSKQTLLEESGLTVSTLTRIXXXXXXXXXXXEVGFGESTGGRRPTLYETNPAYG 79 +R+KG +++ + ++ +STLT I E STGGRR L N YG Sbjct: 24 IREKGEITRTEIAKKCDFGMSTLTYILDDLQQEGIILEGAETSSTGGRRAKLVRFNKDYG 83 Query: 80 YVFGLEISRTFSRXXXXXXXXXXXDEYSWPMDEQATPERLIESVHAQVLRMLEQASIDIS 139 +V +++ + S P + PE IE + V +M + D++ Sbjct: 84 FVVSVKVEEEQLLFALTDLNAEIIENTSIPFSSEKKPEEAIELIAKNVKKMC--GNRDMN 141 Query: 140 QVIGLGIGAVGPLDRKEGMILQPAGFAAPGWSQVPVKERLE-QLLDVPVCLDNGANTALL 198 ++G+GI G ++RK+G +++ GW V ++ L D+PV +D N L Sbjct: 142 HLLGVGIAISGLVNRKKGTVIRSTML---GWENVALEAMLHAHFPDIPVYVDKNINCYTL 198 Query: 199 GEYWAGGDRRQHQLLYLHAGIGLRSAIMNEGRILYGVIDTEGAVGQMIIEXXXXXXXXXX 258 E W G ++ + + G GL +++ +I YG G G I+ Sbjct: 199 AELWLGEGKQSNNFATVSVGAGLGLSVVINRQIYYGAQGGAGEFGHTTIQPG-------- 250 Query: 259 XXXXAWESYVSIR-TLEMQAREEWKRGRPTLLRELAGRPE--DIEFAHLVEALQAGDSVV 315 ++ + + LEM A E + R R L+E E D F + ++ +AGD + Sbjct: 251 ----GYKCHCGQKGCLEMYASEFYFRNRGEELKEAYPTSELNDFHFDKVAKSARAGDEMA 306 Query: 316 NGIFGQAAAYCGIGLANLINILHPEEVILGGPLFSAADFFYREATRTALEKTYYRGQYKV 375 + G+ Y G G+ N+IN +PE+VI+ G D F + A + + ++ Sbjct: 307 TELMGKMGEYLGYGIRNIINTFNPEKVIIVGEGLHHRDLFLTKIDEIASQNFFSGAGFET 366 Query: 376 RFTQGSLSDTXXXXXXXXLILNQL 399 T SL D L+++QL Sbjct: 367 EITTTSLEDPAWLQGAALLVIHQL 390 >ref|NP_469562.1| similar to xylose repressor [Listeria innocua] pir||AB1460 xylose repressor homolog lin0217 [imported] - Listeria innocua (strain Clip11262) emb|CAC95450.1| lin0217 [Listeria innocua] Length = 404 Score = 122 bits (306), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 93/384 (24%), Positives = 162/384 (42%), Gaps = 21/384 (5%) Query: 20 VRKKGTVSKQTLLEESGLTVSTLTRIXXXXXXXXXXXEVGFGESTGGRRPTLYETNPAYG 79 +R+KG +++ + ++ +STLT I E STGGRR L N YG Sbjct: 24 IREKGEITRTEIAKKCDFGMSTLTYILDDLQQEGIILEGAETSSTGGRRAKLVRFNKDYG 83 Query: 80 YVFGLEISRTFSRXXXXXXXXXXXDEYSWPMDEQATPERLIESVHAQVLRMLEQASIDIS 139 +V +++ S P + PE I+ + V +M + D+ Sbjct: 84 FVVSVKVEEEQLLFALTDLNAEIIKNTSIPFSSEKKPEDAIDLIAENVKKMCKNR--DMK 141 Query: 140 QVIGLGIGAVGPLDRKEGMILQPAGFAAPGWSQVPVKERLE-QLLDVPVCLDNGANTALL 198 ++G+GI G ++RK+G +++ GW V ++ L D+PV +D N L Sbjct: 142 NLLGVGIAISGLVNRKKGTVIRSTML---GWENVALEAMLHVHFPDIPVYVDKNINCYTL 198 Query: 199 GEYWAGGDRRQHQLLYLHAGIGLRSAIMNEGRILYGVIDTEGAVGQMIIEXXXXXXXXXX 258 E W G ++ + + G GL +++ +I YG G G I+ Sbjct: 199 AELWLGEGKQSNNFATVSVGAGLGLSVVINRQIYYGAQGGAGEFGHTTIQPG-------- 250 Query: 259 XXXXAWESYVSIR-TLEMQAREEWKRGRPTLLRELAGRPE--DIEFAHLVEALQAGDSVV 315 ++ + + LEM A E + R R ++E E D F ++ ++ +AGD + Sbjct: 251 ----GYKCHCGQKGCLEMYASEFYFRNRGEEIKEAFPTSELNDFHFDNVAKSARAGDEMA 306 Query: 316 NGIFGQAAAYCGIGLANLINILHPEEVILGGPLFSAADFFYREATRTALEKTYYRGQYKV 375 + G+ Y G G+ N+IN +PE+VI+ G D F + A + + ++ Sbjct: 307 IELMGKMGEYLGYGIRNIINTFNPEKVIIVGEGLHHRDLFLTKIDEIASQNFFSGAGFET 366 Query: 376 RFTQGSLSDTXXXXXXXXLILNQL 399 T SL D L+++QL Sbjct: 367 EITTTSLEDPAWLQGAALLVIHQL 390 >ref|NP_623501.1| Transcriptional regulator [Thermoanaerobacter tengcongensis] gb|AAM25105.1| Transcriptional regulator [Thermoanaerobacter tengcongensis] Length = 396 Score = 117 bits (292), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 96/354 (27%), Positives = 161/354 (45%), Gaps = 18/354 (5%) Query: 20 VRKKGTVSKQTLLEESGLTVSTLTRIXXXXXXXXXXXEVGFGESTGGRRPTLYETNPAYG 79 +RK G +S+ + +E+ LT T+T I E GES+GGR P L + NP + Sbjct: 24 IRKMGPISRADIAKETNLTPPTVTNIVNKLLADNVVIEYKVGESSGGRPPILIKLNPDFM 83 Query: 80 YVFGLEISRTFSRXXXXXXXXXXXDEYSWPMDEQATPERLI-ESVHAQVLRMLEQASIDI 138 + + IS T++ E + E+ + + L E V +L LE+A + Sbjct: 84 NIIVIHIS-TYTLHQYTLDA-----ELNTKKSEKHSIKGLKKEEVLDLLLSTLEKAIKEA 137 Query: 139 SQ-VIGLGIGAVGPLDRKEGMILQPAGFAAP--GWSQVPVKERLEQLLDVPVCLDNGANT 195 Q V G+GI GP+ KEG+ AP GW +P+K +E+ +P + N Sbjct: 138 PQNVSGIGIVVRGPVKMKEGI-----SVFAPNIGWRNMPLKSIVEEKFGIPTYIVNDVRA 192 Query: 196 ALLGEYWAGGDRRQHQLLYLHAGIGLRSAIMNEGRILYGVIDTEGAVGQMIIEXXXXXXX 255 LGE+ G + +++L G G+ SAI+ GRI G D+ G +G I+ Sbjct: 193 MALGEFHMGKAKDVVNMIFLKVGYGIGSAILINGRIYTGASDSAGEIGHTTID--VAGPQ 250 Query: 256 XXXXXXXAWESYVSIRTLEMQAREEWKRGRPTLLRELA-GRPEDIEFAHLVEALQAGDSV 314 +E+ S + L + K G +++ ++A G + + + EA + D + Sbjct: 251 CSCGNYGCFEALASEKALVNFVVKAIKEGTDSIVYQMAEGMLDSVTPEMIYEAAKLNDDL 310 Query: 315 VNGIFGQAAAYCGIGLANLINILHPEEVILGGPLFSAADFFYREATRTALEKTY 368 Y GIG+AN+IN +PE +++GG + +FF TA ++ + Sbjct: 311 AVSTLRIIGRYLGIGIANIINTFNPELILIGGGIVQGREFFEDIMRETAKKRAF 364 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 0.319 0.137 0.401 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: 518,169,259 Number of extensions: 19641797 Number of successful extensions: 37817 Number of sequences better than 1.0e-05: 288 Number of HSP's gapped: 37600 Number of HSP's successfully gapped: 288 Length of query: 401 Length of database: 757,237,578 Length adjustment: 128 Effective length of query: 273 Effective length of database: 409,704,906 Effective search space: 111849439338 Effective search space used: 111849439338 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 (21.7 bits) S2: 127 (53.5 bits)