RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780928|ref|YP_003065341.1| histidyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (496 letters) >gnl|CDD|178812 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed. Length = 412 Score = 387 bits (997), Expect = e-108 Identities = 150/495 (30%), Positives = 224/495 (45%), Gaps = 95/495 (19%) Query: 6 KLRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDE-D 64 ++ + PRG D +E + D+IR ++E YGF I TP+ EY++ + + +E D Sbjct: 1 MMKIQAPRGTRDILPEESAKWQYVEDTIREVFERYGFSEIRTPIFEYTELFKRKVGEETD 60 Query: 65 RPNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR 124 K +++ QD G+ ++LR + TAP+ R V E+ P + Y IGP+FR E+ GR Sbjct: 61 IVEKEMYTFQDKGGRSLTLRPEGTAPVVRAVIEHKLQ---PFKLYYIGPMFRYERPQKGR 117 Query: 125 FRQFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRN--------DYHIGINNRKILD 176 +RQF Q V+ +GS + ADAE+ + AD L+A+G+K D+ I N RK L Sbjct: 118 YRQFHQFGVEVIGSDSPLADAEVIALAADILKALGLKGLKLLINSLGDFEIRANYRKALV 177 Query: 177 GILEKIGLHGDDKLNERLI--VLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTS 234 G LEK D+ RL LR +DK DK + K A Sbjct: 178 GFLEKGLDELDEDSKRRLETNPLRILDKKDK----------------EDQELLKDA---- 217 Query: 235 EQIDIMVSFLSIDLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISST 294 ++ +L + ++ F EL EL+ G I Sbjct: 218 ---PKLLDYLDEE-----------------SKEHFEEL---KELLDALGI---PYVIDPR 251 Query: 295 IVRGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIG 354 +VRGL+YYTG V+E + G+V GGGRYDGLV +F G PA GF+IG Sbjct: 252 LVRGLDYYTGTVFEFVTD--------DLGAQGTVCGGGRYDGLVEQFGGPPTPAVGFAIG 303 Query: 355 ISRLIVALKSLESSTNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSS 414 + RL++ L+ L V + + D++ + LR AGIR E+ Sbjct: 304 VERLLLLLEELGEEP------VDVYVVPLGEDAE--LAALKLAEKLRAAGIRVELDY-GG 354 Query: 415 KNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKELSREIKNNESWREARVAQI 474 + Q KYAD+ +I G E + G + +KDL G Q Sbjct: 355 RKLKKQFKYADKSGARFVLILGEDELANGTVTVKDLRTG------------------EQQ 396 Query: 475 TIPISELVSTVKKIL 489 T+P+ ELV +K++L Sbjct: 397 TVPLDELVEALKELL 411 >gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. Length = 397 Score = 363 bits (935), Expect = e-101 Identities = 145/444 (32%), Positives = 220/444 (49%), Gaps = 51/444 (11%) Query: 12 PRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDE-DRPNKGV 70 PRG D +E+ I ++IR ++E YGF I TP+ EY++ + + +E D K + Sbjct: 3 PRGTRDFLPEEMIKWQYIEETIREVFELYGFKEIRTPIFEYTELFARKVGEETDIVEKEM 62 Query: 71 FSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQ 130 ++ +D G+ ++LR + TAP+AR V EN + P + Y IGP+FR E+ GR+RQF Q Sbjct: 63 YTFKDKGGRSLTLRPEGTAPVARAVIENKLLLPKPFKLYYIGPMFRYERPQKGRYRQFHQ 122 Query: 131 CDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKL 190 V+ +GS + ADAE+ + A+ L+ +GIK D+ + IN+ IL+G LE Sbjct: 123 FGVEVIGSDSPLADAEIIALAAEILKELGIK--DFTLEINSLGILEGRLEY--------- 171 Query: 191 NERLIVLRAIDK-LDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLE 249 R +LR +DK LDK G V+ L + + + + L + Sbjct: 172 --REALLRYLDKHLDKLGEDSVRRLE-----------KNPLRILDSKNEKIQELLK-EAP 217 Query: 250 KSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEA 309 K + L E+ + EL+ G KI ++VRGL+YYTG V+E Sbjct: 218 KILDFL---------DEESRAHFEELKELLDALGI---PYKIDPSLVRGLDYYTGTVFEF 265 Query: 310 ILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALKSLESST 369 + +E G++ GGGRYDGLV G PA GF+IGI RL++ L+ L Sbjct: 266 VT-----DELG---AQGTICGGGRYDGLVEELGGPPTPAVGFAIGIERLLLLLEELG-LE 316 Query: 370 NNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNC 429 + V + + ++ + Q LR AGIR E+ LG + QLKYAD+ Sbjct: 317 PPEESSPDVYVVPL--GEEAELEALKLAQKLRKAGIRVEVDLG-GRKLKKQLKYADKLGA 373 Query: 430 PLAIIQGTGERSRGMLQIKDLAKG 453 A+I G E + G + +KDL G Sbjct: 374 RFAVILGEDELANGTVTLKDLETG 397 >gnl|CDD|183519 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional. Length = 423 Score = 208 bits (532), Expect = 2e-54 Identities = 136/449 (30%), Positives = 223/449 (49%), Gaps = 46/449 (10%) Query: 13 RGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFS 72 +G D +E +RN+I ++ +++E YG P+ETP L + + D K +++ Sbjct: 8 KGTKDYLPEEQVLRNKIKRALEDVFERYGCKPLETPTLNMYELMSSKYGGGDEILKEIYT 67 Query: 73 LQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGP---GRFRQFI 129 L D + ++LRYDLT P A+ VA N I P + Y IG VFR+ GP GRFR+FI Sbjct: 68 LTDQGKRDLALRYDLTIPFAKVVAMN-PNIRLPFKRYEIGKVFRD---GPIKQGRFREFI 123 Query: 130 QCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDK 189 QCDVD VG + A+AE+ M + + + + I NNRK+L+GIL+ IG+ + Sbjct: 124 QCDVDIVGVESVMAEAELMSMAFELFRRLNL---EVTIQYNNRKLLNGILQAIGIPTELT 180 Query: 190 LNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLE 249 + V+ ++DK++K G+ GV+ L E ++ E D + + + L+ Sbjct: 181 SD----VILSLDKIEKIGIDGVRKDLLE------------RGISEEMADTICNTVLSCLQ 224 Query: 250 KSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEA 309 S+ + E + E G NEL + + + G N N + + RGL YTG VYE Sbjct: 225 LSIADFKEAFNNPLVAE-GVNELQQLQQYLIALGINEN-CIFNPFLARGLTMYTGTVYEI 282 Query: 310 ILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNV--PATGFSIGISRLIVALKSLES 367 L + + S+G GGRYD ++ F+G ++ P G S G+ + AL E+ Sbjct: 283 FL--------KDGSITSSIGSGGRYDNIIGAFRGDDMNYPTVGISFGLDVIYTALSQKET 334 Query: 368 STNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRR 427 ++ V I + L Q+ Q+ T G++ E+ L + + L YA++ Sbjct: 335 ISSTAD----VFIIPL---GTELQCLQIAQQLRSTTGLKVELEL-AGRKLKKALNYANKE 386 Query: 428 NCPLAIIQGTGERSRGMLQIKDLAKGKEL 456 N P +I G E S G + ++++ +G E+ Sbjct: 387 NIPYVLIIGEEEVSTGTVMLRNMKEGSEV 415 >gnl|CDD|178555 PLN02972, PLN02972, Histidyl-tRNA synthetase. Length = 763 Score = 198 bits (505), Expect = 3e-51 Identities = 138/458 (30%), Positives = 220/458 (48%), Gaps = 53/458 (11%) Query: 10 ELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSL-GKFLPDEDRPNK 68 ++P+G D +++ IR + I ++++ +G ++TP+ E ++L GK+ D +K Sbjct: 328 KIPKGTRDFAKEQMAIREKAFSIITSVFKRHGATALDTPVFELRETLMGKYGED----SK 383 Query: 69 GVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQF 128 ++ L D G+ SLRYDLT P ARYVA N T + Y+I V+R + GR+R+F Sbjct: 384 LIYDLADQGGELCSLRYDLTVPFARYVAMNGITSF---KRYQIAKVYRRDNPSKGRYREF 440 Query: 129 IQCDVDNVGSSAET-ADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGD 187 QCD D G D E+ ++ + L+ + I Y + +N+RK+LDG+LE G+ Sbjct: 441 YQCDFDIAGVYEPMGPDFEIIKVLTELLDELDI--GTYEVKLNHRKLLDGMLEICGV-PP 497 Query: 188 DKLNERLIVLRAIDKLDKFGLQGVKLLLGEGR------TDNSGDF--TKGANLTSEQIDI 239 +K + +IDKLDK + VK + E + D G+F +G L Sbjct: 498 EKFRT---ICSSIDKLDKQSFEQVKKEMVEEKGLSNETADKIGNFVKERGPPLE------ 548 Query: 240 MVSFLSIDLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGL 299 L L + E G + +EL ++ + + KS +I ++ RGL Sbjct: 549 ----LLSKLRQEGSEFL----GNASSRAALDELEIMFKALEKSK-AIGKIVFDLSLARGL 599 Query: 300 EYYTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLI 359 +YYTG +YEA+ K GS+ GGRYD LV F G+ VPA G S+GI R+ Sbjct: 600 DYYTGVIYEAVF---------KGAQVGSIAAGGRYDNLVGMFSGKQVPAVGVSLGIERVF 650 Query: 360 VALKSLESSTNNIKEM--GPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNF 417 ++ E + + VL++ + D L+ L AGI+AE + S Sbjct: 651 AIMEQQEEEKSQVIRPTETEVLVSII--GDDKLALAAELVSELWNAGIKAEYKV--STRK 706 Query: 418 GNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKE 455 LK A P ++ G E S+G +++K+L G E Sbjct: 707 AKHLKRAKESGIPWMVLVGEKELSKGFVKLKNLEAGVE 744 >gnl|CDD|161882 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit. Length = 314 Score = 166 bits (423), Expect = 1e-41 Identities = 101/347 (29%), Positives = 165/347 (47%), Gaps = 45/347 (12%) Query: 22 EIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWI 81 E + I +++++ ++G+ I TP LEY D+ N+ +F L D G+ + Sbjct: 7 EAARKEEIERQLQDVFRSWGYQEIITPTLEYLDT---LSAGGGILNEDLFKLFDSLGRVL 63 Query: 82 SLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAE 141 LR D+T P+AR V+ P R G VFR + G GR R+F Q V+ +G+ Sbjct: 64 GLRPDMTTPIARAVSTRLRDRPLPLRLCYAGNVFRTNESGAGRSREFTQAGVELIGAGGP 123 Query: 142 TADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAID 201 ADAE+ ++ + L+A+G+K D+ I + + ++ +LE+ GL + R + A+ Sbjct: 124 AADAEVIALLIEALKALGLK--DFKIELGHVGLVRALLEEAGLPEE----AREALREALA 177 Query: 202 KLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSI--DLEKSMHELYELV 259 + D L ++ LL E D E + +++ + D E+ + E L Sbjct: 178 RKD---LVALEELLAELGLD------------PEVRERLLALPRLRGDGEEVLEEARALA 222 Query: 260 KGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAI---LGFPVM 316 E +EL + EL+ G I + +VRG YYTG ++E LG P Sbjct: 223 GSE-TAEAALDELEAVLELLEARGVEE-YISLDLGLVRGYHYYTGLIFEGYAPGLGAP-- 278 Query: 317 NEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALK 363 + GGGRYD L+ RF G+ +PATGF++ + RL+ AL Sbjct: 279 -----------IAGGGRYDNLLGRF-GRPLPATGFALNLERLLEALT 313 >gnl|CDD|183410 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 391 Score = 165 bits (419), Expect = 4e-41 Identities = 117/452 (25%), Positives = 202/452 (44%), Gaps = 68/452 (15%) Query: 7 LRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGK--FLPDED 64 + +LP G D +E R I + +++ +G++ + TP LEY D+L + Sbjct: 1 MMWQLPEGIRDLLPEEARKIEEIRRRLLDLFRRWGYEEVITPTLEYLDTLLAGGGAILDL 60 Query: 65 RPNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR 124 R K V G+ + LR D+TA +AR A P R G VFR ++ G GR Sbjct: 61 RTFKLV---DQLSGRTLGLRPDMTAQIARIAATRLANRPGPLRLCYAGNVFRAQERGLGR 117 Query: 125 FRQFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGL 184 R+F+Q V+ +G + ADAE+ +++ + L+A+G+ ++ + + + + +LE GL Sbjct: 118 SREFLQSGVELIGDAGLEADAEVILLLLEALKALGLP--NFTLDLGHVGLFRALLEAAGL 175 Query: 185 HGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFL 244 ++ RA+ D L+ +L+L +L+ E D +++ Sbjct: 176 SE----ELEEVLRRALANKDYVALE--ELVL---------------DLSEELRDALLALP 214 Query: 245 SIDLEKSMHELYELVK--GTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYY 302 L L E K ++ ++ +EL ++E + K GY + + ++R L+YY Sbjct: 215 --RLRGGREVLEEARKLLPSLPIKRALDELEALAEALEKYGYGI-PLSLDLGLLRHLDYY 271 Query: 303 TGCVYEAI---LGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLI 359 TG V+E +G P + GGRYD L+ RF G+ PATGFS+ + RL+ Sbjct: 272 TGIVFEGYVDGVGNP-------------IASGGRYDDLLGRF-GRARPATGFSLDLDRLL 317 Query: 360 VALKSLESSTNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGN 419 LE K++ V+ + + +L+ Q LR G + L +NF + Sbjct: 318 ELQ--LELPVEARKDL--VIAPDSEALAAALA----AAQELRKKGEIVVLALP-GRNFED 368 Query: 420 QLKYADRRNCPLAIIQGTGERSRGMLQIKDLA 451 +YA R + G Q++ LA Sbjct: 369 AREYARDRQI---------VEADGEWQVEPLA 391 >gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase. Length = 487 Score = 162 bits (412), Expect = 2e-40 Identities = 126/464 (27%), Positives = 225/464 (48%), Gaps = 52/464 (11%) Query: 4 KTKLRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDE 63 K K+ P+G D P +++R+RN + D R + +GF+ ++ P+LE S+ L E Sbjct: 65 KPKIDVNPPKGTRDFPPEDMRLRNWLFDHFREVSRLFGFEEVDAPVLE-SEELYIRKAGE 123 Query: 64 DRPNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPG 123 + ++ +++ +D G+ ++LR +LT LAR V + ++ P + + IG +R E+ G Sbjct: 124 EITDQ-LYNFEDKGGRRVALRPELTPSLARLVLQKGKSLSLPLKWFAIGQCWRYERMTRG 182 Query: 124 RFRQFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIG 183 R R+ Q ++D +G A+AE+ + + VGI +D I +++RK+L +L+ G Sbjct: 183 RRREHYQWNMDIIGVPGVEAEAELLAAIVTFFKRVGITSSDVGIKVSSRKVLQAVLKSYG 242 Query: 184 LHGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSF 243 + ++ ++ +DKL+K + ++ L ++ E I+ ++ Sbjct: 243 IP-EESFAPVCVI---VDKLEKLPREEIEKELDT------------LGVSEEAIEGILDV 286 Query: 244 LSIDLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYT 303 LS+ KS+ +L L+ A + +L + L GY + + +++VRGL YYT Sbjct: 287 LSL---KSLDDLEALLG---ADSEAVADLKQLFSLAEAYGY-QDWLVFDASVVRGLAYYT 339 Query: 304 GCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALK 363 G V+E GF + + ++ GGGRYD L+S F G++ PA GF G +IV L Sbjct: 340 GIVFE---GFDRAGKLR------AICGGGRYDRLLSTFGGEDTPACGFGFG-DAVIVEL- 388 Query: 364 SLESSTNNIKEMG--PVLITTMDH-----DSDSLSKYQMYTQMLRTAGIRAEMFLGSSKN 416 +KE G P L +D D D LR G ++ L K Sbjct: 389 --------LKEKGLLPELPHQVDDVVFALDEDLQGAAAGVASRLREKGRSVDLVL-EPKK 439 Query: 417 FGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKELSREI 460 K+A+R ++ G E RGM+++KDL+ G++ ++ Sbjct: 440 LKWVFKHAERIGAKRLVLVGASEWERGMVRVKDLSSGEQTEVKL 483 >gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 373 Score = 84.2 bits (209), Expect = 6e-17 Identities = 92/387 (23%), Positives = 155/387 (40%), Gaps = 86/387 (22%) Query: 29 ILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPD---ED-RPNKGVFSLQDDDGQWISLR 84 +++ +E G ++ P+L+ FL D ED R + +F D++G+ + LR Sbjct: 10 AAEALLASFEAAGAVRVDPPILQ---PAEPFL-DLSGEDIR--RRIFVTSDENGEELCLR 63 Query: 85 YDLTAPLAR-YVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSA-ET 142 D T P+ R ++A P R +G VFR + +F+Q +++ G + Sbjct: 64 PDFTIPVCRRHIATAGGE---PARYAYLGEVFR--QRRDRA-SEFLQAGIESFGRADPAA 117 Query: 143 ADAEMCMMMADTLEAVGIKRNDYHIG-------------------------INNRKILDG 177 ADAE+ + + L A+G + +G + LD Sbjct: 118 ADAEVLALALEALAALGPGDLEVRLGDVGLFAALVDALGLPPGWKRRLLRHFGRPRSLDA 177 Query: 178 ILEKIGLHGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSG------------- 224 +L ++ D L+E VL A+ L+ G + G Sbjct: 178 LLARLAGPRVDPLDEHAGVLAALADEAAARALVEDLMSIAGISPVGGRSPAEIARRLLEK 237 Query: 225 -DFTKGANLTSEQIDIMVSFLSI--DLEKSMHELYELVKGTIAGEKGFNELVVISELVR- 280 A L +E + ++ FL+I + ++ L L A + G + + Sbjct: 238 AALAAAARLPAEALAVLERFLAISGPPDAALAALRAL-----AADAGLDLDAALDRFEAR 292 Query: 281 -----KSGYNSNRIKISSTIVRGLEYYTGCVYE---AILGFPVMNEKQKPVVFGSVGGGG 332 G + R++ S++ R L+YYTG V+E A G P P+ GGG Sbjct: 293 LAALAARGIDLERLRFSASFGRPLDYYTGFVFEIRAAGNGDP-------PLA-----GGG 340 Query: 333 RYDGLVSRF-KGQNVPATGFSIGISRL 358 RYDGL++R G+ +PA GFSI + RL Sbjct: 341 RYDGLLTRLGAGEPIPAVGFSIWLDRL 367 >gnl|CDD|183520 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 392 Score = 67.3 bits (165), Expect = 9e-12 Identities = 99/376 (26%), Positives = 150/376 (39%), Gaps = 62/376 (16%) Query: 11 LPRGFADC-PT---KEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSL----GKFLPD 62 LP G AD P K R+R R+LD + G+ + PL+EY +SL G+ D Sbjct: 9 LPDGVADVLPEEAQKIERLRRRLLDLFAS----RGYQLVMPPLIEYLESLLTGAGQ---D 61 Query: 63 EDRPNKGVFSLQDD-DGQWISLRYDLTAPLARYVAE--NFDTIVFPCRTYRIGPVFRNEK 119 F L D G+ + +R D+T +AR A N + + C Y G V Sbjct: 62 LKLQT---FKLIDQLSGRLMGVRADITPQVARIDAHLLNREGVARLC--Y-AGSVLHTLP 115 Query: 120 HGPGRFRQFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGIL 179 G R +Q + G + AD E+ +M L G+ H+ + + I + Sbjct: 116 QGLFGSRTPLQLGAELYGHAGIEADLEIIRLMLGLLRNAGVPA--LHLDLGHVGIFRRLA 173 Query: 180 EKIGLHGDDKLNERLIVL---RAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQ 236 E GL +++ E L L +A+ +L + Q L +G D F A L Sbjct: 174 ELAGLSPEEE--EELFDLLQRKALPELAEV-CQN--LGVGS---DLRRMFYALARLNG-- 223 Query: 237 IDIMVSFLSIDLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIV 296 LE L L A + +EL ++ ++ + I + Sbjct: 224 ----------GLEALDRALSVLALQDAAIRQALDELKTLAAHLKNRWPELP-VSIDLAEL 272 Query: 297 RGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGIS 356 RG Y+TG V+ A + Q + G GRYDG+ F G+ PATGFS+ + Sbjct: 273 RGYHYHTGLVFAAYIP----GRGQ-ALARG-----GRYDGIGEAF-GRARPATGFSMDLK 321 Query: 357 RLIVALKSLESSTNNI 372 L +AL+ LE I Sbjct: 322 EL-LALQFLEEEAGAI 336 >gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 281 Score = 37.3 bits (87), Expect = 0.011 Identities = 30/118 (25%), Positives = 44/118 (37%), Gaps = 17/118 (14%) Query: 10 ELPRG----FADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDR 65 E+P+G F K +++ I + I GF+ I TP Y Sbjct: 6 EIPQGSKLYFG----KSAKLKREIENVASEILYENGFEEIVTPFFSYHQHQS------IA 55 Query: 66 PNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFR---NEKH 120 K + D+ ISLR D T + R V + + + I PVFR NE + Sbjct: 56 DEKELIRFSDEKNHQISLRADSTLDVVRIVTKRLGRSTEHKKWFYIQPVFRYPSNEIY 113 >gnl|CDD|161893 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. Length = 294 Score = 34.6 bits (80), Expect = 0.059 Identities = 34/118 (28%), Positives = 50/118 (42%), Gaps = 27/118 (22%) Query: 27 NRILDSIRNIYENYGFDPIETPLLEYS----DSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 R++D IR+I+ GF + P +E D+L +P +D P + D +I Sbjct: 75 TRVIDEIRDIFLGLGFTEEKGPEVETDFWNFDAL--NIP-QDHP-----ARDMQDTFYIK 126 Query: 83 ----LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE----KHGPGRFRQFIQCD 132 LR TA R + EN P R + G VFRN+ H P +F Q + Sbjct: 127 DRLLLRTHTTAVQLRTMEENEKP---PIRIFSPGRVFRNDTVDATHLP----EFHQVE 177 >gnl|CDD|178118 PLN02502, PLN02502, lysyl-tRNA synthetase. Length = 553 Score = 34.6 bits (80), Expect = 0.062 Identities = 34/109 (31%), Positives = 44/109 (40%), Gaps = 30/109 (27%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 R R +I+ IR ++ GF +ETP+L + G RP F +D L Sbjct: 230 RTRAKIISYIRRFLDDRGFLEVETPMLN-MIAGGA----AARP----FVTHHND-----L 275 Query: 84 RYDLT---AP---LARYVAENFDTIVFPCRTYRIGPVFRNE----KHGP 122 DL A L R V F+ R Y IG FRNE +H P Sbjct: 276 NMDLYLRIATELHLKRLVVGGFE------RVYEIGRQFRNEGISTRHNP 318 >gnl|CDD|131420 TIGR02367, PylS, pyrrolysyl-tRNA synthetase. PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase. Length = 453 Score = 33.9 bits (77), Expect = 0.089 Identities = 43/189 (22%), Positives = 85/189 (44%), Gaps = 25/189 (13%) Query: 33 IRNIYENYGFDPIETPLL---EYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLRYDLTA 89 I + + GF I++P+L EY + +G + ++ +K +F + + LR L Sbjct: 249 ITKFFVDRGFLEIKSPILIPAEYIERMG--IDNDTELSKQIFRVDKN----FCLRPMLAP 302 Query: 90 PLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAETADAEMCM 149 L Y+ + + P + + IGP +R E G +F + +GS + E Sbjct: 303 NLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLE--A 360 Query: 150 MMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAIDK---LDK- 205 ++ D L+ + I D+ I ++ + L+ +HGD +L+ ++ +D+ +DK Sbjct: 361 IIKDFLDHLEI---DFEIVGDSCMVYGDTLDI--MHGDLELSSAVVGPIPLDREWGIDKP 415 Query: 206 -----FGLQ 209 FGL+ Sbjct: 416 WIGAGFGLE 424 >gnl|CDD|181936 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed. Length = 417 Score = 33.7 bits (77), Expect = 0.10 Identities = 34/129 (26%), Positives = 58/129 (44%), Gaps = 12/129 (9%) Query: 41 GFDPIETPLLEYSDSLGKFLPDEDRP-NKGVFSLQDDDGQWISLRYDLTAPLARYVAENF 99 GF I++P+L ++ + + D D +K +F + + LR L L Y+ Sbjct: 221 GFLEIKSPILIPAEYIERMGIDNDTELSKQIFRVDKN----FCLRPMLAPGLYNYL-RKL 275 Query: 100 DTIV-FPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAETADAEMCMMMADTLEAV 158 D I+ P + + IGP +R E G +F + +GS + E ++ D L+ + Sbjct: 276 DRILPDPIKIFEIGPCYRKESDGKEHLEEFTMVNFCQMGSGCTRENLE--NIIDDFLKHL 333 Query: 159 GIKRNDYHI 167 GI DY I Sbjct: 334 GI---DYEI 339 >gnl|CDD|129550 TIGR00458, aspS_arch, aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). Length = 428 Score = 32.5 bits (74), Expect = 0.24 Identities = 29/125 (23%), Positives = 43/125 (34%), Gaps = 43/125 (34%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLG-------------KFLPDEDRPNKGV 70 RIR+ +L+S+R GF + TP L S + G FL + K Sbjct: 134 RIRSGVLESVREFLAEEGFIEVHTPKLVASATEGGTELFPITYFEREAFLGQSPQLYKQQ 193 Query: 71 FSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR-FRQFI 129 +A F+ R Y IGP+FR E+H R + Sbjct: 194 L-----------------------MAAGFE------RVYEIGPIFRAEEHNTHRHLNEAT 224 Query: 130 QCDVD 134 D++ Sbjct: 225 SIDIE 229 >gnl|CDD|161870 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether.. Length = 563 Score = 32.7 bits (75), Expect = 0.25 Identities = 30/123 (24%), Positives = 47/123 (38%), Gaps = 24/123 (19%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 IRN + D +R YG+ +ETP++ Y L + D + +F + D + L Sbjct: 201 TIRNLLEDFVRQKQIKYGYMEVETPIM-YDLELWEISGHWDNYKERMFPFTELDNREFML 259 Query: 84 RYDLTAPLARYVAENFDTIVF----------PCRTYRIGPVFRNEK----HGPGRFRQFI 129 + + P ++F P R +G R E+ HG R R F Sbjct: 260 KP-MNCP--------GHFLIFKSSLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFT 310 Query: 130 QCD 132 Q D Sbjct: 311 QDD 313 >gnl|CDD|129590 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms. Length = 496 Score = 32.0 bits (73), Expect = 0.34 Identities = 30/106 (28%), Positives = 44/106 (41%), Gaps = 24/106 (22%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 +R++I+ +IR ++ GF +ETP+L+ G RP + D D Sbjct: 173 LVRSKIIKAIRRFLDDRGFIEVETPMLQ-VIPGGA----NARPFITHHNALDMD------ 221 Query: 84 RYDLTAP---LARYVAENFDTIVFPCRTYRIGPVFRNE----KHGP 122 Y AP L R + F+ + Y IG FRNE H P Sbjct: 222 LYLRIAPELYLKRLIVGGFE------KVYEIGRNFRNEGVDTTHNP 261 >gnl|CDD|178491 PLN02903, PLN02903, aminoacyl-tRNA ligase. Length = 652 Score = 32.1 bits (73), Expect = 0.36 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 19/60 (31%) Query: 17 DCPTKEIRIRNRILD------------------SIRNIYEN-YGFDPIETPLLEYSDSLG 57 D +E+R+R R+LD IR E+ +GF IETP+L S G Sbjct: 179 DSIKEEVRLRYRVLDLRRPQMNANLRLRHRVVKLIRRYLEDVHGFVEIETPILSRSTPEG 238 >gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional. Length = 585 Score = 31.1 bits (70), Expect = 0.71 Identities = 28/111 (25%), Positives = 42/111 (37%), Gaps = 22/111 (19%) Query: 26 RNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLRY 85 R +I++ +RN + GF +ETP + P + +D + LR Sbjct: 256 RTKIINYLRNFLNDRGFIEVETPTMNLVAGGANARP--------FITHHNDLDLDLYLRI 307 Query: 86 DLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE----KHGPGRFRQFIQCD 132 PL + D + Y IG VFRNE H P +F C+ Sbjct: 308 ATELPLKMLIVGGID------KVYEIGKVFRNEGIDNTHNP----EFTSCE 348 >gnl|CDD|179042 PRK00476, aspS, aspartyl-tRNA synthetase; Validated. Length = 588 Score = 30.8 bits (71), Expect = 0.75 Identities = 11/28 (39%), Positives = 21/28 (75%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLL 50 +++R+++ +IRN ++ GF IETP+L Sbjct: 141 LKLRSKVTSAIRNFLDDNGFLEIETPIL 168 >gnl|CDD|178496 PLN02908, PLN02908, threonyl-tRNA synthetase. Length = 686 Score = 30.9 bits (70), Expect = 0.85 Identities = 11/25 (44%), Positives = 16/25 (64%) Query: 24 RIRNRILDSIRNIYENYGFDPIETP 48 RI N+++D IR Y G+D + TP Sbjct: 322 RIYNKLMDFIREQYWERGYDEVITP 346 >gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated. Length = 886 Score = 30.1 bits (68), Expect = 1.5 Identities = 11/34 (32%), Positives = 18/34 (52%) Query: 158 VGIKRNDYHIGINNRKILDGILEKIGLHGDDKLN 191 +G R+ YH+ I+ K L L +G G +K+ Sbjct: 670 LGKGRDQYHVHISGAKDLVRFLRHVGAVGAEKVA 703 >gnl|CDD|129558 TIGR00466, kdsB, 3-deoxy-D-manno-octulosonate cytidylyltransferase. Length = 238 Score = 29.9 bits (67), Expect = 1.5 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 19/88 (21%) Query: 126 RQFIQCDVDNVGSSAETADAEMCMMMAD-------TLEAVGIKRNDYHIGINNRKILDGI 178 R + D ++V + + E+CM E V + + + + + Sbjct: 41 RCIVATDDESVAQTCQKFGIEVCMTSKHHNSGTERLAEVVEK------LALKDDERI--- 91 Query: 179 LEKIGLHGDDKLNERLIVLRAIDKLDKF 206 + L GD+ + I+ + D L Sbjct: 92 ---VNLQGDEPFIPKEIIRQVADNLATK 116 >gnl|CDD|161718 TIGR00120, ArgJ, glutamate N-acetyltransferase/amino-acid acetyltransferase. This enzyme can acetylate Glu to N-acetyl-Glu by deacetylating N-2-acetyl-ornithine into ornithine; the two halves of this reaction represent the first and fifth steps in the synthesis of Arg (or citrulline) from Glu by way of ornithine (EC 2.3.1.35). In Bacillus stearothermophilus, but not in Thermus thermophilus HB27, the enzyme is bifunctional and can also use acetyl-CoA to acetylate Glu (EC 2.3.1.1). Length = 404 Score = 29.8 bits (67), Expect = 1.8 Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 3/102 (2%) Query: 173 KILDGILEKIGLHGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANL 232 KI GI + G + N +AI D F + G G KGA + Sbjct: 120 KIRTGINKLYGELKNSS-NSSDNFAKAIMTTDTFPKEVAVEFELPGEKVRIGGVAKGAGM 178 Query: 233 TSEQIDIMVSFLSIDLEKSMHELYELVKGTIAGEKGFNELVV 274 + + M+ F++ D L +++ A +K FN++ V Sbjct: 179 IAPNMATMLGFITTDAAIESKALQKML--RRATDKSFNQITV 218 >gnl|CDD|178244 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic subunit. Length = 1079 Score = 29.5 bits (66), Expect = 2.0 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%) Query: 303 TGCVYE--AILGF--PVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRL 358 TGCV+ A+ G+ P+ + +KP S+ GG R S KG + +G + + Sbjct: 629 TGCVFNRTALYGYEPPIKPKHKKPGFLSSLCGGSRKKSSKSSKKGSDKKKSGKHVDPTVP 688 Query: 359 IVALKSLE 366 + L+ +E Sbjct: 689 VFNLEDIE 696 >gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional. Length = 706 Score = 29.6 bits (66), Expect = 2.1 Identities = 29/117 (24%), Positives = 48/117 (41%), Gaps = 20/117 (17%) Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGK---FLPDEDRPNKGVFSLQDDD 77 + R+RI+ R+ ++ GF IETP+L S G +P P K ++L Sbjct: 154 DHLAKRHRIIKCARDFLDSRGFLEIETPILTKSTPEGARDYLVPSRIHP-KEFYALPQSP 212 Query: 78 GQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVD 134 + L + A RY +++ FR+E P R +F Q D++ Sbjct: 213 QLFKQLL--MIAGFERY--------------FQLARCFRDEDLRPNRQPEFTQLDIE 253 >gnl|CDD|179044 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed. Length = 491 Score = 29.3 bits (67), Expect = 2.2 Identities = 12/27 (44%), Positives = 19/27 (70%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLL 50 R R++I+ +IR +N GF +ETP+L Sbjct: 173 RKRSKIISAIRRFLDNRGFLEVETPML 199 >gnl|CDD|179011 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed. Length = 638 Score = 29.3 bits (67), Expect = 2.3 Identities = 34/137 (24%), Positives = 45/137 (32%), Gaps = 52/137 (37%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLL------EYSDSLGKFLPDEDRPNKGVFSLQDDD 77 IR + IR G+ ++TP + E S + R N +F + D Sbjct: 271 TIRRELERYIRRKLRKAGYQEVKTPQILDRELWETSGHWDHY-----REN--MFPTTESD 323 Query: 78 GQWISLR-----------------Y-DLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEK 119 G+ +L+ Y DL PL R AE G V R E Sbjct: 324 GEEYALKPMNCPGHVQIYKQGLRSYRDL--PL-RL-AE-------------FGTVHRYEP 366 Query: 120 ----HGPGRFRQFIQCD 132 HG R R F Q D Sbjct: 367 SGALHGLMRVRGFTQDD 383 >gnl|CDD|129551 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences. Length = 583 Score = 28.9 bits (65), Expect = 2.8 Identities = 10/30 (33%), Positives = 21/30 (70%) Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLL 50 + +++R+++ ++RN + GF IETP+L Sbjct: 136 QRLKLRHKVTKAVRNFLDQQGFLEIETPML 165 >gnl|CDD|114830 pfam06134, RhaA, L-rhamnose isomerase (RhaA). This family consists of several bacterial L-rhamnose isomerase proteins (EC:5.3.1.14). Length = 416 Score = 28.6 bits (64), Expect = 3.6 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 5/44 (11%) Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIY-----ENYGFDPIETPL 49 +P G+ D P+ + R R+ +++ ++ E Y D +E+ L Sbjct: 184 IPDGYKDIPSDRLTPRKRLKEALDEVFSEKLDEAYNLDAVESKL 227 >gnl|CDD|179948 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional. Length = 437 Score = 28.6 bits (65), Expect = 4.1 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 107 RTYRIGPVFRNEKH 120 R + IGPVFR E+H Sbjct: 204 RVFEIGPVFRAEEH 217 >gnl|CDD|181528 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional. Length = 477 Score = 28.6 bits (65), Expect = 4.1 Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 30/100 (30%) Query: 398 QMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKELS 457 + L+ AGIR ++ S K G + + + PL I G Sbjct: 314 EELKKAGIRVKLDDRSDKTPGWKFNEWELKGVPLRIEIG--------------------P 353 Query: 458 REIKNNESWREARVAQ------ITIPISELVSTVKKILQE 491 R+++NN + + T+P+ ELV V ++L+E Sbjct: 354 RDLENNT----VVLVRRDTLEKETVPLDELVEKVPELLEE 389 >gnl|CDD|179744 PRK04132, PRK04132, replication factor C small subunit; Provisional. Length = 846 Score = 28.3 bits (63), Expect = 4.4 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 5/78 (6%) Query: 126 RQFIQCD--VDNVGSSAETADAEMCMMMADTLEAVGIK---RNDYHIGINNRKILDGILE 180 R + C+ ++ TA EM + L GI R YH+ I+ + L L+ Sbjct: 264 RAYFDCNGGIEKDAIVLSTASKEMAEQIVYALAGFGIIAKLREKYHVIISGSENLKRFLD 323 Query: 181 KIGLHGDDKLNERLIVLR 198 +IG ++KL + L +++ Sbjct: 324 EIGFSQEEKLEKALKLIK 341 >gnl|CDD|178180 PLN02567, PLN02567, alpha,alpha-trehalase. Length = 554 Score = 28.5 bits (64), Expect = 4.6 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 11/36 (30%) Query: 316 MNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGF 351 M+EK G VGGGG Y +P TGF Sbjct: 506 MHEKYDARYCGEVGGGGEY-----------IPQTGF 530 >gnl|CDD|161887 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn. Length = 453 Score = 28.1 bits (63), Expect = 4.9 Identities = 22/99 (22%), Positives = 37/99 (37%), Gaps = 14/99 (14%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 R+RN + +I ++ GF + P+L +D G +F + D + Sbjct: 137 RVRNALSQAIHRYFQENGFTWVSPPILTSNDCEGA---------GELFRVSTDGIDFSQD 187 Query: 84 RYDLTAPLARYVAENFDTIVFPC---RTYRIGPVFRNEK 119 + A L V+ + + Y GP FR EK Sbjct: 188 FFGKEAYLT--VSGQLYLETYALALSKVYTFGPTFRAEK 224 >gnl|CDD|148911 pfam07558, Shugoshin_N, Shugoshin N-terminal coiled-coil region. The Shugoshin protein is found to have this conserved N-terminal coiled-coil region and a highly conserved C-terminal basic region, family Shugoshin_C pfam07557. Shugoshin is a crucial target of Bub1 kinase function at kinetochores, necessary for both meiotic and mitotic localisation of shugoshin to the kinetochore. Human shugoshin is diffusible and mediates kinetochore-driven formation of kinetochore-microtubules during bipolar spindle assembly. Further, the primary role of shugoshin is to ensure bipolar attachment of kinetochores, and its role in protecting cohesion has co-developed to facilitate this process. Length = 46 Score = 27.9 bits (63), Expect = 5.9 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 8/39 (20%) Query: 454 KELSREIKNNESWREARVAQITIPISELVSTVKKILQEN 492 K+ + KNN + ++I ISEL V K+L EN Sbjct: 7 KQNAELAKNN--------SALSIKISELEKEVSKLLNEN 37 >gnl|CDD|182254 PRK10124, PRK10124, putative UDP-glucose lipid carrier transferase; Provisional. Length = 463 Score = 27.8 bits (62), Expect = 6.9 Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 1/70 (1%) Query: 274 VISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQKPVVFG-SVGGGG 332 + + +R GYN + ++ + G E LGF V+ P G S G Sbjct: 131 IGAGWLRNHGYNKRMVAVAGDLPAGQMLLESFRNEPWLGFEVVGVYHDPKPGGVSNDWAG 190 Query: 333 RYDGLVSRFK 342 LV K Sbjct: 191 NLQQLVEDAK 200 >gnl|CDD|132714 TIGR03675, arCOG00543, arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782. Length = 630 Score = 27.6 bits (62), Expect = 7.7 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 3/45 (6%) Query: 452 KGKELSREIKNNESWREARVAQITIPI-SELVSTVKKILQENKEE 495 KG REI W +V + T PI S+ + +++ L+ EE Sbjct: 110 KGGSTLREITAETGWT-PKVVR-TPPIESKTIKNIREYLRSESEE 152 >gnl|CDD|181701 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated. Length = 367 Score = 27.6 bits (62), Expect = 7.8 Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%) Query: 45 IETPLLEYSDS-LGKFLPDEDRPN 67 +ETP+ E DS LG F+ D+D + Sbjct: 262 LETPIGEEDDSHLGDFIEDQDATS 285 >gnl|CDD|185610 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional. Length = 586 Score = 27.3 bits (60), Expect = 9.0 Identities = 14/35 (40%), Positives = 20/35 (57%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLG 57 IRIRN + + +++ GF I TPL+ SD G Sbjct: 215 IRIRNALAIATHLFFQSRGFLYIHTPLITTSDCEG 249 >gnl|CDD|177368 PHA02517, PHA02517, putative transposase OrfB; Reviewed. Length = 277 Score = 27.1 bits (60), Expect = 9.3 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 7/50 (14%) Query: 362 LKSLESSTNNIKEMGPVLITTMDHDSDSLSKY--QMYTQMLRTAGIRAEM 409 L +LE + G ++ H SD S+Y YTQ L+ AGIRA Sbjct: 155 LDALEQALWARGRPGGLI-----HHSDKGSQYVSLAYTQRLKEAGIRAST 199 >gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional. Length = 518 Score = 27.4 bits (61), Expect = 9.3 Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 2/40 (5%) Query: 229 GANLTSEQIDIM--VSFLSIDLEKSMHELYELVKGTIAGE 266 GA+L + I ++ + LSI EKSM E E++K + GE Sbjct: 379 GADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418 >gnl|CDD|185085 PRK15131, PRK15131, mannose-6-phosphate isomerase; Provisional. Length = 389 Score = 27.2 bits (61), Expect = 9.4 Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%) Query: 73 LQDDDGQWISLR----YDLTAPLARYVAENFDTIVF 104 +QD +G +SLR D +A L VA+ F + F Sbjct: 48 VQDANGDIVSLRDVIESDKSALLGEAVAKRFGELPF 83 >gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed. Length = 505 Score = 27.3 bits (60), Expect = 9.8 Identities = 10/28 (35%), Positives = 18/28 (64%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLE 51 +R++IL +IR GF +ETP+++ Sbjct: 185 VVRSKILAAIRQFMVARGFMEVETPMMQ 212 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.138 0.393 Gapped Lambda K H 0.267 0.0763 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,144,822 Number of extensions: 546409 Number of successful extensions: 1234 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1180 Number of HSP's successfully gapped: 61 Length of query: 496 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 399 Effective length of database: 3,898,497 Effective search space: 1555500303 Effective search space used: 1555500303 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 (21.7 bits) S2: 59 (26.4 bits)