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= 0586.0032.p (262 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KIF0.1 B3KIF0_9BACI RNA polymerase sigma factor 410 e-113 B1DLN9.1 B1DLN9_9BACL RNA polymerase sigma factor 374 e-102 C0ZF72.1 C0ZF72_BREBN RNA polymerase sigma-D factor 233 1e-59 B0THD2.1 B0THD2_HELMI RNA polymerase sigma factor 204 7e-51 C5D9B2.1 C5D9B2_9BACI RNA polymerase, sigma 28 subunit, FliA/Whi... 204 8e-51 >B3KIF0.1 B3KIF0_9BACI RNA polymerase sigma factor Length = 262 Score = 410 bits (1054), Expect = e-113, Method: Compositional matrix adjust. Identities = 205/262 (78%), Positives = 224/262 (85%) Query: 1 LNEHKATQSETDGLWEQWKEHGNPEAKKKLIESYLHIVDYVSSRLAVGLPKNVSKDDLAS 60 ++E K + LW WKE G+ EAKKKLIE +LHIVDYVSSRLA+GLPKNVSK DLAS Sbjct: 1 MDERKTSVLNHADLWSAWKEDGDHEAKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLAS 60 Query: 61 NGVMGLIDAIEKFDYKRGLQFQTYASWRVRGAILDSLRQSDWVPRSVREKAKKIEDAYQQ 120 NGVMGLIDAIEKFDYKRGLQF+TYASWRVRGAILDSLRQ DWVPRSVREKAKKIE AYQQ Sbjct: 61 NGVMGLIDAIEKFDYKRGLQFETYASWRVRGAILDSLRQGDWVPRSVREKAKKIETAYQQ 120 Query: 121 LEQKYLRSVSDEEMSQYLNITEPEFQNMLQDVAVMSLCSLEDPIREEESETRMSILVDDK 180 LEQKYLRSVSD EMS YL++TE EF++MLQ+VAVM+L SLEDPIREEESETRMS+LVD+K Sbjct: 121 LEQKYLRSVSDSEMSDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEK 180 Query: 181 AKNPDRKVNEFYLRDTLTKGIEKLTVKERTVVXXXXXXXXXXXXIAEVMSLSPSRISQLH 240 AKNPD KV+EFYLR+ L KGI KLT KERTVV IAEVMSLSPSRISQLH Sbjct: 181 AKNPDHKVHEFYLREALMKGIGKLTPKERTVVSLLYYEDLSLSEIAEVMSLSPSRISQLH 240 Query: 241 SKAILRLRGTLEKNRDLLMQND 262 SKAILRLRG L+K+RDLLMQND Sbjct: 241 SKAILRLRGALDKDRDLLMQND 262 >B1DLN9.1 B1DLN9_9BACL RNA polymerase sigma factor Length = 256 Score = 374 bits (961), Expect = e-102, Method: Compositional matrix adjust. Identities = 175/248 (70%), Positives = 211/248 (85%) Query: 14 LWEQWKEHGNPEAKKKLIESYLHIVDYVSSRLAVGLPKNVSKDDLASNGVMGLIDAIEKF 73 LW WKE G+ EAKK+LIE +L +VDYV++R+A+GLPKNV KDDLASNGVMGLIDAIEKF Sbjct: 9 LWRAWKEEGDLEAKKRLIEQFLPLVDYVTNRMAIGLPKNVLKDDLASNGVMGLIDAIEKF 68 Query: 74 DYKRGLQFQTYASWRVRGAILDSLRQSDWVPRSVREKAKKIEDAYQQLEQKYLRSVSDEE 133 DY RGLQF+TYASWR+RG+I+D LRQ DWVPRSVREKAK+IE+AYQ LEQKYLRSVSD E Sbjct: 69 DYCRGLQFETYASWRIRGSIIDGLRQGDWVPRSVREKAKRIEEAYQSLEQKYLRSVSDAE 128 Query: 134 MSQYLNITEPEFQNMLQDVAVMSLCSLEDPIREEESETRMSILVDDKAKNPDRKVNEFYL 193 +SQYLN++E EF ML ++A+ ++CSLEDPIREEESETR+S+L+D++AKNPD K +EF+L Sbjct: 129 ISQYLNVSEKEFTTMLHEIAITTVCSLEDPIREEESETRLSLLIDERAKNPDHKAHEFFL 188 Query: 194 RDTLTKGIEKLTVKERTVVXXXXXXXXXXXXIAEVMSLSPSRISQLHSKAILRLRGTLEK 253 +D+L GIEKLT KERTV+ IAEVMSLSPSRISQLHSKAILRLRG L K Sbjct: 189 KDSLISGIEKLTEKERTVISLFYYEELSLSEIAEVMSLSPSRISQLHSKAILRLRGALAK 248 Query: 254 NRDLLMQN 261 ++D L+Q+ Sbjct: 249 HKDQLLQH 256 >C0ZF72.1 C0ZF72_BREBN RNA polymerase sigma-D factor Length = 262 Score = 233 bits (594), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 116/247 (46%), Positives = 166/247 (67%), Gaps = 2/247 (0%) Query: 15 WEQWKEHGNPEAKKKLIESYLHIVDYVSSRLAVGLPKNVSKDDLASNGVMGLIDAIEKFD 74 W WK+ G+ EA+ LI +L +VD V++RLA+ LP NV KDDL S G GL+DA+ KFD Sbjct: 16 WVMWKQEGSREAEVDLITRFLPLVDKVANRLAINLPANVDKDDLISYGRFGLLDALAKFD 75 Query: 75 YKRGLQFQTYASWRVRGAILDSLRQSDWVPRSVREKAKKIEDAYQQLEQKYLRSVSDEEM 134 + RGLQF+TYA WR+RGA++D LR++DW+PR+VR+KAKKIE+AY LEQ+ LR +D+E+ Sbjct: 76 HTRGLQFETYAMWRIRGAMIDGLRENDWIPRTVRDKAKKIEEAYTTLEQQMLRMPTDQEV 135 Query: 135 SQYLNITEPEFQNMLQDVAVMSLCSLEDPIREEESE--TRMSILVDDKAKNPDRKVNEFY 192 S YL I++ E Q + + ++ S+ S+++ + +E+ + R S ++D+ PD Sbjct: 136 SDYLGISKKELQQVFLETSLASMVSIDEAVGDEDEQKTARHSYIIDELTPRPDNVAEVSS 195 Query: 193 LRDTLTKGIEKLTVKERTVVXXXXXXXXXXXXIAEVMSLSPSRISQLHSKAILRLRGTLE 252 L++ L I+KL KER V+ IAE+MSLSPSRISQLHSKA+ RLR L Sbjct: 196 LKEVLVTVIDKLPEKERLVISLFYFEEMTLSEIAEIMSLSPSRISQLHSKALFRLRSALS 255 Query: 253 KNRDLLM 259 + + LM Sbjct: 256 RWKSQLM 262 >B0THD2.1 B0THD2_HELMI RNA polymerase sigma factor Length = 266 Score = 204 bits (519), Expect = 7e-51, Method: Compositional matrix adjust. Identities = 110/257 (42%), Positives = 156/257 (60%), Gaps = 16/257 (6%) Query: 9 SETDGLWEQWKEHGNPEAKKKLIESYLHIVDYVSSRLAVGLPKNVSKDDLASNGVMGLID 68 + T LW +K+H +P A+++LI Y +V +V+ RLA+ LP NV ++DL S GV GL+D Sbjct: 12 ARTGPLWASYKDHKDPAAREELILIYAPLVKFVAGRLAISLPPNVEREDLISYGVFGLMD 71 Query: 69 AIEKFDYKRGLQFQTYASWRVRGAILDSLRQSDWVPRSVREKAKKIEDAYQQLEQKYLRS 128 AIEKFD RGL+F+TYA R+RG++LD LR DWVP SVR+K +++E Y L Q+ R Sbjct: 72 AIEKFDLARGLKFETYAIARIRGSMLDGLRAMDWVPVSVRQKTRELEKTYATLSQRLGRE 131 Query: 129 VSDEEMSQYLNITEPEFQNMLQDVAVMSLCSLE----------DPIREEESETRMSILVD 178 +DEE++Q L +T EF +LQDV ++ SL+ DP+R +S L D Sbjct: 132 ATDEEVAQALGLTLNEFAKLLQDVQATTIMSLDEYWLTDSDKGDPVRLIDS------LAD 185 Query: 179 DKAKNPDRKVNEFYLRDTLTKGIEKLTVKERTVVXXXXXXXXXXXXIAEVMSLSPSRISQ 238 ++ + P + R L + I+KL KERTV+ I V+ +S SRISQ Sbjct: 186 EQVEEPTAALEFEETRLLLAQAIDKLPEKERTVIALYYYEGLTLKEIGAVIGVSESRISQ 245 Query: 239 LHSKAILRLRGTLEKNR 255 LH+KAILRLRG L + + Sbjct: 246 LHTKAILRLRGQLARQK 262 >C5D9B2.1 C5D9B2_9BACI RNA polymerase, sigma 28 subunit, FliA/WhiG EC=4.1.1.65 Length = 254 Score = 204 bits (518), Expect = 8e-51, Method: Compositional matrix adjust. Identities = 108/246 (43%), Positives = 160/246 (65%), Gaps = 1/246 (0%) Query: 9 SETDGLWEQWKEHGNPEAKKKLIESYLHIVDYVSSRLAVGLPKNVSKDDLASNGVMGLID 68 SE W++W H +P+A KL+++Y+ +V Y R+A LPK +SK +L S G+MGL D Sbjct: 7 SEERKYWDRWIYHRDPQAGDKLVQTYMPLVHYHVQRIAASLPKTISKQELISLGLMGLYD 66 Query: 69 AIEKFDYKRGLQFQTYASWRVRGAILDSLRQSDWVPRSVREKAKKIEDAYQQLEQKYLRS 128 A+EKFD R L+F TYAS+R+RGAI D LR+ DW+PRSVREKAKKIE+ ++LEQ+Y+RS Sbjct: 67 ALEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDWLPRSVREKAKKIEETIEKLEQRYMRS 126 Query: 129 VSDEEMSQYLNITEPEFQNMLQDVAVMSLCSLEDPIRE-EESETRMSILVDDKAKNPDRK 187 V+ +E++ L ITE E + + ++ S + I E +E E + + D+K +P+ + Sbjct: 127 VTAKEVADELGITEEEVYMAVNENFFANVLSFQHVITENKEEENALLAIRDEKTPSPEEE 186 Query: 188 VNEFYLRDTLTKGIEKLTVKERTVVXXXXXXXXXXXXIAEVMSLSPSRISQLHSKAILRL 247 V + L + L + I++L+ KE+ V+ I E++ LS SRISQLHSKAI +L Sbjct: 187 VLKQELYEKLAEVIQQLSEKEQLVISLFYKEELTFTEIGEILGLSTSRISQLHSKAIFKL 246 Query: 248 RGTLEK 253 R LE+ Sbjct: 247 RKILEQ 252 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 0.313 0.130 0.360 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: 1,391,885,403 Number of extensions: 51164617 Number of successful extensions: 145204 Number of sequences better than 1.0e-05: 4638 Number of HSP's gapped: 142195 Number of HSP's successfully gapped: 4638 Length of query: 262 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 129 Effective length of database: 1,807,701,208 Effective search space: 233193455832 Effective search space used: 233193455832 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 130 (54.7 bits)