RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014355
(426 letters)
>gnl|CDD|215160 PLN02286, PLN02286, arginine-tRNA ligase.
Length = 576
Score = 815 bits (2108), Expect = 0.0
Identities = 323/410 (78%), Positives = 360/410 (87%), Gaps = 3/410 (0%)
Query: 13 RELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKGPQP 71
REL K+F+ +L+ TVP+E V PL+AACT KFGDYQCNNAMGLWSK+KGKGT FK P+
Sbjct: 1 RELAKLFEASLRLTVPDEPSVEPLVAACTNPKFGDYQCNNAMGLWSKLKGKGTSFKNPRA 60
Query: 72 VGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETWAPKLRVKKAV 131
V QAI+KNLP SEMIES SVAGPGFVNV LS +W+AK I++MLVDGI+TWAP L VK+AV
Sbjct: 61 VAQAIVKNLPASEMIESTSVAGPGFVNVRLSASWLAKRIERMLVDGIDTWAPTLPVKRAV 120
Query: 132 VDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEK 191
VDFSSPNIAKEMHVGHLRSTIIGD+LARMLEFS VEVLRRNHVGDWGTQFGMLIE+LFEK
Sbjct: 121 VDFSSPNIAKEMHVGHLRSTIIGDTLARMLEFSGVEVLRRNHVGDWGTQFGMLIEHLFEK 180
Query: 192 FPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQICEI 251
FPN E ++ AIG+LQEFY+ +K RFD D FK RAQQAVVRLQ G+P+Y AWA+ICEI
Sbjct: 181 FPNWESVSDQAIGDLQEFYKAAKKRFDEDEEFKARAQQAVVRLQGGDPEYRAAWAKICEI 240
Query: 252 SRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNIPLI 311
SR+EF+KVY+RLRV+LEEKGESFYNPYIPGVI+EL +GLV ES GARVIF+EG +IPLI
Sbjct: 241 SRREFEKVYQRLRVELEEKGESFYNPYIPGVIEELESKGLVVESDGARVIFVEGFDIPLI 300
Query: 312 IVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDS 371
+VKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQ HFDMVF AAKRAGWL +
Sbjct: 301 VVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQQHFDMVFKAAKRAGWL--PED 358
Query: 372 TYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERG 421
TYP+ HVGFGLVLGEDGKR RTR EVVRLVDLLDEAK+RSKA LIERG
Sbjct: 359 TYPRLEHVGFGLVLGEDGKRFRTRSGEVVRLVDLLDEAKSRSKAALIERG 408
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 332 bits (853), Expect = e-109
Identities = 135/423 (31%), Positives = 220/423 (52%), Gaps = 24/423 (5%)
Query: 10 NVKRELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKG 68
N+K+ L++ AL A + ++ L+ + GD+ N A L +K GK
Sbjct: 2 NIKQLLKEKIAEALSAAGLDVEEIEILVEPPKDPEHGDFATNIAFQL-AKKLGKN----- 55
Query: 69 PQPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETW--APKLR 126
P+ + + I + L E+IE +AGPGF+N LS ++A+ + ++L G + + + +
Sbjct: 56 PREIAEEIAEKLDTDEIIEKVEIAGPGFINFFLSPEFLAELLLEILEKGDDRYGRSKLGK 115
Query: 127 VKKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIE 186
KK V+++SS N +H+GHLR+ IIGDSLAR+LEF +V R N+V DWGTQ GML
Sbjct: 116 GKKVVIEYSSANPTGPLHIGHLRNAIIGDSLARILEFLGYDVTRENYVNDWGTQIGMLAL 175
Query: 187 YLFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAF-KERAQQAVVRLQSGEPKYHEAW 245
++ + G L E+Y + + DP +E A++ V +L+SG+ + E W
Sbjct: 176 SYEKRGREALGLTPEPDGYLGEYYVKIAKDLEEDPGNDEEEAREEVEKLESGDEEA-ELW 234
Query: 246 AQICEISRKEFDKVYKRLRVDLEEK---GESFYNPYIPGVIDELSKQGLVEESQGARVIF 302
+ ++S + + RL V + GESFYN + V+++L ++GL+ E GA V+
Sbjct: 235 RKFVDLSLEGIKETLDRLGVKFDVYDSEGESFYNGKVEKVVEDLEEKGLLYEDDGALVVD 294
Query: 303 IE-----GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVF 357
+ G + ++ KSDG + Y + D+A Y+ E + +IYV Q HF +
Sbjct: 295 LLKFKKFGDDKDRVLQKSDGTYLYFTRDIAYHLYKF-ERGFDKLIYVLGADQHGHFKQLK 353
Query: 358 SAAKRAGWLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVL 417
+ + G+ + H G GLV G +G ++ TR VV L DLLDEA R+ +
Sbjct: 354 AVLELLGYGPDKEVLL----HQGVGLVRGGEGVKMSTRAGNVVTLDDLLDEAGERAPEEM 409
Query: 418 IER 420
E+
Sbjct: 410 EEK 412
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 301 bits (773), Expect = 9e-98
Identities = 120/422 (28%), Positives = 186/422 (44%), Gaps = 79/422 (18%)
Query: 10 NVKRELEKVFDLALKATVPNETDVRPLIAACTAKFGDYQCNNAMGLWSKIKGKGTEFKGP 69
++K L + AL+A E + + GDY N AM L +K K P
Sbjct: 4 DIKELLAEALAAALEAGGLPELPAVLIERPKDPEHGDYATNVAMQL-AKKLKKN-----P 57
Query: 70 QPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETW--APKLRV 127
+ + + I++ IE +AGPGF+N L +A+ + +L G E + + +
Sbjct: 58 REIAEEIVEA------IEKVEIAGPGFINFFLDPAALAELVLAILEAG-ERYGRSDIGKG 110
Query: 128 KKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEY 187
KK VV++ S N +HVGHLRS +IGD+LAR+LEF+ +V R +V D GTQ GMLI
Sbjct: 111 KKVVVEYVSANPTGPLHVGHLRSAVIGDALARILEFAGYDVTREYYVNDAGTQIGMLIAS 170
Query: 188 LFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQ 247
L W +
Sbjct: 171 LE-----------------------------------------------------LLWRK 177
Query: 248 ICEISRKEFDKVYKRLRVDLEE---KGESFYNPYIPGVIDELSKQGL-VEESQGARVIFI 303
+IS E + RL V + + E +YN + V+++L ++GL ES GA + +
Sbjct: 178 AVDISLDEIKEDLDRLGVHFDVWFSESELYYNGKVDEVVEDLKEKGLLYVESDGALWVRL 237
Query: 304 E--GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAK 361
G + +++KSDG + Y + D+A Y+ E+ + +IYV HF + +A K
Sbjct: 238 TEFGDDKDRVLIKSDGTYTYFTRDIAYHLYKF--ERFDRVIYVVGADHHGHFKRLKAALK 295
Query: 362 RAGWLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERG 421
G+ H GLV G +G ++ TR VV L DLLDEA R++ ++ E+
Sbjct: 296 ALGYDPDALE---VLLHQMVGLVRGGEGVKMSTRAGNVVTLDDLLDEAVGRARELIEEKE 352
Query: 422 IY 423
I
Sbjct: 353 IA 354
>gnl|CDD|216097 pfam00750, tRNA-synt_1d, tRNA synthetases class I (R). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only arginyl tRNA
synthetase.
Length = 345
Score = 284 bits (729), Expect = 2e-93
Identities = 126/298 (42%), Positives = 173/298 (58%), Gaps = 9/298 (3%)
Query: 128 KKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEY 187
KK VV+FSSPN AK +HVGHLRSTIIGD+L+R+LEF +V+R N+VGDWGTQFGMLI
Sbjct: 19 KKVVVEFSSPNPAKPIHVGHLRSTIIGDALSRLLEFLGYDVVRENYVGDWGTQFGMLIAS 78
Query: 188 LFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQ 247
L E I +L++ YR K + ++ F + A+ AVV LQSG+ ++ E W
Sbjct: 79 LEAAAKE-ELTVPMPIQDLEDGYRGIKKDYIAEEIFAKEARNAVVLLQSGDEEFREMWVL 137
Query: 248 -ICEISRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIE-- 304
I + ++ +K+Y V L E GES Y + + +L GLV E+ GA +F+
Sbjct: 138 LIFDHIKQSLNKIYDDFDVTLHE-GESVYKGRMNDAVKDLKDNGLVYENDGALWLFLTEF 196
Query: 305 GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAG 364
G + +++KSDGG Y +TDLA RL + + IIYV Q H +F+AA G
Sbjct: 197 GDDKDRVVIKSDGGALYITTDLAYAKERLEQRGFDLIIYVLGADQHGHIQRLFAAAAALG 256
Query: 365 WLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERGI 422
D + H+GFG+VLG+DGKR+ TR VV L DLLDEA R+ + +
Sbjct: 257 ----YDPESVEVLHIGFGVVLGKDGKRMSTRAGNVVTLDDLLDEALERAMDIKEKNRD 310
>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori [Protein synthesis, tRNA
aminoacylation].
Length = 566
Score = 272 bits (697), Expect = 7e-86
Identities = 120/388 (30%), Positives = 193/388 (49%), Gaps = 27/388 (6%)
Query: 43 KFGDYQCNNAMGLWSKIKGKGTEFKGPQPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLS 102
+FGDY N A L +K K P+ + + I+ L E+IE AGP F+N LS
Sbjct: 33 EFGDYASNIAFPLAKVLK------KNPRAIAEEIVLKLKTGEIIEKVEAAGP-FINFFLS 85
Query: 103 KNWMAKNIQKMLVDGIETWAP-KLRVKKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARML 161
+ + + + ++ E + KL+ KK +++FSS N A +H+GHLR+ IIGDSLAR+L
Sbjct: 86 PQKLLERLIQKILTQKEDYGSKKLKNKKIIIEFSSANPAGPLHIGHLRNAIIGDSLARIL 145
Query: 162 EFSNVEVLRRNHVGDWGTQFGMLIEYLFEKFPNSEDANETA--IGELQEFYRRSKNRFDS 219
EF +V+R +V DWG QFG+L EKF N + L+ FY R +
Sbjct: 146 EFLGYDVIREYYVNDWGRQFGLLALG-VEKFGNEKLNEAVKKPDHGLEGFYVEINKRLEE 204
Query: 220 DPAFKERAQQAVVRLQSGEPKYHEAWAQICEISRKEFDKVYKRLRVDLEEK---GESFYN 276
+ +E A++ V+L+SG+ + + W ++ E S + + RL + + GES N
Sbjct: 205 NEELEEEARELFVKLESGDEEAIKLWKRLVEYSLEGIKETLARLNIHFDSFVWEGESVKN 264
Query: 277 PYIPGVIDELSKQGLVEESQGARVIFIEGVNI---PLIIVKSDGGFNYASTDLAALWYRL 333
+P V+++L ++GLV E GA + + ++ KSDG + Y + D+A +L
Sbjct: 265 GMVPKVLEDLKEKGLVVED-GALWLDLTLFGDKDKDRVLQKSDGTYLYLTRDIAYHLDKL 323
Query: 334 NEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDSTYPKASHVGFGLVLGEDGKRLR 393
E + +IYV LH F+ ++ G+ + H+ FG+V K R
Sbjct: 324 -ERGFDKMIYVWGSDHHLHIAQFFAILEKLGFYKK-----KELIHLNFGMVPLGSMKTRR 377
Query: 394 TRFSEVVRLVDLLDEAKNRSKAVLIERG 421
+ L +LLDEA R+ V+ +
Sbjct: 378 GNV---ISLDNLLDEASKRAGNVITIKN 402
>gnl|CDD|183534 PRK12451, PRK12451, arginyl-tRNA synthetase; Reviewed.
Length = 562
Score = 231 bits (592), Expect = 2e-70
Identities = 118/335 (35%), Positives = 179/335 (53%), Gaps = 12/335 (3%)
Query: 90 SVAGPGFVNVVLSKNWMAKNI-QKMLVDGIETWAPKL-RVKKAVVDFSSPNIAKEMHVGH 147
GP +VNV ++ ++ + + +L + E K V+D+SSPNIAK +GH
Sbjct: 74 EAVGP-YVNVFFNRETVSDAVLKTILAEKEEYGQNHFGCEKTVVIDYSSPNIAKPFSMGH 132
Query: 148 LRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEKFPNSEDANETAIGELQ 207
LRST+IG++L + E EV+ N++GDWGTQFG LI ++K+ N E I EL
Sbjct: 133 LRSTMIGNALKHIAEKCGYEVVGINYIGDWGTQFGKLIT-AYKKWGNEAVVKEDPIRELF 191
Query: 208 EFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQICEISRKEFDKVYKRLRVDL 267
+ Y + D +E + +L+ G+ + E W S KEF ++Y+ L V+
Sbjct: 192 KLYVQFHEEVKDDEELEEEGRAWFKKLEEGDEEAVELWNWFRHESLKEFSRIYELLGVEF 251
Query: 268 EE-KGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNI-PLIIVKSDGGFNYASTD 325
+GE+FYN + I L + L+EES+GA V+ +E + P +I KSDG YA+ D
Sbjct: 252 TNFQGEAFYNDLMEDFIGILEEHDLLEESEGALVVNLEEEGMPPCLIRKSDGATIYATRD 311
Query: 326 LAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDSTYPKASHVGFGLVL 385
L A YR N + +YV Q LHF+ F+ K+ G+ D HV FGL+L
Sbjct: 312 LTAALYRQNTFGFDKALYVVGPEQSLHFNQFFTVLKKLGYTWVD-----GMEHVPFGLIL 366
Query: 386 GEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIER 420
+DGK++ TR VV L ++L+EA +K + E+
Sbjct: 367 -KDGKKMSTRKGRVVLLEEVLEEAIELAKQNIEEK 400
>gnl|CDD|185675 cd00671, ArgRS_core, catalytic core domain of arginyl-tRNA
synthetases. Arginyl tRNA synthetase (ArgRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. There
are at least three subgroups of ArgRS. One type contains
both characteristic class I HIGH and KMSKS motifs, which
are involved in ATP binding. The second subtype lacks
the KMSKS motif; however, it has a lysine N-terminal to
the HIGH motif, which serves as the functional
counterpart to the second lysine of the KMSKS motif. A
third group, which is found primarily in archaea and a
few bacteria, lacks both the KMSKS motif and the HIGH
loop lysine.
Length = 212
Score = 218 bits (558), Expect = 1e-69
Identities = 77/269 (28%), Positives = 113/269 (42%), Gaps = 61/269 (22%)
Query: 129 KAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYL 188
K +V+F S N +HVGHLR+ IIGDSLAR+LEF +V R ++ DWG Q G+LI L
Sbjct: 1 KILVEFVSANPTGPLHVGHLRNAIIGDSLARILEFLGYDVTREYYINDWGRQIGLLILSL 60
Query: 189 FEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQI 248
+ E +I E Y R RFD
Sbjct: 61 EK----WRKLVEESIKADLETYGRLDVRFD------------------------------ 86
Query: 249 CEISRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIE--GV 306
GES Y + V++ L + GL+ E GA + + G
Sbjct: 87 -------------------VWFGESSYLGLMGKVVELLEELGLLYEEDGALWLDLTEFGD 127
Query: 307 NIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWL 366
+ ++V+SDG + Y + D+A + E A+ IIYV HF +F+A + G+
Sbjct: 128 DKDRVLVRSDGTYTYFTRDIAYHLDKF-ERGADKIIYVVGADHHGHFKRLFAALELLGYD 186
Query: 367 SADDSTYPKASHVGFGLVLGEDGKRLRTR 395
A K H+ +G+V ++ TR
Sbjct: 187 EAK-----KLEHLLYGMVNLPKEGKMSTR 210
>gnl|CDD|217589 pfam03485, Arg_tRNA_synt_N, Arginyl tRNA synthetase N terminal
domain. This domain is found at the amino terminus of
Arginyl tRNA synthetase, also called additional domain 1
(Add-1). It is about 140 residues long and it has been
suggested that this domain will be involved in tRNA
recognition.
Length = 84
Score = 71.5 bits (176), Expect = 1e-15
Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 14 ELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKGPQPV 72
L+K AL + + P+I +FGDY N AM L K+K K P+ +
Sbjct: 2 LLKKAIAEALAKAGLDLEVIDPVIETPKDPEFGDYATNVAMKLAKKLK------KNPREI 55
Query: 73 GQAIMKNLPPSEMIESCSVAGPGFVNVVL 101
+ I + LP S++IE VAGPGF+N L
Sbjct: 56 AEEIAEKLPKSDLIEKVEVAGPGFINFFL 84
>gnl|CDD|214975 smart01016, Arg_tRNA_synt_N, Arginyl tRNA synthetase N terminal
dom. This domain is found at the amino terminus of
Arginyl tRNA synthetase, also called additional domain 1
(Add-1). It is about 140 residues long and it has been
suggested that this domain will be involved in tRNA
recognition.
Length = 85
Score = 63.4 bits (155), Expect = 8e-13
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 13 RELEKVFDLALKATVPNET-DVRPLIAAC-TAKFGDYQCNNAMGLWSKIKGKGTEFKGPQ 70
L++ ALK + E + + GDY N A L K+K K P+
Sbjct: 1 DLLKEAIAEALKKALGVEGEPIDIALERPKDPDHGDYATNVAFRLAKKLK------KNPR 54
Query: 71 PVGQAIMKNLPPSEMIESCSVAGPGFVNVVL 101
+ + I + LP S+++E +AGPGF+N L
Sbjct: 55 ELAEEIAEKLPKSDLVEKVEIAGPGFINFFL 85
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 143
Score = 50.6 bits (121), Expect = 1e-07
Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 10/90 (11%)
Query: 132 VDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEK 191
FS +H+GHLR+ + D LA+ +V + D G G
Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDP------- 53
Query: 192 FPNSEDANETAIGELQEFYRRSKNRFDSDP 221
+ E A ++ + R K +
Sbjct: 54 ---ANKKGENAKAFVERWIERIKEDVEYMF 80
>gnl|CDD|224661 COG1747, COG1747, Uncharacterized N-terminal domain of the
transcription elongation factor GreA [Function unknown].
Length = 711
Score = 33.7 bits (77), Expect = 0.20
Identities = 29/142 (20%), Positives = 57/142 (40%), Gaps = 15/142 (10%)
Query: 130 AVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLF 189
++ N K V HL + ++ ++M ++ + N + + L+EY
Sbjct: 71 TLLTIFGDNH-KNQIVEHLCTRVLEYGESKMALLELLQCYKENGNEQLYSLWERLVEY-- 127
Query: 190 EKFPNSEDANETAIG-ELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQI 248
D N+ IG EL + Y + K + F + + + R Q+ K E W ++
Sbjct: 128 -------DFNDVVIGRELADKYEKIKKS-KAAEFFGKALYRFIPRRQNAAIK--EVWEKL 177
Query: 249 CEISRKEFDKVYKRLRVDLEEK 270
E+ + D RL+ ++ K
Sbjct: 178 PELIGDDKDFFL-RLQKKIQTK 198
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 33.5 bits (77), Expect = 0.22
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEVL 169
H+GH +TI+ D AR EVL
Sbjct: 15 HLGHAYTTILADVYARYKRLRGYEVL 40
>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
synthetases. Methionine tRNA synthetase (MetRS)
catalytic core domain. This class I enzyme aminoacylates
the 2'-OH of the nucleotide at the 3' of the appropriate
tRNA. MetRS, which consists of the core domain and an
anti-codon binding domain, functions as a monomer.
However, in some species the anti-codon binding domain
is followed by an EMAP domain. In this case, MetRS
functions as a homodimer. The core domain is based on
the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. As a result of a deletion event, MetRS has a
significantly shorter core domain insertion than IleRS,
ValRS, and LeuR. Consequently, the MetRS insertion
lacks the editing function.
Length = 319
Score = 32.5 bits (75), Expect = 0.40
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEVL 169
H+GHL T++ D AR +VL
Sbjct: 16 HLGHLYGTVLADVFARYQRLRGYDVL 41
>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
synthetases. Leucyl tRNA synthetase (LeuRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. In Aquifex
aeolicus, the gene encoding LeuRS is split in two, just
before the KMSKS motif. Consequently, LeuRS is a
heterodimer, which likely superimposes with the LeuRS
monomer found in most other organisms. LeuRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements and thus differs between
prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
editing region hydrolyzes mischarged cognate tRNAs and
thus prevents the incorporation of chemically similar
amino acids.
Length = 314
Score = 32.2 bits (74), Expect = 0.41
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 143 MHVGHLRSTIIGDSLARMLEFSNVEVL 169
+HVGH+R+ IGD +AR VL
Sbjct: 15 LHVGHVRTYTIGDIIARYKRMQGYNVL 41
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 32.2 bits (74), Expect = 0.51
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEVL 169
H+GHL + + D AR L EV
Sbjct: 21 HLGHLYTYLAADVYARYLRLRGYEVF 46
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 32.1 bits (74), Expect = 0.70
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 143 MHVGHLRSTIIGDSLAR 159
+HVGH R+ IGD +AR
Sbjct: 1 LHVGHGRTYTIGDVIAR 17
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 31.5 bits (72), Expect = 0.97
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 143 MHVGHLRSTIIGDSLARMLEFSNVEVL 169
+HVGH+R+ IGD +AR VL
Sbjct: 49 LHVGHVRNYTIGDVIARYKRMQGYNVL 75
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 31.1 bits (71), Expect = 1.0
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 21 LALKATVPNETDVRPLIAACTAKFG--DYQCNNA-MGLWSKI 59
L + V + LI A A+FG D NNA + +WS+
Sbjct: 53 LVVPTDVSDAEACERLIEAAVARFGGIDILVNNAGITMWSRF 94
>gnl|CDD|173899 cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA
synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding.
Length = 213
Score = 30.6 bits (70), Expect = 1.1
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEV 168
H+GH R+ ++ D L R LE +V
Sbjct: 35 HIGHARTYVVFDVLRRYLEDLGYKV 59
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 31.2 bits (71), Expect = 1.1
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEV 168
H+GH R+ I+ D L R L + +V
Sbjct: 36 HIGHARTAIVFDVLRRYLRYLGYKV 60
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 31.2 bits (72), Expect = 1.3
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 144 HVGHLRSTIIGDSLARM 160
H+GH+R+ IGD +AR
Sbjct: 48 HMGHVRNYTIGDVIARY 64
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 30.7 bits (70), Expect = 1.4
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEVL 169
H+GHL +TI D AR L +VL
Sbjct: 15 HIGHLYTTIPADVYARYLRLRGYDVL 40
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 30.3 bits (69), Expect = 1.9
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 22 ALKATVPNETDVRPLIAACTAKFGDYQC--NNA 52
AL+A + +E +VR L+A +A G NNA
Sbjct: 63 ALQADLADEAEVRALVARASAALGPITLLVNNA 95
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 30.5 bits (69), Expect = 2.0
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 119 ETWAPKLRVKKAVVDFSSPNI---------AKEMHVGHLRSTIIGDSLARM 160
+ W + K D S P + +H+GH+R+ I D L+R
Sbjct: 12 QKWDEN-KTFKVTDDSSKPKYYILSMFPYPSGALHMGHVRNYTITDVLSRY 61
>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
Length = 1205
Score = 29.9 bits (67), Expect = 3.6
Identities = 23/68 (33%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 128 KKAVVDFSSPNIAKEM-HVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIE 186
KKA + + P A + H GHL + II D + R V R+ W G+ IE
Sbjct: 101 KKAYIFYDGPPFATGLPHYGHLLAGIIKDCVTRYFYQCGFSVERKF---GWDCH-GLPIE 156
Query: 187 YLFEKFPN 194
Y EK N
Sbjct: 157 YEIEKENN 164
>gnl|CDD|216798 pfam01937, DUF89, Protein of unknown function DUF89. This family
has no known function.
Length = 315
Score = 29.2 bits (66), Expect = 3.7
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 325 DLAALWYRLNEEKAEWIIYVTD-VGQQLHFDMVF 357
D ALW RL +A+ + YV D G +L FD++
Sbjct: 149 DTDALWERLKGSRAKRVDYVLDNAGFELVFDLLL 182
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 29.3 bits (67), Expect = 4.5
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEV 168
H+GH RS ++ D L R L + +V
Sbjct: 38 HIGHARSFVVFDVLRRYLRYLGYKV 62
>gnl|CDD|151393 pfam10946, DUF2625, Protein of unknown function DUF2625. Some
members in this family of proteins are annotated as ybfG
however currently no function is known.
Length = 208
Score = 28.9 bits (65), Expect = 4.8
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 197 DANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQ 235
D E A L+E+ +KN + PA + A ++ LQ
Sbjct: 6 DKEEPAWPLLREWLAEAKNHVEILPADSDLAGTELLALQ 44
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 29.0 bits (66), Expect = 6.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 144 HVGHLRSTIIGDSLAR 159
H+GH +TI D+LAR
Sbjct: 20 HIGHAYTTIAADALAR 35
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 28.9 bits (65), Expect = 6.5
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 251 ISRKEFDKVYKRL--RVDLEEKGESFYNPYIPGVIDELSKQG 290
I + +D+VYK++ + DL E + FY+ GV + S++G
Sbjct: 46 IEPERWDEVYKKITNKGDLYETRKIFYDYIKNGVKIKESQKG 87
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 28.7 bits (65), Expect = 6.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEV 168
H+GH R+ ++ D L R L + +V
Sbjct: 37 HIGHARTYVVFDVLRRYLRYLGYKV 61
>gnl|CDD|216482 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
domain. This family includes only cysteinyl tRNA
synthetases.
Length = 301
Score = 28.5 bits (64), Expect = 7.1
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 144 HVGHLRSTIIGDSLARMLEFSNVEV 168
H+GH RS + D L R L+ +V
Sbjct: 24 HIGHARSAVAFDVLRRYLQALGYDV 48
>gnl|CDD|219491 pfam07632, DUF1593, Protein of unknown function (DUF1593). A
family of proteins in Rhodopirellula baltica that are
predicted to be secreted. Also, a member has been
identified in Caulobacter crescentus. These proteins mat
be related to pfam01156.
Length = 260
Score = 28.4 bits (64), Expect = 7.4
Identities = 18/54 (33%), Positives = 21/54 (38%), Gaps = 13/54 (24%)
Query: 73 GQAIMKNLPPSEMIESCSVAG-------------PGFVNVVLSKNWMAKNIQKM 113
G I KN P I S SV G G N +SK W+ +NIQ
Sbjct: 163 GAWIRKNFPDLFYIASESVHGGNQYGAATWKGIVGGPDNSYVSKEWLKENIQSH 216
>gnl|CDD|216363 pfam01205, UPF0029, Uncharacterized protein family UPF0029.
Length = 110
Score = 27.0 bits (61), Expect = 7.7
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 372 TYPKASHVGFGLVLGEDGKRLRTRFS 397
+PKA+H + +G+ R S
Sbjct: 29 EHPKATHNCWAYRIGDPNGTNVERSS 54
>gnl|CDD|220261 pfam09484, Cas_TM1802, CRISPR-associated protein TM1802
(cas_TM1802). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This minor cas protein is
found in at least five prokaryotic genomes:
Methanosarcina mazei, Sulfurihydrogenibium azorense,
Thermotoga maritima, Carboxydothermus hydrogenoformans,
and Dictyoglomus thermophilum, the first of which is
archaeal while the rest are bacterial.
Length = 584
Score = 28.5 bits (64), Expect = 8.1
Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 16/103 (15%)
Query: 238 EPKYHEAWAQICEISRKEFDKVYK---------------RLRVDLEEKGESFYNPYIPGV 282
KY I ++ K F+K+ K + +K S Y Y V
Sbjct: 114 INKYRYFLKDIKKVLEKNFEKIIKDLIDLKKNEGVLYTIYFLKNDGKKYLSDYEEYRNKV 173
Query: 283 IDELSKQGLVEESQGARVIFIEGVNIPLIIVKSDGGFNYASTD 325
+ ++ ++ ++S+ V I G + D F + +TD
Sbjct: 174 LYKIEQRYFSKKSKEEGVCSICGKEDE-VTGDVDTPFKFYTTD 215
>gnl|CDD|237235 PRK12857, PRK12857, fructose-1,6-bisphosphate aldolase; Reviewed.
Length = 284
Score = 28.2 bits (63), Expect = 8.2
Identities = 22/83 (26%), Positives = 29/83 (34%), Gaps = 14/83 (16%)
Query: 304 EGVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAK-- 361
E P+II S G YA + + R EKA V LH D +
Sbjct: 39 EAEKSPVIIQASQGAIKYAGIEYISAMVRTAAEKA-------SVPVALHLDHGTDFEQVM 91
Query: 362 ---RAGWLSA--DDSTYPKASHV 379
R G+ S D S P ++
Sbjct: 92 KCIRNGFTSVMIDGSKLPLEENI 114
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 27.6 bits (62), Expect = 8.5
Identities = 17/100 (17%), Positives = 32/100 (32%), Gaps = 9/100 (9%)
Query: 252 SRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNIPLI 311
S E + L ++E+ E YI G DE GLV++ ++F+
Sbjct: 60 SAAELEAALAALAAEVEDTREYLVEEYIDG--DEYHVDGLVDDG---ELVFLGV----SR 110
Query: 312 IVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQL 351
+ +L ++ + V + L
Sbjct: 111 YLGPPPPDFSEGVELGSVSPGEDPLPEALRELAERVLKAL 150
>gnl|CDD|173763 cd08223, STKc_Nek4, Catalytic domain of the Protein
Serine/Threonine Kinase, Never In Mitosis gene A-related
kinase 4. Serine/Threonine Kinases (STKs), Never In
Mitosis gene A (NIMA)-related kinase 4 (Nek4) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Nek4 subfamily is
one of a family of 11 different Neks (Nek1-11). The Nek
family is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. Neks are involved in the regulation of
downstream processes following the activation of Cdc2,
and many of their functions are cell cycle-related. They
play critical roles in microtubule dynamics during
ciliogenesis and mitosis. Nek4 is highly abundant in the
testis. Its specific function is unknown.
Length = 257
Score = 28.0 bits (62), Expect = 8.7
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 154 GDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEK 191
G L L+ ++L N V +W Q M ++YL EK
Sbjct: 84 GGDLYHKLKEQKGKLLPENQVVEWFVQIAMALQYLHEK 121
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.400
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,282,703
Number of extensions: 2203503
Number of successful extensions: 2250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2211
Number of HSP's successfully gapped: 56
Length of query: 426
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 326
Effective length of database: 6,502,202
Effective search space: 2119717852
Effective search space used: 2119717852
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: 60 (26.8 bits)