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= 0523.0013.p (626 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q184T0.1 Q184T0_CLOD6 Putative sigma-54-dependent transcriptiona... 375 e-102 Q4MW83.1 Q4MW83_BACCE Carbamoyl-phosphate synthase, large subuni... 374 e-101 B2A0N2.1 B2A0N2_NATTJ Putative sigma54 specific transcriptional ... 367 2e-99 C2Q4M7.1 C2Q4M7_BACCE Carbamoyl-phosphate synthase, large subunit 365 9e-99 C2SUQ6.1 C2SUQ6_BACCE Carbamoyl-phosphate synthase, large subunit 365 1e-98 >Q184T0.1 Q184T0_CLOD6 Putative sigma-54-dependent transcriptional regulator Length = 669 Score = 375 bits (963), Expect = e-102, Method: Compositional matrix adjust. Identities = 211/574 (36%), Positives = 325/574 (56%), Gaps = 15/574 (2%) Query: 1 VIAGAETTSTLLCRQLTSLLGEYMSFHPFSVNGWTGEA----EVDLVIISSHILFIKHSP 56 V G L + L + + + + +N T + ++ LV+I +L IK Sbjct: 7 VTDGLSKLECFLNKNLEMIFKDKVMIKNYYLNKITEKELIKDDIILVMIDDRVLKIKK-- 64 Query: 57 FVLRKQTDVFIMKRTLSRKGWEQIKDLPAGNRYLVVNDERDSVVETISLLYELGLRHVDL 116 + + + + R++ +K ++ LP G LVVND + +V+ETIS LY +G+ H++ Sbjct: 65 -YVEDVSKIITINRSIKQKDIYKLFSLPEGIDVLVVNDNKHTVLETISNLYNIGINHLNF 123 Query: 117 VPCYPGLLENGSVLQAITPGEAHLAPASVEHIIDIGPRVIDIGTIVEILTRFNLVNSKTR 176 +P P E ++ AITPGE+ L P +E +ID+G R ID T ++I+ + L + + Sbjct: 124 IPYNPNE-EYRNIKIAITPGESSLVPKYIEEVIDLGHRYIDSSTFIQIIAKLKLDDKEIT 182 Query: 177 RILDRYASEIMTSSQGLQFTMQEMLDTKNLFEETLNMVQDGVVTYDELGRVTFINRTAEE 236 L +Y EI++ G+ +E+ + +N+ G+ + G + N + + Sbjct: 183 ERLIKYTDEIISLYSGINTKYKELTIKADELNSIINLSNLGMAMVSDKGNIIICNNSLRD 242 Query: 237 ILXXXXAWDGSRLKVGQLFSRHGIELEWQEGEIRDRLVTIRKQNVILSKMAILGRGNAKE 296 IL G + I+ + + D ++ + + ++K I G Sbjct: 243 ILDIQSNIIGKNI---DELENENIKKIFSLSKAHDEVIKFNNKYLNVNKYNIESFGRVTG 299 Query: 297 RVLIFNIAXXXXXXXXXXXXXXXDKGHTSRFTFEDIVTDAEPMKRIIEKAKKMAKNDLSV 356 +KG +R+TF+DI T + M+R + K+A++D ++ Sbjct: 300 YYFCIQEITYIRKLEQNLSKKLREKGQVARYTFDDIKTVSTKMERTKKLGMKIAESDYTI 359 Query: 357 LILGENGTGKELFAHSIHDYSHRSPFAFIAVNCSALPENLLESELFGYEEGAFTGARKGG 416 LI GE+GTGKEL A SIH+ S R FIA+NC+A+PENLLESELFGYEEGAFTGA KGG Sbjct: 360 LITGESGTGKELMAQSIHNASPRHSQPFIAINCAAMPENLLESELFGYEEGAFTGALKGG 419 Query: 417 KPGLFEQAHKGTIFLDEIGDISPHLQARLLRVIQQKEILKVGGTRLLPVDVRVIAATNRN 476 K GLFEQA+ GTIFLDEIGD+ +LQ++LLRV+Q+ ++++VGG ++ +DVRVIAATN+N Sbjct: 420 KKGLFEQANNGTIFLDEIGDMPIYLQSKLLRVLQENQVMRVGGENVIDIDVRVIAATNKN 479 Query: 477 LAELVKSGGFREDLYYRLKVLQIEIVPLRERKEDIPRLIRYFLARRGITRKLPPELSVAL 536 L E++K FR DLYYR+ VL I I PLRERKEDI ++++F+ R+ R + ++ + Sbjct: 480 LLEMIKGDRFRADLYYRINVLPINIPPLRERKEDIEVMLKHFMKRK---RAISQDVQDII 536 Query: 537 AAHDWPGNIRELENTVEYIAIMNGED-FSVEDLP 569 A++WPGNIREL+NT YI IM+ ED + DLP Sbjct: 537 NAYEWPGNIRELKNTAMYINIMSSEDVILINDLP 570 >Q4MW83.1 Q4MW83_BACCE Carbamoyl-phosphate synthase, large subunit EC=6.3.5.5 Length = 677 Score = 374 bits (959), Expect = e-101, Method: Compositional matrix adjust. Identities = 221/582 (37%), Positives = 344/582 (59%), Gaps = 34/582 (5%) Query: 8 TSTLLCRQLTSLLGEYMSFHPFSVNGWTGEAEVDLVIISSHILFIKHSPFVLRKQTDVFI 67 T L +QLT ++G+ + FSV + +I+ + I+ + + +V I Sbjct: 18 TRKALHQQLTEMIGDLIDIESFSVEESIPKVFHSTLIVLPNTFTIETVKDFIGENCEVII 77 Query: 68 MKRTLSRKGWEQIKDLPAGNRYLVVNDERDSVVETISLLYELGLRHVDLVPCYPGLLENG 127 KRTL+ + +Q+ LP G + L VND ++V E+I + +LGL H++ VP YPG Sbjct: 78 AKRTLNYENVDQLLFLPEGTQALYVNDNHETVYESIETMRQLGLNHIEYVPYYPGKTNIQ 137 Query: 128 SVLQAITPGEAHLAPASVEHIIDIGPRVIDIGTIVEILTRFNLVNSKTRRILDRYASEIM 187 + AITPGE + P VE +I+IG R+IDI TI+ IL RF+L+ + +RY +I+ Sbjct: 138 MIKLAITPGELEIIPDFVEKVINIGHRLIDITTIMSILDRFHLMEESGNHVSERYYRKIV 197 Query: 188 TSSQGLQFTMQEMLDTKNLFEETLNMVQDGVVTYDELGRVTFINRTAEEILXXXXAWDGS 247 ++ L +++ + ++ V DG++ D GR+ N E +L S Sbjct: 198 DLTKNLAKAHRQL-------HQVIDGVGDGILAIDYEGRIVVFNEFLESMLKIK-----S 245 Query: 248 RLKVGQLFSRHGIELEWQEGEIRDRLVTIRKQ----------NVILSKMAILGRGNAKER 297 + +G H I++ ++ + +++ ++Q +VI+ ++ I N + Sbjct: 246 KHAIG-----HPIDVIIDNIDLVNFILSDKQQESGIFVVNGLDVIVERLHI----NDQSI 296 Query: 298 VLIFNIAXXXXXXXXXXXXXXXDKGHTSRFTFEDIVTDAEPMKRIIEKAKKMAKNDLSVL 357 ++ F A KG+ +++ F +IV + ++ + AK++AK DL+VL Sbjct: 297 IVTFRNALKTIGFERKLRKEFVKKGYVAKYNFHNIVGISPTIQDTKQIAKRLAKTDLTVL 356 Query: 358 ILGENGTGKELFAHSIHDYSHRSPFAFIAVNCSALPENLLESELFGYEEGAFTGARKGGK 417 I GE+GTGKELFA +IH+ S R+ F+AVN SAL ++L+ESELFGYE+GAFTGA+KGGK Sbjct: 357 IEGESGTGKELFASAIHNASQRNSGPFLAVNFSALSDDLVESELFGYEDGAFTGAKKGGK 416 Query: 418 PGLFEQAHKGTIFLDEIGDISPHLQARLLRVIQQKEILKVGGTRLLPVDVRVIAATNRNL 477 GLFEQA+ GTIFLDEIGDIS LQARLLRV+Q+KEI++VGG++++P+DVR+IAATN++L Sbjct: 417 MGLFEQANGGTIFLDEIGDISLKLQARLLRVLQEKEIMRVGGSQIIPIDVRIIAATNKDL 476 Query: 478 AELVKSGGFREDLYYRLKVLQIEIVPLRERKEDIPRLIRYFLARRGITRKLPPELSVALA 537 ++++ FREDLY+RLKVL I + LR R+ DI L ++F+A K+ EL L Sbjct: 477 LKMIQENVFREDLYHRLKVLFIHLPELRARRNDIELLAKHFVALSDPKVKIEQELIEELQ 536 Query: 538 AHDWPGNIRELENTVEY-IAIMNGEDFSVEDLPFET--NSPP 576 + W GN+REL+NT++Y +A+ G + DLP + PP Sbjct: 537 GYPWYGNVRELKNTIDYMLAVRTGNQITKNDLPNQHYFQKPP 578 >B2A0N2.1 B2A0N2_NATTJ Putative sigma54 specific transcriptional regulator Length = 706 Score = 367 bits (942), Expect = 2e-99, Method: Compositional matrix adjust. Identities = 203/521 (38%), Positives = 315/521 (60%), Gaps = 24/521 (4%) Query: 61 KQTDVFIMKRTLSRKGWEQIKDLPAGNRYLVVNDERDSVVETISLLYELGLRHVDLVPCY 120 K ++V I RT++ + ++I LP+ + L VND ++S +E I L E+G+ H++ P Y Sbjct: 72 KSSEVIIADRTINYEFIDRIVLLPSRTKVLFVNDAKESALEGIEALQEIGIDHLEFHPYY 131 Query: 121 PGLLENGSVLQ----AITPGEAHLAPASVEHIIDIGPRVIDIGTIVEILTRFNLVNSKTR 176 PG+ S L+ AITPGE P + I DIGPR++D TI+++L + S+ R Sbjct: 132 PGIEFCDSKLKDINIAITPGEKDRVPKHINKIYDIGPRLLDFTTIMKVLKSIGQLESRGR 191 Query: 177 RILDRYASEIMTSSQGLQFTMQEMLDTKNLFEETLNMVQDGVVTYDELGRVTFINRTAEE 236 + + Y +I+T ++ L + + + ++ +QDG+V +D GR++ N Sbjct: 192 QFSNNYLQKIITMAKRLSHSANCISELNQHLNTVIDGLQDGLVVFDTQGRISVYNENFRR 251 Query: 237 ILXXXXAWDGSRLKVGQLFSRHGIELEWQEGEIRDRLVTIRKQNVILSKMAIL------G 290 ++ A R ++ + E ++ + + K +++SK+ ++ G Sbjct: 252 MMEIPEANLRGRKISDVIYQKPLKEFLMNYDTEQELSIDLDKDKLLVSKIKLMDNNYLVG 311 Query: 291 RGNAKERVLIFNIAXXXXXXXXXXXXXXXDKGHTSRFTFEDIVTDAEPMKRIIEKAKKMA 350 R +++ + A +KGH ++ TF++IV + + A K++ Sbjct: 312 RFRSQKNSTEYREAKNI------------EKGHFAKHTFDNIVGKSSIVTYTKNIAHKLS 359 Query: 351 KNDLSVLILGENGTGKELFAHSIHDYSHRSPFAFIAVNCSALPENLLESELFGYEEGAFT 410 K +L++L+ GE+GTGKEL+A++IH+ SHR F+AVN SALP+NL+ESELFGYEEGAFT Sbjct: 360 KTELTILLEGESGTGKELYANAIHNSSHRKDAPFLAVNFSALPDNLIESELFGYEEGAFT 419 Query: 411 GARKGGKPGLFEQAHKGTIFLDEIGDISPHLQARLLRVIQQKEILKVGGTRLLPVDVRVI 470 GA KGGKPGLFEQA GTIFLDEIGD S +QARLLRV+Q+KE++++G T++ PV+VRV+ Sbjct: 420 GASKGGKPGLFEQADGGTIFLDEIGDSSLKVQARLLRVLQEKEVMRIGATKIRPVNVRVV 479 Query: 471 AATNRNLAELVKSGGFREDLYYRLKVLQIEIVPLRERKEDIPRLIRYFLA-RRGITRKLP 529 AATN+NL +L+ G FR+DLYYRLK+ I+I LR+RKEDIP+L+ Y + K Sbjct: 480 AATNKNLKQLIAQGNFRQDLYYRLKMGYIKIPALRDRKEDIPKLLDYLIKIETAADIKFD 539 Query: 530 PELSVALAAHDWPGNIRELENTVEYIAIMNGEDF-SVEDLP 569 E+ L +DWPGNIREL+N V Y+ + D+ ++ED+P Sbjct: 540 DEVLNILKNYDWPGNIRELKNVVSYMLAVRQNDYLTIEDIP 580 >C2Q4M7.1 C2Q4M7_BACCE Carbamoyl-phosphate synthase, large subunit Length = 681 Score = 365 bits (936), Expect = 9e-99, Method: Compositional matrix adjust. Identities = 211/571 (36%), Positives = 324/571 (56%), Gaps = 6/571 (1%) Query: 1 VIAGAETTSTLLCRQLTSLLGEYMSFHPFSVN-GWTGEAEVDLVIISSHILFIKHSPFVL 59 +IAG+ T+ L QL LLG+Y+ + + G E +++ SS ++ + + Sbjct: 8 LIAGSSKTTQALQEQLEQLLGDYVYIKSHAADEGIPQSLEDTIILYSSASVYDQTNGMYS 67 Query: 60 RKQTDVFIMKRTLSRKGWEQIKDLPAGNRYLVVNDERDSVVETISLLYELGLRHVDLVPC 119 + + KRT+ + +++ +P + LVVND D+ + I LY+LG+ H+ +P Sbjct: 68 VNAEKIIVGKRTVHHEYIDKLLRIPEDSSVLVVNDNDDATINLIESLYQLGINHIQFIPF 127 Query: 120 YPGLLENGSVLQAITPGEAHLAPASVEHIIDIGPRVIDIGTIVEILTRFNLVNSKTRRIL 179 G+L V A++PGE HL P+ ++ +IDIG R+ D+ TI+E++ L + +I Sbjct: 128 RKGVLFYDDVRIAVSPGETHLCPSYIKEVIDIGVRLFDMTTILEVVECCGLSKDISSKIS 187 Query: 180 DRYASEIMTSSQGLQFTMQEMLDTKNLFEETLNMVQDGVVTYDELGRVTFINRTAEEILX 239 +RY S I+ + L ++ + L V DG++ ++ GR+T N L Sbjct: 188 ERYISNIIELQRKLLHAERDAKQMSEHIQNVLGTVDDGILVVNQEGRITVFNERLTA-LF 246 Query: 240 XXXAWDGSRLKVGQLFSRHGIELEWQEGEIRDRLVTIRKQNVILSKMAILGRGNAKERVL 299 A D V + SR I G+ + I +V++ ++ ++ V Sbjct: 247 HIVAQDVVNEYVEHVMSRRDITDFIMNGKDESKFFDIDGVDVVIFRLQMMQENTI---VA 303 Query: 300 IFNIAXXXXXXXXXXXXXXXDKGHTSRFTFEDIVTDAEPMKRIIEKAKKMAKNDLSVLIL 359 F +KG +++ FEDI+ + MK AKK+A ++ +LI Sbjct: 304 TFKSVHQAFEIEKTAQREMRNKGFHTKYGFEDIIGEHIVMKERKRIAKKLALSEHPILIQ 363 Query: 360 GENGTGKELFAHSIHDYSHRSPFAFIAVNCSALPENLLESELFGYEEGAFTGARKGGKPG 419 GE GTGKELFAH+IH++S R F+AVNCSAL E+LLESELFGYEEG FTGA+KGGK G Sbjct: 364 GETGTGKELFAHAIHEHSLRKNGPFLAVNCSALTESLLESELFGYEEGTFTGAQKGGKKG 423 Query: 420 LFEQAHKGTIFLDEIGDISPHLQARLLRVIQQKEILKVGGTRLLPVDVRVIAATNRNLAE 479 LFE A GTIFLDEIGDIS +Q+ LLRV+Q+ EI ++GG R++PV+VRVI ATN++L Sbjct: 424 LFELADNGTIFLDEIGDISLTVQSHLLRVLQEGEIRRIGGVRIIPVNVRVITATNKDLQG 483 Query: 480 LVKSGGFREDLYYRLKVLQIEIVPLRERKEDIPRLIRYFLARRGITRKLPPELSVALAAH 539 +++G F+ DL+YRL VL + I PL ER+ DIP LI++F+ + G K+ ++ + Sbjct: 484 KIRAGSFKVDLFYRLNVLNLCIPPLIERRADIPILIKHFITKSGKWVKIEQDVLEYFMQY 543 Query: 540 DWPGNIRELENTVEY-IAIMNGEDFSVEDLP 569 +WPGNIREL++T++Y + I G + DLP Sbjct: 544 EWPGNIRELKSTIDYMLTICEGNIVTKGDLP 574 >C2SUQ6.1 C2SUQ6_BACCE Carbamoyl-phosphate synthase, large subunit Length = 681 Score = 365 bits (936), Expect = 1e-98, Method: Compositional matrix adjust. Identities = 211/571 (36%), Positives = 323/571 (56%), Gaps = 6/571 (1%) Query: 1 VIAGAETTSTLLCRQLTSLLGEYMSFHPFSVN-GWTGEAEVDLVIISSHILFIKHSPFVL 59 +IAG+ T+ L QL LLG+Y+ + + G E +++ SS ++ + Sbjct: 8 LIAGSSKTTQALQEQLEQLLGDYVYIKSHAADEGIPQSLEDTIILYSSASVYDQTKGMYS 67 Query: 60 RKQTDVFIMKRTLSRKGWEQIKDLPAGNRYLVVNDERDSVVETISLLYELGLRHVDLVPC 119 + + KRT+ + +++ +P + LVVND D+ + I LY+LG+ H+ +P Sbjct: 68 VNAEKIIVGKRTVHHEYIDKLLRIPEDSSVLVVNDNDDATINLIESLYQLGINHIQFIPF 127 Query: 120 YPGLLENGSVLQAITPGEAHLAPASVEHIIDIGPRVIDIGTIVEILTRFNLVNSKTRRIL 179 G+L V A++PGE HL P+ ++ +IDIG R+ D+ TI+E++ L + +I Sbjct: 128 RKGVLFYDDVRIAVSPGETHLCPSYIKEVIDIGVRLFDMTTILEVVECCGLSKDISSKIS 187 Query: 180 DRYASEIMTSSQGLQFTMQEMLDTKNLFEETLNMVQDGVVTYDELGRVTFINRTAEEILX 239 +RY S I+ + L ++ + L V DG++ ++ GR+T N L Sbjct: 188 ERYISNIIELQRKLLHAERDAKQMSEHIQNVLGTVDDGILVVNQEGRITVFNERLTA-LF 246 Query: 240 XXXAWDGSRLKVGQLFSRHGIELEWQEGEIRDRLVTIRKQNVILSKMAILGRGNAKERVL 299 A D V + SR I G+ + I +V++ ++ ++ V Sbjct: 247 HIVAQDVVNEYVEHVMSRRDITDFIMNGKDESKFFDIDGVDVVIFRLQMMQENTI---VA 303 Query: 300 IFNIAXXXXXXXXXXXXXXXDKGHTSRFTFEDIVTDAEPMKRIIEKAKKMAKNDLSVLIL 359 F +KG +++ FEDI+ + MK AKK+A ++ +LI Sbjct: 304 TFKSVHQAFEIEKTAQREMRNKGFHTKYGFEDIIGEHIVMKERKRIAKKLALSEHPILIQ 363 Query: 360 GENGTGKELFAHSIHDYSHRSPFAFIAVNCSALPENLLESELFGYEEGAFTGARKGGKPG 419 GE GTGKELFAH+IH++S R F+AVNCSAL E+LLESELFGYEEG FTGA+KGGK G Sbjct: 364 GETGTGKELFAHAIHEHSLRKNGPFLAVNCSALTESLLESELFGYEEGTFTGAQKGGKKG 423 Query: 420 LFEQAHKGTIFLDEIGDISPHLQARLLRVIQQKEILKVGGTRLLPVDVRVIAATNRNLAE 479 LFE A GTIFLDEIGDIS +Q+ LLRV+Q+ EI ++GG R++PV+VRVI ATN++L Sbjct: 424 LFELADNGTIFLDEIGDISLTVQSHLLRVLQEGEIRRIGGVRIIPVNVRVITATNKDLQG 483 Query: 480 LVKSGGFREDLYYRLKVLQIEIVPLRERKEDIPRLIRYFLARRGITRKLPPELSVALAAH 539 +++G F+ DL+YRL VL + I PL ER+ DIP LI++F+ + G K+ ++ + Sbjct: 484 KIRAGSFKVDLFYRLNVLNLCIPPLIERRADIPILIKHFITKSGKWVKIEQDVLEYFMQY 543 Query: 540 DWPGNIRELENTVEY-IAIMNGEDFSVEDLP 569 +WPGNIREL++T++Y + I G + DLP Sbjct: 544 EWPGNIRELKSTIDYMLTICEGNVVTKGDLP 574 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 0.320 0.138 0.396 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: 3,371,782,530 Number of extensions: 135318833 Number of successful extensions: 392189 Number of sequences better than 1.0e-05: 9486 Number of HSP's gapped: 374594 Number of HSP's successfully gapped: 9513 Length of query: 626 Length of database: 3,060,696,203 Length adjustment: 142 Effective length of query: 484 Effective length of database: 1,722,912,073 Effective search space: 833889443332 Effective search space used: 833889443332 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: 134 (56.2 bits)