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= 0053.0004.p (324 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|AAM19069.1| repressor FruR [Bacillus megaterium] 301 1e-80 emb|CAD90945.1| repressor [Lactobacillus fermentum] 259 6e-68 ref|ZP_00046868.1| COG1609: Transcriptional regulators [Lactobac... 256 5e-67 ref|NP_965738.1| sucrose operon repressor [Lactobacillus johnson... 255 1e-66 ref|NP_843192.1| ribose operon repressor [Bacillus anthracis str... 254 2e-66 >gb|AAM19069.1| repressor FruR [Bacillus megaterium] Length = 327 Score = 301 bits (772), Expect = 1e-80, Method: Compositional matrix adjust. Identities = 147/326 (45%), Positives = 229/326 (70%), Gaps = 4/326 (1%) Query: 2 ATINDVAEQAGVSVTTVSRVLNNRGYISEKTRQKVYQVMDELNYQPNELARSLLRKHSNV 61 A I+DVA+ AGVS TTVSRVLNNRGYIS++TR+ VY+ M E+NY PN++ARSL K +N+ Sbjct: 3 AKISDVAKIAGVSPTTVSRVLNNRGYISKETRENVYKAMKEINYFPNDIARSLFNKRTNL 62 Query: 62 LGLIIPSVAHPFFGELANAIESVAYQHGFKLLLCNSQLDSAKEREYVDMMRRNRVDGMIL 121 +G+I+P ++PFFGELA IES+ +K+LLCNS KE++YV+M+ RN+VDG+I Sbjct: 63 IGMIVPQTSNPFFGELAFHIESICASLNYKVLLCNSLNRIDKEKKYVEMLIRNQVDGVIA 122 Query: 122 GSHTLEIGDYTHLNYPLVTIDRRIG-DIPFVASDNENGGALAARLLIAKGCRKIGHLSGN 180 ++ I D + P+V +D + DIP V+SDN +GG A LLI+K C+ I H++G Sbjct: 123 VTYNRGIFDSESQSLPVVAVDHYLSTDIPTVSSDNYSGGKQATELLISKDCKHIIHINGP 182 Query: 181 MKLDMLSNLRTTGFEREARQGGVKFVTYQTELDVFDEQIYNEIIRKMFTEHPDIDGVFAT 240 +KL+ +NLR +E ++ G + +TY+ + FD I E I K+F E+P++DG+FA+ Sbjct: 183 LKLETPANLRRKAYENVMKKYGKQPITYEIS-NTFDRNIQRETISKVFEENPEVDGIFAS 241 Query: 241 SDLMALFVMKWCRTFGKEVPRDVRIIGYDDIDAASWYMPGLSTIKQPIKDMARRAVELLL 300 DL+A V+ + GK +PRD++I+GYD +A+ +PGL+T++QPI+ +A+ A+++LL Sbjct: 242 DDLLAALVVAEAQKRGKNIPRDLKIVGYDGTEASQTLLPGLTTVQQPIESIAQTAIDILL 301 Query: 301 EQMDDK--TVERETVLPVELVEREST 324 ++++ + + RE LPV+L+E ++T Sbjct: 302 KEIEGEFSNIPREICLPVKLLEGQTT 327 >emb|CAD90945.1| repressor [Lactobacillus fermentum] Length = 329 Score = 259 bits (662), Expect = 6e-68, Method: Compositional matrix adjust. Identities = 127/318 (39%), Positives = 199/318 (62%), Gaps = 2/318 (0%) Query: 4 INDVAEQAGVSVTTVSRVLNNRGYISEKTRQKVYQVMDELNYQPNELARSLLRKHSNVLG 63 + DVA AGVS TTVSRVLNNRGY+SE T+Q+V++ M++L+Y PN +AR L + +N++G Sbjct: 9 LEDVAALAGVSKTTVSRVLNNRGYLSEATKQRVHEAMEQLHYCPNAIARQLFTQKTNLVG 68 Query: 64 LIIPSVAHPFFGELANAIESVAYQHGFKLLLCNSQLDSAKEREYVDMMRRNRVDGMILGS 123 L+ P+V PFFG+L ++ Y++G++ L+ NSQ + KE +Y+ ++ +++DG+I+G+ Sbjct: 69 LVFPTVNDPFFGQLEAGLDECLYENGYRTLMGNSQNNPQKEEQYLQLLLNHQIDGLIVGA 128 Query: 124 HTLEIGDYTHLNYPLVTIDRRIG-DIPFVASDNENGGALAARLLIAKGCRKIGHLSGNMK 182 H + DY N P+V+I+R + IP VASDN GG LA + L+ GC+ I H + Sbjct: 129 HNQAMPDYLQTNLPIVSIERAVAPQIPVVASDNYRGGQLATQRLLDAGCQHIIHTNYPKD 188 Query: 183 LDMLSNLRTTGFEREARQGGVKFVTYQTELDVFDEQIYNEIIRKMFTEHPDIDGVFATSD 242 + + R +E Q G +TY+ D E+ I ++F EHP++DG+FA +D Sbjct: 189 VMTTNQDRRKAYEDLMSQAGYPAITYKVNYDTPMEE-KKAIFARLFDEHPEVDGIFADND 247 Query: 243 LMALFVMKWCRTFGKEVPRDVRIIGYDDIDAASWYMPGLSTIKQPIKDMARRAVELLLEQ 302 A + G+ P D++IIG+D D +P L+TI+QPI++MA AVELL E+ Sbjct: 248 TNARLALTAATEAGRRCPEDIKIIGFDGADMTRLLLPELTTIQQPIQEMAEAAVELLKEE 307 Query: 303 MDDKTVERETVLPVELVE 320 + + ++ LPV+LVE Sbjct: 308 IAGEPADQYRTLPVKLVE 325 >ref|ZP_00046868.1| COG1609: Transcriptional regulators [Lactobacillus gasseri] Length = 330 Score = 256 bits (654), Expect = 5e-67, Method: Compositional matrix adjust. Identities = 142/335 (42%), Positives = 207/335 (61%), Gaps = 20/335 (5%) Query: 1 MATINDVAEQAGVSVTTVSRVLNNRGYISEKTRQKVYQVMDELNYQPNELARSLLRKHSN 60 M + DVA +AG SVTTVSRV+NN GYIS+KTR+KV++ M ELNYQPN +ARSL K + Sbjct: 3 MVKLTDVAAKAGCSVTTVSRVINNYGYISQKTRKKVHEAMRELNYQPNSVARSLQGKKTK 62 Query: 61 VLGLIIPSVAHPFFGELANAIESVAYQHGFKLLLCNSQLDSAKEREYVDMMRRNRVDGMI 120 ++GLI P V++PFFGEL + IE + HG+K +LCN+ D+ KER Y+ M+ N+VDG+I Sbjct: 63 LIGLIFPDVSNPFFGELVSKIEDQLFNHGYKTILCNAGNDTEKERTYLQMLMANQVDGII 122 Query: 121 LGSHTLEIGDYTHLNYPLVTIDRRIGD-IPFVASDNENGGALAARLLIAKGCRKIGHLSG 179 G+H L I +Y P+V+ DR++ D IP V++DN GG+LA + L G R I + G Sbjct: 123 AGAHNLGIEEYQRTGLPIVSFDRKLSDNIPIVSADNFKGGSLATQELYNHGARHI-YFVG 181 Query: 180 NMKLDMLSNLRTTGFEREARQGGVKFVTYQTELD------VFDEQI-YNEIIRKMFTEHP 232 N LD G + R G K + +L +F+E + E+ K E+ Sbjct: 182 NPTLD--------GHPTQKRLLGYKETIKELQLTEHIHPVIFNETLALKEMAIKDLLENH 233 Query: 233 DIDGVFATSDLMALFVMKWCRTFGKEVPRDVRIIGYDDIDAASWYMPGLSTIKQPIKDMA 292 +DG+ A+ DL AL +M G ++P+D++IIG+D + P LSTI QPI +A Sbjct: 234 KVDGIVASDDLTALLIMNISHDLGIKIPKDLKIIGFDGSKVVRDFEPRLSTIVQPIPSIA 293 Query: 293 RRAVELLLEQMDDKTVERET---VLPVELVEREST 324 + V+LL +++D+ T + + LPVEL++RES+ Sbjct: 294 QLLVKLLEKRIDNPTEKLDNYTYYLPVELLKRESS 328 >ref|NP_965738.1| sucrose operon repressor [Lactobacillus johnsonii NCC 533] gb|AAS09704.1| sucrose operon repressor [Lactobacillus johnsonii NCC 533] Length = 328 Score = 255 bits (651), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 143/336 (42%), Positives = 205/336 (61%), Gaps = 22/336 (6%) Query: 1 MATINDVAEQAGVSVTTVSRVLNNRGYISEKTRQKVYQVMDELNYQPNELARSLLRKHSN 60 M + DVA +AG SVTTVSRV+NN GYIS+KTR+KV++ M ELNYQPN +ARSL K + Sbjct: 1 MVKLTDVAAKAGCSVTTVSRVINNYGYISQKTRKKVHEAMKELNYQPNSVARSLQGKKTK 60 Query: 61 VLGLIIPSVAHPFFGELANAIESVAYQHGFKLLLCNSQLDSAKEREYVDMMRRNRVDGMI 120 ++GLI P V++PFFGEL + IE ++HG+K +LCN+ D KER Y+ M+ N+VDG+I Sbjct: 61 LIGLIFPDVSNPFFGELVSKIEDQLFKHGYKTILCNAGNDKEKERTYLQMLMANQVDGII 120 Query: 121 LGSHTLEIGDYTHLNYPLVTIDRRIGD-IPFVASDNENGGALAARLLIAKGCRKIGHLSG 179 G+H L I +Y P+V+ DR++ D IP V++DN GG+LA + L G R I + G Sbjct: 121 AGAHNLGIEEYQRTGLPIVSFDRKLSDNIPIVSADNFKGGSLATQELYNHGARHI-YFVG 179 Query: 180 NMKLDMLSNLRTTGFEREARQGGVKFVTYQTEL-DVFDEQIYNEI-------IRKMFTEH 231 N LD G + R G K + +L + I+NE IR + H Sbjct: 180 NPTLD--------GHPTQKRLLGYKETIKELKLTEHIHPVIFNETLALKEMAIRDLLENH 231 Query: 232 PDIDGVFATSDLMALFVMKWCRTFGKEVPRDVRIIGYDDIDAASWYMPGLSTIKQPIKDM 291 +DG+ A+ DL AL ++ G +P+D++IIG+D + P LSTI QPI + Sbjct: 232 -KVDGIVASDDLTALLILNISHDLGIHIPKDLKIIGFDGSKIVRDFEPRLSTIVQPIPSI 290 Query: 292 ARRAVELLLEQMDDKTVERET---VLPVELVEREST 324 A+ V+LL +++D+ T E + LPVEL++RES+ Sbjct: 291 AQLLVKLLEKRIDNPTEELDNYTYYLPVELLKRESS 326 >ref|NP_843192.1| ribose operon repressor [Bacillus anthracis str. Ames] gb|AAP24678.1| ribose operon repressor [Bacillus anthracis str. Ames] Length = 323 Score = 254 bits (648), Expect = 2e-66, Method: Compositional matrix adjust. Identities = 129/326 (39%), Positives = 207/326 (63%), Gaps = 6/326 (1%) Query: 1 MATINDVAEQAGVSVTTVSRVLNNRGYISEKTRQKVYQVMDELNYQPNELARSLLRKHSN 60 M+TI DVA+ AGVSV+TVSRVLN GY+ E T +KV + ++ L+Y+P+ +ARSL K S Sbjct: 1 MSTIKDVAKLAGVSVSTVSRVLNKNGYVHEDTLKKVERAIEMLDYKPSTVARSLYNKKSR 60 Query: 61 VLGLIIPSVAHPFFGELANAIESVAYQHGFKLLLCNSQLDSAKEREYVDMMRRNRVDGMI 120 ++GL++P++ +PFF E+A A+E VA++ G+ ++LCNS KE++Y+D++R+N VDG I Sbjct: 61 LIGLVVPNIVNPFFPEVARAVEDVAHKQGYTVVLCNSDESLEKEKQYIDVLRQNNVDGFI 120 Query: 121 LGSHTLEIGDYTHLNYPLVTIDRRIGD-IPFVASDNENGGALAARLLIAKGCRKIGHLSG 179 + ++ +Y +L+ P+V IDR + IP V +DN G A +LLI KGC++I H+ G Sbjct: 121 VATNPQNSVNYMNLSVPVVAIDRMFNERIPAVYADNYAGSQAATKLLIDKGCKRIAHIRG 180 Query: 180 NMKLDMLSNLRTTGFEREARQGGVKFVTYQTELDVFDEQIYNEIIRKMFTEHPDIDGVFA 239 + +N R GF Q + ++ ++ FD + ++ E+P IDG+ A Sbjct: 181 PRDVST-ANERFEGFVDVITQNNLSYMIAES---TFDPANSERVAVELLEEYPHIDGIVA 236 Query: 240 TSDLMALFVMKWCRTFGKEVPRDVRIIGYDDIDAASWYMPGLSTIKQPIKDMARRAVELL 299 +DL+A+ ++K G +P D++IIG+D I P ++T+ QPI +M + A ELL Sbjct: 237 GNDLIAIGIVKAALQKGISIPDDLQIIGFDGISLTEMMYPSITTVAQPIYEMGKVATELL 296 Query: 300 LEQMDDKTVERETV-LPVELVEREST 324 LEQM+ +E + LP+E++ER +T Sbjct: 297 LEQMEGNVLEEKHYRLPIEIIERNTT 322 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 0.320 0.137 0.391 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: 451,892,083 Number of extensions: 18383025 Number of successful extensions: 49661 Number of sequences better than 1.0e-05: 1233 Number of HSP's gapped: 48165 Number of HSP's successfully gapped: 1246 Length of query: 324 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 198 Effective length of database: 415,135,104 Effective search space: 82196750592 Effective search space used: 82196750592 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 (21.8 bits) S2: 126 (53.1 bits)