RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780928|ref|YP_003065341.1| histidyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (496 letters) >gnl|CDD|30473 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 429 Score = 350 bits (900), Expect = 5e-97 Identities = 155/471 (32%), Positives = 241/471 (51%), Gaps = 47/471 (9%) Query: 10 ELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDE-DRPNK 68 + PRG D +++ +R I +IR ++E+YGF I TP+ EY++ + +E D K Sbjct: 5 QRPRGTRDFLPEDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETDVVEK 64 Query: 69 GVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQF 128 +++ +D G+ ++LR +LTAP+AR VAEN + P + Y GPVFR E+ GR+RQF Sbjct: 65 EMYTFKDKGGRSLALRPELTAPVARAVAENKLDLPKPLKLYYFGPVFRYERPQKGRYRQF 124 Query: 129 IQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDD 188 Q V+ +GS + ADAE+ + + LEA+GI + + IN+R IL+G LE +G Sbjct: 125 YQFGVEVIGSDSPDADAEVIALAVEILEALGIG--GFTLEINSRGILEGRLEYLG----- 177 Query: 189 KLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDL 248 +++R +LR +DKLDK KL L E L + + ++ S D Sbjct: 178 -IDQREALLRYLDKLDKI----GKLELDEDSKR---------RLKTNPLRVLDSKKDSDQ 223 Query: 249 EKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYE 308 E + EL+ E+ L + L+ G + +I ++VRGL+YYTG V+E Sbjct: 224 E-LLKNAPELLDYL--DEESLEHLEELLALLDALGIS---YEIDPSLVRGLDYYTGTVFE 277 Query: 309 AILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALKSLESS 368 A+ GSV GGGRYDGLV F G+ PA GF+IG+ RLI+AL+ Sbjct: 278 AVT--------DGLGAQGSVCGGGRYDGLVEEFGGKPTPAVGFAIGVERLILALEEEGKE 329 Query: 369 TNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRN 428 ++ V + + D++ + Q LR AGI E+ S + Q KYAD+ Sbjct: 330 D-PVETRVDVYVVPLGEDAE--PEALKLAQKLRAAGISVEVDY-SGRKLKKQFKYADKLG 385 Query: 429 CPLAIIQGTGERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPIS 479 A+I G E + G++ +KDLA G++ E + V ++ + Sbjct: 386 ARFAVILGEDELANGVVTVKDLATGEQ-------EEVPLDELVEELKELLE 429 >gnl|CDD|37147 KOG1936, KOG1936, KOG1936, Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 518 Score = 233 bits (595), Expect = 9e-62 Identities = 143/473 (30%), Positives = 225/473 (47%), Gaps = 45/473 (9%) Query: 2 GKKTKLRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSL-GKFL 60 K K + P+G D +++ +R +I +I+ +++ +G + I+TP+ E + L GK+ Sbjct: 53 IFKKKFSLKTPKGTRDFSPEQMALREKIFSTIKEVFKRHGAETIDTPVFELKEILTGKYG 112 Query: 61 PDEDRPNKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFR--NE 118 D +K ++ L+D G+ SLRYDLT P ARY+A N T + + Y I V+R Sbjct: 113 ED----SKLIYDLKDQGGELCSLRYDLTVPFARYLAMNKITSI---KRYHIAKVYRRDQP 165 Query: 119 KHGPGRFRQFIQCDVDNVGSSAE-TADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDG 177 GR+R+F QCD D G DAE ++ + L +GI DY I +N+RKILDG Sbjct: 166 AMTRGRYREFYQCDFDIAGQFDPMIPDAECLKIVVEILSRLGIG--DYGIKVNHRKILDG 223 Query: 178 ILEKIGLHGDDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQI 237 + G+ +DK + +IDKLDK + VK + F KG L+ E Sbjct: 224 MFAVCGV-PEDKFRT---ICSSIDKLDKMPWEDVKKEMV---------FEKG--LSEEAA 268 Query: 238 DIMVSFLSIDLEKSMHELY---ELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISST 294 D + ++S+ + E + A ++ +L + E + G S RI + Sbjct: 269 DRIGEYVSLKGLDELLEKLIADPKLSQNEAAKEALADLKQLFEYLEIFGI-SERISFDLS 327 Query: 295 IVRGLEYYTGCVYEAIL---------GFPVMNEKQKPVVFGSVGGGGRYDGLVSRF--KG 343 + RGL+YYTG +YEA+L G +P GSV GGRYD LV F KG Sbjct: 328 LARGLDYYTGVIYEAVLRGLRLICPAGRYDQAGSTEPGGVGSVAAGGRYDNLVGMFDKKG 387 Query: 344 QNVPATGFSIGISRLIVALKS-LESSTNNIKEMGPVLITTMDHDSDSLSKYQMYTQMLRT 402 VP G S+G+ R+ L+ + I+ + + L + L Sbjct: 388 DKVPCVGQSVGVERIFSILEQRAATVATKIRTTE-TQVYVAAAGKNLLFERLKVVNALWD 446 Query: 403 AGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDLAKGKE 455 AGI+AE ++ Q +YA+ PLA+I G E + G +++K++ +E Sbjct: 447 AGIKAEYLYKANPKLLKQFQYAEEAGIPLAVILGEEELADGSVKVKNVGTREE 499 >gnl|CDD|73226 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.. Length = 261 Score = 207 bits (529), Expect = 5e-54 Identities = 105/342 (30%), Positives = 166/342 (48%), Gaps = 81/342 (23%) Query: 22 EIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWI 81 E +R I D++R ++E YG++ I+TP+ EY++ + DE K ++ +D G+ + Sbjct: 1 EAALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVS--KEMYRFKDKGGRDL 58 Query: 82 SLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAE 141 +LR DLTAP+AR VAEN ++ P + Y IGPVFR E+ GR+R+F Q V+ +GS + Sbjct: 59 ALRPDLTAPVARAVAENLLSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSDSP 118 Query: 142 TADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAID 201 ADAE+ + + LEA+ G+ + +I K+N R I Sbjct: 119 LADAEVIALAVEILEAL---------GLKDFQI--------------KINHRGI------ 149 Query: 202 KLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLEKSMHELYELVKG 261 L G+ LL + E I+ ++ L + + +L + ++ Sbjct: 150 ------LDGIAGLLEDRE---------------EYIERLIDKLDKEALAHLEKLLDYLEA 188 Query: 262 TIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQK 321 K I ++VRGL+YYTG V+EA+ Sbjct: 189 LGVDIK---------------------YSIDLSLVRGLDYYTGIVFEAVA--------DG 219 Query: 322 PVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVALK 363 GS+ GGGRYDGL+ F G++VPA GF+IG+ RL++AL+ Sbjct: 220 LGAQGSIAGGGRYDGLLEEFGGEDVPAVGFAIGLERLLLALE 261 >gnl|CDD|33500 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]. Length = 390 Score = 135 bits (340), Expect = 3e-32 Identities = 97/366 (26%), Positives = 154/366 (42%), Gaps = 48/366 (13%) Query: 7 LRAELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRP 66 + +LP G D E R + I D + ++ +G++ +ETP LE +D L ED Sbjct: 1 MTWQLPEGIRDVLPLEARRKEEIRDQLLALFRAWGYERVETPTLEPADPLLD-GAGEDLR 59 Query: 67 NKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFR 126 + +F L+D+ G + LR D T P+AR A P R G VFR + GR Sbjct: 60 RR-LFKLEDETGGRLGLRPDFTIPVARIHATLLAG--TPLRLSYAGKVFRAREGRHGRRA 116 Query: 127 QFIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHG 186 +F+Q ++ +G + ADAE+ + L+A+G+ D + + + I +L GL G Sbjct: 117 EFLQAGIELLGDDSAAADAEVIALALAALKALGLA--DLKLELGHAGIFRALLAAAGLPG 174 Query: 187 DDKLNERLIVLRAIDKLDKFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSI 246 RL RA D GL+ A L+ E + L++ Sbjct: 175 G--WRARL--RRAFGDKDLLGLE---------------LLVLAAPLSPELRGRLSELLAL 215 Query: 247 -----DLEKSMHELYELVKGTIAGEKGFNELVVISELVRKSGYNSNRIKISSTIVRGLEY 301 LE L+ +A NE ++++ R+ I + +R +Y Sbjct: 216 LGGREVLE----RARGLLDELMAQGIALNEGRALADIARRLIEK---IALDLGRLRHFDY 268 Query: 302 YTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPATGFSIGISRLIVA 361 YTG V+ A + ++ GGRYDGL+ F G+ PATGF++ + L Sbjct: 269 YTGLVFLAY----------ADGLGDALASGGRYDGLLGLF-GRAAPATGFALRLDALAQG 317 Query: 362 LKSLES 367 LE Sbjct: 318 GLPLEE 323 >gnl|CDD|144252 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G, H, P, S and T). Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. Length = 170 Score = 98.1 bits (245), Expect = 5e-21 Identities = 45/168 (26%), Positives = 79/168 (47%), Gaps = 16/168 (9%) Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSL---GKFLPDEDRPNKGVFSLQDDDGQWI 81 +RN + + IR++++ YG+ ++TP+LE + G + D ++ +D G+ + Sbjct: 1 LRNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDE----MYRFKDRGGEEL 56 Query: 82 SLRYDLTAPLARYVAENFDT-IVFPCRTYRIGPVFRNEK---HGPGRFRQFIQCDVDNVG 137 LR + R + P + Y+IGP FR E G GR R+F Q D + G Sbjct: 57 YLRPTAEVGITRLFKNEILSYRDLPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFG 116 Query: 138 SS--AETADAEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIG 183 + +E D E+ + + L+ +G+ Y + +N R L G K G Sbjct: 117 TPEQSEEEDEELLKLAEEILQDLGL---PYRVVLNTRGDLGGYASKTG 161 >gnl|CDD|36253 KOG1035, KOG1035, KOG1035, eIF-2alpha kinase GCN2 [Translation, ribosomal structure and biogenesis]. Length = 1351 Score = 81.2 bits (200), Expect = 6e-16 Identities = 78/409 (19%), Positives = 148/409 (36%), Gaps = 41/409 (10%) Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLR 84 +R +++ + I+ +G +ETP L ++ L D G + L Sbjct: 934 LREYVVEEVVKIFRKHGAIELETPPL-------SLRNACAYFSRKAVELLDHSGDVVELP 986 Query: 85 YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVDNVGSSAETAD 144 YDL P ARYV+ N + Y I V+R H ++ ++CD D +G + + Sbjct: 987 YDLRLPFARYVSRNSVLSF---KRYCISRVYRPAIHNHP--KECLECDFDIIGPTTSLTE 1041 Query: 145 AEMCMMMADTLEAVGIKRNDYHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAIDKLD 204 AE+ + + + + + I +N+ +L+ IL G+ D+ + +L + Sbjct: 1042 AEL-LKVIVEITTEILHEGNCDIHLNHADLLEAILSHCGIP-KDQRRKVAELLSDMGSSR 1099 Query: 205 KFGLQGVKLLLGEGRTDNSGDFTKGANLTSEQIDIMVSFLSIDLEKSMHELYELVKGTIA 264 + + R+ + A L + L + +L++G + Sbjct: 1100 PQRSEKELKWVFIRRSSL-----QLAKL------PEFVLNRLFLVAGRFQALKLIRGKLR 1148 Query: 265 GE---KGFNELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQK 321 + + EL + L+R G + + I G ++ + Sbjct: 1149 ADSLVRALKELENVVGLLRSLGIEEH-VHIYVGPTESRHRNGGIQFQ----ITAEIKSNT 1203 Query: 322 PVVFGSVGGGGRYDGLVSRFKGQ---NVP-ATGFSIGISRLIVALKSLESSTNNIKEMGP 377 + GGRYD L+ + + N+P A G S + A K LE Sbjct: 1204 SGDPVLLAAGGRYDSLLQEVRDEQKMNLPGAIGVSALSTIRQHAPKDLEPIKTPSS--CD 1261 Query: 378 VLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADR 426 VLI + + + L + GI+AE+ S + +YA+ Sbjct: 1262 VLICSRGSGLLTQRMELV--AKLWSKGIKAEIVPDPSPSLEELTEYANE 1308 >gnl|CDD|29799 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.. Length = 91 Score = 72.1 bits (177), Expect = 3e-13 Identities = 33/110 (30%), Positives = 49/110 (44%), Gaps = 21/110 (19%) Query: 377 PVLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQG 436 V + + +LS+ + LR AGI+AE+ G K Q KYADR A+I G Sbjct: 3 DVYVVPLG--EGALSEALELAEQLRDAGIKAEIDYGGRK-LKKQFKYADRSGARFAVILG 59 Query: 437 TGERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPISELVSTVK 486 E + G++ +KDL G+ Q T+ + ELV +K Sbjct: 60 EDELAAGVVTVKDLETGE------------------QETVALDELVEELK 91 >gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional. Length = 430 Score = 62.6 bits (152), Expect = 2e-10 Identities = 51/164 (31%), Positives = 72/164 (43%), Gaps = 20/164 (12%) Query: 290 KISSTIVRGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVGGGGRYDGLVSRFKGQNVPAT 349 KI+ +VRGL+YY +E ++ GGGRYD L+ + G PA Sbjct: 251 KINYKLVRGLDYYNDTAFEI-----KTLSSNGQ---DTICGGGRYDSLIHQLGGPKTPAV 302 Query: 350 GFSIGISRLIVALKSLESSTNNI---KEMGPVLITTMDHDSDSLSKYQMYTQMLRTAGIR 406 G +IG+ RL++ K +NI K+ V I T + K Q L I+ Sbjct: 303 GCAIGLERLLLIAK------DNIILPKQSIDVYIAT--QGLKAQKKGWEIIQFLEKQNIK 354 Query: 407 AEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGMLQIKDL 450 E+ L SS NF Q+K A ++ II G E + IK L Sbjct: 355 FELDL-SSSNFHKQIKQAGKKRAKACIILGDNEIMDNCITIKWL 397 Score = 60.3 bits (146), Expect = 1e-09 Identities = 45/164 (27%), Positives = 69/164 (42%), Gaps = 10/164 (6%) Query: 13 RGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSD----SLGKFLPDEDRPNK 68 RG D EI I D + + I TP+ E S +G+ D NK Sbjct: 8 RGTKDILPDEINYWQFIHDKALTLLSLANYSEIRTPIFENSSLYDRGIGE---TTDIVNK 64 Query: 69 GVFSLQDDDGQWISLRYDLTAPLARYVAEN-FDTIVFPCRTYRIGPVFRNEKHGPGRFRQ 127 ++ D + I+LR + TA + R EN D R + GP+FR E+ GR RQ Sbjct: 65 EMYRFTDRSNRDITLRPEGTAGIVRAFIENKMDYHSNLQRLWYSGPMFRYERPQSGRQRQ 124 Query: 128 FIQCDVDNVGSSAETADAEMCMMMADTLEAVGIKRNDYHIGINN 171 F Q ++ +GS AD E+ + + + + + IN+ Sbjct: 125 FHQLGIEFIGSIDARADTEVIHLAMQIFNELQV--KNLILDINS 166 >gnl|CDD|29813 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.. Length = 211 Score = 50.1 bits (119), Expect = 1e-06 Identities = 41/141 (29%), Positives = 59/141 (41%), Gaps = 10/141 (7%) Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLR 84 IR++I +R GF +ETP++E L K + ++D LR Sbjct: 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDL----YLR 56 Query: 85 YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH--GPGRFRQFIQCDVDNVGSSAET 142 L L R + + P R IGP FRNE G R R+F Q + + G E Sbjct: 57 PTLEPGLVRLFVSHIRKL--PLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEE 114 Query: 143 AD--AEMCMMMADTLEAVGIK 161 A E+ + + L A+GIK Sbjct: 115 ASEFEELIELTEELLRALGIK 135 >gnl|CDD|145985 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain. Length = 93 Score = 47.6 bits (114), Expect = 7e-06 Identities = 23/111 (20%), Positives = 46/111 (41%), Gaps = 19/111 (17%) Query: 378 VLITTMDHDSDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGT 437 V++ + + Q + LR AGIR E+ +++ G + + AD P ++ G Sbjct: 2 VVVIPLGEKDELEDYAQKLAEELREAGIRVELDD-RNESLGKKFRDADLIGIPFRLVVGE 60 Query: 438 GERSRGMLQIKDLAKGKELSREIKNNESWREARVAQITIPISELVSTVKKI 488 E G + ++D G+ + T+ + ELV +K++ Sbjct: 61 KELENGTVTVRDRDTGE------------------KETVSLEELVEKLKEL 93 >gnl|CDD|143920 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N). Length = 341 Score = 42.6 bits (101), Expect = 2e-04 Identities = 31/136 (22%), Positives = 52/136 (38%), Gaps = 29/136 (21%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 +++R++I+ +IR + GF +ETP+L S G R F + + Sbjct: 22 LKLRSKIIRAIREFLDERGFLEVETPILTKSTPEGGA-----RD----FLVPKFYAKEAY 72 Query: 83 LRYDLTAP---LARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR-FRQFIQCDVDNVGS 138 L +P + FD R ++I P FR+E R +F Q D Sbjct: 73 LP---QSPQLYKQLLMVAGFD------RVFQIAPCFRDEDLRTDRHPPEFTQLD------ 117 Query: 139 SAETADAEMCMMMADT 154 E + + +M T Sbjct: 118 -LEMSFVDYEDVMDLT 132 >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 41.8 bits (98), Expect = 4e-04 Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 13/165 (7%) Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQW 80 K IRN + D +R +YG+ ++TP+L L + D + +F + DD + Sbjct: 218 KGATIRNLLEDYVRTKLRSYGYQEVKTPVL-ADLELWELSGHWDNYKEDMFLTESDD-RE 275 Query: 81 ISLRYDLTAPLARYVAENFDTIV--FPCRTYRIGPVFRNEK----HGPGRFRQFIQCDVD 134 +L+ + P + ++ P R G V+R EK HG R R F Q D Sbjct: 276 YALKP-MNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAH 334 Query: 135 NVGSSAETAD--AEMCMMMADTLEAVGIKRNDYHIGINNRKILDG 177 + + D + ++ + + G DY + ++ R G Sbjct: 335 IFCTPDQIKDEFKGILELILEVYKDFGF--TDYEVKLSTRPKFIG 377 >gnl|CDD|29810 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.. Length = 235 Score = 41.8 bits (98), Expect = 4e-04 Identities = 29/159 (18%), Positives = 57/159 (35%), Gaps = 14/159 (8%) Query: 25 IRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQW---- 80 + + + + YG+ I P L + K + K +++ +D + Sbjct: 4 LWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYR-KEMYTFEDKGRELRDTD 62 Query: 81 ISLRYDLTAPLARYVAENFD-TIVFPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDNV 136 + LR P+ + + P R +IGP FR+E + G R R+F Q + Sbjct: 63 LVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVF 122 Query: 137 G--SSAETADAEMCMMMADTLEAVGIKRNDYHIGINNRK 173 G AE E + + +G+ + + + Sbjct: 123 GEPEEAEEERREWLELAEEIARELGL---PVRVVVADDP 158 >gnl|CDD|37535 KOG2324, KOG2324, KOG2324, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 457 Score = 40.3 bits (94), Expect = 0.001 Identities = 37/128 (28%), Positives = 61/128 (47%), Gaps = 10/128 (7%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 +R+ N++ + N ++ G I P+L S L + D +F L D G+ + Sbjct: 52 LRVLNKLCRLLDNEMQSGGAQKISLPILS-SKELWEKTGRWDAMGSELFRLHDRKGKQMC 110 Query: 83 L----RYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDN 135 L D+TA +A Y+ ++ P R Y+IG FR+E + G R R+F+ D+ + Sbjct: 111 LTPTHEEDITALMATYIPLSYKQ--LPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYS 168 Query: 136 VGSSAETA 143 S ETA Sbjct: 169 FDSDEETA 176 Score = 34.2 bits (78), Expect = 0.086 Identities = 32/177 (18%), Positives = 65/177 (36%), Gaps = 31/177 (17%) Query: 270 NELVVISELVRKSGYNSNRIKISSTIVRGLEYYTGCVYEAILGFPVMNEKQKPVVFGSVG 329 +E + +S++ N R+ + +I G + G Y L +N + KP Sbjct: 239 SEDLDLSKIASCPKCNEGRLTKTKSIEVGHTFLLGTKYSKPLNAKFVNVEGKP------- 291 Query: 330 GGGRYDGLVSRFKGQNVPATGFSIGISRLIVALKSLESSTNNI---KEMGP--VLITTMD 384 + + + IG++RL+ A + S + + P V + Sbjct: 292 --------------EFLHMGCYGIGVTRLLAAAAEVLSDDKGLRWPSLIAPYKVCLIGPK 337 Query: 385 HDSDSLSKYQMYTQMLRTAGIRA---EMFLGSSKN--FGNQLKYADRRNCPLAIIQG 436 S S ++ +++L + E+ L + G ++K A+R P I+ G Sbjct: 338 KGSKSQRAQEVISELLNDEAVGNLHGEILLDDREELTIGKRIKDANRLGIPFVIVVG 394 >gnl|CDD|29816 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.. Length = 298 Score = 38.6 bits (90), Expect = 0.004 Identities = 29/130 (22%), Positives = 45/130 (34%), Gaps = 39/130 (30%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLL-------------EYSDSLGKFLPDED----RP 66 IRN + D +R + G+ +ETP++ Y +++ F +++ +P Sbjct: 31 IIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFEEEDEEYGLKP 90 Query: 67 NKGVFSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEK----HGP 122 + S R DL P R G V R E+ HG Sbjct: 91 MNCPGHCLIFKSKPRSYR-DL-----------------PLRLAEFGTVHRYEQSGALHGL 132 Query: 123 GRFRQFIQCD 132 R R F Q D Sbjct: 133 TRVRGFTQDD 142 >gnl|CDD|31383 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 502 Score = 37.9 bits (88), Expect = 0.006 Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 14/96 (14%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 R++I+ +IR ++ GF +ETP+L G RP + D D + Sbjct: 180 FIKRSKIIRAIREFLDDRGFLEVETPML--QPIPGG---AAARPFITHHNALDMD---LY 231 Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE 118 LR L R + F+ R + IG FRNE Sbjct: 232 LRIAPELYLKRLIVGGFE------RVFEIGRNFRNE 261 >gnl|CDD|30366 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]. Length = 335 Score = 37.9 bits (88), Expect = 0.006 Identities = 30/113 (26%), Positives = 52/113 (46%), Gaps = 14/113 (12%) Query: 27 NRILDSIRNIYENYGFDPIETPLLEYS----DSLGKFLPDEDRPNK---GVFSLQDDDGQ 79 + ++ I +I+ GF +E P +E D+L +P +D P + F L+DD + Sbjct: 114 TQTIEEIEDIFLGMGFTEVEGPEIETDFYNFDAL--NIP-QDHPARDMQDTFYLKDDREK 170 Query: 80 WISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCD 132 + LR + AR +AEN P + + G V+RN+ +F Q + Sbjct: 171 LL-LRTHTSPVQARTLAENAKI---PIKIFSPGRVYRNDTVDATHSPEFHQIE 219 >gnl|CDD|29820 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.. Length = 329 Score = 35.9 bits (83), Expect = 0.023 Identities = 29/103 (28%), Positives = 42/103 (40%), Gaps = 18/103 (17%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 +R++I+ IR ++ GF +ETP+L+ RP + D D + L Sbjct: 9 IVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGA-----AARPFITHHNALDMD---LYL 60 Query: 84 RYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNE----KHGP 122 R L R + F+ R Y IG FRNE H P Sbjct: 61 RIAPELYLKRLIVGGFE------RVYEIGRNFRNEGIDLTHNP 97 >gnl|CDD|58337 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.. Length = 269 Score = 35.3 bits (81), Expect = 0.041 Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 14/111 (12%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 ++R++I+ +IR+ ++ GF +ETP+L+ K + G Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAG---ARPFLVK-----YNALGLDYY 52 Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDV 133 LR R + D R + I FRNE +F D+ Sbjct: 53 LRISPQLFKKRLMVGGLD------RVFEINRNFRNEDLRARHQPEFTMMDL 97 >gnl|CDD|73228 cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.. Length = 280 Score = 34.4 bits (79), Expect = 0.078 Identities = 33/115 (28%), Positives = 51/115 (44%), Gaps = 20/115 (17%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLG--KFL-PDEDRPNKGVFSLQDDDGQ 79 +R+R+R++ +IRN + GF IETP+L S G FL P P K ++L Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEGARDFLVPSRLHPGK-FYALPQSPQL 59 Query: 80 WISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVD 134 + L + FD R ++I FR+E R +F Q D++ Sbjct: 60 FKQL----------LMVSGFD------RYFQIARCFRDEDLRADRQPEFTQIDIE 98 >gnl|CDD|37096 KOG1885, KOG1885, KOG1885, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 34.1 bits (78), Expect = 0.082 Identities = 37/150 (24%), Positives = 54/150 (36%), Gaps = 41/150 (27%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISL 83 RIR +I+ IR ++ GF +ETP++ +P F +D L Sbjct: 226 RIRAKIISYIRKFLDSRGFLEVETPMMN-----MIAGGATAKP----FITHHND-----L 271 Query: 84 RYDLT---AP---LARYVAENFDTIVFPCRTYRIGPVFRNE----KHGPGRFRQFIQC-- 131 DL AP L V D R Y IG FRNE H P +F C Sbjct: 272 DMDLYLRIAPELYLKMLVVGGLD------RVYEIGRQFRNEGIDLTHNP----EFTTCEF 321 Query: 132 -----DVDNVGSSAETADAEMCMMMADTLE 156 D +++ E + M + + + Sbjct: 322 YMAYADYEDLMDMTEELLSGMVKNITGSYK 351 >gnl|CDD|37622 KOG2411, KOG2411, KOG2411, Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]. Length = 628 Score = 33.5 bits (76), Expect = 0.14 Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 19/117 (16%) Query: 21 KEIRIRNRILDSIRNIYENY-GFDPIETPLLEYSDSLG--KFLPDEDRPNKGVFSLQDDD 77 +R+R+ ++ IR N GF +ETP L G +F+ P ++L Sbjct: 176 NNLRLRSNVVKKIRRYLNNRHGFVEVETPTLFKRTPGGAREFVVPTRTPRGKFYALPQSP 235 Query: 78 GQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQFIQCDVD 134 Q+ L + D R Y+I FR+E R +F Q D++ Sbjct: 236 QQFKQL----------LMVSGID------RYYQIARCFRDEDLRADRQPEFTQVDME 276 >gnl|CDD|30522 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 585 Score = 32.1 bits (73), Expect = 0.40 Identities = 12/30 (40%), Positives = 22/30 (73%) Query: 21 KEIRIRNRILDSIRNIYENYGFDPIETPLL 50 K +++R+++ +IRN ++ GF IETP+L Sbjct: 139 KNLKLRSKVTKAIRNFLDDQGFLEIETPIL 168 >gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]. Length = 637 Score = 30.6 bits (69), Expect = 0.95 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%) Query: 450 LAKGKELSREIKNNESWREARVAQITIPISELVSTVKKILQENKEE 495 + KG REI W V I S + ++++IL+ ++E Sbjct: 114 IGKGGSTLREITAETGWAPKIVRTPPIQ-SRTIKSIREILRSERKE 158 >gnl|CDD|30367 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]. Length = 435 Score = 29.8 bits (67), Expect = 1.6 Identities = 28/119 (23%), Positives = 43/119 (36%), Gaps = 32/119 (26%) Query: 23 IRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWIS 82 +IR+ IL +IR + GF + TP++ S + G +F + Sbjct: 134 FKIRSSILRAIREFFYENGFTEVHTPIITASATEG---------GGELFKVDY------- 177 Query: 83 LRYDLTAPLA-------RYVAENFDTIVFPCRTYRIGPVFRNEKHGPGR-FRQFIQCDV 133 +D A L +A + R + IGP FR EK R +F D Sbjct: 178 --FDKEAYLTQSPQLYKEALAAALE------RVFTIGPTFRAEKSNTRRHLSEFWMLDP 228 >gnl|CDD|29821 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.. Length = 322 Score = 29.7 bits (67), Expect = 1.7 Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 19/98 (19%) Query: 24 RIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQ-WIS 82 RIR+ +L + R GF + TP + +D+ G +F + +++ Sbjct: 25 RIRSEVLRAFREFLRENGFTEVHTPKITSTDTEG---------GAELFKVSYFGKPAYLA 75 Query: 83 LRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH 120 L + E R Y IGPVFR EK Sbjct: 76 QSPQLYKEMLIAALE---------RVYEIGPVFRAEKS 104 >gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 28.8 bits (64), Expect = 3.5 Identities = 29/126 (23%), Positives = 47/126 (37%), Gaps = 14/126 (11%) Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGV 70 LP G RI N ++D IR Y GF + TP + Y+ L + ++ + Sbjct: 188 LPHG--------TRIYNTLVDFIRAEYRKRGFTEVITPNI-YNKKLWETSGHWQNYSENM 238 Query: 71 FSLQDDDGQWISLRYDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKHGP----GRFR 126 F + + ++ + + + P R G + RNE G R R Sbjct: 239 FKFEVEKEEFALKPMNCPGHCLMFAHRDRSYRELPLRFADFGVLHRNEASGALSGLTRVR 298 Query: 127 QFIQCD 132 +F Q D Sbjct: 299 RF-QQD 303 >gnl|CDD|48070 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).. Length = 417 Score = 28.6 bits (64), Expect = 4.0 Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%) Query: 30 LDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRP 66 ++ +++I E +G +PI P L S SL L D+ P Sbjct: 173 VEELKDIIEAFGLEPIILPDL--SGSLDGHLADDWSP 207 >gnl|CDD|30791 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 500 Score = 28.3 bits (63), Expect = 4.8 Identities = 32/150 (21%), Positives = 57/150 (38%), Gaps = 31/150 (20%) Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLL------EYSDSLGKFLPDED 64 LP G R+ +I + IR + G + P L + S F P+ Sbjct: 43 LPLGL--------RVLEKIENIIREEMDKIGAQEVLFPTLIPAELWKESGRWEGFGPE-- 92 Query: 65 RPNKGVFSLQDDDGQWISLR----YDLTAPLARYVAENFDTIVFPCRTYRIGPVFRNEKH 120 +F ++D + ++LR +T +++ D P + Y+I FR+EK Sbjct: 93 -----LFRVKDRGDRPLALRPTSEEVITDMFRKWIRSYKD---LPLKLYQIQSKFRDEKR 144 Query: 121 GPG---RFRQFIQCDVDNVGSSAETADAEM 147 R R+F+ D + + E A+ Sbjct: 145 PRFGLLRGREFLMKDAYSFHADEEDAEETY 174 >gnl|CDD|38484 KOG3274, KOG3274, KOG3274, Uncharacterized conserved protein, AMMECR1 [Function unknown]. Length = 210 Score = 28.4 bits (63), Expect = 4.8 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%) Query: 263 IAGEKGFNELVVISELVRKSGYNSN-----RIKISSTIVRGLEYYTGCVYE 308 +A E+G++++ I L+RK+GY R I T R + YE Sbjct: 147 VAAEQGWDQIETIDSLIRKAGYKGPITEELRKSIKLTRYRSEKI--SITYE 195 >gnl|CDD|48408 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.. Length = 145 Score = 28.3 bits (63), Expect = 5.6 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%) Query: 450 LAKGKELSREIKNNESWREARVAQITIPISELVSTVKKILQENKEE 495 + KG REI W V I S V ++++ L+ +EE Sbjct: 91 IGKGGSTLREITRETGWAPKVVRTPPIQ-SRTVKSIRRFLRREREE 135 >gnl|CDD|73229 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.. Length = 255 Score = 28.2 bits (63), Expect = 5.8 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%) Query: 104 FPCRTYRIGPVFRNE---KHGPGRFRQFIQCDVDNVGSSAETADAE 146 P Y+I FR+E + G R R+F+ D + E+ + Sbjct: 112 LPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEET 157 >gnl|CDD|39385 KOG4183, KOG4183, KOG4183, RNA polymerase I 49 kDa subunit [Transcription]. Length = 413 Score = 28.1 bits (62), Expect = 6.1 Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 6/74 (8%) Query: 48 PLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQWISLRYDLTAPLAR--YVAENFDTIVFP 105 PL+ +SD G F E+ ++ +D + L R YV NF T Sbjct: 24 PLVAFSDPNGGFRSPEN-TRFTLYKKKDSSKPRN--QRVLAGETERLEYVGNNFSTGALK 80 Query: 106 CRTYRIGPVFRNEK 119 C TY +G VF E Sbjct: 81 CNTYCVG-VFNKES 93 >gnl|CDD|34415 COG4806, RhaA, L-rhamnose isomerase [Carbohydrate transport and metabolism]. Length = 419 Score = 28.1 bits (62), Expect = 6.1 Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 5/45 (11%) Query: 11 LPRGFADCPTKEIRIRNRILDSIRNIY-----ENYGFDPIETPLL 50 +P G D P + R R+L+++ + + D +E+ L Sbjct: 186 IPDGMKDIPVDRLAPRQRLLEALDEVISEKLDPAHHIDAVESKLF 230 >gnl|CDD|146135 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognized by T cells. Length = 577 Score = 27.8 bits (62), Expect = 7.1 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 9/66 (13%) Query: 439 ERSRGMLQIKDLAKGKE-LSREIKNNESWREARVAQ-------ITI-PISELVSTVKKIL 489 + R + Q K E ++R+I +S E A+ I I SE V +++K Sbjct: 321 AKQRRLKQKKRKKLRPEDIARQIAEEKSEDEEEAAEAENNDNGIVIDETSEFVRSLQKEP 380 Query: 490 QENKEE 495 E + E Sbjct: 381 LEEEPE 386 >gnl|CDD|33846 COG4089, COG4089, Predicted membrane protein [Function unknown]. Length = 235 Score = 27.6 bits (61), Expect = 7.3 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 7/41 (17%) Query: 302 YTGCVYEAILGFPVMNEKQ-----KPVVFGSVGGGGRYDGL 337 Y V ++G ++N K+ PVV S+GG G +DG+ Sbjct: 186 YITGVLGTLIGADLLNLKKIINEGPPVV--SIGGAGTFDGI 224 >gnl|CDD|176105 cd08413, PBP2_CysB_like, The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 198 Score = 27.6 bits (62), Expect = 8.9 Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 7/37 (18%) Query: 165 YHIGINNRKILDGILEKIGLHGDDKLNERLIVLRAID 201 Y G R +D + GL + IVL A+D Sbjct: 104 YDFGFTGRSSIDRAFARAGLEPN-------IVLTALD 133 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.138 0.393 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,835,000 Number of extensions: 318339 Number of successful extensions: 829 Number of sequences better than 10.0: 1 Number of HSP's gapped: 791 Number of HSP's successfully gapped: 49 Length of query: 496 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 398 Effective length of database: 4,146,055 Effective search space: 1650129890 Effective search space used: 1650129890 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 (26.6 bits)