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= 0282.0005.p (149 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value pir||S71440 hypothetical protein 3 - Bacillus circulans (fragmen... 236 1e-61 ref|ZP_00059828.1| COG0219: Predicted rRNA methylase (SpoU class... 199 2e-50 gb|AAB02738.1| CspR 188 3e-47 ref|NP_654479.1| SpoU_methylase, SpoU rRNA Methylase family [Bac... 188 3e-47 ref|NP_388774.1| rRNA methylase homolog [Bacillus subtilis] >gi|... 187 7e-47 >pir||S71440 hypothetical protein 3 - Bacillus circulans (fragment) emb|CAA86559.1| orf [Bacillus circulans subsp. alkalophilus] Length = 144 Score = 236 bits (602), Expect = 1e-61, Method: Compositional matrix adjust. Identities = 110/139 (79%), Positives = 121/139 (87%) Query: 1 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFRTDDATLKRAGLDYWHAVHIEYHDSFG 60 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGF TDD TLKRAGLDYW+AVHIEYHDSF Sbjct: 6 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFNTDDKTLKRAGLDYWYAVHIEYHDSFE 65 Query: 61 EVLEKYAEGRFFYATTKADKRYTDFTFRDGDFFVFGKETKGLSAEILEAGKETVMRMPMS 120 E+ +KY EGRFFY +TKA KRY D F+DGDF VFGKETKGL E+L A ++ +RMPM+ Sbjct: 66 ELQQKYPEGRFFYTSTKATKRYCDIAFQDGDFLVFGKETKGLPPELLAANPDSCIRMPMT 125 Query: 121 EAVRSLNLSNSAAIIVYEA 139 + VRSLNLSNSAAIIVYEA Sbjct: 126 DKVRSLNLSNSAAIIVYEA 144 >ref|ZP_00059828.1| COG0219: Predicted rRNA methylase (SpoU class) [Clostridium thermocellum ATCC 27405] Length = 164 Score = 199 bits (506), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 96/148 (64%), Positives = 112/148 (75%) Query: 1 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFRTDDATLKRAGLDYWHAVHIEYHDSFG 60 VLVEPEIP NTGNIARTCAA G +LHLV+PLGF +D LKRAGLDYW V+I+Y+DSF Sbjct: 6 VLVEPEIPQNTGNIARTCAAVGANLHLVKPLGFSVEDRYLKRAGLDYWDKVNIKYYDSFS 65 Query: 61 EVLEKYAEGRFFYATTKADKRYTDFTFRDGDFFVFGKETKGLSAEILEAGKETVMRMPMS 120 E+ +KY E F+Y+TTKA K YTD + D F VFGKET GL E+L KE +R+PM Sbjct: 66 ELRDKYKEHIFYYSTTKAQKLYTDVKYPDDCFIVFGKETAGLPEELLVENKEWCIRIPMR 125 Query: 121 EAVRSLNLSNSAAIIVYEALRQLNFPQL 148 + +RSLNLSNS AIIVYEALRQ NF L Sbjct: 126 DDIRSLNLSNSVAIIVYEALRQNNFAGL 153 >gb|AAB02738.1| CspR Length = 157 Score = 188 bits (478), Expect = 3e-47, Method: Compositional matrix adjust. Identities = 89/151 (58%), Positives = 112/151 (74%), Gaps = 3/151 (1%) Query: 1 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFRTDDATLKRAGLDYWHAVHIEYHDSFG 60 VL +PEIPANTGNIARTCAAT T LHL+RPLGF TDD LKRAGLDYW V++ YHDS Sbjct: 6 VLYQPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLKRAGLDYWEFVNVVYHDSLE 65 Query: 61 EVLEKYAEGRFFYATTKADKRYTDFTFRDGD---FFVFGKETKGLSAEILEAGKETVMRM 117 E+ E Y +G+FF+ T + +T F + D D FFVFG+ET GL ++++ + +R+ Sbjct: 66 ELFEAYKKGKFFFITKFGQQPHTSFDYTDLDEDYFFVFGRETSGLPKDLIQNNMDRCLRL 125 Query: 118 PMSEAVRSLNLSNSAAIIVYEALRQLNFPQL 148 PM+E VRSLNLSN+AAI+VYEALRQ N+ L Sbjct: 126 PMTEHVRSLNLSNTAAILVYEALRQQNYRDL 156 >ref|NP_654479.1| SpoU_methylase, SpoU rRNA Methylase family [Bacillus anthracis A2012] ref|NP_830365.1| 23S rRNA methyltransferase [Bacillus cereus ATCC 14579] ref|NP_843082.1| RNA methyltransferase, TrmH family, group 2 [Bacillus anthracis str. Ames] ref|NP_976929.1| RNA methyltransferase, TrmH family, group 2 [Bacillus cereus ATCC 10987] gb|AAP07566.1| 23S rRNA methyltransferase [Bacillus cereus ATCC 14579] gb|AAP24568.1| RNA methyltransferase, TrmH family, group 2 [Bacillus anthracis str. Ames] gb|AAS39537.1| RNA methyltransferase, TrmH family, group 2 [Bacillus cereus ATCC 10987] Length = 162 Score = 188 bits (477), Expect = 3e-47, Method: Compositional matrix adjust. Identities = 91/151 (60%), Positives = 113/151 (74%), Gaps = 3/151 (1%) Query: 1 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFRTDDATLKRAGLDYWHAVHIEYHDSFG 60 VL +PEIPANTGNIARTCAATGT LHL+RPLGF TDD LKRAGLDYW V I Y+DS Sbjct: 6 VLYQPEIPANTGNIARTCAATGTELHLIRPLGFSTDDKMLKRAGLDYWQHVKITYYDSIE 65 Query: 61 EVLEKYAEGRFFYATTKADKRYT--DFTFRDGD-FFVFGKETKGLSAEILEAGKETVMRM 117 E EK +G FFY T +K +T D++ R+ D +FVFG+ET GL A ++E + +R+ Sbjct: 66 EFYEKNKDGEFFYLTKYGEKAHTAFDYSKREKDYYFVFGRETNGLPANVIEENFDHCLRI 125 Query: 118 PMSEAVRSLNLSNSAAIIVYEALRQLNFPQL 148 PM++ VRSLNLSN+AAI++YEA RQ N+P L Sbjct: 126 PMTDKVRSLNLSNTAAILIYEAFRQQNYPGL 156 >ref|NP_388774.1| rRNA methylase homolog [Bacillus subtilis] pir||G69608 rRNA methylase homolog cspR - Bacillus subtilis emb|CAB12721.1| rRNA methylase homolog [Bacillus subtilis subsp. subtilis str. 168] Length = 160 Score = 187 bits (475), Expect = 7e-47, Method: Compositional matrix adjust. Identities = 89/151 (58%), Positives = 111/151 (73%), Gaps = 3/151 (1%) Query: 1 VLVEPEIPANTGNIARTCAATGTHLHLVRPLGFRTDDATLKRAGLDYWHAVHIEYHDSFG 60 VL PEIPANTGNIARTCAAT T LHL+RPLGF TDD LKRAGLDYW V++ YHDS Sbjct: 9 VLYHPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLKRAGLDYWEFVNVVYHDSLE 68 Query: 61 EVLEKYAEGRFFYATTKADKRYTDFTFRDGD---FFVFGKETKGLSAEILEAGKETVMRM 117 E+ E Y +G+FF+ T + +T F + D D FFVFG+ET GL ++++ + +R+ Sbjct: 69 ELFEAYKKGKFFFITKFGQQPHTSFDYTDLDEDYFFVFGRETSGLPKDLIQNNMDRCLRL 128 Query: 118 PMSEAVRSLNLSNSAAIIVYEALRQLNFPQL 148 PM+E VRSLNLSN+AAI+VYEALRQ N+ L Sbjct: 129 PMTEHVRSLNLSNTAAILVYEALRQQNYRDL 159 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.322 0.137 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 215,959,890 Number of extensions: 8434917 Number of successful extensions: 21429 Number of sequences better than 1.0e-05: 471 Number of HSP's gapped: 21196 Number of HSP's successfully gapped: 471 Length of query: 149 Length of database: 757,237,578 Length adjustment: 108 Effective length of query: 41 Effective length of database: 464,006,886 Effective search space: 19024282326 Effective search space used: 19024282326 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 (21.9 bits) S2: 120 (50.8 bits)