RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780191|ref|YP_003064604.1| alanyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (898 letters) >gnl|CDD|30363 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 879 Score = 988 bits (2557), Expect = 0.0 Identities = 432/911 (47%), Positives = 583/911 (63%), Gaps = 51/911 (5%) Query: 1 MSNVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQA 60 + IR FL+FF+K GH ++PSS L+P NDPTL+FTN+GMV FK FTG P Sbjct: 5 KLTTNEIRQKFLDFFEKKGHTVVPSSPLVPRNDPTLLFTNAGMVQFKPYFTGGVTPPANR 64 Query: 61 VTTVQKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDL 120 T QKC+R ND+DNVG T RHHTFFEMLGNFSFG YFKE AI+ AW+ LTK L Sbjct: 65 AVTSQKCIRT----NDIDNVGYTARHHTFFEMLGNFSFGDYFKEEAIEFAWEFLTKVLGL 120 Query: 121 DQRRLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQG 180 + +LY+TVY++D+EA+ W+KI G+ ++IIRI +DNFW M GPCGPCSEIF+D+G Sbjct: 121 PKEKLYVTVYEDDDEAYNEWEKIIGIPPERIIRIGASDNFWEMG-DGPCGPCSEIFYDRG 179 Query: 181 ECIPGGLPGS-SEEGERYIEIWNLVFMQFEQQNKQERFI-LPKMSIDTGMGLERMATVLQ 238 E I GG PGS E+G+RY+EIWNLVFMQ+ + + LPK +IDTGMGLER+A VLQ Sbjct: 180 EEIGGGPPGSPDEDGDRYLEIWNLVFMQYNRDPGDGNYTPLPKKNIDTGMGLERIAAVLQ 239 Query: 239 EKTNNYDIDLFKHLIQASEQVTGMKYEGNN---IVNHRVIVDHLRSSSFLIADGILPANE 295 NYD DLF+ +I+A E++TG KY + V+ RVI DH+RS +F+IADG+LP+NE Sbjct: 240 GVPTNYDTDLFRPIIKAIEKLTGKKYGEDEEDPDVSFRVIADHIRSLAFMIADGVLPSNE 299 Query: 296 GRGYVLRRIMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSED 355 GRGYVLRRI+RRA+ + +LLG EP + L+ + EMG AYPEL + + I+E L+ E+ Sbjct: 300 GRGYVLRRIIRRALRHGKLLGIKEPFLYKLVDTVIDEMGDAYPELKEKEDFIKEVLKLEE 359 Query: 356 ERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCARGLAGIDI 415 ERF KTL+RGL LL+ L+ L K + L+G+ AFKLYDT+G P+++ ++I RGL +D Sbjct: 360 ERFAKTLERGLKLLEKELAKLKKSKTLDGEDAFKLYDTYGFPVELTEEIAEERGL-KVDE 418 Query: 416 ISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKV 475 F A+E QR RARA + G G G E L +K T+F+GYD Sbjct: 419 PGFEYAMEAQRERARASA-GSGEGAKESEDLELIDKLPETEFLGYD-------------- 463 Query: 476 LCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAI 535 + V + G+ V E GQ+V VV DQTPFYAE+GGQ+GDTG Sbjct: 464 ---------DLEMEFKVLVLFVDGKEVSELNEGQEVYVVLDQTPFYAESGGQVGDTGYIF 514 Query: 536 GD-GIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHSATHLLH 594 GD G R ++TDVQK G+ VH VE G L+ + +D + RR+L NH+ATHLLH Sbjct: 515 GDGGGRFEVTDVQKVGNGVIVHKGKVESGELKVGDEVTAEVDEERRRRLMRNHTATHLLH 574 Query: 595 HALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLPVVTRIM 654 AL +LG HV Q GS + P+ LRFD +H K +T+ ELK IE VN+II +NLPV T M Sbjct: 575 AALRKVLGDHVWQAGSLVDPEKLRFDFSHYKALTAEELKEIERLVNEIIRENLPVKTEEM 634 Query: 655 NREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIMLLYIVSES 714 + ++A A GA AL G KY D VRVV + G S LCGGTHVS+TG+I L I+SE Sbjct: 635 DLDEAKAKGAMALFGEKYGDEVRVVEI-----GDFSVELCGGTHVSNTGDIGLFKIISEE 689 Query: 715 SIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEIWEEYRKLQ--L 772 I AG+RRIEA+TG+ A +L Q++ LK +AS LKV ++ +VE + EE ++L+ L Sbjct: 690 GIAAGVRRIEAVTGEAALEYLQEQEDLLKEIASLLKVPP-ELLPKVERLLEELKELEKEL 748 Query: 773 IHAKRKLQL-----NVEDLSCHKIADVNFMSHIISEVDSKELKSVMDALQKKIQSGIIML 827 K+KL + + +I V ++ + D KEL+ + D L+KK+ S +I+L Sbjct: 749 ERLKKKLAAAELADLLSNAKAEEIGGVKVLAKEVDGADMKELREIADDLKKKLGSAVIVL 808 Query: 828 VGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGGPNGNKADQ 887 ++ K S+++ V++DL D+ A +L + A ++ GG GGGRP MAQ GG + K D+ Sbjct: 809 ASVADG-KVSLVVAVSKDLTDKVKAGELVKELAAIV-GGKGGGRPDMAQGGGKDPEKLDE 866 Query: 888 AIAGVASFLKK 898 A+ V ++K+ Sbjct: 867 ALELVIEWVKE 877 >gnl|CDD|144852 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases. Length = 545 Score = 712 bits (1839), Expect = 0.0 Identities = 280/574 (48%), Positives = 370/574 (64%), Gaps = 35/574 (6%) Query: 7 IRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQE-KPVYQAVTTVQ 65 IR TFL+FF+K GH +PSS ++P NDPTL+FTN+GM FK IF G E KP Y Q Sbjct: 2 IRQTFLDFFEKKGHTRVPSSPVVPRNDPTLLFTNAGMNQFKPIFLGGEDKPPYNRAVNSQ 61 Query: 66 KCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRL 125 KC+RAG DLDNVGRT RHHTFFEMLGNFSFG YFKE AI+ AW+LLTKE LD RL Sbjct: 62 KCIRAG----DLDNVGRTARHHTFFEMLGNFSFGDYFKEEAIEFAWELLTKELGLDPERL 117 Query: 126 YITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPG 185 Y+TVY+ D+EA +W+KI G ++I+R DNFW M +TGPCGPCSEI +D+GE I G Sbjct: 118 YVTVYEWDDEAGPIWEKIVGGPEERILRFGDKDNFWEMGDTGPCGPCSEIDYDRGEEIGG 177 Query: 186 GLPGSSEE--GERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQEKTNN 243 G + +R++EIWNLVFMQF +++ LPK SIDTGMGLER+ VLQ +N Sbjct: 178 WPSGGTPTADDDRFLEIWNLVFMQFNRESDGTLKPLPKKSIDTGMGLERLVAVLQNVRSN 237 Query: 244 YDIDLFKHLIQASEQVTGMKYEGNNIVNHRVIVDHLRSSSFLIADGILPANEGRGYVLRR 303 YD D+F LI+ E ++G KY +RVI DH R+ +F IADG++P+NEGRGYVLRR Sbjct: 238 YDTDVFIPLIELIEAISGAKYYDETDEAYRVIADHTRALTFAIADGVVPSNEGRGYVLRR 297 Query: 304 IMRRAMCYARLLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIEETLRSEDERFGKTLD 363 I+RRA+ +A+ LG EP + L+P + EMG AYPEL + + I+E L E+ERF KTL+ Sbjct: 298 ILRRALRHAKKLGLKEPFLYDLVPTVIEEMGDAYPELKEKEDTIQEILELEEERFAKTLE 357 Query: 364 RGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCARGLAGIDIISFNQALE 423 RGL LL+ ++ L K + L G+ AFKLYDT+G P+D+ ++I RGL +D+ F A+ Sbjct: 358 RGLRLLERLIKSLKKKKTLPGEDAFKLYDTYGFPVDLTKEIAEERGL-TVDMPGFEYAMV 416 Query: 424 EQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMKEDRKVLCQKPPID 483 EQR R++ G E +LKE T+F+GYD L Sbjct: 417 EQRERSKQAKKEKGE---ELDNSALKELPATTEFLGYDDLE------------------- 454 Query: 484 LTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQI 543 + + A+ GE V E ++GQ+ V+ D+TPFYAE+GGQ+GDTG IG+G ++ Sbjct: 455 ----AEAKIIALPDDGEFVAEVLAGQEGGVILDRTPFYAESGGQIGDTGYIIGNGGEFRV 510 Query: 544 TDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDY 577 TDVQK G+ VH +E G L+ +++ +D Sbjct: 511 TDVQKYG-GVVVHKGKLESGSLKVGDTVIAVVDE 543 >gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 895 Score = 593 bits (1531), Expect = e-170 Identities = 325/933 (34%), Positives = 485/933 (51%), Gaps = 85/933 (9%) Query: 5 SSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTV 64 S +R TFL+FF+ H+++ SSS+IP +DPTL+F N+GM FK IF G + +A + Sbjct: 5 SEVRKTFLDFFKSKHHKIVHSSSVIPFDDPTLLFANAGMNQFKPIFLGTMAKLKRAANS- 63 Query: 65 QKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRR 124 QKC+RAGGKHNDLD+VG+ HHTFFEMLGN+SFG YFKE A AW+LLT + + R Sbjct: 64 QKCIRAGGKHNDLDDVGKDFYHHTFFEMLGNWSFGDYFKEEACAWAWELLTFVYGIPTDR 123 Query: 125 LYITVYDEDE--------EAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIF 176 LY+T + DE E ++W ++ G+ +I+ DNFW M +TGPCGPC+EI Sbjct: 124 LYVTYFGGDEKLGLEPDLECREIWNEL-GVPDSRILPFGMKDNFWEMGDTGPCGPCTEIH 182 Query: 177 FDQGECIPGGLPGSS---EEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERM 233 +D+ GG + +EIWN+VF+Q+ ++ LPK IDTGMG ER+ Sbjct: 183 YDR----IGGRDAVKLVNHDDPDVLEIWNIVFIQYNREADGSLKPLPKKHIDTGMGFERL 238 Query: 234 ATVLQEKTNNYDIDLFKHLIQASEQVTGMKYEGNNI----VNHRVIVDHLRSSSFLIADG 289 +VLQ KT+NYD DLF + +A ++ TG +Y G + +RV+ DH R+ + ++DG Sbjct: 239 VSVLQNKTSNYDTDLFTPIFEAIQEGTGARYTGEDADGIDTAYRVVADHARTLTVALSDG 298 Query: 290 ILPANEGRGYVLRRIMRRAMCYAR-LLGYTEPLMMHLLPALCTEMGSAYPELIQAKLLIE 348 +P N GRGYVLRRI+RRA+ YA L L+P + +G A+PEL + + Sbjct: 299 GVPDNTGRGYVLRRILRRAVRYAHEKLNAPPGFFSTLVPVVVETLGDAFPELKRDPQHVI 358 Query: 349 ETLRSEDERFGKTLDRGLVLLDGVLSHLGKDEILNGDVAFKLYDTHGLPLDIMQDILCAR 408 + + E+ +F KTLDRG L D V LG + + GDVA++LYDT+G P+D+ + + + Sbjct: 359 DIINEEEAQFLKTLDRGRKLFDRVARELGSSKTIPGDVAWRLYDTYGFPVDLTELMAEEK 418 Query: 409 GLAGIDIISFNQALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKF 468 GL ID F E R A+ S G G I + + Sbjct: 419 GLK-IDETGF----EAARQEAQEKSKG-AGGGKLSIDLDVLSELVPPT------------ 460 Query: 469 MKEDRKVLCQKPPIDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQL 528 +D + + + A+ ++ + VE GQ+ +V D+T FYAE GGQ+ Sbjct: 461 --DDSFKYNEFGV------CKTRILALYREDQFVESIPKGQECGIVLDKTNFYAEQGGQI 512 Query: 529 GDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINHS 588 DTG + DG + +V++ G +V H V G L + L +D + R+ + NH+ Sbjct: 513 YDTGKLVIDGDEDFVFNVKRVQVGGYVVHIGVLEGDLSVGDQVELHVDEERRQLIMRNHT 572 Query: 589 ATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAELKSIEDNVNDIIAQNLP 648 ATHLL+ AL +L Q GS + PD LRFD + +T +LK +ED +N+ I +N P Sbjct: 573 ATHLLNFALRQVLKG-TDQKGSLVAPDKLRFDFSTKGALTKEQLKKVEDKINEFIQKNAP 631 Query: 649 VVTRIMNREDAIA-SGAAALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTHVSSTGEIML 707 V + + +A G A+ Y D VRVVSV G + S CGGTH+++T I Sbjct: 632 VYAKELPLAEAKKIPGLRAVFDEVYPDPVRVVSV--GAGQLTSVEFCGGTHLTNTSHIGD 689 Query: 708 LYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVEEI---- 763 IVSE I GIRRI A+TG+ A+ L ++ K L K + + E + Sbjct: 690 FVIVSEEGIAKGIRRIVAVTGKEAQEALRLAEDLDKDLRKTDKALEKEIQELGENLDHAV 749 Query: 764 ---WEEYRKLQLIHAKRKLQLNVEDLSCHKIADVNF---------------MSHIISEVD 805 W++ +L+ +KLQ ++DLS A V ++ ++ Sbjct: 750 IPYWQKDEIRELL---KKLQKRMDDLSRALKAAVQKEVLEEAKQLKESNPNQPLLVHYIE 806 Query: 806 SKELKSVMDALQKKIQSGIIMLVGISKEKKASVLIVVTEDLLDR-FNAVDLARLSAKVLG 864 S +L A K IML+ + K + L V ++ ++ A + + + + Sbjct: 807 SSKL-LKKQAPDKS-----IMLLSDDESGKVTCLCQVPQNAANKGLKASEWVQSVSGTM- 859 Query: 865 GGGGGGRPHMAQSGGPNGNKADQAIAGVASFLK 897 GG GGG+ +AQ+ G N D+A++ F Sbjct: 860 GGKGGGKGVLAQATGNNVGCLDEAVSLATEFAL 892 >gnl|CDD|29811 cd00673, AlaRS_core, Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine 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 predicted structure and the presence of three characteristic sequence motifs.. Length = 232 Score = 331 bits (849), Expect = 7e-91 Identities = 122/237 (51%), Positives = 153/237 (64%), Gaps = 5/237 (2%) Query: 4 VSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTT 63 S IR TFL FF+K GH +PSS ++P +DPTL+FTN+GM FK IF G+ P + Sbjct: 1 ASEIRETFLSFFEKKGHTRVPSSPVVPRDDPTLLFTNAGMNQFKPIFLGEVPPPANRLVN 60 Query: 64 VQKCVRAGGKHNDLDNVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQR 123 QKC+RAG N G+T RHHTFFEMLGNFSFG YFKE AI AW+LLT+ L + Sbjct: 61 SQKCIRAGDIDNV----GKTGRHHTFFEMLGNFSFGDYFKEEAIAFAWELLTEVLGLPKD 116 Query: 124 RLYITVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECI 183 RLY++V++ D+E +W GL +I RI DNFW M GPCGPCSEIF+D+GE Sbjct: 117 RLYVSVFEGDDEEEAIWWWKIGLPGIRIERIGFKDNFWEMGGNGPCGPCSEIFYDRGEE- 175 Query: 184 PGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMATVLQEK 240 +E+ +RY+EIWNLVFMQ+ + LPK +DTGMGLER+ VLQ Sbjct: 176 RDAASLPNEDDDRYLEIWNLVFMQYNRDADGTYRPLPKKIVDTGMGLERLVWVLQGV 232 >gnl|CDD|32699 COG2872, COG2872, Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]. Length = 241 Score = 113 bits (283), Expect = 3e-25 Identities = 71/222 (31%), Positives = 101/222 (45%), Gaps = 7/222 (3%) Query: 512 EVVFDQTPFYAEAGGQLGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSL 571 E+V D+T FY GGQ GDTG I G + DV K E I H + E L+ + Sbjct: 26 EIVLDRTIFYPTGGGQPGDTGTLIWAGGEYVVEDVTKDGEEIV--HVLAEHAKLKVGDKV 83 Query: 572 VLTIDYQNRRQLSINHSATHLLHHALSTILGSHVSQNGSCITPDGLRFDVTHSKPITSAE 631 L ID++ R + H+A HLL L + G+ + I D R D T E Sbjct: 84 KLKIDWERRYRHMRMHTALHLLSAVLYKVYGALTTGFE--IGEDYARIDF--DGEDTEDE 139 Query: 632 LKSIEDNVNDIIAQNLPVVTRIMNREDAIASGAAALLGTKYNDRVRVVSVEYEDGGVHSS 691 ++ +E N+++ +NLPV+ + RE+A L K V E G + Sbjct: 140 IEEVEALANELVKENLPVIIYFIPREEAEKLPGLVKLKNKVPPDVEGKIRIVEIGDIDVQ 199 Query: 692 ALCGGTHVSSTGEIMLLYIVSESSIRAGIRRIEAITGQRARS 733 CGGTHV +TGEI + I+ G RR+ G+RA + Sbjct: 200 P-CGGTHVKNTGEIGEIKILKTEKKGKGNRRVYFTLGERASA 240 >gnl|CDD|37316 KOG2105, KOG2105, KOG2105, Predicted metal-dependent hydrolase, contains AlaS domain [General function prediction only]. Length = 415 Score = 66.3 bits (161), Expect = 3e-11 Identities = 80/418 (19%), Positives = 152/418 (36%), Gaps = 58/418 (13%) Query: 473 RKVLCQKPP-----IDLTNGVSSIVKAIVQQGEIVEEAVSGQKVEVVFDQTPFYAEAGGQ 527 KV D V S ++GEI + E+ T + E GGQ Sbjct: 8 VKVGALACQRNSFLFDFKTLVVSCEPTKNKKGEI-------EGYEIELQDTILFPEGGGQ 60 Query: 528 LGDTGCAIGDGIRLQITDVQKKAEGIFVHHAIVERGILRTEMSLVLTIDYQNRRQLSINH 587 D+G + ++ A+ HH + ++ + +D Q R H Sbjct: 61 PSDSG-FLKIVEVSHVSRFGLHAK----HHV---NDYIEPGTTVEVAVDEQKRMDYMQQH 112 Query: 588 SATHLLHHALSTILGSHVSQNGSCITPDGLRFDVT-HSKPITSAELKSIEDNVNDIIAQN 646 S HL+ + + + R + + +T+ ++ +IE +VN+ I Sbjct: 113 SGQHLI----TAVADHLFKLKTTSWELGRFRSAIELDTPSMTAEQVAAIEQSVNEKIRDR 168 Query: 647 LPVVTRIMNREDAIASGAAALLGTK--YNDR---VRVVSVEYEDGGVHSSALCGGTHVSS 701 LPV R E ++ + + +D +RVV++E D S +C GTHVS+ Sbjct: 169 LPVNVR----ELSLDDPEVEQVSGRGLPDDHAGPIRVVNIEGVD-----SNMCCGTHVSN 219 Query: 702 TGEIMLLYIVSESSIRAGIRRIEAITGQRARSHLMGQDEKLKSLASFLKVSQGNVVGRVE 761 ++ ++ I+ + + ++G R + K+L + LK + V V+ Sbjct: 220 LSDLQVIKILGTEKGKKNRTNLIFLSGNRVLKWMERSHGTEKALTALLKCGAEDHVEAVK 279 Query: 762 EIWEEYRKLQLIHAKRKLQLNVEDLS---CHKIADVNFMSHIISEVDSKELKSVMDALQK 818 ++ + LQ K L L + DL+ H + + ++ + M+ + Sbjct: 280 KLQNSTKILQ----KNNLNL-LRDLAVHIAHSLRNSPDWGGVVILHRKEGDSEFMNIIAN 334 Query: 819 KIQSGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVL-----GGGGGGGR 871 +I S +L ++K L ++ + L +V G G GR Sbjct: 335 EIGSEETLLFLTVGDEKGGGLFLLAG------PPASVETLGPRVAEVLEGKGAGKKGR 386 >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 = 57.8 bits (139), Expect = 1e-08 Identities = 44/233 (18%), Positives = 66/233 (28%), Gaps = 63/233 (27%) Query: 13 EFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQKCVRAGG 72 +K GHE + N+ L + +F + + + + R G Sbjct: 30 PLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFVSHIRKLPLRLAEIGPAFRNEG 89 Query: 73 KHNDLDNVGRTNRHHTFFEMLGNFSFGGYF-----KERAIQLAWDLLTKEFDLDQRRLYI 127 L R F L FG E I+L +LL Sbjct: 90 GRRGL-------RRVREFTQLEGEVFGEDGEEASEFEELIELTEELLRAL---------- 132 Query: 128 TVYDEDEEAFKLWKKISGLSADKIIRITTNDNFWSMAETGPCGPCSEIFFDQGECIPGGL 187 G+ D + T F G GP EI D E Sbjct: 133 -----------------GIKLDIVFVEKTPGEFSP----GGAGPGFEIEVDHPE------ 165 Query: 188 PGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKM-------SIDTGMGLERM 233 R +EI + + Q EQ + + L + +I G+GLER+ Sbjct: 166 -------GRGLEIGSGGYRQDEQARAADLYFLDEALEYRYPPTIGFGLGLERL 211 >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 49.1 bits (117), Expect = 6e-06 Identities = 39/135 (28%), Positives = 60/135 (44%), Gaps = 20/135 (14%) Query: 585 INHSATHLLHHALSTILGSHVSQNGSCITP---DGLRFDVTHSKPITSAELKSIEDNVND 641 I HS H+L A+ + I P +G +D +PIT +L IE + + Sbjct: 29 IRHSCAHVLAQAVKRLYP------DVTIGPVIEEGFYYDFDVKEPITPEDLLKIEKEMKE 82 Query: 642 IIAQNLPVVTRIMNREDAIASGA---AALLGTKYNDRVRVVSVEYEDGGVHSSALCGGTH 698 I +NLP+ +++RE+A A A L+ K + E+ D LC G H Sbjct: 83 IAKENLPIEREVVSREEARAPFGPYKAELIDCKGHPLSEYSQGEFVD-------LCRGPH 135 Query: 699 VSSTGEIML-LYIVS 712 V STG+I L ++ Sbjct: 136 VPSTGKIAFKLLKLA 150 >gnl|CDD|145431 pfam02272, DHHA1, DHHA1 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif. Length = 69 Score = 46.1 bits (110), Expect = 5e-05 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 4/71 (5%) Query: 822 SGIIMLVGISKEKKASVLIVVTEDLLDRFNAVDLARLSAKVLGGGGGGGRPHMAQSGGPN 881 ++L ++ K V ++ L + +L + A++LGGGGGG P A +GG + Sbjct: 1 DKPVVLFAE-EDGKVKVSARSSKGLDVKGG--ELLKEVAEILGGGGGG-HPDAAGAGGKD 56 Query: 882 GNKADQAIAGV 892 +K ++A+ + Sbjct: 57 PSKLEEALELL 67 >gnl|CDD|173967 cd08048, TAF11, TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex. Each TAF, with the help of a specific activator, is required only for the expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. The TAF11 domain is structurally analogous to histone H3 and interacts with TAF13, making a novel histone-like heterodimer. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex. Length = 85 Score = 29.8 bits (68), Expect = 3.0 Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 11/57 (19%) Query: 456 QFIGYDLLRGSKFMKEDRKVLCQK-------PPIDLTNGVSSIVKAIVQQGEIVEEA 505 Q Y++ R S F K K L Q + + V+ I K V GEIVEEA Sbjct: 5 QMNRYEMFRRSSFPKAAIKRLIQSVTGQSVSQNVVIA--VAGIAKVFV--GEIVEEA 57 >gnl|CDD|31229 COG1026, COG1026, Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]. Length = 978 Score = 29.5 bits (66), Expect = 4.6 Identities = 15/47 (31%), Positives = 20/47 (42%) Query: 20 HELLPSSSLIPCNDPTLMFTNSGMVPFKNIFTGQEKPVYQAVTTVQK 66 H +L S P DP + F N FT +K VY A + +K Sbjct: 65 HTVLCGSKKYPVKDPFFKMLKRSLNTFLNAFTFPDKTVYPASSANEK 111 >gnl|CDD|146284 pfam03564, DUF1759, Protein of unknown function (DUF1759). This is a family of proteins of unknown function. Length = 146 Score = 29.3 bits (66), Expect = 5.1 Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 17/101 (16%) Query: 414 DIISFN---QALEEQRSRARAHSLGLGSGTTEKIWFSLKEKYGATQFIGYDLLRGSKFMK 470 +I FN ALE + + H L + + + W +LKE+Y + I LL K MK Sbjct: 27 EIQKFNYLKSALEGEAATLVTH-LPITAANYDVAWEALKERYDNPRVIIRSLLN--KLMK 83 Query: 471 ------EDRKVLCQKPPIDLTNGVSSIVKAIVQQGEIVEEA 505 + L + L + + I++ + Q GE ++ Sbjct: 84 LPSTNNDSVSQLRR-----LYDEANEIIRQLEQLGENADDT 119 >gnl|CDD|39628 KOG4427, KOG4427, KOG4427, E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]. Length = 1096 Score = 29.2 bits (65), Expect = 5.2 Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 13/64 (20%) Query: 66 KCVRAGGKHN-DLDNVGRTNRHHTFFEMLGNFSFGGYF-KERAIQLAWDLLTKEFDLDQR 123 + + +G + DLD++ + +T + +GG+ R I+ WD+L +F ++R Sbjct: 949 QRLISGDNSDIDLDDL----KRNTKY-------YGGFHDSHRVIKWLWDILAGDFTPEER 997 Query: 124 RLYI 127 +L++ Sbjct: 998 KLFL 1001 >gnl|CDD|31095 COG0752, GlyQ, Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]. Length = 298 Score = 28.6 bits (64), Expect = 7.2 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 229 GLERMATVLQEKTNNYDID 247 GLER+A +Q N YD++ Sbjct: 164 GLERLAMYIQGVDNVYDLE 182 >gnl|CDD|32597 COG2605, COG2605, Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]. Length = 333 Score = 28.7 bits (64), Expect = 7.4 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 10/71 (14%) Query: 807 KELKSVMDALQKKIQS------GIIMLVGISKEKKASVLIVVTEDLLDRF--NAVDLARL 858 E+K++ ++ + G I+ G +KK S I + D +DR A+ Sbjct: 224 HEMKALAYEMKDALVRNDIPEFGQILDRGWEAKKKLSSRI--SNDAIDRIYELALKNGAY 281 Query: 859 SAKVLGGGGGG 869 K+ G GGGG Sbjct: 282 GGKLSGAGGGG 292 >gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 28.8 bits (64), Expect = 7.9 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 10/53 (18%) Query: 587 HSATHLLHHALSTILGSHVSQNGSCITP---DGLRFDVTHSKPITSAELKSIE 636 HS+ H+L AL G+H+ CI P +G +D+ I+S + SIE Sbjct: 71 HSSAHVLGEALEQEYGAHL-----CIGPPIEEGFYYDML--DEISSNDFPSIE 116 >gnl|CDD|111033 pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit. Length = 284 Score = 28.2 bits (63), Expect = 9.7 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 222 MSIDTGMGLERMATVLQEKTNNYDI 246 +S + GLER+A LQ+ + YD+ Sbjct: 151 VSGEITYGLERLAMYLQKVDSVYDL 175 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 0.319 0.136 0.393 Gapped Lambda K H 0.267 0.0700 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 10,636,780 Number of extensions: 585112 Number of successful extensions: 1550 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1510 Number of HSP's successfully gapped: 23 Length of query: 898 Length of database: 6,263,737 Length adjustment: 103 Effective length of query: 795 Effective length of database: 4,038,010 Effective search space: 3210217950 Effective search space used: 3210217950 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 (21.8 bits) S2: 62 (27.7 bits)