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= 0183.0002.p (329 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KAF2.1 B3KAF2_9BACI Dihydrouridine synthase DuS 585 e-165 A7Z2I6.1 A7Z2I6_BACA2 YfjN 540 e-152 O31546.1 DUS2_BACSU Probable tRNA-dihydrouridine synthase 2 EC=1... 537 e-151 Q8ES60.1 Q8ES60_OCEIH Hypothetical conserved protein 531 e-149 B4AI30.1 B4AI30_BACPU Probable tRNA-dihydrouridine synthase EC=1... 531 e-149 >B3KAF2.1 B3KAF2_9BACI Dihydrouridine synthase DuS Length = 329 Score = 585 bits (1508), Expect = e-165, Method: Compositional matrix adjust. Identities = 279/329 (84%), Positives = 300/329 (91%) Query: 1 MTENFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHAVR 60 MT+NFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHP+GNH+VR Sbjct: 1 MTDNFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPDGNHSVR 60 Query: 61 GRLTFTEDEQPIVAHIWGDKPEFFRQMSIGIAQEGFKGIDINMGCPVANVAENGKGSGLI 120 GRLTFTEDEQP+VAHIWGDKPE+FRQMSIG+A+EGFKGIDINMGCPVANVAENGKGSGLI Sbjct: 61 GRLTFTEDEQPMVAHIWGDKPEYFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLI 120 Query: 121 CRPELAAEIIQAAKAGGLPVSVKTRLGFSSLDEWRGWLTHILQQDIVNLSIHLRTREEMS 180 CRP++AAE+IQAAKAGGLPVSVKTRLGFS++DEWR WLTHIL+QDIVNLSIHLRTREEMS Sbjct: 121 CRPDIAAELIQAAKAGGLPVSVKTRLGFSAVDEWRDWLTHILKQDIVNLSIHLRTREEMS 180 Query: 181 KADAHWELIPEIKKLRDEVAPDTLLTINRDIPDRQTGLKLAERYGVDGIMIGRGIFHNPF 240 K DAHWELIPEIKKLRDEVAPDTLLTIN DIPDRQTGLKLAE+YGVDGIMIGRGIFHNPF Sbjct: 181 KVDAHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFHNPF 240 Query: 241 AFEKEPKEHSSTEXXXXXXXXXXXXXQYSVQAPRSFSPLQRFFKIYVRGFRGASELRNSL 300 AFEKEP++HSS E QYS Q RSFS L RFFKIYVRGFRGASELRN+L Sbjct: 241 AFEKEPRDHSSEELLDLLRLHLDLHDQYSAQMRRSFSALVRFFKIYVRGFRGASELRNNL 300 Query: 301 MNTRSTNEVRALLGEFGGKEQDGAEEHGD 329 MN +ST+EVRALL EFG K D A+E G+ Sbjct: 301 MNAKSTSEVRALLDEFGSKHSDEADERGN 329 >A7Z2I6.1 A7Z2I6_BACA2 YfjN Length = 327 Score = 540 bits (1391), Expect = e-152, Method: Compositional matrix adjust. Identities = 256/326 (78%), Positives = 284/326 (87%) Query: 1 MTENFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHAVR 60 MT+NFWR+LPRPFF+LAPMEDVTDVVFRHVVSEA RPDVFFTEF N+ESYCHP+G +VR Sbjct: 1 MTDNFWRELPRPFFVLAPMEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVR 60 Query: 61 GRLTFTEDEQPIVAHIWGDKPEFFRQMSIGIAQEGFKGIDINMGCPVANVAENGKGSGLI 120 GRLTFTEDEQP+VAHIWGDKPE FRQMSIG+A+ GFKG+DINMGCPV NVA NGKGSGLI Sbjct: 61 GRLTFTEDEQPMVAHIWGDKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLI 120 Query: 121 CRPELAAEIIQAAKAGGLPVSVKTRLGFSSLDEWRGWLTHILQQDIVNLSIHLRTREEMS 180 CRPE+AAE+IQAAKAGGLPVSVKTRLG++ +DEWRGWLTHIL+QDI NLSIHLRTR EMS Sbjct: 121 CRPEVAAELIQAAKAGGLPVSVKTRLGYTDIDEWRGWLTHILKQDIANLSIHLRTRAEMS 180 Query: 181 KADAHWELIPEIKKLRDEVAPDTLLTINRDIPDRQTGLKLAERYGVDGIMIGRGIFHNPF 240 K DAHWELIPEIKKLRDE+APDTLLTIN DIPDR+TGLKLAE+YGVDGIMIGRGIF NPF Sbjct: 181 KVDAHWELIPEIKKLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTNPF 240 Query: 241 AFEKEPKEHSSTEXXXXXXXXXXXXXQYSVQAPRSFSPLQRFFKIYVRGFRGASELRNSL 300 AFEKEP+EHSS E +YS R++ PL RFFKIY+RGFRGASELRN Sbjct: 241 AFEKEPREHSSKELLDLLRLHLDLHDEYSKAEARAYKPLPRFFKIYLRGFRGASELRNQC 300 Query: 301 MNTRSTNEVRALLGEFGGKEQDGAEE 326 MNT+ST+EVRALL +F K DG E+ Sbjct: 301 MNTKSTDEVRALLDDFERKYLDGMEQ 326 >O31546.1 DUS2_BACSU Probable tRNA-dihydrouridine synthase 2 EC=1.-.-.- Length = 325 Score = 537 bits (1384), Expect = e-151, Method: Compositional matrix adjust. Identities = 258/325 (79%), Positives = 281/325 (86%) Query: 1 MTENFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHAVR 60 MTENFWR+LPRPFF+LAPMEDVTDVVFRHVVSEA RPDVFFTEF N+ESYCHP+G +VR Sbjct: 1 MTENFWRELPRPFFVLAPMEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVR 60 Query: 61 GRLTFTEDEQPIVAHIWGDKPEFFRQMSIGIAQEGFKGIDINMGCPVANVAENGKGSGLI 120 GRLTFTEDEQPIVAHIWGDKPE FR+MSIG+A+ GFKG+DINMGCPV NVA NGKGSGLI Sbjct: 61 GRLTFTEDEQPIVAHIWGDKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLI 120 Query: 121 CRPELAAEIIQAAKAGGLPVSVKTRLGFSSLDEWRGWLTHILQQDIVNLSIHLRTREEMS 180 CRP +AAE+IQAAKAGGLPVSVKTRLG++ +DEWR WLTHIL+QDI NLSIHLRTR EMS Sbjct: 121 CRPAVAAELIQAAKAGGLPVSVKTRLGYTDVDEWREWLTHILKQDIANLSIHLRTRAEMS 180 Query: 181 KADAHWELIPEIKKLRDEVAPDTLLTINRDIPDRQTGLKLAERYGVDGIMIGRGIFHNPF 240 K DAHWELIPEIKKLRDEVAPDTLLTIN DIPDRQTGLKLAE+YGVDGIMIGRGIF NPF Sbjct: 181 KVDAHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPF 240 Query: 241 AFEKEPKEHSSTEXXXXXXXXXXXXXQYSVQAPRSFSPLQRFFKIYVRGFRGASELRNSL 300 AFEKEPKEHSS E +YS + R + PL RFFKIY+RGFRGASELRN Sbjct: 241 AFEKEPKEHSSKELLDLLRLHLDLHDEYSKEEARPYKPLPRFFKIYLRGFRGASELRNQC 300 Query: 301 MNTRSTNEVRALLGEFGGKEQDGAE 325 MNT+ST+EVRALL +F K DG E Sbjct: 301 MNTKSTDEVRALLDDFERKYLDGIE 325 >Q8ES60.1 Q8ES60_OCEIH Hypothetical conserved protein Length = 326 Score = 531 bits (1369), Expect = e-149, Method: Compositional matrix adjust. Identities = 249/316 (78%), Positives = 275/316 (87%) Query: 1 MTENFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHAVR 60 M +NFWRDLPRPFF+LAPMEDVTDVVFRHVV+EAARPDVFFTEF N+ESYCHP+G +VR Sbjct: 1 MIDNFWRDLPRPFFVLAPMEDVTDVVFRHVVTEAARPDVFFTEFTNSESYCHPDGRQSVR 60 Query: 61 GRLTFTEDEQPIVAHIWGDKPEFFRQMSIGIAQEGFKGIDINMGCPVANVAENGKGSGLI 120 GRLTFTEDEQPIVAHIWGDKPE+FRQMSIG+A+ GFKG+DINMGCPVANVA NGKGSGLI Sbjct: 61 GRLTFTEDEQPIVAHIWGDKPEYFRQMSIGMAEMGFKGLDINMGCPVANVAGNGKGSGLI 120 Query: 121 CRPELAAEIIQAAKAGGLPVSVKTRLGFSSLDEWRGWLTHILQQDIVNLSIHLRTREEMS 180 RPE+AAE+IQAAKAGGLPVSVKTRLG++ +DEW+ WL H+L+QDIVNLSIHLRTR+EMS Sbjct: 121 NRPEIAAELIQAAKAGGLPVSVKTRLGYTYIDEWKEWLKHVLEQDIVNLSIHLRTRKEMS 180 Query: 181 KADAHWELIPEIKKLRDEVAPDTLLTINRDIPDRQTGLKLAERYGVDGIMIGRGIFHNPF 240 K DAHWELIPEIKKLRDE+APDTLLTIN DIPDRQTGLKL E YGVDG+MIGRG+F NPF Sbjct: 181 KVDAHWELIPEIKKLRDEIAPDTLLTINGDIPDRQTGLKLVEEYGVDGVMIGRGVFKNPF 240 Query: 241 AFEKEPKEHSSTEXXXXXXXXXXXXXQYSVQAPRSFSPLQRFFKIYVRGFRGASELRNSL 300 AFEKE KEHSS E +Y RSF PL RFFKIYV+GFRGASELRN + Sbjct: 241 AFEKEQKEHSSQEMLDLLRLHLDLHDKYDELESRSFKPLHRFFKIYVKGFRGASELRNQM 300 Query: 301 MNTRSTNEVRALLGEF 316 MNT+ST EVRALL F Sbjct: 301 MNTKSTAEVRALLDNF 316 >B4AI30.1 B4AI30_BACPU Probable tRNA-dihydrouridine synthase EC=1.-.-.- Length = 324 Score = 531 bits (1368), Expect = e-149, Method: Compositional matrix adjust. Identities = 252/322 (78%), Positives = 281/322 (87%) Query: 1 MTENFWRDLPRPFFILAPMEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHAVR 60 M++NFWRDLPRPFFILAPME+VTDVVFRHVVSEAARPDVFFTEF N+ESYCHP+G +V+ Sbjct: 1 MSKNFWRDLPRPFFILAPMEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGIQSVK 60 Query: 61 GRLTFTEDEQPIVAHIWGDKPEFFRQMSIGIAQEGFKGIDINMGCPVANVAENGKGSGLI 120 GRLTFTEDEQPIVAHIWGDKPE FRQMSIG+A+ GF+G+DINMGCPV NV +NGKGSGLI Sbjct: 61 GRLTFTEDEQPIVAHIWGDKPENFRQMSIGMAELGFQGLDINMGCPVPNVTQNGKGSGLI 120 Query: 121 CRPELAAEIIQAAKAGGLPVSVKTRLGFSSLDEWRGWLTHILQQDIVNLSIHLRTREEMS 180 RP++AAE+IQAAKAGGLPVSVKTRLGF+ +DEWRGWL HIL+QDIVNLSIHLRTR+EMS Sbjct: 121 LRPDVAAELIQAAKAGGLPVSVKTRLGFTEVDEWRGWLRHILEQDIVNLSIHLRTRKEMS 180 Query: 181 KADAHWELIPEIKKLRDEVAPDTLLTINRDIPDRQTGLKLAERYGVDGIMIGRGIFHNPF 240 + DAHWELIPEIKKLRDEVAPDTLLTIN DIPDRQTGLKLAE+YGVDG+MIGRGIFHNPF Sbjct: 181 QVDAHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGVMIGRGIFHNPF 240 Query: 241 AFEKEPKEHSSTEXXXXXXXXXXXXXQYSVQAPRSFSPLQRFFKIYVRGFRGASELRNSL 300 AFEKEPK+H+S E QYS R F L RFFKIYV+GFRGAS LRN L Sbjct: 241 AFEKEPKDHTSDELLGLLRLHLDLHDQYSSLGLRPFKALHRFFKIYVKGFRGASFLRNQL 300 Query: 301 MNTRSTNEVRALLGEFGGKEQD 322 MNT ST+EVRA+L EF + Q+ Sbjct: 301 MNTSSTDEVRAMLDEFEARNQE 322 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 0.417 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: 1,952,204,041 Number of extensions: 78981555 Number of successful extensions: 204100 Number of sequences better than 1.0e-05: 2821 Number of HSP's gapped: 198310 Number of HSP's successfully gapped: 2826 Length of query: 329 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 193 Effective length of database: 1,779,438,163 Effective search space: 343431565459 Effective search space used: 343431565459 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: 131 (55.1 bits)