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= 0264.0027.p (260 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KGA4.1 B3KGA4_9BACI RNA-binding S4 domain protein 350 6e-95 B1DKM3.1 B1DKM3_9BACL RNA-binding S4 domain protein 270 9e-71 Q65JV9.1 Q65JV9_BACLD YlmH 192 2e-47 C0ZG88.1 C0ZG88_BREBN Putative uncharacterized protein ylmH 190 9e-47 A7GRM2.1 A7GRM2_BACCN RNA-binding S4 domain protein 184 7e-45 >B3KGA4.1 B3KGA4_9BACI RNA-binding S4 domain protein Length = 261 Score = 350 bits (899), Expect = 6e-95, Method: Compositional matrix adjust. Identities = 163/259 (62%), Positives = 207/259 (79%) Query: 1 MKNEIYGHFHPDERQFVDKALEWVTGAGEYHESKLTEFLDPRQGFILQTLVNRHPDVSVR 60 MK +IY HFH DER+FVD+A EWV AG+YHE+KLT+FLDPRQ FIL++LVNRHPDV Sbjct: 2 MKLDIYDHFHKDEREFVDRAWEWVVNAGQYHETKLTDFLDPRQRFILESLVNRHPDVHAL 61 Query: 61 WDGGSAEAERKRALVAPDYLDLEAEDMELKVLAISSGEQKFLALEHGDYMGAXXXXXXXX 120 +DGG A+AER RA++APDY LE ED+++KVL+ISSG+QKFL LEHGDYMG+ Sbjct: 62 FDGGHADAERVRAMIAPDYRALEGEDLKMKVLSISSGDQKFLELEHGDYMGSILGLGIKR 121 Query: 121 XXXXXXHVLEDGCHVVVAADIADYLAMNLTGVHRMNVSTEVLPVSGLRSSQVKLETIDLT 180 HVL DGCH VVA DI+ +L +NL+ VHR++V T++LP+ L+ ++ E +D+T Sbjct: 122 SKIGDIHVLADGCHAVVADDISAFLHLNLSQVHRVHVMTDLLPLDKLQVARTNFEAMDIT 181 Query: 181 VASLRLDGIAADVTRLSRSKILAPIKAGRVRVNWKVEEDPSCGLKDGDMVSIQGFGRFKI 240 V+S+RLDGIA+D R+SR+KI+ PIKAGR RVNWKVEEDPS LK+GD+VSIQGFGRFK+ Sbjct: 182 VSSMRLDGIASDAYRISRTKIIVPIKAGRCRVNWKVEEDPSTNLKEGDVVSIQGFGRFKV 241 Query: 241 LEIGSLTKKGRYRVQVGKF 259 LE G LTKKGRYR++VGK+ Sbjct: 242 LETGGLTKKGRYRIKVGKY 260 >B1DKM3.1 B1DKM3_9BACL RNA-binding S4 domain protein Length = 257 Score = 270 bits (690), Expect = 9e-71, Method: Compositional matrix adjust. Identities = 136/260 (52%), Positives = 179/260 (68%), Gaps = 3/260 (1%) Query: 1 MKNEIYGHFHPDERQFVDKALEWVTGAGEYHESKLTEFLDPRQGFILQTLVNRHPDVSVR 60 MK +Y HFHPDE+ FVD+ALEWV + + HE K T+FLDPRQ ILQ L NR+PDV +R Sbjct: 1 MKPTVYEHFHPDEKPFVDRALEWVERSAQLHELKRTDFLDPRQAQILQMLANRNPDVQLR 60 Query: 61 WDGGSAEAERKRALVAPDYLDLEAEDMELKVLAISSGEQKFLALEHGDYMGAXXXXXXXX 120 GG EAER RA++ P+Y L+ E + L VLA++ G + L+HGDY+GA Sbjct: 61 LAGGYPEAERCRAIIGPEYRYLDDEPIGLSVLAVTGGGSE---LDHGDYLGALLGLGVKR 117 Query: 121 XXXXXXHVLEDGCHVVVAADIADYLAMNLTGVHRMNVSTEVLPVSGLRSSQVKLETIDLT 180 HV ED H++V +IADYL ++L VHR +V TE++P L+ L+ + T Sbjct: 118 DRIGDIHVHEDYSHIIVLDEIADYLNVHLRQVHRASVLTEIIPTLKLKPVVPALQEMSFT 177 Query: 181 VASLRLDGIAADVTRLSRSKILAPIKAGRVRVNWKVEEDPSCGLKDGDMVSIQGFGRFKI 240 VAS+RLDGIA+DV R+SR+KI+ PI+AGR RVNWK E+PS LK GD+VS +G GRFK+ Sbjct: 178 VASMRLDGIASDVYRISRTKIVDPIRAGRCRVNWKTAENPSEQLKLGDVVSFKGLGRFKV 237 Query: 241 LEIGSLTKKGRYRVQVGKFV 260 +EI +TKKGR RV+VGKF+ Sbjct: 238 MEIDGMTKKGRIRVKVGKFI 257 >Q65JV9.1 Q65JV9_BACLD YlmH Length = 258 Score = 192 bits (489), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 103/257 (40%), Positives = 157/257 (61%), Gaps = 3/257 (1%) Query: 3 NEIYGHFHPDERQFVDKALEWVTGAGEYHESKLTEFLDPRQGFILQTLVNRHPDVSVRWD 62 ++IY HF DE F+D+ALEW E + KLT+FLDPR+ ILQ+++ + +V + + Sbjct: 2 SDIYQHFRKDEEPFIDQALEWKRIVAEQYRMKLTDFLDPREQVILQSVIGQSDEVRLEFF 61 Query: 63 GGSAEAERKRALVAPDYLDLEAEDMELKVLAISSGEQKFLALEHGDYMGAXXXXXXXXXX 122 GG EAERKRA++ P+Y + AED +L+ + QKF ++EH + +G+ Sbjct: 62 GGFPEAERKRAVLFPEYAEPSAEDFQLQAWEVIYP-QKFASIEHRELLGSLMGIGLKRQK 120 Query: 123 XXXXHVLEDGC-HVVVAADIADYLAMNLTGVHRMNVSTEVLPVSGLRSSQVKLETIDLTV 181 + DG + + ++AD++ LT + ++ VS E +P+S L+ + +E D TV Sbjct: 121 FGDL-IFSDGTWQFICSEEVADFVFTQLTQIGKVKVSLEKIPLSKLKVPEQDVEIRDDTV 179 Query: 182 ASLRLDGIAADVTRLSRSKILAPIKAGRVRVNWKVEEDPSCGLKDGDMVSIQGFGRFKIL 241 +SLRLD I + ++R SR K +K G V+VNWKV EDPS L +GDMVSI+GFGRF++ Sbjct: 180 SSLRLDAICSAMSRQSRQKAQVLVKNGLVKVNWKVIEDPSYALAEGDMVSIRGFGRFRMK 239 Query: 242 EIGSLTKKGRYRVQVGK 258 I TKKG++R+ K Sbjct: 240 NIDGKTKKGKWRLTFEK 256 >C0ZG88.1 C0ZG88_BREBN Putative uncharacterized protein ylmH Length = 257 Score = 190 bits (483), Expect = 9e-47, Method: Compositional matrix adjust. Identities = 103/253 (40%), Positives = 148/253 (58%), Gaps = 1/253 (0%) Query: 5 IYGHFHPDERQFVDKALEWVTGAGEYHESKLTEFLDPRQGFILQTLVNRHPDVSVRWDGG 64 I+ HF +ER FV++ALE +T +LT+F+DPRQ I Q+L ++ DV V GG Sbjct: 3 IFDHFSKEERPFVERALEMLTQVERKQAMRLTDFVDPRQLLIFQSLSSQVTDVKVSPYGG 62 Query: 65 SAEAERKRALVAPDYLDLEAEDMELKVLAISSGEQKFLALEHGDYMGAXXXXXXXXXXXX 124 AER R ++ P+YL +E +D L +LAI + +Q+F LEH D MGA Sbjct: 63 YEGAERVRIIIHPEYLPVEPDDYRLTLLAIKA-DQRFHVLEHRDVMGAMLGVGMKREKFG 121 Query: 125 XXHVLEDGCHVVVAADIADYLAMNLTGVHRMNVSTEVLPVSGLRSSQVKLETIDLTVASL 184 G + +VA ++AD++ +T +HR +V E + K +TV S Sbjct: 122 DMLTDSAGSYAIVAEEVADFVCAQVTQIHRTSVQFERVAWEAFTPPAPKFVEKTITVPSG 181 Query: 185 RLDGIAADVTRLSRSKILAPIKAGRVRVNWKVEEDPSCGLKDGDMVSIQGFGRFKILEIG 244 R+D I +V +SR+K L PI+AG+V++NWKV EDPS L+ GDMVS+ G+GRFKILE+ Sbjct: 182 RIDAIIGEVHNMSRAKALVPIRAGKVKINWKVIEDPSYQLQMGDMVSLAGYGRFKILEVA 241 Query: 245 SLTKKGRYRVQVG 257 T+ GR R+ VG Sbjct: 242 GPTRSGRIRMIVG 254 >A7GRM2.1 A7GRM2_BACCN RNA-binding S4 domain protein Length = 257 Score = 184 bits (467), Expect = 7e-45, Method: Compositional matrix adjust. Identities = 104/255 (40%), Positives = 149/255 (58%), Gaps = 5/255 (1%) Query: 5 IYGHFHPDERQFVDKALEWVTGAGEYHESKLTEFLDPRQGFILQTLVNRHPDVSVRWDGG 64 IY HF P+E FVDK LEW EYH+ KLT+FLDPRQ I+ T+V + DVS++++G Sbjct: 3 IYEHFRPEEASFVDKVLEWERAVEEYHQVKLTDFLDPRQQQIVTTIVGQQGDVSLQFNGA 62 Query: 65 SAEAERKRALVAPDYLDLEAEDMELKVLAISSGEQKFLALEHGDYMGAXXXXXXXXXXXX 124 + +AERKRAL+ PDYL L E+ +++VL I KF LEH +GA Sbjct: 63 APKAERKRALIYPDYLALNEEEFQVEVLEIDYPS-KFYTLEHRQILGALMSLGLKREKYG 121 Query: 125 XXHVLEDGCHVVVAADIADYLAMNLTGVHRMNVSTEVLPVSGLRSSQVKLETIDL--TVA 182 + E+ +VVA ++ Y+ MNL + + VS + VS Q++ E + TV+ Sbjct: 122 DIFIQENRVQIVVAKEVVSYIEMNLQSIGKTKVS--LFSVSAENVLQLQDEWREQFGTVS 179 Query: 183 SLRLDGIAADVTRLSRSKILAPIKAGRVRVNWKVEEDPSCGLKDGDMVSIQGFGRFKILE 242 SLRLD + A++ LSR K+ IK G V+VNWKV + S GD++S++G GR K+ Sbjct: 180 SLRLDVVLAEILHLSRQKVQPLIKNGLVKVNWKVVDQTSYECLPGDILSVRGHGRSKLFS 239 Query: 243 IGSLTKKGRYRVQVG 257 + TKK ++RV G Sbjct: 240 VDGRTKKDKWRVLYG 254 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 0.137 0.397 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: 1,404,420,547 Number of extensions: 50573685 Number of successful extensions: 125298 Number of sequences better than 1.0e-05: 437 Number of HSP's gapped: 124579 Number of HSP's successfully gapped: 437 Length of query: 260 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 127 Effective length of database: 1,807,701,208 Effective search space: 229578053416 Effective search space used: 229578053416 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 (21.7 bits) S2: 130 (54.7 bits)