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= 0035.0014.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 B3K8Y2.1 B3K8Y2_9BACI Transcription factor CarD 378 e-103 C0ZHD9.1 C0ZHD9_BREBN Transcription-repair coupling factor 244 4e-63 B7GFI2.1 B7GFI2_ANOFW Transcription-repair coupling factor (Heli... 229 1e-58 Q5L3U5.1 Q5L3U5_GEOKA Transcription-repair coupling factor 227 6e-58 C3J4P7.1 C3J4P7_9BACI Transcription-repair coupling factor 227 1e-57 >B3K8Y2.1 B3K8Y2_9BACI Transcription factor CarD Length = 849 Score = 378 bits (971), Expect = e-103, Method: Compositional matrix adjust. Identities = 181/249 (72%), Positives = 213/249 (85%) Query: 4 LLQGIIEAFSKDPDFQSVTRGVAAGMKEQLISGLSGSARQIMLAALHEETGRPLLIVTHN 63 +LQ +I+ FSKD DF+S+T GV AGM+EQLISGLSGS+RQI++AALH++ RPLL+VTHN Sbjct: 1 MLQALIDVFSKDSDFKSITSGVHAGMREQLISGLSGSSRQILMAALHQDQQRPLLVVTHN 60 Query: 64 MFSAQKMAEDLQEALSPDRVLLYPANELVAAEAAVSSPETLAQRIDVLTKCAQGFRGVVV 123 MFSAQK+A+DLQEALS D+VLLYPANELVAAE+AVSSPETLAQRIDVL +CA+GFRG+VV Sbjct: 61 MFSAQKIADDLQEALSSDQVLLYPANELVAAESAVSSPETLAQRIDVLVRCARGFRGIVV 120 Query: 124 VPYSGVRRLLPSPHVMAGAELTLSQDGTLVLDDFLMSMIEMGYERVERVENRGELSVRGG 183 P+SGVRRLLP+P VM+ A + L GTLVLD FL MIEMGYERVERVE RGE+SVRGG Sbjct: 121 APFSGVRRLLPAPEVMSDARIVLHDGGTLVLDAFLNRMIEMGYERVERVERRGEMSVRGG 180 Query: 184 IIDFFPMTSPLAYRVELFDDEVDSIRTFDPQDQRSIDKVRSVKITPAKEIIADQIRLDSA 243 IIDF+PMT+ +AYRVELFD+++DSIRTFDP DQRSIDKVR V ITP KEIIAD RL Sbjct: 181 IIDFYPMTTAMAYRVELFDEDIDSIRTFDPTDQRSIDKVREVMITPCKEIIADAERLSRT 240 Query: 244 SSEAAAMLE 252 + +LE Sbjct: 241 AETVVRLLE 249 >C0ZHD9.1 C0ZHD9_BREBN Transcription-repair coupling factor Length = 1182 Score = 244 bits (624), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 120/255 (47%), Positives = 173/255 (67%), Gaps = 7/255 (2%) Query: 5 LQGIIEAFSKDPDFQSVTRGVAAGMKEQLISGLSGSARQIMLAALHEETGRPLLIVTHNM 64 +Q II +D + ++ G+ G+ EQL+SGL+GSARQ+++A+L + RP+ +VTHNM Sbjct: 1 MQVIINPMKQDTNVGTIVAGLEKGLHEQLVSGLAGSARQVLMASLQQMADRPVCVVTHNM 60 Query: 65 FSAQKMAEDLQEALSPDRVLLYPANELVAAEAAVSSPETLAQRIDVLTKCAQGFRGVVVV 124 + AQK+ EDL E + D+VLLYP NEL+ +E A++SPE LAQRI V + AQGF G +V Sbjct: 61 YQAQKVYEDLIELVPSDQVLLYPGNELIGSELAIASPEMLAQRIHVFNRLAQGFTGFLVA 120 Query: 125 PYSGVRRLLPSPHVMAGAELTLSQDGTLVLDDFLMSMIEMGYERVERVENRGELSVRGGI 184 P++G+RRL+ P V A++ LS L ++ FL+ IE+GYERV+ VE +GE+S+RGGI Sbjct: 121 PFAGLRRLVVPPQVWKEAQIQLSVGNELDIESFLLRCIELGYERVDMVERKGEMSIRGGI 180 Query: 185 IDFFPMTSPLAYRVELFDDEVDSIRTFDPQDQRSIDKVRSVKITPAKEIIADQ------- 237 ID +P+ S R+ELFD E+DSIRTFD QRS++ V++ + PAKE+IA Sbjct: 181 IDLYPIDSEWPVRIELFDVEIDSIRTFDMLSQRSLESVQTYILGPAKEMIASTPLLQESA 240 Query: 238 IRLDSASSEAAAMLE 252 +RL+ E A L+ Sbjct: 241 VRLEQKLGETLANLK 255 >B7GFI2.1 B7GFI2_ANOFW Transcription-repair coupling factor (Helicase, mfd) Length = 1189 Score = 229 bits (585), Expect = 1e-58, Method: Compositional matrix adjust. Identities = 115/249 (46%), Positives = 162/249 (65%) Query: 3 LLLQGIIEAFSKDPDFQSVTRGVAAGMKEQLISGLSGSARQIMLAALHEETGRPLLIVTH 62 + L+G+ + F D QSV GV G+KEQL++GLSGSAR + +++L+E+T RPL IVTH Sbjct: 18 VFLRGLRQYFIHHADMQSVAEGVRNGLKEQLVTGLSGSARSVFISSLYEDTERPLCIVTH 77 Query: 63 NMFSAQKMAEDLQEALSPDRVLLYPANELVAAEAAVSSPETLAQRIDVLTKCAQGFRGVV 122 N+F AQK+ +DL + + + V LYP NEL+AAE AV+SPE AQR++VL + +G+V Sbjct: 78 NLFQAQKIYDDLIQLIDEEEVFLYPVNELIAAELAVASPELRAQRLEVLNYWCERKKGIV 137 Query: 123 VVPYSGVRRLLPSPHVMAGAELTLSQDGTLVLDDFLMSMIEMGYERVERVENRGELSVRG 182 + P + +RRLLP V +L + ++ L + MGYERV V GE SVRG Sbjct: 138 IAPIAALRRLLPPKDVWQRYQLHFRVGEQMDVEHCLKQFVAMGYERVSVVSTPGEFSVRG 197 Query: 183 GIIDFFPMTSPLAYRVELFDDEVDSIRTFDPQDQRSIDKVRSVKITPAKEIIADQIRLDS 242 GIID +P+T+ L YR+ELFD E++SIRTF DQRS+ ++ V I PA E+I +Q ++ Sbjct: 198 GIIDIYPLTAELPYRIELFDVEIESIRTFSVDDQRSVAEIDEVLIGPATELIVEQQHINE 257 Query: 243 ASSEAAAML 251 A A L Sbjct: 258 AIQRLEAQL 266 >Q5L3U5.1 Q5L3U5_GEOKA Transcription-repair coupling factor Length = 1177 Score = 227 bits (579), Expect = 6e-58, Method: Compositional matrix adjust. Identities = 108/225 (48%), Positives = 153/225 (68%) Query: 12 FSKDPDFQSVTRGVAAGMKEQLISGLSGSARQIMLAALHEETGRPLLIVTHNMFSAQKMA 71 +++ D +++ G+ +KEQL++GLSGSAR + ++ L++ETGRPLL+V+HN+F AQKM Sbjct: 8 LAENQDVRTIIEGLHVRLKEQLVAGLSGSARSVFISTLYKETGRPLLVVSHNLFQAQKMY 67 Query: 72 EDLQEALSPDRVLLYPANELVAAEAAVSSPETLAQRIDVLTKCAQGFRGVVVVPYSGVRR 131 +DL L P+ V LY NE++AAE AV+SPE AQR++++ QG +GVVV P +G+RR Sbjct: 68 DDLVSLLGPEDVFLYSVNEVIAAEMAVASPELKAQRLEIMNHWVQGGKGVVVCPVAGLRR 127 Query: 132 LLPSPHVMAGAELTLSQDGTLVLDDFLMSMIEMGYERVERVENRGELSVRGGIIDFFPMT 191 LLP P + T S ++ ++MGY+RV V GE SVRGGIID +P+T Sbjct: 128 LLPPPSLWKQYLFTFSVGQEFDVERCKQKFVQMGYKRVGTVSAPGEFSVRGGIIDIYPLT 187 Query: 192 SPLAYRVELFDDEVDSIRTFDPQDQRSIDKVRSVKITPAKEIIAD 236 + L YR+ELFD E++SIRTF P DQRS ++ + I PA EII D Sbjct: 188 AELPYRIELFDTEIESIRTFTPDDQRSQGQIERIMIGPADEIILD 232 >C3J4P7.1 C3J4P7_9BACI Transcription-repair coupling factor Length = 1177 Score = 227 bits (578), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 108/225 (48%), Positives = 153/225 (68%) Query: 12 FSKDPDFQSVTRGVAAGMKEQLISGLSGSARQIMLAALHEETGRPLLIVTHNMFSAQKMA 71 +++ D +++ G+ +KEQL++GLSGSAR + ++ L++ETGRPLL+V+HN+F AQKM Sbjct: 8 LAENQDVRTIIEGLHVRLKEQLVAGLSGSARSVFISTLYKETGRPLLVVSHNLFQAQKMY 67 Query: 72 EDLQEALSPDRVLLYPANELVAAEAAVSSPETLAQRIDVLTKCAQGFRGVVVVPYSGVRR 131 +DL L P+ V LY NE++AAE AV+SPE AQR++++ AQG +GVVV P +G+RR Sbjct: 68 DDLVSLLGPEDVFLYSVNEVIAAEMAVASPELKAQRLEIMNHWAQGGKGVVVCPVAGLRR 127 Query: 132 LLPSPHVMAGAELTLSQDGTLVLDDFLMSMIEMGYERVERVENRGELSVRGGIIDFFPMT 191 LLP P + T ++ ++MGY+RV V GE SVRGGIID +P+T Sbjct: 128 LLPPPSLWKQYLFTFFVGQEFDVERCKQKFVQMGYKRVGTVSAPGEFSVRGGIIDIYPLT 187 Query: 192 SPLAYRVELFDDEVDSIRTFDPQDQRSIDKVRSVKITPAKEIIAD 236 + L YR+ELFD E++SIRTF P DQRS ++ + I PA EII D Sbjct: 188 AELPYRIELFDTEIESIRTFTPDDQRSQGQIERIMIGPADEIILD 232 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 0.319 0.135 0.370 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: 1,400,780,330 Number of extensions: 53851262 Number of successful extensions: 172415 Number of sequences better than 1.0e-05: 2846 Number of HSP's gapped: 169997 Number of HSP's successfully gapped: 2846 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 130 (54.7 bits)