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= 0345.0004.p (464 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 ref|NP_623708.1| tRNA and rRNA cytosine-C5-methylases [Thermoana... 332 1e-89 ref|ZP_00059686.1| COG0144: tRNA and rRNA cytosine-C5-methylases... 326 6e-88 ref|ZP_00037859.1| COG0144: tRNA and rRNA cytosine-C5-methylases... 296 7e-79 ref|ZP_00069293.1| COG0144: tRNA and rRNA cytosine-C5-methylases... 288 2e-76 ref|NP_688004.1| NOL1/NOP2/sun family protein [Streptococcus aga... 280 8e-74 >ref|NP_623708.1| tRNA and rRNA cytosine-C5-methylases [Thermoanaerobacter tengcongensis] gb|AAM25312.1| tRNA and rRNA cytosine-C5-methylases [Thermoanaerobacter tengcongensis] Length = 460 Score = 332 bits (851), Expect = 1e-89, Method: Compositional matrix adjust. Identities = 184/473 (38%), Positives = 267/473 (56%), Gaps = 47/473 (9%) Query: 10 YTAAIREMLGQEADAFLESYTARRTQGLRFNTLKSNSLSGRAAAEHTAVRFDLTPVPWCP 69 + ++E+L +E +AFL+ Y + +GLR NTLK + + + A F++ P+PWCP Sbjct: 9 FLKRMKELLKEEYEAFLKEYEKKPQKGLRVNTLKIDVENFKKIAP-----FEIEPIPWCP 63 Query: 70 SGYYYEEPVRPGRHAYHTAGLYYIQEPSAMSAAELLAPRPGETVLDLAAAPGGKTSHIAA 129 +G+YYE+ + G H YH GLYYIQEP+AM+ E+L P+PGE +LD++AAPGGKT+HIA+ Sbjct: 64 TGFYYEKEEKAGNHLYHVLGLYYIQEPTAMAVVEVLDPKPGEKILDVSAAPGGKTTHIAS 123 Query: 130 LMQGQGLLVSNEIHPERAKILAENVERLGISHAVVTSAAPGELSRRFPEVFDRIMLDAPC 189 + +GL+V+NEI +R + L ENV R+GI + V+ + P L + F FD+I++DAPC Sbjct: 124 KIGDEGLIVANEIDRKRIRALEENVARMGIRNIVLLNERPERLIQAFEGYFDKIVVDAPC 183 Query: 190 SGEGMFRKDPAAIGEWSPEHVEMCAARQWDILQDAYIMLKPGGSLAYSTCTFNRKENEET 249 SGEGMFRKDPAA WS +V C+ Q +IL+ +LK GG L YSTCTF+ +ENE Sbjct: 184 SGEGMFRKDPAARRIWSLNNVLSCSITQRNILRSVAPLLKRGGVLVYSTCTFSPEENEGV 243 Query: 250 ISRFLDHYPDMERIAEK-----------------------RLWPHLEKGEGHFVALLRKA 286 I +FL+ P+ E + + RLWPH +GEGHF+A L+K Sbjct: 244 IKKFLEENPEFEVVESELSHFFDKGHPEWVDGPKELEKCMRLWPHKVRGEGHFIAKLKKN 303 Query: 287 ASEEEAPGRNKRGSGRGKTSHKLPANASDAYQQFMSWAADELPGFAGQGVPLLFGEALYL 346 E+ KR + K +L + + QF AD+ + + L Sbjct: 304 G--EDVNVNFKRKVEKKKHQKEL-----ELFYQF----ADKYLDLDLEILNLQVDNNF-- 350 Query: 347 LPEAFGASLHTSLLEGLKVPRAGLHIAHLKKNRIEPAHALAMALQPEQAARSYNLAADSQ 406 + L L+G+++ R G + LKKNR EP+H LAM L+P Q R L D Sbjct: 351 ---VYHVPLDLPELKGIRIYRHGWLMGELKKNRFEPSHWLAMGLKPSQIKRV--LELDKF 405 Query: 407 DIQAWLRGESLPVPLELHGWTLVTVDGLPVSWGKASSGQLKNHLPKGLRIIKA 459 + +L GE+ + E GW L T + P WG+ + G +KN+ PK LR I+ Sbjct: 406 QREKYLNGETFELD-EEDGWILFTAENFPAGWGRVAKGVVKNYFPKWLRDIEV 457 >ref|ZP_00059686.1| COG0144: tRNA and rRNA cytosine-C5-methylases [Clostridium thermocellum ATCC 27405] Length = 470 Score = 326 bits (836), Expect = 6e-88, Method: Compositional matrix adjust. Identities = 186/480 (38%), Positives = 261/480 (54%), Gaps = 53/480 (11%) Query: 3 EERLPAAYTAAIREMLG----QEADAFLESYTARRTQGLRFNTLKSNSLSGRAAAEHTAV 58 E +LP + +R+M G E + FL+SY R GLR NTLK + + Sbjct: 14 EMKLPEEF---LRKMEGLFDAGEFEEFLKSYDMPRFYGLRVNTLKIGVEEFKKLSP---- 66 Query: 59 RFDLTPVPWCPSGYYYEEPVRPGRHAYHTAGLYYIQEPSAMSAAELLAPRPGETVLDLAA 118 F+L P+PW G+YY E PG+H Y+ AGLYYIQEPSAM ++ G+ VLDL A Sbjct: 67 -FELEPIPWTKDGFYYNEGENPGKHPYYHAGLYYIQEPSAMLPGAVINAEEGDYVLDLCA 125 Query: 119 APGGKTSHIAALMQGQGLLVSNEIHPERAKILAENVERLGISHAVVTSAAPGELSRRFPE 178 APGGKT +AA M+G+GLL++N+I +R K L +N+E GI++A+VT+ +P L+++ Sbjct: 126 APGGKTVQMAAGMKGKGLLIANDISSDRVKALVKNIELCGITNAIVTNESPDRLAKKLCA 185 Query: 179 VFDRIMLDAPCSGEGMFRKDPAAIGEWSPEHVEMCAARQWDILQDAYIMLKPGGSLAYST 238 FDRI++DAPCSGEGMFRKD A W + C A Q +IL+ A +MLKPGG L YST Sbjct: 186 FFDRILVDAPCSGEGMFRKDEDAAKSWGKFKCDKCCAMQREILESADVMLKPGGYLVYST 245 Query: 239 CTFNRKENEETISRFLDHYPDM-----------------------ERIAEKRLWPHLEKG 275 CTF+ +ENE IS FL + + E + R+WPH +G Sbjct: 246 CTFSPEENEGMISEFLSRHKNYDILEIPKAYGIDNGRPEWWDNNKELLKTARIWPHKVRG 305 Query: 276 EGHFVALLRKAASEEEAPGRNKRGSGRGKTSHKLPANASDAYQQFMSWAADELPGFAGQG 335 EGHFVALL+K R K +N + F +A + L G Sbjct: 306 EGHFVALLKKKGDRTVNEKRRKNAD----------SNVIKLMEPFYKFAGENL-NINIDG 354 Query: 336 VPLLFGEALYLLPEAFGASLHTSLLEGLKVPRAGLHIAHLKKNRIEPAHALAMALQPEQA 395 + G LY LPE L G+KV + G ++ + K R EP+H+ A++L+ E Sbjct: 355 FFTVKGNNLYCLPE------EPPDLSGIKVAKFGWYLGEIAKGRFEPSHSFALSLKKEDI 408 Query: 396 ARSYNLAADSQDIQAWLRGESLPVPLELHGWTLVTVDGLPVSWGKASSGQLKNHLPKGLR 455 ++ N +ADS ++ +L+GE+L + E G+T + VDG + W K + LKN PKG R Sbjct: 409 RKTLNFSADSVEVLKYLKGETLMIEGE-PGYTGILVDGYTLGWAKQTGDMLKNLYPKGWR 467 >ref|ZP_00037859.1| COG0144: tRNA and rRNA cytosine-C5-methylases [Enterococcus faecium] Length = 456 Score = 296 bits (758), Expect = 7e-79, Method: Compositional matrix adjust. Identities = 190/480 (39%), Positives = 257/480 (53%), Gaps = 49/480 (10%) Query: 1 MNEE--RLPAAYTAAIREMLGQEADAFLESY-TARRTQGLRFNTLKSNSLSGRAAAEHTA 57 M EE LP + R +LG+EA F + +G R+N LK L H+ Sbjct: 1 MKEEATTLPQQFIKKYRLLLGEEASDFFSALEQGSVKKGFRWNPLKPAGLD-MVQTYHSE 59 Query: 58 VRFDLTPVPWCPSGYYYEEPVRPGRHAYHTAGLYYIQEPSAMSAAELLAPRPGETVLDLA 117 +L P P+ G+ G+ H AG Y QEPSAM A +PGE VLDL Sbjct: 60 ---ELQPAPYSNEGFL---GTVNGKSFLHQAGYEYSQEPSAMIVGTAAAAKPGEKVLDLC 113 Query: 118 AAPGGKTSHIAALMQGQGLLVSNEIHPERAKILAENVERLGISHAVVTSAAPGELSRRFP 177 AAPGGK++ +AA M+G+GLLV+NEI P+RAKIL+EN+ER G+S+A+VT+ AP EL F Sbjct: 114 AAPGGKSTQLAAQMKGKGLLVTNEIFPKRAKILSENIERWGVSNAIVTNHAPAELVPHFS 173 Query: 178 EVFDRIMLDAPCSGEGMFRKDPAAIGEWSPEHVEMCAARQWDILQDAYIMLKPGGSLAYS 237 FDRI++DAPCSGEGMFRKDP AI EW+ E C RQ +IL A MLK G L YS Sbjct: 174 GFFDRIVVDAPCSGEGMFRKDPNAIKEWTEESPLYCQKRQQEILSSAIKMLKNKGQLIYS 233 Query: 238 TCTFNRKENEETISRFLDHYP-DMERI------------------AEK--RLWPHLEKGE 276 TCTF +ENEE IS +++YP +E I EK R+WPH ++GE Sbjct: 234 TCTFAPEENEEIISWLVENYPVTIEEIPLTQSVSSGRSEWGSVAGLEKTIRIWPHKDQGE 293 Query: 277 GHFVALLRKAASEEEAPGRNKRGSGRGKTSHKLPANASDAYQQFMSWAADELPGFAGQGV 336 GHFVA L G+N+ + + + + ++ D + G Sbjct: 294 GHFVAKLT-------FHGQNQMHKEKKTRKKSKVQMTKEQEKLWTEFSNDF--HYEATGR 344 Query: 337 PLLFGEALYLLPEAFGASLHTSLLEGLKVPRAGLHIAHLKKNRIEPAHALAMALQPEQAA 396 L+F + L+ +PE L+GLKV R GLH+ KKNR EP++ALA+A + + Sbjct: 345 LLVFNDHLWEVPEL------APSLDGLKVVRTGLHLGDFKKNRFEPSYALALATKKIENI 398 Query: 397 RSYNLAADSQDIQAWLRGESLPVPLELHGWTLVTVDGLPVSWGKASSGQLKNHLPKGLRI 456 L ++ Q++ GE+ GW L+ +D +PV +GK G +KN PKGLR Sbjct: 399 PC--LPITQKEWQSYTAGETFQRDGN-QGWVLLVLDKIPVGFGKQVKGTVKNFFPKGLRF 455 >ref|ZP_00069293.1| COG0144: tRNA and rRNA cytosine-C5-methylases [Oenococcus oeni MCW] Length = 458 Score = 288 bits (737), Expect = 2e-76, Method: Compositional matrix adjust. Identities = 179/478 (37%), Positives = 255/478 (53%), Gaps = 60/478 (12%) Query: 6 LPAAYTAAIREMLGQEADAFLESYTARRTQGLRFNTLKSNSLSGRAAAEHTAVRFDLTPV 65 LP + A R +LG+EAD FL S+ G N LK L A+ + A P+ Sbjct: 4 LPKEFIAKYRRLLGKEADDFLASFQMEADNGFHLNPLKD--LRQFASLKRQA------PI 55 Query: 66 PWCPSGYYYEEPVRPGRHAYHTAGLYYIQEPSAMSAAELLAPRPGETVLDLAAAPGGKTS 125 PW Y + G +G+ Y QEPSA A ++ +PGE +LDLAAAPGGK++ Sbjct: 56 PWNRENGRYGKIF--GESVAFLSGVAYSQEPSAQFVARVVDAQPGEKILDLAAAPGGKST 113 Query: 126 HIAALMQGQGLLVSNEIHPERAKILAENVERLGISHAVVTSAAPGELSRRFPEVFDRIML 185 IAA M QGLL++NEI RAKIL+EN+ER GI++ +VT+ P EL+ F FD+I+L Sbjct: 114 QIAADMNNQGLLIANEISFSRAKILSENIERSGITNCIVTNHRPDELAEHFENYFDKILL 173 Query: 186 DAPCSGEGMFRKDPAAIGEWSPEHVEMCAARQWDILQDAYIMLKPGGSLAYSTCTFNRKE 245 DAPCSGEGMFRKDP AI W ++ CA RQ +IL+ ML+P G L YSTCTF +E Sbjct: 174 DAPCSGEGMFRKDPQAIKYWHSDYSSECANRQKEILKSVLSMLRPNGQLIYSTCTFAPEE 233 Query: 246 NEETISRFLDHYPDME--RIAEK---------------------RLWPHLEKGEGHFVAL 282 +E+ ++ LD+Y ++ +I +K RLWP+ KGEGHFVA Sbjct: 234 DEQIVAWLLDNYSELSLLKIRKKDGIEDGRPQWADGNRELKNTARLWPNKIKGEGHFVAR 293 Query: 283 LRKAASEEEAPGRNKRGSGRGKTSHKLPANASDAYQ--QFMSWAADELPGFAGQGVPLLF 340 L K+ + + +NK R S N + ++ QF F + + F Sbjct: 294 LIKSKGKNQ---KNKVNQLRSNLSRNDSQNLQNTFKENQF---------DFPIKQI-YRF 340 Query: 341 GEALYLLPEAFGASLHTSLLEGLKVPRAGLHIAHLKKNRIEPAHALAMALQPEQAARSYN 400 G+ LYL PE + + GLKV R GL I LK R P H+LA++ + +++Y+ Sbjct: 341 GDYLYLFPE------NCPEISGLKVLRLGLQIGRLKNKRFLPTHSLALSSLGNKISQTYD 394 Query: 401 LAADSQDIQAWLRGESLPVPLE---LHGWTLVTVDGLPVSWGKASSGQLKNHLPKGLR 455 L+ + + ++ G+ + L+ + GW L+T + G+ S +KN PKGLR Sbjct: 395 LS--DYEFRQFIHGDII-TNLKGNFVKGWVLMTKQSNGIGIGRYSDKVIKNFYPKGLR 449 >ref|NP_688004.1| NOL1/NOP2/sun family protein [Streptococcus agalactiae 2603V/R] ref|NP_735477.1| Unknown, conserved protein [Streptococcus agalactiae NEM316] gb|AAM99876.1| NOL1/NOP2/sun family protein [Streptococcus agalactiae 2603V/R] emb|CAD46687.1| Unknown, conserved protein [Streptococcus agalactiae NEM316] Length = 436 Score = 280 bits (715), Expect = 8e-74, Method: Compositional matrix adjust. Identities = 174/468 (37%), Positives = 243/468 (51%), Gaps = 51/468 (10%) Query: 5 RLPAAYTAAIREMLGQEADAFLESYTARRTQGLRFNTLKSNSLSGRAAAEHTAVRFDLTP 64 +LP + + +L EA+AF +S+ + R N LK L A Sbjct: 2 KLPNEFIEKYQTILKDEAEAFFDSFEQKPISAYRTNPLKEKQLDFPNA------------ 49 Query: 65 VPWCPSGYYYEEPVRPGRHAYHTAGLYYIQEPSAMSAAELLAPRPGETVLDLAAAPGGKT 124 +P P G+Y + G+ HT GL Y QEP+A A++ P+ G VLDLAAAPGGKT Sbjct: 50 IPSTPWGHYGK---ISGKSIEHTTGLVYSQEPAAQIVAQIAEPQEGMKVLDLAAAPGGKT 106 Query: 125 SHIAALMQGQGLLVSNEIHPERAKILAENVERLGISHAVVTSAAPGELSRRFPEVFDRIM 184 +H+ + + GLLVSNEI +R+KIL ENVER G + +VT+ + L++ F FD I+ Sbjct: 107 THLLSYLNNTGLLVSNEISNKRSKILVENVERFGARNVIVTNESSQRLAKCFNSFFDLIV 166 Query: 185 LDAPCSGEGMFRKDPAAIGEWSPEHVEMCAARQWDILQDAYIMLKPGGSLAYSTCTFNRK 244 D PCSGEGMFRKDP AI W ++ CA Q DIL++A ML GG L YSTCT++ + Sbjct: 167 FDGPCSGEGMFRKDPQAIQYWHKDYPTECAQLQRDILKEAIKMLAHGGILVYSTCTWSPE 226 Query: 245 ENEETISRFLDHY--------PDMERIAE-------KRLWPHLEKGEGHFVALLRKAASE 289 ENEE ++ L Y P + + E R++PH +GEG FVA LR S+ Sbjct: 227 ENEEVVNWLLQEYDYLELVDIPKLNGMVEGINVPQVARMYPHHFQGEGQFVAKLRDTRSK 286 Query: 290 EEAPGRNKRGSGRGKTSHKLPANASDAYQQFMSWAADELPGFAGQGVPLLFGEALYLLPE 349 E + K + K+ +QQF A D L GV +FG+ LYLLP Sbjct: 287 EAQKIKPK--------AQKINKMQLQLWQQF---AQDHLK-IDLNGVLDVFGDQLYLLPN 334 Query: 350 AFGASLHTSLLEGLKVPRAGLHIAHLKKNRIEPAHALAMALQPEQAARSYNLAADSQDIQ 409 L LK+ R GLH+ KKNR EP+ AL MAL +S + D + + Sbjct: 335 GLPD------LSKLKIARNGLHLGTFKKNRFEPSFALGMALSEHDLVQS--IEIDIEQFE 386 Query: 410 AWLRGESLPVPLEL-HGWTLVTVDGLPVSWGKASSGQLKNHLPKGLRI 456 ++ G + + + +GW + V G + + K ++ LKN+ PKGLR Sbjct: 387 VYVSGNVVKLDKTVPNGWYQILVKGNGLGFAKVTNNTLKNYYPKGLRF 434 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 0.317 0.133 0.399 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: 719,523,059 Number of extensions: 31491464 Number of successful extensions: 78105 Number of sequences better than 1.0e-05: 488 Number of HSP's gapped: 77285 Number of HSP's successfully gapped: 489 Length of query: 464 Length of database: 757,237,578 Length adjustment: 129 Effective length of query: 335 Effective length of database: 406,989,807 Effective search space: 136341585345 Effective search space used: 136341585345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 128 (53.9 bits)