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= 0340.0045.p (333 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_00180754.1| hypothetical protein Mther123301 [Moorella th... 80 6e-14 ref|NP_812034.1| transcriptional regulator [Bacteroides thetaiot... 80 7e-14 ref|ZP_00060872.1| COG2207: AraC-type DNA-binding domain-contain... 77 4e-13 ref|NP_534775.1| transcriptional regulator, AraC family [Agrobac... 77 7e-13 ref|NP_356357.1| AGR_L_1135p [Agrobacterium tumefaciens] >gi|255... 77 8e-13 >ref|ZP_00180754.1| hypothetical protein Mther123301 [Moorella thermoacetica ATCC 39073] Length = 439 Score = 80.1 bits (196), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 45/128 (35%), Positives = 76/128 (59%), Gaps = 1/128 (0%) Query: 191 LAKLILPAASVPFTQQPQINEDPLHDVILYMISNFSEKITLKEISRQIAMSSRQFQRLFK 250 L +L+ A V T++ Q N + Y+ +NFS+ +TL+E++RQ+ +S F +LFK Sbjct: 308 LERLMALVAQVAETRE-QRNSSLIDRASKYIEANFSQDLTLEEVARQVYLSPCYFSKLFK 366 Query: 251 IKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIYDMKYFYRLFREYSGMTPACY 310 G ++I L ++R+K + LL+ TKL + IA VG D +YF ++F++ G TP+ + Sbjct: 367 QFKGLNFIDYLTKVRLKAARELLLNTKLPVAEIATRVGYRDARYFGQVFKKQEGYTPSVF 426 Query: 311 RNRFHSHF 318 R +HF Sbjct: 427 RKIGGAHF 434 >ref|NP_812034.1| transcriptional regulator [Bacteroides thetaiotaomicron VPI-5482] gb|AAO78228.1| transcriptional regulator [Bacteroides thetaiotaomicron VPI-5482] Length = 289 Score = 80.1 bits (196), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 66/262 (25%), Positives = 115/262 (43%), Gaps = 20/262 (7%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 H H E+ YV +G G+ + + GD+L++ + H + ++ E Sbjct: 32 HFHTEYEIIYVKEGTGMRFVGNNAEKYADGDILLLGSDLPHYMKSDEVYRQE-----GST 86 Query: 120 LRPELCRIPGELPGQYSEEDMVP----LLKLLELKQWFGYRENNVELSFLLRRMQGIHNN 175 LR I E + + P + LLE Q Y L+ ++ I Sbjct: 87 LRTTGTIIQFEKDFMHHAFNYYPHFMKIKNLLEEAQRGIYFPAGCSPR-LVDLLESIPVE 145 Query: 176 GSAEDQQQLYPLLFELAKLILPAASVPFTQQPQINEDPLHD------VILYMISNFSEKI 229 + LL E+A + AS D ++D +I+Y+ N++ +I Sbjct: 146 TGVDQITSFLQLLKEMANV----ASRSVLSTSDFENDIIYDGSRIDKIIVYLNKNYTRQI 201 Query: 230 TLKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGI 289 L EIS AM+ F R FK KTG+S+ + E+R+ Y+C LL+ + I I++E G Sbjct: 202 DLNEISSLAAMNPAAFCRFFKSKTGKSFKNYILEMRIGYACKLLLMGDMNISQISVECGF 261 Query: 290 YDMKYFYRLFREYSGMTPACYR 311 + +F + F++++G TP+ Y+ Sbjct: 262 DTISHFNKSFKKHTGFTPSYYK 283 >ref|ZP_00060872.1| COG2207: AraC-type DNA-binding domain-containing proteins [Clostridium thermocellum ATCC 27405] Length = 305 Score = 77.4 bits (189), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 69/261 (26%), Positives = 122/261 (46%), Gaps = 18/261 (6%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 ++H+ E+ Y+ +G+ + A ++ D+++I P H F +G E I+L+ Sbjct: 46 NKHECFEMVYIKRGKAVFEIAGYPAEIGPNDIIIIKPNQPHKFIVKSESGCE-FIVLSF- 103 Query: 120 LRPELCRIPGELPGQYSEEDMVPLLKLLELKQWFGYRENNV----ELSFLLRRMQGIHNN 175 + GQYS+ + L + K+ + V ++ LL R+ N Sbjct: 104 ------KFVNRFDGQYSDVSLENFLDFVSGKETGPFITLKVSQKNDIIVLLNRILKEREN 157 Query: 176 GSAEDQQQLYPLLFELAKLILPAASVPF-----TQQPQINEDPLHDVILYMISNFSEKIT 230 + Y L+ EL LI A + + + P+I E + + Y+ +N+ I+ Sbjct: 158 PDIGSEFLNYLLVMELFVLISRALKMEWENSIKNKSPKIKE-LIQASVNYINNNYERDIS 216 Query: 231 LKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIY 290 LK+I+R + +S+ F R FK + G S I L +IR++ + LL T I IAL VG Sbjct: 217 LKDIARYVFLSTSYFTRAFKEEMGISPINYLLKIRVERAKELLKDTDNRISDIALSVGFS 276 Query: 291 DMKYFYRLFREYSGMTPACYR 311 + + F +F++Y +TP YR Sbjct: 277 NQQRFNDIFKKYVKLTPLQYR 297 >ref|NP_534775.1| transcriptional regulator, AraC family [Agrobacterium tumefaciens str. C58 (U. Washington)] pir||AE3084 transcription regulator, AraC family Atu4297 [imported] - Agrobacterium tumefaciens (strain C58, Dupont) gb|AAL45091.1| transcriptional regulator, AraC family [Agrobacterium tumefaciens str. C58 (U. Washington)] Length = 297 Score = 76.6 bits (187), Expect = 7e-13, Method: Compositional matrix adjust. Identities = 69/264 (26%), Positives = 116/264 (43%), Gaps = 20/264 (7%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 H H EL + G+ + GDL+++ P + H +Q S LI + Sbjct: 31 HYHPEFELTLTLNSAGMRFVGDSVENYGDGDLVLLGPNLPHAWQ------SHGLINAPGV 84 Query: 120 LRPELCR-----IPGELPGQYSEEDMVPLLKLLELKQWFGYRENNVELSFLLRRMQGIHN 174 R +C I G + + PLL +E + E+ L+ + R+ +H Sbjct: 85 HRAVVCWFTRDWIEGLIALTPELSAITPLL--VESGHGICFGED--ALAKVGERLATLHK 140 Query: 175 NGSAEDQQQLYPLLFELAKLI----LPAASVPFTQQPQINEDPLHDVILYMISNFSEKIT 230 + L +L +LA++ L A V + P+ + + V+ ++ +++ I+ Sbjct: 141 IAPEQQILTLLGVLVDLARVSDRRPLSAGEVTASTAPR-DRARMQRVLNHIHAHYIGTIS 199 Query: 231 LKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIY 290 +K +S +S Q QRLFK T + Q + ++R+ +C LL T L + IA E G Sbjct: 200 IKPLSEIAHLSDSQLQRLFKRSTRMTISQYIGQLRVGGACRLLAQTDLSLARIAEETGFS 259 Query: 291 DMKYFYRLFREYSGMTPACYRNRF 314 D +F R FR GMTP YR +F Sbjct: 260 DAAHFSRQFRAARGMTPGDYRRQF 283 >ref|NP_356357.1| AGR_L_1135p [Agrobacterium tumefaciens] pir||D98202 transcription regulator araC/xylS family VC1260 [imported] - Agrobacterium tumefaciens (strain C58, Cereon) gb|AAK89142.1| AGR_L_1135p [Agrobacterium tumefaciens str. C58 (Cereon)] Length = 313 Score = 76.6 bits (187), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 69/264 (26%), Positives = 116/264 (43%), Gaps = 20/264 (7%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 H H EL + G+ + GDL+++ P + H +Q S LI + Sbjct: 47 HYHPEFELTLTLNSAGMRFVGDSVENYGDGDLVLLGPNLPHAWQ------SHGLINAPGV 100 Query: 120 LRPELCR-----IPGELPGQYSEEDMVPLLKLLELKQWFGYRENNVELSFLLRRMQGIHN 174 R +C I G + + PLL +E + E+ L+ + R+ +H Sbjct: 101 HRAVVCWFTRDWIEGLIALTPELSAITPLL--VESGHGICFGED--ALAKVGERLATLHK 156 Query: 175 NGSAEDQQQLYPLLFELAKLI----LPAASVPFTQQPQINEDPLHDVILYMISNFSEKIT 230 + L +L +LA++ L A V + P+ + + V+ ++ +++ I+ Sbjct: 157 IAPEQQILTLLGVLVDLARVSDRRPLSAGEVTASTAPR-DRARMQRVLNHIHAHYIGTIS 215 Query: 231 LKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIY 290 +K +S +S Q QRLFK T + Q + ++R+ +C LL T L + IA E G Sbjct: 216 IKPLSEIAHLSDSQLQRLFKRSTRMTISQYIGQLRVGGACRLLAQTDLSLARIAEETGFS 275 Query: 291 DMKYFYRLFREYSGMTPACYRNRF 314 D +F R FR GMTP YR +F Sbjct: 276 DAAHFSRQFRAARGMTPGDYRRQF 299 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 0.324 0.139 0.416 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: 480,149,218 Number of extensions: 19346680 Number of successful extensions: 43487 Number of sequences better than 1.0e-05: 239 Number of HSP's gapped: 43651 Number of HSP's successfully gapped: 239 Length of query: 333 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 207 Effective length of database: 415,135,104 Effective search space: 85932966528 Effective search space used: 85932966528 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 126 (53.1 bits)