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= 0440.0012.p (391 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1D5V1.1 B1D5V1_9BACL Regulatory protein GntR HTH 225 5e-57 B3K3S1.1 B3K3S1_9BACI Regulatory protein GntR HTH 204 1e-50 B7DVD9.1 B7DVD9_9BACL Regulatory protein GntR HTH 197 1e-48 A0AGL7.1 A0AGL7_LISW6 Complete genome 180 2e-43 A4IPD0.1 A4IPD0_GEOTN Transcriptional regulator 177 2e-42 >B1D5V1.1 B1D5V1_9BACL Regulatory protein GntR HTH Length = 383 Score = 225 bits (574), Expect = 5e-57, Method: Compositional matrix adjust. Identities = 127/374 (33%), Positives = 208/374 (55%), Gaps = 13/374 (3%) Query: 11 KPLYQTIYQSIKEGIQSGKYAPGDQVPTEKELTDMYDVSRLTAKNAMNLLAEEGWIHRVS 70 KP+Y+ I+++++E I KY PGD+VP+EKEL D Y+VSR+T+K A+ LLA EG+I R Sbjct: 6 KPMYERIFEALREDIIEKKYIPGDRVPSEKELGDEYNVSRITSKKALELLANEGYIIRQP 65 Query: 71 GKGSFVSELAVEQANRS-----------EQRQARLIGLILAGFSDSYGTELLRTMIHELT 119 G+GSFVS+ Q + ++ LIGL++ F+DSYG L+ M Sbjct: 66 GRGSFVSDQPAPQPKQPAAAGAIAQKARKEDGKLLIGLVITDFADSYGNGLIYGMEEASR 125 Query: 120 RRGYHAILKISNESQEMETQYLNELIALGVQGILILPVQAEFHNVALLKVTLSNFPIVLV 179 + +L+ + +E + + L+ LGV G++I P Q E+ N +LK+ ++ FP VLV Sbjct: 126 HHNCYLVLRRTFGMPALEEEAIKGLLELGVDGLIIFPAQGEYFNAEILKLVINQFPFVLV 185 Query: 180 DRRLSGVSVPYVGSNNKEIAHQLTMKLLNSGHNKISVISHENLNNSSLNDRMDGIRDAYM 239 DR L G+S + ++N A T L GH I+ ++ ++ +++ +R++G A+ Sbjct: 186 DRHLKGISASSIATDNVGAAKDGTNHLFELGHKSIAFLTPPPVDTTAIEERIEGFIQAHA 245 Query: 240 EKQVXXXXXXXXXXXETSYWNLSDTQLLERDFQKIYQKLQEKPEITCFFALDYLSGQILW 299 EK + ++ + + + D QKI L + P+IT FA +Y GQI + Sbjct: 246 EKGIVVDREVWMENITSTLPKHNTEENKQEDIQKIISHLNKHPQITALFATEYNIGQIAF 305 Query: 300 YALHQIGKSIPEDYSLLSFDGPLQNFLSPSFTRIIQNQPEIGLHAVGLLLQMIESGQPDY 359 A+ Q+GKS+P DYS++ FD P N P FT + QNQ E+G A +L++ +GQ Sbjct: 306 QAVQQMGKSVPRDYSIICFDCPETNGRYP-FTHLSQNQHEMGRVAFENVLKLW-AGQSVP 363 Query: 360 KEVIVKTRFLDNDS 373 ++++ + +DS Sbjct: 364 NKILLDASLVVSDS 377 >B3K3S1.1 B3K3S1_9BACI Regulatory protein GntR HTH Length = 386 Score = 204 bits (520), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 115/359 (32%), Positives = 192/359 (53%), Gaps = 11/359 (3%) Query: 5 KQTMKKKPLYQTIYQSIKEGIQSGKYAPGDQVPTEKELTDMYDVSRLTAKNAMNLLAEEG 64 K KP+Y+ I+ +K I + + GD+VP+EKEL D Y VSR+T+K A++LLA EG Sbjct: 2 KDAASTKPMYEQIFNEMKRKISTHMFRIGDKVPSEKELADEYGVSRITSKKALDLLAAEG 61 Query: 65 WIHRVSGKGSFVSE----------LAVEQANRSEQRQARLIGLILAGFSDSYGTELLRTM 114 I R GKGSFV++ ++ E + ++IGL++ FS SYGT L+ +M Sbjct: 62 VIVRKPGKGSFVADPDEPVVHREPISSESTETGTAGREKMIGLVITDFSSSYGTRLIYSM 121 Query: 115 IHELTRRGYHAILKISNESQEMETQYLNELIALGVQGILILPVQAEFHNVALLKVTLSNF 174 +L+ + Q+ E + +L LGV G+++ P Q E+ N +LK+ ++ F Sbjct: 122 EQYSRENDCFLVLRRTFGDQDNEELSIQKLRNLGVNGLIVFPAQGEYFNAEILKMVIARF 181 Query: 175 PIVLVDRRLSGVSVPYVGSNNKEIAHQLTMKLLNSGHNKISVISHENLNNSSLNDRMDGI 234 P+VL+DR+L GV+ + ++N A Q L + GH I ++S + +++ +R++G Sbjct: 182 PLVLIDRKLKGVAAASISTDNLGAAVQAVEHLFDLGHRHICLLSPPPRDTTAVEERIEGF 241 Query: 235 RDAYMEKQVXXXXXXXXXXXETSYWNLSDTQLLERDFQKIYQKLQEKPEITCFFALDYLS 294 A+ + + + N +ER+ Q+I Q LQ+ P IT FFA++Y Sbjct: 242 VQAHAARGIAFDKEIWISDVTATLPNAFYESNIEREIQRIMQHLQDHPSITAFFAIEYNI 301 Query: 295 GQILWYALHQIGKSIPEDYSLLSFDGPLQNFLSPS-FTRIIQNQPEIGLHAVGLLLQMI 352 + A ++G +PED S++ FD P N FT + QN+ E+G A+ +L ++ Sbjct: 302 ALLAKVAAERLGLRVPEDLSIICFDSPQLNIGEGYLFTHMRQNEEEMGRLAIETVLGIM 360 >B7DVD9.1 B7DVD9_9BACL Regulatory protein GntR HTH Length = 379 Score = 197 bits (502), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 130/379 (34%), Positives = 206/379 (54%), Gaps = 25/379 (6%) Query: 10 KKPLYQTIYQSIKEGIQSGKYAPGDQVPTEKELTDMYDVSRLTAKNAMNLLAEEGWIHRV 69 +K LY+ IY+ ++ I SG+Y PGD +PTE EL + + VSR+T A+ +LA+EG I R Sbjct: 4 RKVLYKKIYKDLRARILSGEYRPGDAIPTEHELMNQFGVSRITTNRALKMLADEGLIVRK 63 Query: 70 SGKGSFVSELAVEQANR----SEQRQARLIGLILAGFSDSYGTELLRTMIHELTRRGYHA 125 G G+FVS A+R S Q ARL+G +L F S+G LL + L Sbjct: 64 VGLGTFVSNSVSSSASRDNEHSGQPAARLVGFVLP-FLHSFGPRLLAALERHLRDHDICL 122 Query: 126 ILKISNESQEMETQYLNELIALGVQGILILPVQAEFHNVALLKVTLSNFPIVLVDRRLSG 185 + S SQ++E ++ L+ +G +G++I+PV E++N ++LK+ FPIVLVD+RL G Sbjct: 123 AIACSEGSQDIEAYCIDRLVEIGAKGLIIMPVNGEYYNHSILKLHTLGFPIVLVDKRLPG 182 Query: 186 VSVPYVGSNNKEIAHQLTMKLLNSGHNKISVISHENLNNSSLNDRMDGIRDAYMEKQVXX 245 + VP V ++N E + +LT LL+ GH +I+ S + S+L DR G A + + Sbjct: 183 IPVPSVCTDNVEASRRLTEHLLSLGHRQIAFFSPKIKGTSTLEDRFKGFSMALNQAGI-- 240 Query: 246 XXXXXXXXXETSYW---NLSDTQLLERDFQKIYQ--KLQEKPEITCFFAL-DYLSGQILW 299 SY +L D +L E D ++ + K E++ FA DYL+ + W Sbjct: 241 -------EVNPSYCIEASLPDYRLEELDKNQLSTICEFMRKTEVSAVFATDDYLA--LYW 291 Query: 300 Y-ALHQIGKSIPEDYSLLSFDG--PLQNFLSPSFTRIIQNQPEIGLHAVGLLLQMIESGQ 356 Y A +G+ IP+D++++ FD P + SFT IQ++ I AV LLL ++++ Sbjct: 292 YEAARCLGRQIPDDFAIVCFDAYRPHYYYHLESFTSAIQDEQSIAAEAVRLLLSLLQNDN 351 Query: 357 PDYKEVIVKTRFLDNDSIR 375 + V+VK + + S + Sbjct: 352 VEVSNVLVKAKIVVGASTK 370 >A0AGL7.1 A0AGL7_LISW6 Complete genome Length = 372 Score = 180 bits (457), Expect = 2e-43, Method: Compositional matrix adjust. Identities = 130/374 (34%), Positives = 193/374 (51%), Gaps = 18/374 (4%) Query: 10 KKPLYQTIYQSIKEGIQSGKYAPGDQVPTEKELTDMYDVSRLTAKNAMNLLAEEGWIHRV 69 KK LYQ +Y +K IQ GK G ++PTE EL +DVS +T K A+ LL ++G+I R Sbjct: 2 KKLLYQKVYDQLKLSIQEGKIPVGSKMPTENELMAQFDVSSITLKKALELLKKDGYISRR 61 Query: 70 SGKGSFVSELAVEQANRSEQRQAR-----LIGLILAGFSDSYGTELLRTMIHELTRRGYH 124 G+FV + + SEQ + R L G I+ F D++GT LL M+ E + H Sbjct: 62 PRVGTFV----INASPISEQIETRMFDKPLFGCIMTNFDDTFGTILLSGML-EHSDTKAH 116 Query: 125 AILKISNESQEMETQYLNELIALGVQGILILPVQAEFHNVALLKVTLSNFPIVLVDRRLS 184 I+K S E E + L E I + V GILILP ++F + LL++ FP+V++DR L Sbjct: 117 IIVKKSLGDTEREEEILQEFIEMNVAGILILPASSKFVSPTLLELASQKFPLVVIDRTLE 176 Query: 185 GVSVPYVGSNNKEIAHQLTMKLLNSGHNKISVISHENLNNSSLNDRMDGIRDAYMEKQVX 244 G+ + + S+N E +T KL GH I +I+ + S+L+ R++G + Sbjct: 177 GLPISSISSDNTEAGRIITEKLFEIGHKHIGMITSTS-PVSTLDSRVNGFIRGHASFHTA 235 Query: 245 XXXXXXXXXXETSYWNLSDTQLLERDFQKIYQKLQEKPEITCFFALDYLSGQILWYALHQ 304 E+ N T ++ D KI L+ PEIT A +Y ++ A ++ Sbjct: 236 FHSDYVFREIESVMPN--STVSIQTDIDKIADFLKTHPEITALVATEYNIALLIKQACNK 293 Query: 305 IGKSIPEDYSLLSFDGPLQNFLSPS---FTRIIQNQPEIGLHAVGLLLQMIESGQPDYKE 361 +GKSIP D S++ FD P NF S FT I Q Q EIG+ AV +LL + KE Sbjct: 294 LGKSIPADLSVVCFDHP-DNFFDSSAFQFTHIKQAQYEIGVKAVDMLLNQVHKPDAINKE 352 Query: 362 VIVKTRFLDNDSIR 375 ++ ++ DSI+ Sbjct: 353 ML-PPMLVEGDSIK 365 >A4IPD0.1 A4IPD0_GEOTN Transcriptional regulator Length = 377 Score = 177 bits (449), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 116/378 (30%), Positives = 195/378 (51%), Gaps = 13/378 (3%) Query: 12 PLYQTIYQSIKEGIQSGKYAPGDQVPTEKELTDMYDVSRLTAKNAMNLLAEEGWIHRVSG 71 P Y I Q I + IQ GK+ P D++P+E EL + + VSR+T K A++ L EEG I+R+ G Sbjct: 4 PFYMQIRQYIMDHIQQGKWKPNDKIPSENELAEKFQVSRITVKKALDALVEEGIIYRIQG 63 Query: 72 KGSFV-----SELAVEQANRSEQRQARLIGLILAGFSDSYGTELLRTMIHELTRRGYHAI 126 +GSFV SE + N S+Q ++LI I+ + + T ++ + L + GY I Sbjct: 64 RGSFVAKKEDSEHIIYPNNVSQQNSSKLIACIIPRLNSQFITIMMSEIEELLAQHGYRVI 123 Query: 127 LKISNESQEMETQYLNELIALGVQGILILPVQAEFHNVALLKVTLSNFPIVLVDRRLSGV 186 L + +SQ++ETQ L E++ LGV G++I P + E +N +LK+T+ FP+VL+DR G+ Sbjct: 124 LCQTYDSQQLETQILKEVLRLGVDGLIIYPAEGETYNEEILKLTIEKFPLVLIDRYFRGI 183 Query: 187 SVPYVGSNNKEIAHQLTMKLLNSGHNKISVISHENLNNSSLNDRMDGIRDAYMEKQVXXX 246 V ++N A++ T LL GH KI ++S +S+ DR+ G A E + Sbjct: 184 GANSVCTDNVLGAYEATKHLLELGHTKIGIVSSIPEGTTSIEDRIKGFEKALTEYNIPID 243 Query: 247 XXXXXXXXETSYWNLSDTQLLERDFQKIYQKLQEKPEITCFFALDYLSGQILWYALHQIG 306 + L + + +D KI L +IT F ++ +G + A ++G Sbjct: 244 HRLYLLDLHLT---LEEHDHINKD--KIKNFLSNHRDITALFLVN--NGLTVIEAALEMG 296 Query: 307 KSIPEDYSLLSFDG-PLQNFLSPSFTRIIQNQPEIGLHAVGLLLQMIESGQPDYKEVIVK 365 +IP+D S++ FD + T I Q + + AV L++ IE+ +++ V Sbjct: 297 YTIPQDLSMIMFDDYEFSHLHKVPPTCIRQQETLLAQEAVKLMISTIENPLQKRQQIFVP 356 Query: 366 TRFLDNDSIRINKKQTGE 383 + + S + + T + Sbjct: 357 PKLIVRSSTDVCQTSTNQ 374 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.316 0.134 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 2,180,289,256 Number of extensions: 88230132 Number of successful extensions: 257270 Number of sequences better than 1.0e-05: 2974 Number of HSP's gapped: 258172 Number of HSP's successfully gapped: 2976 Length of query: 391 Length of database: 3,060,696,203 Length adjustment: 138 Effective length of query: 253 Effective length of database: 1,760,596,133 Effective search space: 445430821649 Effective search space used: 445430821649 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 132 (55.5 bits)