RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007251
(611 letters)
>gnl|CDD|215160 PLN02286, PLN02286, arginine-tRNA ligase.
Length = 576
Score = 1091 bits (2823), Expect = 0.0
Identities = 435/543 (80%), Positives = 480/543 (88%), Gaps = 3/543 (0%)
Query: 69 RELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKGPQP 127
REL K+F+ +L+ TVP+E V PL+AACT KFGDYQCNNAMGLWSK+KGKGT FK P+
Sbjct: 1 RELAKLFEASLRLTVPDEPSVEPLVAACTNPKFGDYQCNNAMGLWSKLKGKGTSFKNPRA 60
Query: 128 VGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETWAPKLRVKKAV 187
V QAI+KNLP SEMIES SVAGPGFVNV LS +W+AK I++MLVDGI+TWAP L VK+AV
Sbjct: 61 VAQAIVKNLPASEMIESTSVAGPGFVNVRLSASWLAKRIERMLVDGIDTWAPTLPVKRAV 120
Query: 188 VDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEK 247
VDFSSPNIAKEMHVGHLRSTIIGD+LARMLEFS VEVLRRNHVGDWGTQFGMLIE+LFEK
Sbjct: 121 VDFSSPNIAKEMHVGHLRSTIIGDTLARMLEFSGVEVLRRNHVGDWGTQFGMLIEHLFEK 180
Query: 248 FPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQICEI 307
FPN E ++ AIG+LQEFY+ +K RFD D FK RAQQAVVRLQ G+P+Y AWA+ICEI
Sbjct: 181 FPNWESVSDQAIGDLQEFYKAAKKRFDEDEEFKARAQQAVVRLQGGDPEYRAAWAKICEI 240
Query: 308 SRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNIPLI 367
SR+EF+KVY+RLRV+LEEKGESFYNPYIPGVI+EL +GLV ES GARVIF+EG +IPLI
Sbjct: 241 SRREFEKVYQRLRVELEEKGESFYNPYIPGVIEELESKGLVVESDGARVIFVEGFDIPLI 300
Query: 368 IVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDS 427
+VKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQ HFDMVF AAKRAGWL +
Sbjct: 301 VVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQQHFDMVFKAAKRAGWL--PED 358
Query: 428 TYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERGKDKEWTEEEL 487
TYP+ HVGFGLVLGEDGKR RTR EVVRLVDLLDEAK+RSKA LIERGKD EWT EEL
Sbjct: 359 TYPRLEHVGFGLVLGEDGKRFRTRSGEVVRLVDLLDEAKSRSKAALIERGKDSEWTPEEL 418
Query: 488 EQTAEAVGYGAAKYFDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYAHARICSIIRKSGKD 547
EQ AEAVGYGA KY DLKNNRLTNYTFSFDQML+ KGNTAVYLLYAHARICSIIRKSGKD
Sbjct: 419 EQAAEAVGYGAVKYADLKNNRLTNYTFSFDQMLDLKGNTAVYLLYAHARICSIIRKSGKD 478
Query: 548 IEELKKTGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNVVCEYLYNLSEYFTRFYSN 607
I+ELKKTG +VLDH DERALGLHLL F EV+EEA T+LLPN +CEYLYNLSE FT+FYSN
Sbjct: 479 IDELKKTGKIVLDHPDERALGLHLLQFPEVVEEACTDLLPNRLCEYLYNLSEKFTKFYSN 538
Query: 608 CQV 610
C+V
Sbjct: 539 CKV 541
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 459 bits (1183), Expect = e-156
Identities = 191/557 (34%), Positives = 298/557 (53%), Gaps = 31/557 (5%)
Query: 66 NVKRELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKG 124
N+K+ L++ AL A + ++ L+ + GD+ N A L +K GK
Sbjct: 2 NIKQLLKEKIAEALSAAGLDVEEIEILVEPPKDPEHGDFATNIAFQL-AKKLGKN----- 55
Query: 125 PQPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETW--APKLR 182
P+ + + I + L E+IE +AGPGF+N LS ++A+ + ++L G + + + +
Sbjct: 56 PREIAEEIAEKLDTDEIIEKVEIAGPGFINFFLSPEFLAELLLEILEKGDDRYGRSKLGK 115
Query: 183 VKKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIE 242
KK V+++SS N +H+GHLR+ IIGDSLAR+LEF +V R N+V DWGTQ GML
Sbjct: 116 GKKVVIEYSSANPTGPLHIGHLRNAIIGDSLARILEFLGYDVTRENYVNDWGTQIGMLAL 175
Query: 243 YLFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAF-KERAQQAVVRLQSGEPKYHEAW 301
++ + G L E+Y + + DP +E A++ V +L+SG+ + E W
Sbjct: 176 SYEKRGREALGLTPEPDGYLGEYYVKIAKDLEEDPGNDEEEAREEVEKLESGDEEA-ELW 234
Query: 302 AQICEISRKEFDKVYKRLRVDLEEK---GESFYNPYIPGVIDELSKQGLVEESQGARVIF 358
+ ++S + + RL V + GESFYN + V+++L ++GL+ E GA V+
Sbjct: 235 RKFVDLSLEGIKETLDRLGVKFDVYDSEGESFYNGKVEKVVEDLEEKGLLYEDDGALVVD 294
Query: 359 IE-----GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVF 413
+ G + ++ KSDG + Y + D+A Y+ E + +IYV Q HF +
Sbjct: 295 LLKFKKFGDDKDRVLQKSDGTYLYFTRDIAYHLYKF-ERGFDKLIYVLGADQHGHFKQLK 353
Query: 414 SAAKRAGWLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVL 473
+ + G+ + H G GLV G +G ++ TR VV L DLLDEA R+ +
Sbjct: 354 AVLELLGYGPDKEVLL----HQGVGLVRGGEGVKMSTRAGNVVTLDDLLDEAGERAPEEM 409
Query: 474 IERGKDKEWTEEELEQTAEAVGYGAAKYFDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYA 533
E+ + E + AE VG A +Y DL +R +Y F +D+ L+ +GNTA Y+ YA
Sbjct: 410 EEKEEKNE-------EIAEVVGIDAVRYADLSRSRDKDYVFDWDKALSFEGNTAPYVQYA 462
Query: 534 HARICSIIRKSGKDIEELKKTGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNVVCEY 593
HARICSI+RK+G+D +L +L +ER L LL F EV+EEA L P+ + Y
Sbjct: 463 HARICSILRKAGEDELDLSTEADALLTELEERELVKKLLEFPEVLEEAAEELEPHRLANY 522
Query: 594 LYNLSEYFTRFYSNCQV 610
LY+L+ F FY+ C V
Sbjct: 523 LYDLAGSFNSFYNACPV 539
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 434 bits (1119), Expect = e-147
Identities = 166/551 (30%), Positives = 249/551 (45%), Gaps = 94/551 (17%)
Query: 66 NVKRELEKVFDLALKATVPNETDVRPLIAACTAKFGDYQCNNAMGLWSKIKGKGTEFKGP 125
++K L + AL+A E + + GDY N AM L +K K P
Sbjct: 4 DIKELLAEALAAALEAGGLPELPAVLIERPKDPEHGDYATNVAMQL-AKKLKKN-----P 57
Query: 126 QPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLSKNWMAKNIQKMLVDGIETW--APKLRV 183
+ + + I++ IE +AGPGF+N L +A+ + +L G E + + +
Sbjct: 58 REIAEEIVEA------IEKVEIAGPGFINFFLDPAALAELVLAILEAG-ERYGRSDIGKG 110
Query: 184 KKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEY 243
KK VV++ S N +HVGHLRS +IGD+LAR+LEF+ +V R +V D GTQ GMLI
Sbjct: 111 KKVVVEYVSANPTGPLHVGHLRSAVIGDALARILEFAGYDVTREYYVNDAGTQIGMLIAS 170
Query: 244 LFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQ 303
L W +
Sbjct: 171 LE-----------------------------------------------------LLWRK 177
Query: 304 ICEISRKEFDKVYKRLRVDLEE---KGESFYNPYIPGVIDELSKQGL-VEESQGARVIFI 359
+IS E + RL V + + E +YN + V+++L ++GL ES GA + +
Sbjct: 178 AVDISLDEIKEDLDRLGVHFDVWFSESELYYNGKVDEVVEDLKEKGLLYVESDGALWVRL 237
Query: 360 E--GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAK 417
G + +++KSDG + Y + D+A Y+ E+ + +IYV HF + +A K
Sbjct: 238 TEFGDDKDRVLIKSDGTYTYFTRDIAYHLYKF--ERFDRVIYVVGADHHGHFKRLKAALK 295
Query: 418 RAGWLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERG 477
G+ H GLV G +G ++ TR VV L DLLDEA R++ ++ E+
Sbjct: 296 ALGYDPDALE---VLLHQMVGLVRGGEGVKMSTRAGNVVTLDDLLDEAVGRARELIEEK- 351
Query: 478 KDKEWTEEELEQTAEAVGYGAAKYFDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYAHARI 537
+ AEAVG A +YFDL +R + F D L+ +GN Y+ YAHARI
Sbjct: 352 -----------EIAEAVGIDAVRYFDLSRSRDKDLDFDLDLALSFEGNNPPYVQYAHARI 400
Query: 538 CSIIRKSGKDIEELKKTGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNVVCEYLYNL 597
CSI+RK+ E +L +E+ L L F EV+E A L P+ + YLY L
Sbjct: 401 CSILRKAA---EAGIDLLLALLTEEEEKELIKKLAEFPEVVESAAEELEPHRIANYLYEL 457
Query: 598 SEYFTRFYSNC 608
+ F FY+
Sbjct: 458 AGAFHSFYNRV 468
>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 = 393 bits (1012), Expect = e-130
Identities = 181/521 (34%), Positives = 273/521 (52%), Gaps = 34/521 (6%)
Query: 99 KFGDYQCNNAMGLWSKIKGKGTEFKGPQPVGQAIMKNLPPSEMIESCSVAGPGFVNVVLS 158
+FGDY N A L +K K P+ + + I+ L E+IE AGP F+N LS
Sbjct: 33 EFGDYASNIAFPLAKVLK------KNPRAIAEEIVLKLKTGEIIEKVEAAGP-FINFFLS 85
Query: 159 KNWMAKNIQKMLVDGIETWAP-KLRVKKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARML 217
+ + + + ++ E + KL+ KK +++FSS N A +H+GHLR+ IIGDSLAR+L
Sbjct: 86 PQKLLERLIQKILTQKEDYGSKKLKNKKIIIEFSSANPAGPLHIGHLRNAIIGDSLARIL 145
Query: 218 EFSNVEVLRRNHVGDWGTQFGMLIEYLFEKFPNSEDANETA--IGELQEFYRRSKNRFDS 275
EF +V+R +V DWG QFG+L EKF N + L+ FY R +
Sbjct: 146 EFLGYDVIREYYVNDWGRQFGLLALG-VEKFGNEKLNEAVKKPDHGLEGFYVEINKRLEE 204
Query: 276 DPAFKERAQQAVVRLQSGEPKYHEAWAQICEISRKEFDKVYKRLRVDLEEK---GESFYN 332
+ +E A++ V+L+SG+ + + W ++ E S + + RL + + GES N
Sbjct: 205 NEELEEEARELFVKLESGDEEAIKLWKRLVEYSLEGIKETLARLNIHFDSFVWEGESVKN 264
Query: 333 PYIPGVIDELSKQGLVEESQGARVIFIEGVNI---PLIIVKSDGGFNYASTDLAALWYRL 389
+P V+++L ++GLV E GA + + ++ KSDG + Y + D+A +L
Sbjct: 265 GMVPKVLEDLKEKGLVVED-GALWLDLTLFGDKDKDRVLQKSDGTYLYLTRDIAYHLDKL 323
Query: 390 NEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDSTYPKASHVGFGLVLGEDGKRLR 449
E + +IYV LH F+ ++ G+ + H+ FG+V K R
Sbjct: 324 -ERGFDKMIYVWGSDHHLHIAQFFAILEKLGFYKK-----KELIHLNFGMVPLGSMKTRR 377
Query: 450 TRFSEVVRLVDLLDEAKNRSKAVLIERGKDKEWTEEELEQTAEAVGYGAAKYFDLKNNRL 509
+ L +LLDEA R+ V+ + + E E A+AVG GA +YFDL NR
Sbjct: 378 GNV---ISLDNLLDEASKRAGNVITIK------NDLEEEDVADAVGIGAVRYFDLSQNRE 428
Query: 510 TNYTFSFDQMLNDKGNTAVYLLYAHARICSIIRKSGKDIEELKKTGSLVLDHADERALGL 569
T+Y F +D ML+ +GNTA Y+ YAHARICSI+RK+ D E+L +L E+ L
Sbjct: 429 THYVFDWDAMLSFEGNTAPYIQYAHARICSILRKADIDGEKLIADDFSLL-EEKEKELLK 487
Query: 570 HLLHFSEVIEEALTNLLPNVVCEYLYNLSEYFTRFYSNCQV 610
LL F +V+EEA L P+V+ YLY L+ F+ FY C V
Sbjct: 488 LLLQFPDVLEEAAEELEPHVLTNYLYELASLFSSFYKACPV 528
>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 = 325 bits (834), Expect = e-106
Identities = 143/336 (42%), Positives = 197/336 (58%), Gaps = 12/336 (3%)
Query: 184 KKAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEY 243
KK VV+FSSPN AK +HVGHLRSTIIGD+L+R+LEF +V+R N+VGDWGTQFGMLI
Sbjct: 19 KKVVVEFSSPNPAKPIHVGHLRSTIIGDALSRLLEFLGYDVVRENYVGDWGTQFGMLIAS 78
Query: 244 LFEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQ 303
L E I +L++ YR K + ++ F + A+ AVV LQSG+ ++ E W
Sbjct: 79 LEAAAKE-ELTVPMPIQDLEDGYRGIKKDYIAEEIFAKEARNAVVLLQSGDEEFREMWVL 137
Query: 304 -ICEISRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIE-- 360
I + ++ +K+Y V L E GES Y + + +L GLV E+ GA +F+
Sbjct: 138 LIFDHIKQSLNKIYDDFDVTLHE-GESVYKGRMNDAVKDLKDNGLVYENDGALWLFLTEF 196
Query: 361 GVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAG 420
G + +++KSDGG Y +TDLA RL + + IIYV Q H +F+AA G
Sbjct: 197 GDDKDRVVIKSDGGALYITTDLAYAKERLEQRGFDLIIYVLGADQHGHIQRLFAAAAALG 256
Query: 421 WLSADDSTYPKASHVGFGLVLGEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERGKDK 480
D + H+GFG+VLG+DGKR+ TR VV L DLLDEA R+ + + +
Sbjct: 257 ----YDPESVEVLHIGFGVVLGKDGKRMSTRAGNVVTLDDLLDEALERAMDIKEKN---R 309
Query: 481 EWTEEELEQTAEAVGYGAAKYFDLKNNRLTNYTFSF 516
+ T +ELE A A+G AA+Y DL +NR T+Y F
Sbjct: 310 DLTADELEAVATAIGVDAARYADLSSNRDTDYIFDL 345
>gnl|CDD|183534 PRK12451, PRK12451, arginyl-tRNA synthetase; Reviewed.
Length = 562
Score = 311 bits (799), Expect = 1e-98
Identities = 162/469 (34%), Positives = 253/469 (53%), Gaps = 20/469 (4%)
Query: 146 SVAGPGFVNVVLSKNWMAKNI-QKMLVDGIETWAPKL-RVKKAVVDFSSPNIAKEMHVGH 203
GP +VNV ++ ++ + + +L + E K V+D+SSPNIAK +GH
Sbjct: 74 EAVGP-YVNVFFNRETVSDAVLKTILAEKEEYGQNHFGCEKTVVIDYSSPNIAKPFSMGH 132
Query: 204 LRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEKFPNSEDANETAIGELQ 263
LRST+IG++L + E EV+ N++GDWGTQFG LI ++K+ N E I EL
Sbjct: 133 LRSTMIGNALKHIAEKCGYEVVGINYIGDWGTQFGKLIT-AYKKWGNEAVVKEDPIRELF 191
Query: 264 EFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQICEISRKEFDKVYKRLRVDL 323
+ Y + D +E + +L+ G+ + E W S KEF ++Y+ L V+
Sbjct: 192 KLYVQFHEEVKDDEELEEEGRAWFKKLEEGDEEAVELWNWFRHESLKEFSRIYELLGVEF 251
Query: 324 EE-KGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNI-PLIIVKSDGGFNYASTD 381
+GE+FYN + I L + L+EES+GA V+ +E + P +I KSDG YA+ D
Sbjct: 252 TNFQGEAFYNDLMEDFIGILEEHDLLEESEGALVVNLEEEGMPPCLIRKSDGATIYATRD 311
Query: 382 LAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWLSADDSTYPKASHVGFGLVL 441
L A YR N + +YV Q LHF+ F+ K+ G+ D HV FGL+L
Sbjct: 312 LTAALYRQNTFGFDKALYVVGPEQSLHFNQFFTVLKKLGYTWVD-----GMEHVPFGLIL 366
Query: 442 GEDGKRLRTRFSEVVRLVDLLDEAKNRSKAVLIERGKDKEWTEEELEQTAEAVGYGAAKY 501
+DGK++ TR VV L ++L+EA +K + ++K ++ E+ A+ VG GA +
Sbjct: 367 -KDGKKMSTRKGRVVLLEEVLEEAIELAKQNI----EEKNPNLKQKEEVAKQVGVGAVIF 421
Query: 502 FDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYAHARICSIIRKSGKDIEELKKTGSLVLDH 561
DLKN R+ N FS + ML +G T Y+ Y HAR CSI+RK + E T +L D+
Sbjct: 422 HDLKNERMHNIEFSLENMLKFEGETGPYVQYTHARACSILRKESVEFETC--TFALKDDY 479
Query: 562 ADERALGLHLLHFSEVIEEALTNLLPNVVCEYLYNLSEYFTRFYSNCQV 610
+ ++ L F +VIE A P+V+ +Y+ ++++ F ++Y N ++
Sbjct: 480 S--WSVVKLLNKFPQVIEAAFNKNEPSVISKYVLDVAQSFNKYYGNVRI 526
>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 = 220 bits (563), Expect = 3e-68
Identities = 77/269 (28%), Positives = 113/269 (42%), Gaps = 61/269 (22%)
Query: 185 KAVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYL 244
K +V+F S N +HVGHLR+ IIGDSLAR+LEF +V R ++ DWG Q G+LI L
Sbjct: 1 KILVEFVSANPTGPLHVGHLRNAIIGDSLARILEFLGYDVTREYYINDWGRQIGLLILSL 60
Query: 245 FEKFPNSEDANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQI 304
+ E +I E Y R RFD
Sbjct: 61 EK----WRKLVEESIKADLETYGRLDVRFD------------------------------ 86
Query: 305 CEISRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIE--GV 362
GES Y + V++ L + GL+ E GA + + G
Sbjct: 87 -------------------VWFGESSYLGLMGKVVELLEELGLLYEEDGALWLDLTEFGD 127
Query: 363 NIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAKRAGWL 422
+ ++V+SDG + Y + D+A + E A+ IIYV HF +F+A + G+
Sbjct: 128 DKDRVLVRSDGTYTYFTRDIAYHLDKF-ERGADKIIYVVGADHHGHFKRLFAALELLGYD 186
Query: 423 SADDSTYPKASHVGFGLVLGEDGKRLRTR 451
A K H+ +G+V ++ TR
Sbjct: 187 EAK-----KLEHLLYGMVNLPKEGKMSTR 210
>gnl|CDD|153410 cd07956, Anticodon_Ia_Arg, Anticodon-binding domain of arginyl tRNA
synthetases. This domain is found in arginyl tRNA
synthetases (ArgRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. ArgRS catalyzes the
transfer of arginine to the 3'-end of its tRNA.
Length = 156
Score = 129 bits (327), Expect = 4e-35
Identities = 54/119 (45%), Positives = 77/119 (64%)
Query: 492 EAVGYGAAKYFDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYAHARICSIIRKSGKDIEEL 551
E VG GA KY DL N R+ +YTF +++ML+ +G+T YL YAHAR+CSI+RK+G+ IE
Sbjct: 1 EEVGVGAVKYQDLSNKRIKDYTFDWERMLSFEGDTGPYLQYAHARLCSILRKAGETIEAE 60
Query: 552 KKTGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNVVCEYLYNLSEYFTRFYSNCQV 610
+L DER L L L F EV++ A L P+ + YL++L+ F++FY+ C V
Sbjct: 61 ADADLSLLPEPDERDLILLLAKFPEVVKNAAETLEPHTIATYLFDLAHAFSKFYNACPV 119
>gnl|CDD|218729 pfam05746, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain in
Arginyl and glycyl tRNA synthetase. This domain is known
as the DALR domain after characteristic conserved amino
acids.
Length = 117
Score = 92.3 bits (230), Expect = 2e-22
Identities = 38/81 (46%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 530 LLYAHARICSIIRKSGKDIEELKKTGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNV 589
L YAHARICSI+RK+G+ L L L +E+ L LL F EV+EEA L P+
Sbjct: 1 LQYAHARICSILRKAGELGINLDIDADL-LTEEEEKELLKALLQFPEVLEEAAEELEPHR 59
Query: 590 VCEYLYNLSEYFTRFYSNCQV 610
+ YLY L+ F FY+NC+V
Sbjct: 60 LANYLYELASAFHSFYNNCRV 80
>gnl|CDD|214846 smart00836, DALR_1, DALR anticodon binding domain. This all alpha
helical domain is the anticodon binding domain of
Arginyl tRNA synthetase. This domain is known as the
DALR domain after characteristic conserved amino acids.
Length = 122
Score = 89.2 bits (222), Expect = 3e-21
Identities = 33/84 (39%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 530 LLYAHARICSIIRKS---GKDIEELKKTGSLVLDHADERALGLHLLHFSEVIEEALTNLL 586
+ YAHARICSI+RK+ G+ + ++ +L +E AL L L F EV+E A L
Sbjct: 1 VQYAHARICSILRKAGEAGETLPDIADADLSLLTEPEEWALLLKLARFPEVLEAAAEQLE 60
Query: 587 PNVVCEYLYNLSEYFTRFYSNCQV 610
P+ + YLY+L+ F FY+ +V
Sbjct: 61 PHRLANYLYDLAAAFHSFYNRVRV 84
>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 = 72.7 bits (179), Expect = 6e-16
Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 70 ELEKVFDLALKATVPNETDVRPLIAACT-AKFGDYQCNNAMGLWSKIKGKGTEFKGPQPV 128
L+K AL + + P+I +FGDY N AM L K+K K P+ +
Sbjct: 2 LLKKAIAEALAKAGLDLEVIDPVIETPKDPEFGDYATNVAMKLAKKLK------KNPREI 55
Query: 129 GQAIMKNLPPSEMIESCSVAGPGFVNVVL 157
+ 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 = 64.5 bits (158), Expect = 5e-13
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 69 RELEKVFDLALKATVPNET-DVRPLIAAC-TAKFGDYQCNNAMGLWSKIKGKGTEFKGPQ 126
L++ ALK + E + + GDY N A L K+K K P+
Sbjct: 1 DLLKEAIAEALKKALGVEGEPIDIALERPKDPDHGDYATNVAFRLAKKLK------KNPR 54
Query: 127 PVGQAIMKNLPPSEMIESCSVAGPGFVNVVL 157
+ + 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 = 50.9 bits (122), Expect = 1e-07
Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 10/90 (11%)
Query: 188 VDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLFEK 247
FS +H+GHLR+ + D LA+ +V + D G G
Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDP------- 53
Query: 248 FPNSEDANETAIGELQEFYRRSKNRFDSDP 277
+ E A ++ + R K +
Sbjct: 54 ---ANKKGENAKAFVERWIERIKEDVEYMF 80
>gnl|CDD|235726 PRK06181, PRK06181, short chain dehydrogenase; Provisional.
Length = 263
Score = 35.7 bits (83), Expect = 0.054
Identities = 27/92 (29%), Positives = 36/92 (39%), Gaps = 18/92 (19%)
Query: 34 SDILRATTRRLA-------LAATKTRSITSMATEEENTGNVKRELEKVFDLALKATVPNE 86
I RA RLA LAA + S+A E + G L + V +
Sbjct: 11 EGIGRALAVRLARAGAQLVLAARNETRLASLAQELADHGGEA--------LVVPTDVSDA 62
Query: 87 TDVRPLIAACTAKFG--DYQCNNA-MGLWSKI 115
LI A A+FG D NNA + +WS+
Sbjct: 63 EACERLIEAAVARFGGIDILVNNAGITMWSRF 94
>gnl|CDD|235953 PRK07188, PRK07188, nicotinate phosphoribosyltransferase;
Provisional.
Length = 352
Score = 34.5 bits (80), Expect = 0.15
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 508 RLTNYTFSFDQMLNDKGNTAVYLLYAHARICSIIRKSGKD 547
RLTN TF FD+ + + +AVY L + II K +
Sbjct: 1 RLTNKTFKFDERIGEGWYSAVYFL----KTREIIEKFNPN 36
>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 = 0.32
Identities = 29/142 (20%), Positives = 57/142 (40%), Gaps = 15/142 (10%)
Query: 186 AVVDFSSPNIAKEMHVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIEYLF 245
++ N K V HL + ++ ++M ++ + N + + L+EY
Sbjct: 71 TLLTIFGDNH-KNQIVEHLCTRVLEYGESKMALLELLQCYKENGNEQLYSLWERLVEY-- 127
Query: 246 EKFPNSEDANETAIG-ELQEFYRRSKNRFDSDPAFKERAQQAVVRLQSGEPKYHEAWAQI 304
D N+ IG EL + Y + K + F + + + R Q+ K E W ++
Sbjct: 128 -------DFNDVVIGRELADKYEKIKKS-KAAEFFGKALYRFIPRRQNAAIK--EVWEKL 177
Query: 305 CEISRKEFDKVYKRLRVDLEEK 326
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 = 0.32
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEVL 225
H+GH +TI+ D AR EVL
Sbjct: 15 HLGHAYTTILADVYARYKRLRGYEVL 40
>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 = 32.6 bits (75), Expect = 0.52
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 199 MHVGHLRSTIIGDSLARMLEFSNVEVL 225
+HVGH+R+ IGD +AR VL
Sbjct: 15 LHVGHVRTYTIGDIIARYKRMQGYNVL 41
>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 = 0.56
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEVL 225
H+GHL T++ D AR +VL
Sbjct: 16 HLGHLYGTVLADVFARYQRLRGYDVL 41
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 32.6 bits (75), Expect = 0.73
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEVL 225
H+GHL + + D AR L EV
Sbjct: 21 HLGHLYTYLAADVYARYLRLRGYEVF 46
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 32.5 bits (75), Expect = 0.78
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 199 MHVGHLRSTIIGDSLAR 215
+HVGH R+ IGD +AR
Sbjct: 1 LHVGHGRTYTIGDVIAR 17
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 32.3 bits (74), Expect = 1.1
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 199 MHVGHLRSTIIGDSLARMLEFSNVEVL 225
+HVGH+R+ IGD +AR VL
Sbjct: 49 LHVGHVRNYTIGDVIARYKRMQGYNVL 75
>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 = 1.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEV 224
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 = 31.6 bits (73), Expect = 1.6
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 200 HVGHLRSTIIGDSLARM 216
H+GH+R+ IGD +AR
Sbjct: 48 HMGHVRNYTIGDVIARY 64
>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 = 1.8
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEV 224
H+GH R+ ++ D L R LE +V
Sbjct: 35 HIGHARTYVVFDVLRRYLEDLGYKV 59
>gnl|CDD|212504 cd11645, Precorrin_2_C20_MT, Precorrin-2 C20-methyltransferase,
also named CobI or CbiL. Precorrin-2
C20-methyltransferase participates in the pathway toward
the biosynthesis of cobalamin (vitamin B12). There are
two distinct cobalamin biosynthetic pathways in
bacteria. The aerobic pathway requires oxygen, and
cobalt is inserted late in the pathway; the anaerobic
pathway does not require oxygen, and cobalt insertion is
the first committed step towards cobalamin synthesis.
Precorrin-2 C20-methyltransferase catalyzes methylation
at the C-20 position of a cyclic tetrapyrrole ring of
precorrin-2 using S-adenosylmethionine as a methyl group
source to produce precorrin-3A. In the anaerobic
pathway, cobalt is inserted into precorrin-2 by CbiK to
generate cobalt-precorrin-2, which is the substrate for
CbiL, a C20 methyltransferase. In Clostridium difficile,
CbiK and CbiL are fused into a bifunctional enzyme. In
the aerobic pathway, the precorrin-2
C20-methyltransferase is named CobI. This family
includes CbiL and CobI precorrin-2
C20-methyltransferases, both as stand-alone enzymes and
when CbiL forms part of a bifunctional enzyme.
Length = 226
Score = 30.6 bits (70), Expect = 1.9
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 23/88 (26%)
Query: 432 ASHVGFGLVLGEDG----------KRLRTRFSE---VV---------RLVDLLDEAKNRS 469
A+ +G L G++ + L VV + +LL+EA
Sbjct: 132 AARLGIPLAEGDERLAILPATLGEEELEEALELFDTVVLMKVGRNLDEVRELLEEAGLLD 191
Query: 470 KAVLIER-GKDKEWTEEELEQTAEAVGY 496
+AV +ER G + E +LE E + Y
Sbjct: 192 RAVYVERCGMEGERIVRDLEADPEKLPY 219
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 31.1 bits (71), Expect = 1.9
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEVL 225
H+GHL +TI D AR L +VL
Sbjct: 15 HIGHLYTTIPADVYARYLRLRGYDVL 40
>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 = 31.3 bits (71), Expect = 2.1
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 175 ETWAPKLRVKKAVVDFSSPNI---------AKEMHVGHLRSTIIGDSLARM 216
+ W + K D S P + +H+GH+R+ I D L+R
Sbjct: 12 QKWDEN-KTFKVTDDSSKPKYYILSMFPYPSGALHMGHVRNYTITDVLSRY 61
>gnl|CDD|238164 cd00264, BPI, BPI/LBP/CETP domain; Bactericidal
permeability-increasing protein (BPI) /
Lipopolysaccharide-binding protein (LBP) / Cholesteryl
ester transfer protein (CETP) domain; binds to and
neutralizes lipopolysaccharides from the outer membrane
of Gram-negative bacteria.; Apolar pockets on the
concave surface bind a molecule of phosphatidylcholine,
primarily by interacting with their acyl chains; this
suggests that the pockets may also bind the acyl chains
of lipopolysaccharide.
Length = 208
Score = 30.0 bits (68), Expect = 2.9
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 554 TGSLVLDHADERALGLHLLHFSEVIEEALTNLLPNVVCEYLY 595
T SL L + L ++ F I L +L ++C +
Sbjct: 120 TLSLSLCSSTVELLSSNIGGFGNFIVSLLQKVLNTILCPVVL 161
>gnl|CDD|236389 PRK09134, PRK09134, short chain dehydrogenase; Provisional.
Length = 258
Score = 29.9 bits (68), Expect = 3.0
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 78 ALKATVPNETDVRPLIAACTAKFGDYQC--NNA 108
AL+A + +E +VR L+A +A G NNA
Sbjct: 63 ALQADLADEAEVRALVARASAALGPITLLVNNA 95
>gnl|CDD|187616 cd05358, GlcDH_SDR_c, glucose 1 dehydrogenase (GlcDH), classical
(c) SDRs. GlcDH, is a tetrameric member of the SDR
family, it catalyzes the NAD(P)-dependent oxidation of
beta-D-glucose to D-glucono-delta-lactone. GlcDH has a
typical NAD-binding site glycine-rich pattern as well as
the canonical active site tetrad (YXXXK motif plus
upstream Ser and Asn). SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 253
Score = 29.3 bits (66), Expect = 4.7
Identities = 27/85 (31%), Positives = 36/85 (42%), Gaps = 14/85 (16%)
Query: 32 SPSDILRATTRRLALAATKT----RSITSMATEEENTGNVKRELEKV--FDLALKATVPN 85
+ S I +A RLA A RS A E V E++ V +A++A V
Sbjct: 11 ASSGIGKAIAIRLATAGANVVVNYRSKEDAAEE------VVEEIKAVGGKAIAVQADVSK 64
Query: 86 ETDVRPLIAACTAKFG--DYQCNNA 108
E DV L + +FG D NNA
Sbjct: 65 EEDVVALFQSAIKEFGTLDILVNNA 89
>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
Length = 1205
Score = 29.9 bits (67), Expect = 5.5
Identities = 23/68 (33%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 184 KKAVVDFSSPNIAKEM-HVGHLRSTIIGDSLARMLEFSNVEVLRRNHVGDWGTQFGMLIE 242
KKA + + P A + H GHL + II D + R V R+ W G+ IE
Sbjct: 101 KKAYIFYDGPPFATGLPHYGHLLAGIIKDCVTRYFYQCGFSVERKF---GWDCH-GLPIE 156
Query: 243 YLFEKFPN 250
Y EK N
Sbjct: 157 YEIEKENN 164
>gnl|CDD|222260 pfam13609, Porin_4, Gram-negative porin.
Length = 310
Score = 29.3 bits (66), Expect = 5.6
Identities = 9/44 (20%), Positives = 13/44 (29%), Gaps = 2/44 (4%)
Query: 493 AVGYGAAKYFDLKNNRLTNYTFSFDQMLNDKGNTAVYLLYAHAR 536
GYG + T Y L+ T +Y Y +
Sbjct: 265 GAGYGNGDATGGADADATAYGLGATYNLS--KRTTLYAEYGYVD 306
>gnl|CDD|216798 pfam01937, DUF89, Protein of unknown function DUF89. This family
has no known function.
Length = 315
Score = 29.2 bits (66), Expect = 5.8
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 381 DLAALWYRLNEEKAEWIIYVTD-VGQQLHFDMVF 413
D ALW RL +A+ + YV D G +L FD++
Sbjct: 149 DTDALWERLKGSRAKRVDYVLDNAGFELVFDLLL 182
>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 = 6.0
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 253 DANETAIGELQEFYRRSKNRFDSDPAFKERAQQAVVRLQ 291
D E A L+E+ +KN + PA + A ++ LQ
Sbjct: 6 DKEEPAWPLLREWLAEAKNHVEILPADSDLAGTELLALQ 44
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 29.5 bits (66), Expect = 6.2
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 504 LKNNRLTNYTFSFDQMLNDKGNTAVYL 530
++ N++ TF+ Q++NDKG AV+L
Sbjct: 497 IETNKVIGKTFTVPQLMNDKGFDAVFL 523
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 29.3 bits (67), Expect = 6.4
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEV 224
H+GH RS ++ D L R L + +V
Sbjct: 38 HIGHARSFVVFDVLRRYLRYLGYKV 62
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 28.8 bits (65), Expect = 7.9
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 11/68 (16%)
Query: 43 RLALAATKTRSITSMATEEENTGNVKRELEKVFDLALKATVPNETDVRPLIAACTAKFG- 101
++A+ A + + A E N GNV L L A V +E DV+ + A A FG
Sbjct: 32 KVAITARDQKELEEAAAELNNKGNV---------LGLAADVRDEADVQRAVDAIVAAFGG 82
Query: 102 -DYQCNNA 108
D NA
Sbjct: 83 LDVLIANA 90
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 29.0 bits (66), Expect = 8.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 200 HVGHLRSTIIGDSLAR 215
H+GH +TI D+LAR
Sbjct: 20 HIGHAYTTIAADALAR 35
>gnl|CDD|237235 PRK12857, PRK12857, fructose-1,6-bisphosphate aldolase; Reviewed.
Length = 284
Score = 28.9 bits (65), Expect = 8.3
Identities = 22/83 (26%), Positives = 29/83 (34%), Gaps = 14/83 (16%)
Query: 360 EGVNIPLIIVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQLHFDMVFSAAK-- 417
E P+II S G YA + + R EKA V LH D +
Sbjct: 39 EAEKSPVIIQASQGAIKYAGIEYISAMVRTAAEKA-------SVPVALHLDHGTDFEQVM 91
Query: 418 ---RAGWLSA--DDSTYPKASHV 435
R G+ S D S P ++
Sbjct: 92 KCIRNGFTSVMIDGSKLPLEENI 114
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 28.6 bits (65), Expect = 8.3
Identities = 25/77 (32%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 36 ILRATTRRLALAATKTRSITSMATEEENTGNVKRELEKVFD--LALKATVPNETDVRPLI 93
I RA RLA K + + EE + EL L V +E VR LI
Sbjct: 17 IGRAIALRLAADGAK---VVIYDSNEEAAEALAAELRAAGGEARVLVFDVSDEAAVRALI 73
Query: 94 AACTAKFG--DYQCNNA 108
A FG D NNA
Sbjct: 74 EAAVEAFGALDILVNNA 90
>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 = 28.8 bits (65), Expect = 8.3
Identities = 18/54 (33%), Positives = 21/54 (38%), Gaps = 13/54 (24%)
Query: 129 GQAIMKNLPPSEMIESCSVAG-------------PGFVNVVLSKNWMAKNIQKM 169
G I KN P I S SV G G N +SK W+ +NIQ
Sbjct: 163 GAWIRKNFPDLFYIASESVHGGNQYGAATWKGIVGGPDNSYVSKEWLKENIQSH 216
>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 = 8.8
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 307 ISRKEFDKVYKRL--RVDLEEKGESFYNPYIPGVIDELSKQG 346
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 = 9.0
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEV 224
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 = 9.5
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 200 HVGHLRSTIIGDSLARMLEFSNVEV 224
H+GH RS + D L R L+ +V
Sbjct: 24 HIGHARSAVAFDVLRRYLQALGYDV 48
>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 = 28.0 bits (63), Expect = 9.7
Identities = 17/100 (17%), Positives = 32/100 (32%), Gaps = 9/100 (9%)
Query: 308 SRKEFDKVYKRLRVDLEEKGESFYNPYIPGVIDELSKQGLVEESQGARVIFIEGVNIPLI 367
S E + L ++E+ E YI G DE GLV++ ++F+
Sbjct: 60 SAAELEAALAALAAEVEDTREYLVEEYIDG--DEYHVDGLVDDG---ELVFLGV----SR 110
Query: 368 IVKSDGGFNYASTDLAALWYRLNEEKAEWIIYVTDVGQQL 407
+ +L ++ + V + L
Sbjct: 111 YLGPPPPDFSEGVELGSVSPGEDPLPEALRELAERVLKAL 150
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 0.134 0.390
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: 31,759,631
Number of extensions: 3192223
Number of successful extensions: 3378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3328
Number of HSP's successfully gapped: 63
Length of query: 611
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 508
Effective length of database: 6,369,140
Effective search space: 3235523120
Effective search space used: 3235523120
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: 62 (27.5 bits)