RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043787
(452 letters)
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 847 bits (2189), Expect = 0.0
Identities = 340/429 (79%), Positives = 377/429 (87%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNIL 60
MKTG +EV E V +LN V LPFLVTTAD+ KD +KEE+RLRYR LDLRR QMN N+
Sbjct: 145 MKTGSVEVVAESVDILNVVTKSLPFLVTTADEQKDSIKEEVRLRYRVLDLRRPQMNANLR 204
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFK 120
LRH+VVKLIRRYLEDVHGFVEIETP+LSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFK
Sbjct: 205 LRHRVVKLIRRYLEDVHGFVEIETPILSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFK 264
Query: 121 QMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFLE 180
QMLMVSGFD+YYQIARCFRDEDLRADRQPEFTQLDMELAFTPL+DML+LNEDLIR++F E
Sbjct: 265 QMLMVSGFDRYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLEDMLKLNEDLIRQVFKE 324
Query: 181 IKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLESPFRVFSDSLKSGGII 240
IK VQLPNPFPRLTYAEAMS+YGSD+PD R+ L+L DVSD+F ES F+VF+ +L+SGG++
Sbjct: 325 IKGVQLPNPFPRLTYAEAMSKYGSDKPDLRYGLELVDVSDVFAESSFKVFAGALESGGVV 384
Query: 241 KVLCVPSGAKTYSNTALKKGDIYNEAIKSGAKGLPFLKVLDAGGVEGIPALVSSLGPSNK 300
K +CVP G K +NTALKKGDIYNEAIKSGAKGL FLKVLD G +EGI ALV SL P
Sbjct: 385 KAICVPDGKKISNNTALKKGDIYNEAIKSGAKGLAFLKVLDDGELEGIKALVESLSPEQA 444
Query: 301 EQLLIRCSAGPSDLILFAVGHPASVNKTLDRLRTFVAHELGLIDNSKHSILWITDFPMFE 360
EQLL C AGP DLILFA G +SVNKTLDRLR F+A L LID S+HSILW+TDFPMFE
Sbjct: 445 EQLLAACGAGPGDLILFAAGPTSSVNKTLDRLRQFIAKTLDLIDPSRHSILWVTDFPMFE 504
Query: 361 WNDSEQRLEALHHPFTAPNPEDMDDLSSARALAYDMVYNGVEIGGGSLRIYKREVQQKVL 420
WN+ EQRLEALHHPFTAPNPEDM DLSSARALAYDMVYNGVEIGGGSLRIY+R+VQQKVL
Sbjct: 505 WNEDEQRLEALHHPFTAPNPEDMGDLSSARALAYDMVYNGVEIGGGSLRIYRRDVQQKVL 564
Query: 421 EIVGISPEQ 429
E +G+SPE+
Sbjct: 565 EAIGLSPEE 573
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 658 bits (1700), Expect = 0.0
Identities = 235/436 (53%), Positives = 298/436 (68%), Gaps = 20/436 (4%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSK-LPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNI 59
+ TG IEV ++VLN SK LPF + +D V EE+RL+YR LDLRR +M N+
Sbjct: 88 LPTGEIEVLASELEVLNK--SKTLPFPIDDEED----VSEELRLKYRYLDLRRPEMQKNL 141
Query: 60 LLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLF 119
LR KV IR +L+D +GF+EIETP+L++STPEGARDYLVPSRV PG FYALPQSPQLF
Sbjct: 142 KLRSKVTSAIRNFLDD-NGFLEIETPILTKSTPEGARDYLVPSRVHPGKFYALPQSPQLF 200
Query: 120 KQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFL 179
KQ+LMV+GFD+YYQIARCFRDEDLRADRQPEFTQ+D+E++F +D++ L E LIR +F
Sbjct: 201 KQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDIEMSFVTQEDVMALMEGLIRHVFK 260
Query: 180 EIKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLESPFRVFSDSLKSGGI 239
E+ V LP PFPR+TYAEAM RYGSD+PD RF L+L DV+D+F +S F+VF+ + GG
Sbjct: 261 EVLGVDLPTPFPRMTYAEAMRRYGSDKPDLRFGLELVDVTDLFKDSGFKVFAGAANDGGR 320
Query: 240 IKVLCVPSGAKTYSNTALKKGDIYNEAIKS-GAKGLPFLKVLDAGGVEGIPALVSSLGPS 298
+K + VP GA S K+ D E K GAKGL ++KV + G++G + L
Sbjct: 321 VKAIRVPGGAAQLSR---KQIDELTEFAKIYGAKGLAYIKV-NEDGLKG--PIAKFLSEE 374
Query: 299 NKEQLLIRCSAGPSDLILFAVGHPASVNKTLDRLRTFVAHELGLIDNSKHSILWITDFPM 358
LL R A DLI F VN L LR + ELGLID K + LW+ DFPM
Sbjct: 375 ELAALLERTGAKDGDLIFFGADKAKVVNDALGALRLKLGKELGLIDEDKFAFLWVVDFPM 434
Query: 359 FEWNDSEQRLEALHHPFTAPNPEDMDDL-----SSARALAYDMVYNGVEIGGGSLRIYKR 413
FE+++ E R A HHPFT P ED+D+L ARA AYD+V NG E+GGGS+RI++
Sbjct: 435 FEYDEEEGRWVAAHHPFTMPKDEDLDELETTDPGKARAYAYDLVLNGYELGGGSIRIHRP 494
Query: 414 EVQQKVLEIVGISPEQ 429
E+Q+KV EI+GIS E+
Sbjct: 495 EIQEKVFEILGISEEE 510
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 589 bits (1520), Expect = 0.0
Identities = 234/434 (53%), Positives = 301/434 (69%), Gaps = 18/434 (4%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNIL 60
+ TG IEV E ++VLNA LPF + + EEIRL+YR LDLRR +M N+
Sbjct: 88 LPTGEIEVLAEEIEVLNA-SKTLPFQIEDETN----ASEEIRLKYRYLDLRRPEMQKNLK 142
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFK 120
LR KV K IR +L D GF+EIETP+L++STPEGARD+LVPSRV PG FYALPQSPQLFK
Sbjct: 143 LRSKVTKAIRNFL-DDQGFLEIETPILTKSTPEGARDFLVPSRVHPGKFYALPQSPQLFK 201
Query: 121 QMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFLE 180
Q+LMV+GFD+YYQIARCFRDEDLRADRQPEFTQ+D+E++F +D++ L E L+R +F E
Sbjct: 202 QLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDLEMSFVDEEDVMELIEKLLRYVFKE 261
Query: 181 IKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLESPFRVFSDSLKSGGII 240
+K ++L PFPR+TYAEAM RYGSD+PD RF L+L DV+D+F +S F+VFS++L +GG +
Sbjct: 262 VKGIELKTPFPRMTYAEAMRRYGSDKPDLRFPLELIDVTDLFKDSEFKVFSNALANGGRV 321
Query: 241 KVLCVPSGAKTYSNTALKKGDIYNE-AIKSGAKGLPFLKVLDAGGVEGIPALVSSLGPSN 299
K + VP GA S K+ D E A GAKGL ++KV + G++G + L
Sbjct: 322 KAIVVPGGAS-LSR---KQIDELTEFAKIYGAKGLAYIKV-EEDGLKG--PIAKFLSEEI 374
Query: 300 KEQLLIRCSAGPSDLILFAVGHPASVNKTLDRLRTFVAHELGLIDNSKHSILWITDFPMF 359
E+L+ R A D+I F VNK L LR + ELGLID + LW+ DFP+F
Sbjct: 375 LEELIERLGAEDGDIIFFVADKKKVVNKALGALRLKLGKELGLIDKDQFKFLWVVDFPLF 434
Query: 360 EWNDSEQRLEALHHPFTAPNPEDMDDLS----SARALAYDMVYNGVEIGGGSLRIYKREV 415
EW++ E R A HHPFT P PED++ L S RA AYD+V NG E+GGGS+RI+ E+
Sbjct: 435 EWDEEEGRYVAAHHPFTMPKPEDLELLEADPESVRARAYDLVLNGYELGGGSIRIHDPEI 494
Query: 416 QQKVLEIVGISPEQ 429
Q+KV EI+GISPE+
Sbjct: 495 QEKVFEILGISPEE 508
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 496 bits (1280), Expect = e-173
Identities = 226/433 (52%), Positives = 290/433 (66%), Gaps = 17/433 (3%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNIL 60
+ TG IE+ E + +LN SK P L+ DA+ EE+RL+YR LDLRR +M +
Sbjct: 86 LDTGEIEILAESITLLNK--SKTPPLIIEKTDAE----EEVRLKYRYLDLRRPEMQQRLK 139
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFK 120
LRHKV K +R +L+ GF+EIETP+L++STPEGARDYLVPSRV G FYALPQSPQLFK
Sbjct: 140 LRHKVTKAVRNFLDQ-QGFLEIETPMLTKSTPEGARDYLVPSRVHKGEFYALPQSPQLFK 198
Query: 121 QMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFLE 180
Q+LMVSG D+YYQIARCFRDEDLRADRQPEFTQ+DME++F +D++ L E L+ +FLE
Sbjct: 199 QLLMVSGVDRYYQIARCFRDEDLRADRQPEFTQIDMEMSFMTQEDVMELIEKLVSHVFLE 258
Query: 181 IKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLESPFRVFSDSLKSGGII 240
+K + L PFP +TYAEAM RYGSD+PD RF L+L DV+D+F +S F+VFS+ + GG +
Sbjct: 259 VKGIDLKKPFPVMTYAEAMERYGSDKPDLRFPLELIDVTDLFKDSEFKVFSNLINDGGRV 318
Query: 241 KVLCVPSGAKTYSNTALKKGDIYNEAIKSGAKGLPFLKVLDAGGVEGIPALVSSLGPSNK 300
K + VP G S ++K+ A + GAKGL +LKV + G + L
Sbjct: 319 KAIRVPGGWAELSRKSIKELR--KFAKEYGAKGLAYLKVNEDG---INSPIKKFLDEKKG 373
Query: 301 EQLLIRCSAGPSDLILFAVGHPASVNKTLDRLRTFVAHELGLIDNSKHSILWITDFPMFE 360
+ LL R A D++LF G V L LR + +LGL+D S LW+ DFPMFE
Sbjct: 374 KILLERTDAQNGDILLFGAGSKKIVLDALGALRLKLGKDLGLVDPDLFSFLWVVDFPMFE 433
Query: 361 WNDSEQRLEALHHPFTAPNPEDMDDL----SSARALAYDMVYNGVEIGGGSLRIYKREVQ 416
D E RL A HHPFT P ED+++L A A AYD+V NGVE+GGGS+RI+ EVQ
Sbjct: 434 K-DKEGRLCAAHHPFTMPKDEDLENLEAAPEEALAEAYDLVLNGVELGGGSIRIHDPEVQ 492
Query: 417 QKVLEIVGISPEQ 429
+KV EI+GI PE+
Sbjct: 493 KKVFEILGIDPEE 505
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 376 bits (967), Expect = e-124
Identities = 197/442 (44%), Positives = 275/442 (62%), Gaps = 20/442 (4%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPF------LVTTADDAK-DFVKEEIRLRYRCLDLRRQ 53
++TG IEV V + +L A + LPF + A A D V E++RL+YR LD+RR
Sbjct: 92 IETGDIEVFVRELSILAASEA-LPFAISDKAMTAGAGSAGADAVNEDLRLQYRYLDIRRP 150
Query: 54 QMNHNILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALP 113
M ++ RH+++K R +L D GF+EIETP+L++STPEGARDYLVPSR+ P FYALP
Sbjct: 151 AMQDHLAKRHRIIKCARDFL-DSRGFLEIETPILTKSTPEGARDYLVPSRIHPKEFYALP 209
Query: 114 QSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDL 173
QSPQLFKQ+LM++GF++Y+Q+ARCFRDEDLR +RQPEFTQLD+E +F + + L E+L
Sbjct: 210 QSPQLFKQLLMIAGFERYFQLARCFRDEDLRPNRQPEFTQLDIEASFIDEEFIFELIEEL 269
Query: 174 IRKIFLEIKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLESPFRVFSDS 233
++F I + LP PFPR+ YAEAM GSDRPD RF L+ D +DIF + + +F
Sbjct: 270 TARMF-AIGGIALPRPFPRMPYAEAMDTTGSDRPDLRFDLKFADATDIFENTRYGIFKQI 328
Query: 234 LKSGGIIKVLCVPSGAKTYSNTALKKGDIYNEAIKSGAKGLPFLKVLDAGGVEGIPALVS 293
L+ GG IK + + ++ S L+ A GAKG+ +++ +AGG++ +V
Sbjct: 329 LQRGGRIKGINIKGQSEKLSKNVLQNEYAKEIAPSFGAKGMTWMRA-EAGGLDS--NIVQ 385
Query: 294 SLGPSNKEQLLIRCSAGPSD-LILFAVGHPASVNKTLDRLRTFVAHELGLIDNSKHSILW 352
KE L R A D +I+ A A V L +LR +A LGLI LW
Sbjct: 386 FFSADEKEALKRRFHAEDGDVIIMIADASCAIVLSALGQLRLHLADRLGLIPEGVFHPLW 445
Query: 353 ITDFPMFEWNDSEQRLEALHHPFTAPNPEDMD-----DLSSARALAYDMVYNGVEIGGGS 407
ITDFP+FE D + + + HHPFTAP+ ED D +L R+ AYD+V NG E+GGGS
Sbjct: 446 ITDFPLFEATD-DGGVTSSHHPFTAPDREDFDPGDIEELLDLRSRAYDLVVNGEELGGGS 504
Query: 408 LRIYKREVQQKVLEIVGISPEQ 429
+RI +++Q ++ +G+S E
Sbjct: 505 IRINDKDIQLRIFAALGLSEED 526
>gnl|CDD|238400 cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core
domain. Class II assignment is based upon its structure
and the presence of three characteristic sequence
motifs. AspRS is a homodimer, which attaches a specific
amino acid to the 3' OH group of ribose of the
appropriate tRNA. The catalytic core domain is primarily
responsible for the ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. AspRS in this family
differ from those found in the AsxRS family by a GAD
insert in the core domain.
Length = 280
Score = 280 bits (718), Expect = 3e-92
Identities = 97/145 (66%), Positives = 124/145 (85%), Gaps = 1/145 (0%)
Query: 59 ILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQL 118
+ LR +V+K IR +L++ GFVEIETP+L++STPEGARD+LVPSR+ PG FYALPQSPQL
Sbjct: 1 LRLRSRVIKAIRNFLDE-QGFVEIETPILTKSTPEGARDFLVPSRLHPGKFYALPQSPQL 59
Query: 119 FKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIF 178
FKQ+LMVSGFD+Y+QIARCFRDEDLRADRQPEFTQ+D+E++F +D++ L E L++ +F
Sbjct: 60 FKQLLMVSGFDRYFQIARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKYVF 119
Query: 179 LEIKDVQLPNPFPRLTYAEAMSRYG 203
E+ V+L PFPR+TYAEAM RYG
Sbjct: 120 KEVLGVELTTPFPRMTYAEAMERYG 144
Score = 132 bits (335), Expect = 1e-35
Identities = 48/85 (56%), Positives = 63/85 (74%), Gaps = 4/85 (4%)
Query: 349 SILWITDFPMFEWNDSEQRLEALHHPFTAPNPEDMDDLS----SARALAYDMVYNGVEIG 404
LWI DFP+FEW++ E RL + HHPFTAP ED+D L ARA AYD+V NGVE+G
Sbjct: 146 KFLWIVDFPLFEWDEEEGRLVSAHHPFTAPKEEDLDLLEKDPEDARAQAYDLVLNGVELG 205
Query: 405 GGSLRIYKREVQQKVLEIVGISPEQ 429
GGS+RI+ ++Q+KV EI+G+S E+
Sbjct: 206 GGSIRIHDPDIQEKVFEILGLSEEE 230
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 272 bits (697), Expect = 3e-88
Identities = 115/215 (53%), Positives = 156/215 (72%), Gaps = 22/215 (10%)
Query: 39 EEIRLRYRCLDLRRQQMNHNILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEG-ARD 97
EE RL+YR LDLRR +M N+ LR K++K IR +L++ GF+E+ETP+L++STPEG ARD
Sbjct: 2 EETRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDE-RGFLEVETPILTKSTPEGGARD 60
Query: 98 YLVPSRVQPGTFYA----LPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQP-EFT 152
+LVPS FYA LPQSPQL+KQ+LMV+GFD+ +QIA CFRDEDLR DR P EFT
Sbjct: 61 FLVPS-----KFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFT 115
Query: 153 QLDMELAFTPLDDMLRLNEDLIRKIFLEIK---------DVQLPNPFPRLTYAEAMSRYG 203
QLD+E++F +D++ L EDLI+ +F ++ ++LP FPR+TYAEA+ RYG
Sbjct: 116 QLDLEMSFVDYEDVMDLTEDLIKYVFKKVLGKREELELLGIELP-EFPRITYAEAIERYG 174
Query: 204 SDRPDTRFSLQLNDVSDIFLESPFRVFSDSLKSGG 238
SD+PD RF L+L DV++IF S F+VF+++
Sbjct: 175 SDKPDLRFGLELKDVTEIFKGSEFKVFAEAGDVVD 209
Score = 99.2 bits (248), Expect = 6e-23
Identities = 41/106 (38%), Positives = 56/106 (52%), Gaps = 17/106 (16%)
Query: 324 SVNKTLDRLRTFVAHELGLIDNSKHSILWITDFPMFEWNDSEQRLEALHHPFTAPNPEDM 383
V+K L LR+ E L D K + +++TDFP+FE HPF P ED
Sbjct: 207 VVDKALGALRSE-LGEENLGDKDKDNPVFVTDFPLFE------------HPFYMPKDEDP 253
Query: 384 DDLSSARALAYDMVYNGVEIGGGSLRIYKREVQQKVLEIVGISPEQ 429
A +D+V NG EIGGGS+RI+ E Q+K E +G+ PE+
Sbjct: 254 ----PGLAERFDLVLNGGEIGGGSIRIHDPEEQRKRFEELGLDPEE 295
>gnl|CDD|238358 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II
core domain. This domain is the core catalytic domain of
class II aminoacyl-tRNA synthetases of the subgroup
containing aspartyl, lysyl, and asparaginyl tRNA
synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. Nearly all class II tRNA synthetases
are dimers and enzymes in this subgroup are homodimers.
These enzymes attach a specific amino acid to the 3' OH
group of ribose of the appropriate tRNA.
Length = 269
Score = 181 bits (460), Expect = 5e-54
Identities = 69/156 (44%), Positives = 95/156 (60%), Gaps = 13/156 (8%)
Query: 59 ILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTP-EGARDYLVPSRVQPGTFYALPQSPQ 117
+R K++K IR +++D GF+E+ETP+L + T GAR +LV G Y L SPQ
Sbjct: 1 FKVRSKIIKAIRDFMDD-RGFLEVETPMLQKITGGAGARPFLVKYNA-LGLDYYLRISPQ 58
Query: 118 LFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKI 177
LFK+ LMV G D+ ++I R FR+EDLRA QPEFT +D+E+AF +D++ L E L+R +
Sbjct: 59 LFKKRLMVGGLDRVFEINRNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHL 118
Query: 178 FLEIK----------DVQLPNPFPRLTYAEAMSRYG 203
E+ PFPRLTY EA+ RYG
Sbjct: 119 AREVLGVTAVTYGFELEDFGLPFPRLTYREALERYG 154
Score = 63.6 bits (155), Expect = 3e-11
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 16/82 (19%)
Query: 351 LWITDFPMFEWNDSEQRLEALHHPFTAPNPEDMDDLSSARALAYDMVYNGVEIGGGSLRI 410
L++TD+P +H P +P+ + A A+D+ NGVE+G GS R+
Sbjct: 157 LFLTDYPAE-----------MHSPLASPHDVN-----PEIADAFDLFINGVEVGNGSSRL 200
Query: 411 YKREVQQKVLEIVGISPEQFIF 432
+ ++Q +V + GI+ E +
Sbjct: 201 HDPDIQAEVFQEQGINKEAGME 222
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 123 bits (311), Expect = 6e-31
Identities = 65/211 (30%), Positives = 98/211 (46%), Gaps = 28/211 (13%)
Query: 6 IEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNILLRHKV 65
E+ VE ++VL P D K+ + E L R LDLR ++ +R +
Sbjct: 87 FELQVEKIEVLGEADPPYPI------DKKEHSELETLLDNRHLDLRTPKIQAVFKIRSSI 140
Query: 66 VKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQMLMV 125
++ IR + + +GF E+ TP+++ S EG + L Y L QSPQL+K+ L
Sbjct: 141 LRAIREFFYE-NGFTEVHTPIITASATEGGGE-LFKVDYFDKEAY-LTQSPQLYKEALAA 197
Query: 126 SGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPLDDMLRLNEDLIRKIF------ 178
+ ++ + I FR E R EF LD E+AF L+D++ L E+LI+ +F
Sbjct: 198 A-LERVFTIGPTFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLEE 256
Query: 179 ----LEIKDVQLP-------NPFPRLTYAEA 198
LE PFPR+TY EA
Sbjct: 257 CADELEFLGRDNSELKRPESAPFPRITYKEA 287
Score = 37.6 bits (88), Expect = 0.011
Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 19/96 (19%)
Query: 337 AHELGLIDNSKHSILWITDFPMFEWNDSEQRLEALHHPF-TAPNPEDMDDLSSARALAYD 395
HE L + +++T++P E + PF P+P++ ++D
Sbjct: 308 EHERYLGEEYFKPPVFVTNYP------KEIK------PFYMRPDPDNPG-----TVASFD 350
Query: 396 MVYNGV-EIGGGSLRIYKREVQQKVLEIVGISPEQF 430
++ G EI GGS R + ++ + ++ G+ PE +
Sbjct: 351 LLAPGGGEIIGGSQREHDYDLLVERIKEKGLDPESY 386
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 118 bits (298), Expect = 3e-29
Identities = 70/218 (32%), Positives = 112/218 (51%), Gaps = 35/218 (16%)
Query: 2 KTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEI--RLRYRCLDLRRQQMNHNI 59
G EV E ++VLN LP ++ V E+ RL R LDLRR ++
Sbjct: 84 PGGV-EVIPEEIEVLNKAEEPLPLDIS------GKVLAELDTRLDNRFLDLRRPRVRAIF 136
Query: 60 LLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYA----LPQS 115
+R +V++ R +L + +GF EI TP + S EG + + P ++ L QS
Sbjct: 137 KIRSEVLRAFREFLYE-NGFTEIFTPKIVASGTEGG------AELFPIDYFEKEAYLAQS 189
Query: 116 PQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPLD-DMLRLNEDL 173
PQL+KQM++ +GF++ ++I FR E+ R E+T +D+E+ F D++ L E+L
Sbjct: 190 PQLYKQMMVGAGFERVFEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENL 249
Query: 174 IRKIF----------LEIKDVQLP---NPFPRLTYAEA 198
+R ++ LE+ ++LP P PR+TY EA
Sbjct: 250 LRYMYEDVAENCEKELELLGIELPVPETPIPRITYDEA 287
Score = 40.9 bits (97), Expect = 9e-04
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 18/81 (22%)
Query: 353 ITDFPMFEWNDSEQRLEALHHPF-TAPNPEDMDDLSSARALAYDMVYNGVEIGGGSLRIY 411
ITD+P E+R PF T P+ +D ++S ++D+++ G+EI G RI+
Sbjct: 327 ITDYPS------EKR------PFYTMPDEDD-PEIS----KSFDLLFRGLEITSGGQRIH 369
Query: 412 KREVQQKVLEIVGISPEQFIF 432
+ ++ + ++ G++PE F F
Sbjct: 370 RYDMLVESIKEKGLNPESFEF 390
>gnl|CDD|129550 TIGR00458, aspS_nondisc, nondiscriminating aspartyl-tRNA
synthetase. In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_arch, represents
aspartyl-tRNA synthetases from the eukaryotic cytosol
and from the Archaea. In some species, this enzyme
aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn)
is subsequently transamidated to Asn-tRNA(asn) [Protein
synthesis, tRNA aminoacylation].
Length = 428
Score = 117 bits (295), Expect = 5e-29
Identities = 71/216 (32%), Positives = 109/216 (50%), Gaps = 33/216 (15%)
Query: 4 GFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEI--RLRYRCLDLRRQQMNHNILL 61
G E+ ++V+N + LP T + V E+ RL YR LDLRR + +
Sbjct: 82 GGFEIIPTKIEVINEAKEPLPLDPT------EKVPAELDTRLDYRFLDLRRPTVQAIFRI 135
Query: 62 RHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYA----LPQSPQ 117
R V++ +R +L + GF+E+ TP L S EG + + P T++ L QSPQ
Sbjct: 136 RSGVLESVREFLAE-EGFIEVHTPKLVASATEGG------TELFPITYFEREAFLGQSPQ 188
Query: 118 LFKQMLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPLDDMLRLNEDLIRK 176
L+KQ LM +GF++ Y+I FR E+ R E T +D+E+AF D++ + E+L+ +
Sbjct: 189 LYKQQLMAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDIEMAFEDHHDVMDILEELVVR 248
Query: 177 IF-------------LEIKDVQLPNPFPRLTYAEAM 199
+F LE K + F RLTY EA+
Sbjct: 249 VFEDVPERCAHQLETLEFKLEKPEGKFVRLTYDEAI 284
Score = 34.4 bits (79), Expect = 0.11
Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 18/82 (21%)
Query: 352 WITDFPMFEWNDSEQRLEALHHPF-TAPNPEDMDDLSSARALAYDMVYNGVEIGGGSLRI 410
+ITD+P +E R PF T P+ ++ + + ++D++Y +EI G+ RI
Sbjct: 317 FITDWP------TEIR------PFYTMPDEDNPE-----ISKSFDLMYRDLEISSGAQRI 359
Query: 411 YKREVQQKVLEIVGISPEQFIF 432
+ ++ + ++ G++PE F
Sbjct: 360 HLHDLLVERIKAKGLNPEGFKD 381
>gnl|CDD|238399 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II
core domain. Assignment to class II aminoacyl-tRNA
synthetases (aaRS) based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This family includes AsnRS as well as a
subgroup of AspRS. AsnRS and AspRS are homodimers,
which attach either asparagine or aspartate to the 3'OH
group of ribose of the appropriate tRNA. While archaea
lack asnRS, they possess a non-discriminating aspRS,
which can mischarge Asp-tRNA with Asn. Subsequently, a
tRNA-dependent aspartate amidotransferase converts the
bound aspartate to asparagine. The catalytic core domain
is primarily responsible for the ATP-dependent formation
of the enzyme bound aminoacyl-adenylate.
Length = 322
Score = 112 bits (282), Expect = 8e-28
Identities = 54/182 (29%), Positives = 90/182 (49%), Gaps = 32/182 (17%)
Query: 40 EIRLRYRCLDLRRQQMNHNIL-LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDY 98
E L R LDLR I +R +V++ R +L + +GF E+ TP ++ + EG
Sbjct: 5 ETLLDNRHLDLRTP-KVQAIFRIRSEVLRAFREFLRE-NGFTEVHTPKITSTDTEG---- 58
Query: 99 LVPSRVQPGTFYA----LPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQ 153
+ + +++ L QSPQL+K+M +++ ++ Y+I FR E R EF
Sbjct: 59 --GAELFKVSYFGKPAYLAQSPQLYKEM-LIAALERVYEIGPVFRAEKSNTRRHLSEFWM 115
Query: 154 LDMELAF-TPLDDMLRLNEDLIRKIF----------------LEIKDVQLPNPFPRLTYA 196
L+ E+AF ++++ L E+LI+ IF L + ++ PFPR+TY
Sbjct: 116 LEAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRITYD 175
Query: 197 EA 198
EA
Sbjct: 176 EA 177
Score = 38.3 bits (90), Expect = 0.006
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 19/80 (23%)
Query: 353 ITDFPMFEWNDSEQRLEALHHPF-TAPNPEDMDDLSSARALAYDMVYNGV-EIGGGSLRI 410
+TD+P E + PF P+ ++ + ++D++ GV EI GGS RI
Sbjct: 215 VTDYP------KEIK------PFYMKPDDDNPE-----TVESFDLLMPGVGEIVGGSQRI 257
Query: 411 YKREVQQKVLEIVGISPEQF 430
+ + ++ ++ G+ PE F
Sbjct: 258 HDYDELEERIKEHGLDPESF 277
>gnl|CDD|232998 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and
non-spirochete bacterial. This model represents the
lysyl-tRNA synthetases that are class II amino-acyl tRNA
synthetases. It includes all eukaryotic and most
bacterial examples of the enzyme, but not archaeal or
spirochete forms [Protein synthesis, tRNA
aminoacylation].
Length = 496
Score = 104 bits (262), Expect = 3e-24
Identities = 76/259 (29%), Positives = 119/259 (45%), Gaps = 35/259 (13%)
Query: 2 KTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMN----H 57
KTG + V V +Q+L LP D +E R R R LDL +N
Sbjct: 120 KTGELSVHVTELQILTKALRPLP------DKFHGLTDQETRYRQRYLDL---IVNPDSRQ 170
Query: 58 NILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGA--RDYLVPSRVQPGTFYALPQS 115
L+R K++K IRR+L+D GF+E+ETP+L P GA R ++ Y L +
Sbjct: 171 TFLVRSKIIKAIRRFLDD-RGFIEVETPMLQ-VIPGGANARPFITHHNALDMDLY-LRIA 227
Query: 116 PQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIR 175
P+L+ + L+V GF+K Y+I R FR+E + PEFT ++ A+ +D++ L E+L +
Sbjct: 228 PELYLKRLIVGGFEKVYEIGRNFRNEGVDTTHNPEFTMIEFYQAYADYEDLMDLTENLFK 287
Query: 176 KIFLEI----------KDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLES 225
+ E+ ++ PF R+T EA+ +Y +T +
Sbjct: 288 FLAQELLGTTKITYGELEIDFKKPFKRITMVEAIKKY---DMETGIDFDDLKDFETAKAL 344
Query: 226 PFR----VFSDSLKSGGII 240
+ V SL G I+
Sbjct: 345 AKKIGIEVAEKSLTLGHIL 363
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 99.2 bits (248), Expect = 2e-22
Identities = 68/227 (29%), Positives = 117/227 (51%), Gaps = 24/227 (10%)
Query: 2 KTGFIEVAVEHVQVLN-AVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDL-RRQQMNHNI 59
KTG + V+VE +++L+ ++R LP + +EIR R R LDL +
Sbjct: 128 KTGELSVSVEELRLLSKSLRP-LP------EKFHGLTDKEIRYRQRYLDLIVNPESRQTF 180
Query: 60 LLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGA--RDYLVPSRVQPGTFYALPQSPQ 117
+ R K+++ IR +L+D GF+E+ETP+L P GA R ++ Y L +P+
Sbjct: 181 IKRSKIIRAIREFLDD-RGFLEVETPMLQ-PIPGGAAARPFITHHNALDMDLY-LRIAPE 237
Query: 118 LFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKI 177
L+ + L+V GF++ ++I R FR+E + PEFT L+ A+ +D++ L E+LI+++
Sbjct: 238 LYLKRLIVGGFERVFEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKEL 297
Query: 178 FLEI-KDVQLPN---------PFPRLTYAEAMSRYGSDRPDTRFSLQ 214
E+ ++ PF R+T +A+ Y D F +
Sbjct: 298 AKEVNGTTKVTYGGQEIDFSKPFKRITMVDALKEYLGVDFDDLFDDE 344
>gnl|CDD|238398 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core
domain. Class II LysRS is a dimer which attaches a
lysine to the 3' OH group of ribose of the appropriate
tRNA. Its assignment to class II aaRS is based upon its
structure and the presence of three characteristic
sequence motifs in the core domain. It is found in
eukaryotes as well as some prokaryotes and archaea.
However, LysRS belongs to class I aaRS's in some
prokaryotes and archaea. The catalytic core domain is
primarily responsible for the ATP-dependent formation of
the enzyme bound aminoacyl-adenylate.
Length = 329
Score = 95.7 bits (239), Expect = 7e-22
Identities = 52/178 (29%), Positives = 86/178 (48%), Gaps = 40/178 (22%)
Query: 57 HNILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGA-------------RD-YLVPS 102
++R K++ IR++L+D GF+E+ETP+L GA D YL
Sbjct: 6 QTFIVRSKIISYIRKFLDD-RGFLEVETPMLQ-PIAGGAAARPFITHHNALDMDLYL--- 60
Query: 103 RVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTP 162
R+ +P+L+ + L+V GF++ Y+I R FR+E + PEFT ++ A+
Sbjct: 61 RI----------APELYLKRLIVGGFERVYEIGRNFRNEGIDLTHNPEFTMIEFYEAYAD 110
Query: 163 LDDMLRLNEDLIRKIFLEI----------KDVQLPNPFPRLTYAEAMSRY-GSDRPDT 209
+DM+ L EDL + +I K++ PF R+T +A+ G D P+
Sbjct: 111 YNDMMDLTEDLFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALKEKTGIDFPEL 168
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 93.2 bits (233), Expect = 2e-20
Identities = 67/230 (29%), Positives = 104/230 (45%), Gaps = 52/230 (22%)
Query: 2 KTGFIEVAVEHVQVLN-AVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDL-RRQQMNHNI 59
KTG + V + +L ++R LP D E R R R +DL +
Sbjct: 120 KTGELSVKATELTLLTKSLRP-LP------DKFHGLTDVETRYRQRYVDLIVNPESRETF 172
Query: 60 LLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEG--AR---------D---YLVPSRVQ 105
R K++ IRR+L++ GF+E+ETP+L G AR D YL R+
Sbjct: 173 RKRSKIISAIRRFLDN-RGFLEVETPMLQ-PIAGGAAARPFITHHNALDIDLYL---RI- 226
Query: 106 PGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMEL--AFTPL 163
+P+L+ + L+V GF++ Y+I R FR+E + PEFT +E A+
Sbjct: 227 ---------APELYLKRLIVGGFERVYEIGRNFRNEGIDTRHNPEFTM--LEFYQAYADY 275
Query: 164 DDMLRLNEDLIRKIFLEI----------KDVQLPNPFPRLTYAEAMSRYG 203
+DM+ L E+LIR + + ++ PF RLT +A+ Y
Sbjct: 276 NDMMDLTEELIRHLAQAVLGTTKVTYQGTEIDFGPPFKRLTMVDAIKEYT 325
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 84.3 bits (209), Expect = 5e-18
Identities = 54/227 (23%), Positives = 94/227 (41%), Gaps = 33/227 (14%)
Query: 26 LVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNILLRHKVVKLIRRYLEDVHGFVEIETP 85
L + ++F++ + + ++ + ++ +++ R +L+ GFVE+ P
Sbjct: 3 LERYPKEYEEFLRMSWKH------ISSEKYRKVLKVQSSILRYTREFLDG-RGFVEVLPP 55
Query: 86 VLSRSTPEGARD-----YLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRD 140
++S ST S G Y L S L KQ L + K + ++ FR
Sbjct: 56 IISPSTDPLMGLGSDLPVKQISIDFYGVEYYLADSMILHKQ-LALRMLGKIFYLSPNFRL 114
Query: 141 EDLRADRQP---EFTQLDMELAFTPLDDMLRLNEDLIRKIFLEIKDV----------QLP 187
E + D EFTQLD+E+ LD+++ L EDLI+ + E+ + LP
Sbjct: 115 EPVDKDTGRHLYEFTQLDIEIEGADLDEVMDLIEDLIKYLVKELLEEHEDELEFFGRDLP 174
Query: 188 ---NPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFL----ESPF 227
PF R+T+ EA+ + +L + L E PF
Sbjct: 175 HLKRPFKRITHKEAVEILNEEGCRGIDLEELGSEGEKSLSEHFEEPF 221
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 84.7 bits (209), Expect = 1e-17
Identities = 61/224 (27%), Positives = 111/224 (49%), Gaps = 25/224 (11%)
Query: 2 KTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDL-RRQQMNHNIL 60
+TG + + +++L LP D +E+R R R LDL + +
Sbjct: 132 QTGELSIHCTELRLLTKALRPLP------DKFHGLQDQEVRYRQRYLDLIANDKSRQTFV 185
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGA--RDYLVPSRVQPGTFYALPQSPQL 118
+R K++ IR+++ GF+E+ETP++ + P GA R ++ Y L +P+L
Sbjct: 186 VRSKILAAIRQFMV-ARGFMEVETPMM-QVIPGGASARPFITHHNALDLDMY-LRIAPEL 242
Query: 119 FKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIF 178
+ + L+V GF++ ++I R FR+E + PEFT +++ +A+ D++ L E L R +
Sbjct: 243 YLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLA 302
Query: 179 LEI-KDVQLP---------NPFPRLTYAEAMSRYGSDRPDTRFS 212
E+ ++ PF +LT EA+ +Y RP+T +
Sbjct: 303 QEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKY---RPETDMA 343
>gnl|CDD|145868 pfam02938, GAD, GAD domain. This domain is found in some members
of the GatB and aspartyl tRNA synthetases.
Length = 94
Score = 75.4 bits (186), Expect = 6e-17
Identities = 36/100 (36%), Positives = 50/100 (50%), Gaps = 6/100 (6%)
Query: 230 FSDSLKSGGIIKVLCVPSGAKTYSNTALKKGDIYNEAIKSGAKGLPFLKVLDAGGVEGIP 289
FS++LK GG +K LCVP GA S + + + A + GAKGL ++KV G I
Sbjct: 1 FSEALKKGGSVKALCVPGGAG-LSRKQIDELE--RFAKEFGAKGLAWIKVEGGGHTGPIA 57
Query: 290 ALVSSLGPSNKEQLLIRCSAGPSDLILFAVGHPASVNKTL 329
++ E+LL R A D++LF VNK L
Sbjct: 58 KFLTE---EEVEELLERVGAQNGDILLFVADKEKVVNKAL 94
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 82.7 bits (205), Expect = 7e-17
Identities = 52/186 (27%), Positives = 84/186 (45%), Gaps = 46/186 (24%)
Query: 40 EIRLRYRCLDLRRQQMNHNI----LLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGA 95
E R R R LDL N + R K++ IRR+L+D GF+E+ETP+L+ GA
Sbjct: 209 ETRYRQRYLDL---IANPEVRDIFRTRAKIISYIRRFLDD-RGFLEVETPMLN-MIAGGA 263
Query: 96 -------------RD-YLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDE 141
D YL R+ + +L + L+V GF++ Y+I R FR+E
Sbjct: 264 AARPFVTHHNDLNMDLYL---RI----------ATELHLKRLVVGGFERVYEIGRQFRNE 310
Query: 142 DLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFLEIK----------DVQLPNPFP 191
+ PEFT + A+ +DM+ L E+++ + E+ ++ PF
Sbjct: 311 GISTRHNPEFTTCEFYQAYADYNDMMELTEEMVSGMVKELTGSYKIKYHGIEIDFTPPFR 370
Query: 192 RLTYAE 197
R++
Sbjct: 371 RISMIS 376
>gnl|CDD|238391 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 = 77.9 bits (192), Expect = 1e-16
Identities = 35/159 (22%), Positives = 65/159 (40%), Gaps = 23/159 (14%)
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARD----YLVPSRVQPGTFYALPQSP 116
+R K+ + +RR++ + GF E+ETP++ R L+P + L +
Sbjct: 1 IRSKIEQKLRRFMAE-LGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTL 59
Query: 117 QLFKQMLMVS----GFDKYYQIARCFRDEDLRAD--RQPEFTQLDMELAFTPLDD----- 165
+ L VS + +I FR+E R R EFTQL+ E+ ++
Sbjct: 60 EPGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEFE 119
Query: 166 -MLRLNEDLIRKIFLEIKDVQLPNPFPRLTYAEAMSRYG 203
++ L E+L+R + +++ + S G
Sbjct: 120 ELIELTEELLRALGIKL------DIVFVEKTPGEFSPGG 152
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 77.8 bits (192), Expect = 2e-15
Identities = 66/231 (28%), Positives = 93/231 (40%), Gaps = 45/231 (19%)
Query: 6 IEVAVEHVQVLNAVRSKLPFLV-----------TTADDAKDFVK--EEIRLRYRCLDLRR 52
+E+ V + ++ + LPF V + V+ ++ RL R LDLR
Sbjct: 159 VEIQVRKIYCVSKALATLPFNVEDAARSESEIEKALQTGEQLVRVGQDTRLNNRVLDLRT 218
Query: 53 QQMNHNILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGAR-----DYLVPSRVQPG 107
++ +V L R +L GFVEI TP L EG DY G
Sbjct: 219 PANQAIFRIQSQVCNLFREFLLS-KGFVEIHTPKLIAGASEGGSAVFRLDYK-------G 270
Query: 108 TFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTP-LDD 165
L QSPQL KQM + F + ++I FR ED R EFT LD+E+ +
Sbjct: 271 QPACLAQSPQLHKQMAICGDFRRVFEIGPVFRAEDSFTHRHLCEFTGLDLEMEIKEHYSE 330
Query: 166 MLRLNEDLIRKIF----------LEIKDVQLP-------NPFPRLTYAEAM 199
+L + ++L IF LE Q P RLT+AE +
Sbjct: 331 VLDVVDELFVAIFDGLNERCKKELEAIREQYPFEPLKYLPKTLRLTFAEGI 381
>gnl|CDD|239812 cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia coli
aspartyl-tRNA synthetase (AspRS), the human
mitochondrial (mt) AspRS-2, the discriminating (D)
Thermus thermophilus AspRS-1, and the nondiscriminating
(ND) Helicobacter pylori AspRS. These homodimeric
enzymes are class2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs catalyze
the specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic synthesis, whereas the other exclusively
with mitochondrial protein synthesis. Human mtAspRS
participates in mitochondrial biosynthesis; this enzyme
been shown to charge E.coli native tRNAsp in addition to
in vitro transcribed human mitochondrial tRNAsp. T.
thermophilus is rare among bacteria in having both a
D_AspRS and a ND_AspRS. H.pylori ND-AspRS can charge
both tRNAASp and tRNAAsn, it is fractionally more
efficient at aminoacylating tRNAAsp over tRNAAsn. The
H.pylori genome does not contain AsnRS.
Length = 135
Score = 69.1 bits (170), Expect = 3e-14
Identities = 24/55 (43%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQM 55
+ TG IEV ++VLN + LPF + + V EE+RL+YR LDLRR +M
Sbjct: 86 LPTGEIEVVASELEVLNKAK-TLPFEIDDDVN----VSEELRLKYRYLDLRRPKM 135
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 73.1 bits (179), Expect = 1e-13
Identities = 55/233 (23%), Positives = 106/233 (45%), Gaps = 34/233 (14%)
Query: 1 MKTGFIEVAVEHVQVLNAVRSKLPFLVT---TADDAKDFVK---EEIRLRYRCLDLRRQQ 54
M+ G + VA + +L+ P++ T + + F +++ RYR D+
Sbjct: 174 MQRGELSVAASRMLILS------PYVCTDQVVCPNLRGFTVLQDNDVKYRYRFTDMMTNP 227
Query: 55 -MNHNILLRHKVVKLIRRYLEDVHGFVEIETPVL-SRSTPEGARDYLVPSRVQPGTFYAL 112
+ I RH +++ +R Y + + FVE+ETPVL + ++ A+ ++ + L
Sbjct: 228 CVIETIKKRHVMLQALRDYFNERN-FVEVETPVLHTVASGANAKSFVTHHNANAMDLF-L 285
Query: 113 PQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNED 172
+P+L + +V G ++ Y+I + FR+ED PEFT + A+ +D++ + ED
Sbjct: 286 RVAPELHLKQCIVGGMERIYEIGKVFRNEDADRSHNPEFTSCEFYAAYHTYEDLMPMTED 345
Query: 173 LIRKIFLEI-----------------KDVQLPNPFPRLT-YAEAMSRYGSDRP 207
+ R++ + + V L PF R++ Y E G + P
Sbjct: 346 IFRQLAMRVNGTTVVQIYPENAHGNPVTVDLGKPFRRVSVYDEIQRMSGVEFP 398
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 70.8 bits (174), Expect = 2e-13
Identities = 39/151 (25%), Positives = 70/151 (46%), Gaps = 15/151 (9%)
Query: 58 NILLRHKVVKLIRRYLEDVHGFVEIETPVLSRST-PEG-----ARDYLVPSRVQPGTFYA 111
N+L R ++ IRR+ + G +E+ETP LS + + ++L P + +
Sbjct: 15 NLLKRAAIIAAIRRFFAE-RGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLW- 72
Query: 112 LPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNE 171
L SP+ + L+ +G +Q+ + FR+E++ PEFT L+ + D RL
Sbjct: 73 LHTSPEYHMKRLLAAGSGPIFQLGKVFRNEEMGRLHNPEFTMLEW---YRVGCDYYRLMN 129
Query: 172 DLIRKIFLEIKDVQLPNPFPRLTYAEAMSRY 202
+ + + + + RL+Y EA RY
Sbjct: 130 E-VDDLLQLVLEC---VEAERLSYQEAFLRY 156
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 70.0 bits (171), Expect = 8e-13
Identities = 53/207 (25%), Positives = 93/207 (44%), Gaps = 37/207 (17%)
Query: 40 EIRLRYRCLDLR-RQQMNHNILLRHKVVKLIRRYLEDVHGFVEIETPVLSR-STPEGARD 97
EIR R R LDL + + R K++ +R +L D GF+E+ETP ++ + AR
Sbjct: 233 EIRYRQRYLDLMINESTRSTFITRTKIINYLRNFLND-RGFIEVETPTMNLVAGGANARP 291
Query: 98 YLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDME 157
++ Y L + +L +ML+V G DK Y+I + FR+E + PEFT +
Sbjct: 292 FITHHNDLDLDLY-LRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFY 350
Query: 158 LAFTPLDDMLRLNEDLIRKIFLEI---------KD--------VQLPNPFPRLTYAEAMS 200
A+ D+++ +ED ++ + + KD + P+P+++ E
Sbjct: 351 WAYADFYDLIKWSEDFFSQLVMHLFGTYKILYNKDGPEKDPIEIDFTPPYPKVSIVE--- 407
Query: 201 RYGSDRPDTRFSLQLNDVSDIFLESPF 227
+L +++ LE PF
Sbjct: 408 -------------ELEKLTNTKLEQPF 421
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 66.2 bits (161), Expect = 1e-11
Identities = 60/214 (28%), Positives = 90/214 (42%), Gaps = 19/214 (8%)
Query: 6 IEVAVEHVQVLNAVRSKLPFLVTTA----DDAKDFVKEEIRLRYRCLDLRRQQMNHNILL 61
IE+ V+ + + LPF + A D V + RL R +DLR L
Sbjct: 156 IELKVKKIHTVTESLRTLPFTLEDASRKESDEGAKVNFDTRLNSRWMDLRTPASGAIFRL 215
Query: 62 RHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQ 121
+ +V + R++L D F EI +P + + EG + F L QSPQL+KQ
Sbjct: 216 QSRVCQYFRQFLID-SDFCEIHSPKIINAPSEGGANVFKLEYFN--RFAYLAQSPQLYKQ 272
Query: 122 MLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTP-LDDMLRLNEDLIRKIF- 178
M++ + +++ FR E+ R EF LD+E+ ++L L E L IF
Sbjct: 273 MVLQGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDLAESLFNYIFE 332
Query: 179 ------LEIKDVQLPNPFPRLTY---AEAMSRYG 203
E+K V PF L + E M G
Sbjct: 333 RLATHTKELKAVCQQYPFEPLVWKLTPERMKELG 366
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 64.7 bits (158), Expect = 3e-11
Identities = 56/229 (24%), Positives = 101/229 (44%), Gaps = 40/229 (17%)
Query: 2 KTGFIEVAVEHVQVLNAVRSKLPFLVTTADDAKDFVKEEIRLRYRCLDLRRQQMNHNIL- 60
K +E+ V+ ++V+ + + + + +F+++ LR R L ++
Sbjct: 85 KGQPVELQVKKIEVVGEAEPD-DYPLQKKEHSLEFLRDIAHLRLRTNTL------GAVMR 137
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGT---FYA----LP 113
+R+ + + I RY ++ +GF + P+L+ + EGA + S F+ L
Sbjct: 138 VRNALSQAIHRYFQE-NGFTWVSPPILTSNDCEGAGELFRVSTGNIDFSQDFFGKEAYLT 196
Query: 114 QSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPLDDMLRLNED 172
S QL+ + ++ K Y FR E R EF ++ E+AF L+D+L+L E
Sbjct: 197 VSGQLYLETYALA-LSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFANLNDLLQLAET 255
Query: 173 LIRKI-------------FLEI---KDVQ------LPNPFPRLTYAEAM 199
LI+ I FLE KD+ + N F R+TY +A+
Sbjct: 256 LIKYIIKAVLENCSQELKFLEKNFDKDLIKRLENIINNKFARITYTDAI 304
>gnl|CDD|232984 TIGR00462, genX, EF-P lysine aminoacylase GenX. Many Gram-negative
bacteria have a protein closely homologous to the
C-terminal region of lysyl-tRNA synthetase (LysS).
Multiple sequence alignment of these proteins with the
homologous regions of collected LysS proteins shows that
these proteins form a distinct set rather than just
similar truncations of LysS. The protein is termed GenX
after its designation in E. coli. Interestingly, genX
often is located near a homolog of
lysine-2,3-aminomutase. Its function is unknown [Unknown
function, General].
Length = 290
Score = 63.3 bits (155), Expect = 4e-11
Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 11/130 (8%)
Query: 78 GFVEIETPVLSRST-PEGARDYLVPSRVQPG----TFYALPQSPQLFKQMLMVSGFDKYY 132
G +E+ETP+LS + + D V P Y L SP+ + L+ +G +
Sbjct: 6 GVLEVETPLLSPAPVTDPHLDAFATEFVGPDGQGRPLY-LQTSPEYAMKRLLAAGSGPIF 64
Query: 133 QIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIRKIFLEIKDVQLPNPFPR 192
QI + FR+ + PEFT L+ D++ E L++++ P R
Sbjct: 65 QICKVFRNGERGRRHNPEFTMLEWYRPGFDYHDLMDEVEALLQELL-----GDPFAPAER 119
Query: 193 LTYAEAMSRY 202
L+Y EA RY
Sbjct: 120 LSYQEAFLRY 129
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 63.1 bits (154), Expect = 2e-10
Identities = 48/160 (30%), Positives = 73/160 (45%), Gaps = 30/160 (18%)
Query: 31 DDAKDFVKEEIRLRYRCLDL--RRQQMNHNILLRHKVVKLIRRYLEDVHGFVEIETPVLS 88
D K E R+R R LDL + + + R VV+ +R L GF+E+ETP+L
Sbjct: 741 DKWKGLTDPEARVRQRYLDLAVNPEARD-LLRARSAVVRAVRETLVA-RGFLEVETPILQ 798
Query: 89 R----------STPEGARD---YLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIA 135
+ T A D YL R+ +P+L+ + L V G ++ +++
Sbjct: 799 QVHGGANARPFVTHINAYDMDLYL---RI----------APELYLKRLCVGGVERVFELG 845
Query: 136 RCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNEDLIR 175
R FR+E + A PEFT L+ A D M L +LI+
Sbjct: 846 RNFRNEGVDATHNPEFTLLEAYQAHADYDTMRDLTRELIQ 885
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 57.2 bits (139), Expect = 5e-09
Identities = 46/151 (30%), Positives = 75/151 (49%), Gaps = 15/151 (9%)
Query: 58 NILLRHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGAR------DYLVPSRVQPGTFYA 111
N+L R K++ IRR+ D G +E+ETP+LS++T ++ P Q T +
Sbjct: 4 NLLKRAKIIAEIRRFFAD-RGVLEVETPILSQATVTDIHLVPFETRFVGPGASQGKTLW- 61
Query: 112 LPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLDDMLRLNE 171
L SP+ + L+ +G +QI + FR+E+ PEFT L+ + P DM RL
Sbjct: 62 LMTSPEYHMKRLLAAGSGPIFQICKSFRNEEAGRYHNPEFTMLEW---YRPHYDMYRLMN 118
Query: 172 DLIRKIFLEIKDVQLPNPFPRLTYAEAMSRY 202
+ + + ++ D P L+Y +A RY
Sbjct: 119 E-VDDLLQQVLDC---EPAESLSYQQAFLRY 145
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 50.7 bits (122), Expect = 1e-07
Identities = 42/150 (28%), Positives = 64/150 (42%), Gaps = 30/150 (20%)
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRS--------TPEGARDYLVPSRVQPGTFYAL 112
LR+ + IR L+ +G+ E++TP+L + + + + + G L
Sbjct: 1 LRNALENFIRELLKR-YGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYL 59
Query: 113 PQSP-------QLFKQMLMVSGFD---KYYQIARCFRDE--DLR-ADRQPEFTQLDMELA 159
P +LFK ++ S + K YQI CFR E R R EFTQ+D E+
Sbjct: 60 --RPTAEVGITRLFKNEIL-SYRELPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIF 116
Query: 160 FTPLDDMLRLNE--DLIRKIFLEIKDVQLP 187
TP L E L +I +D+ LP
Sbjct: 117 GTPEQSEEELEELLKLAEEIL---QDLGLP 143
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 50.1 bits (121), Expect = 1e-06
Identities = 41/177 (23%), Positives = 73/177 (41%), Gaps = 52/177 (29%)
Query: 62 RHKVVKLIRRYLEDVHGFVEIETPVLSRSTPEGARDYLVPSRVQPGTFYALPQSPQLFKQ 121
R+ + + I + + +GFV ++TP+++ S EGA G + + F +
Sbjct: 136 RNTLAQAIHEFFNE-NGFVWVDTPIITASDCEGA-----------GELFRVTTLDLDFSK 183
Query: 122 -------MLMVSG----------FDKYYQIARCFRDEDLRADRQ-PEFTQLDMELAFTPL 163
L VSG K Y FR E+ R EF ++ E+AF L
Sbjct: 184 DFFGKEAYLTVSGQLYAEAYAMALGKVYTFGPTFRAENSNTRRHLAEFWMIEPEMAFADL 243
Query: 164 DDMLRLNEDLIRKI-----------------FLEIKDVQ-----LPNPFPRLTYAEA 198
+D + L E++++ + ++ D++ + +PFPR+TY EA
Sbjct: 244 EDNMDLAEEMLKYVVKYVLENCPDDLEFLNRRVDKGDIERLENFIESPFPRITYTEA 300
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 38.4 bits (90), Expect = 0.007
Identities = 28/153 (18%), Positives = 54/153 (35%), Gaps = 44/153 (28%)
Query: 59 ILLRHKVVKLIRRYLEDVHGFVEIETPV------LSRSTPEGARDYLVPSRVQPGTFY-- 110
+ LR + IR+ E +GF EI TP+ +R + E V+ +
Sbjct: 18 MALREYIESTIRKVFES-YGFSEIRTPIFEYTELFARKSGEETDV------VEKEMYTFK 70
Query: 111 -------------------ALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEF 151
A+ ++ + L K Y FR E + R +F
Sbjct: 71 DKGGRSLALRPELTAPVARAVAENKLDLPKPL------KLYYFGPVFRYERPQKGRYRQF 124
Query: 152 TQLDMEL--AFTPLDD--MLRLNEDLIRKIFLE 180
Q +E+ + +P D ++ L +++ + +
Sbjct: 125 YQFGVEVIGSDSPDADAEVIALAVEILEALGIG 157
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 36.3 bits (85), Expect = 0.030
Identities = 33/160 (20%), Positives = 54/160 (33%), Gaps = 52/160 (32%)
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETP------VLSRSTPE---------------GARDY- 98
+ + IR E +GF EI TP + +R E G R
Sbjct: 16 KWQYIEETIREVFEL-YGFKEIRTPIFEYTELFARKVGEETDIVEKEMYTFKDKGGRSLT 74
Query: 99 --------LVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPE 150
+ + ++ P K Y I FR E + R +
Sbjct: 75 LRPEGTAPVARAVIENKLLLPKPF---------------KLYYIGPMFRYERPQKGRYRQ 119
Query: 151 FTQLDMEL--AFTPLDD--MLRLNEDLIRKIFLEIKDVQL 186
F Q +E+ + +PL D ++ L ++++ L IKD L
Sbjct: 120 FHQFGVEVIGSDSPLADAEIIALAAEILKA--LGIKDFTL 157
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 35.7 bits (83), Expect = 0.035
Identities = 26/131 (19%), Positives = 38/131 (29%), Gaps = 53/131 (40%)
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETPVLSRS----------------------------TP 92
LR + +R E +G+ EI+TPV + P
Sbjct: 4 LRRYIEDTLREVFE-RYGYEEIDTPVFEYTELFLRKSGDEVSKEMYRFKDKGGRDLALRP 62
Query: 93 EG----ARDYLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQ 148
+ AR + LP K Y I FR E + R
Sbjct: 63 DLTAPVARAV-----AENLLSLPLPL---------------KLYYIGPVFRYERPQKGRY 102
Query: 149 PEFTQLDMELA 159
EF Q+ +E+
Sbjct: 103 REFYQVGVEII 113
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH 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. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 34.4 bits (80), Expect = 0.073
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 129 DKYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLD--DMLRLNEDLIRKIFLEIKDVQL 186
+ + I R +R++++ A PEF Q++ + L D+ E+ +++F I V+
Sbjct: 81 IRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKELFGPITKVRF 140
Query: 187 -PNPFP 191
P+ FP
Sbjct: 141 RPSYFP 146
>gnl|CDD|236132 PRK07922, PRK07922, N-acetylglutamate synthase; Validated.
Length = 169
Score = 33.4 bits (77), Expect = 0.11
Identities = 20/40 (50%), Positives = 24/40 (60%), Gaps = 8/40 (20%)
Query: 77 HGFVEIE-TPV-------LSRSTPEGARDYLVPSRVQPGT 108
HGFVEI+ TPV L RS EG ++L SRV+P T
Sbjct: 120 HGFVEIDGTPVTPEVYAELLRSYDEGVAEFLDLSRVKPNT 159
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 33.9 bits (78), Expect = 0.12
Identities = 35/161 (21%), Positives = 57/161 (35%), Gaps = 38/161 (23%)
Query: 66 VKLIRRYLEDV-------HGFVEIETPVLSRS-------TPEGARDYLV----PSRVQPG 107
+ R LE +G+ EI P L+ + +G R + R
Sbjct: 1 GTALWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRD 60
Query: 108 TFYAL-PQSPQLFKQMLMVSGFD------KYYQIARCFRDE-----DLRADRQPEFTQLD 155
T L P + + Q+ + QI CFR E L R EF Q++
Sbjct: 61 TDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHEPSGRRGL--MRVREFRQVE 118
Query: 156 MELAFTPLDD------MLRLNEDLIRKIFLEIKDVQLPNPF 190
+ P + L L E++ R++ L ++ V +PF
Sbjct: 119 YVVFGEPEEAEEERREWLELAEEIARELGLPVRVVVADDPF 159
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 33.1 bits (76), Expect = 0.28
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 130 KYYQIARCFRDEDLRADRQPEFTQL-----DMELAFTPLDDMLRLNEDLIRKIFLEIKDV 184
+ + R FR++ + A PEF Q+ D ++FT ++ E+ ++K+F E +
Sbjct: 152 RIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFT---NLKGFLEEFLKKMFGETEIR 208
Query: 185 QLPNPFP 191
P+ FP
Sbjct: 209 FRPSYFP 215
>gnl|CDD|216992 pfam02358, Trehalose_PPase, Trehalose-phosphatase. This family
consist of trehalose-phosphatases EC:3.1.3.12 these
enzyme catalyze the de-phosphorylation of
trehalose-6-phosphate to trehalose and orthophosphate.
The aligned region is present in trehalose-phosphatases
and comprises the entire length of the protein it is
also found in the C-terminus of trehalose-6-phosphate
synthase EC:2.4.1.15 adjacent to the
trehalose-6-phosphate synthase domain - pfam00982. It
would appear that the two equivalent genes in the E.
coli otsBA operon otsA the trehalose-6-phosphate
synthase and otsB trehalose-phosphatase (this family)
have undergone gene fusion in most eukaryotes. Trehalose
is a common disaccharide of bacteria, fungi and
invertebrates that appears to play a major role in
desiccation tolerance.
Length = 235
Score = 32.7 bits (75), Expect = 0.30
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 199 MSRYGSDRPDTRFSLQL-NDVSDIFLESPFRVFSDSLKSGGIIKVLCVPSGAK 250
+ GS F L + +D +D E F V + + SG I+V G+K
Sbjct: 174 LEELGSAGSPPDFPLCIGDDRTD---EDMFDVVNPTKMSGLSIEVGATSVGSK 223
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 32.2 bits (74), Expect = 0.42
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 9/68 (13%)
Query: 130 KYYQIARCFRDEDLRADRQPEFTQL-----DMELAFTPLDDMLRLNEDLIRKIFLEIKDV 184
K + I R FR + + A PEF Q+ D ++F D+ + E+ +RK F V
Sbjct: 104 KIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVSF---ADLKGVLEEFLRKFFGFEVKV 160
Query: 185 QL-PNPFP 191
+ P+ FP
Sbjct: 161 RFRPSYFP 168
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 32.0 bits (73), Expect = 0.70
Identities = 30/117 (25%), Positives = 44/117 (37%), Gaps = 36/117 (30%)
Query: 69 IRRYLEDV---HGFVEIETPVLS--------------------RSTPEGARDYLVPSRVQ 105
I+R LEDV +G +ETP L+ T +G RD
Sbjct: 24 IKRALEDVFERYGCKPLETPTLNMYELMSSKYGGGDEILKEIYTLTDQGKRDL------- 76
Query: 106 PGTFYALPQSPQLFKQMLMVSGFD---KYYQIARCFRDEDLRADRQPEFTQLDMELA 159
Y L + K + M K Y+I + FRD ++ R EF Q D+++
Sbjct: 77 -ALRYDL--TIPFAKVVAMNPNIRLPFKRYEIGKVFRDGPIKQGRFREFIQCDVDIV 130
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 29.9 bits (68), Expect = 2.5
Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 21/96 (21%)
Query: 102 SRVQPGTFYALPQSPQLFKQMLMVSGFDKYYQIARCFRDEDLRADRQPEFTQL-----DM 156
S VQ T + P K + R +R++ + A PEF Q+ D
Sbjct: 178 SPVQARTLAENAKIPI------------KIFSPGRVYRNDTVDATHSPEFHQIEGLVVDK 225
Query: 157 ELAFTPLDDMLRLNEDLIRKIFLEIKDVQL-PNPFP 191
++F L L E+ +K F E V+ P+ FP
Sbjct: 226 NISFADLKGTL---EEFAKKFFGEDVKVRFRPSYFP 258
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 29.8 bits (68), Expect = 2.9
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 130 KYYQIARCFRDEDLRADRQPEFTQLD 155
KY+ I R FR + + A PEF QL+
Sbjct: 352 KYFSIGRVFRPDTIDATHLPEFYQLE 377
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 29.7 bits (68), Expect = 3.0
Identities = 12/39 (30%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 61 LRHKVVKLIRRYLEDVHGFVEIETP------VLSRSTPE 93
V IR E +GF EI TP + R E
Sbjct: 20 KWQYVEDTIREVFER-YGFSEIRTPIFEYTELFKRKVGE 57
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 29.6 bits (67), Expect = 3.5
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 405 GGSLRIYKREVQQKVLEIVGISPEQFIFA-EVVAIPA 440
GGS RI VQ+ V + G P + + EVVAI A
Sbjct: 332 GGSTRIPA--VQELVKDFFGKEPNKSVNPDEVVAIGA 366
>gnl|CDD|178154 PLN02539, PLN02539, glucose-6-phosphate 1-dehydrogenase.
Length = 491
Score = 29.3 bits (66), Expect = 4.8
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 275 PFLKVLDAGGVEGIPALVSSLGPSNKEQLLIR 306
P L +DAG V+ IP S GP+ ++LL +
Sbjct: 451 PLLHRIDAGKVKPIPYKQGSRGPAEADELLEK 482
>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34
[Transcription].
Length = 301
Score = 29.2 bits (65), Expect = 5.1
Identities = 19/119 (15%), Positives = 43/119 (36%), Gaps = 13/119 (10%)
Query: 165 DMLRLNEDLIRKIFLEIKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSLQLNDVSDIFLE 224
+M+R D + + + ++ + FP+ M + L D++
Sbjct: 3 EMIRGLLDNAKSRPEGVVEKEISSEFPQQELQMQMGKA-----------SLTDLASELNA 51
Query: 225 SPFRVFSDSLKSGGIIKVLCV-PSGAKTYSNTALKKGDIYNEAIKSGAKGLPFLKVLDA 282
R + G++ V S A + + +Y+ +SG +G+ +LK +
Sbjct: 52 LLKRQLISLFRQKGVLYYKGVLESEASPINTMDDYELTVYSLISQSGGEGI-WLKTIKD 109
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 28.7 bits (65), Expect = 6.3
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 9/82 (10%)
Query: 220 DIFLESPFRVFSDSLKSGGIIKVL---CVPSGAKTYSNTAL----KKGDIYNEAIKSGAK 272
++ +E RVF S + ++ L G + +N+ + K + +++
Sbjct: 88 ELKVEEDGRVFPCSDSAADVLDALLNELKELGVEILTNSKVKSIKKDDGGFG--VETSGG 145
Query: 273 GLPFLKVLDAGGVEGIPALVSS 294
KV+ A G P L S+
Sbjct: 146 EYEADKVIIATGGLSYPQLGST 167
>gnl|CDD|238397 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class
II core catalytic domain. GlyRS functions as a homodimer
in eukaryotes, archaea and some bacteria and as a
heterotetramer in the remainder of prokaryotes. It is
responsible for the attachment of glycine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP binding and hydrolysis.
This alignment contains only sequences from the GlyRS
form which homodimerizes. The heterotetramer glyQ is in
a different family of class II aaRS. Class II assignment
is based upon its structure and the presence of three
characteristic sequence motifs. This domain is also
found at the N-terminus of the accessory subunit of
mitochondrial polymerase gamma (Pol gamma b). Pol gamma
b stimulates processive DNA synthesis and is functional
as a homodimer, which can associate with the catalytic
subunit Pol gamma alpha to form a heterotrimer. Despite
significant both structural and sequence similarity with
GlyRS, Pol gamma b lacks conservation of several class
II functional residues.
Length = 254
Score = 28.3 bits (64), Expect = 7.0
Identities = 36/195 (18%), Positives = 64/195 (32%), Gaps = 52/195 (26%)
Query: 59 ILLRHKVVKLIRRY---LEDVHGFVEIETPVLSRSTPE-------GARD------YLVPS 102
+ L++ + R+ E+ +EI++P++ TPE G + YL P
Sbjct: 32 VELKNNIKSAWRKSFVLEEE--DMLEIDSPII---TPELMFKTSIGPVESGGNLGYLRPE 86
Query: 103 RVQPGTFYALPQSPQLF-KQMLMVSGFDKYYQIARCFRDE--------DLRADRQPEFTQ 153
Q G F + +++ QI + FR+E +R EFTQ
Sbjct: 87 TAQ-GIFVNFKNLLEFNRRKLPFGVA-----QIGKSFRNEISPRNGLFRVR-----EFTQ 135
Query: 154 LDMELAFTPLDDMLRLNEDLIRKIFLEIKDVQLPNPFPRLTYAEAMSRYGSDRPDTRFSL 213
++E P + +++ K Q P +D +
Sbjct: 136 AEIEFFVDPEKSHPWFDYWADQRLKWLPKFAQSPENLR-----------LTDHEKEELAH 184
Query: 214 QLNDVSDIFLESPFR 228
N+ D F P
Sbjct: 185 YANETLDYFYAFPHG 199
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and
related proteins) [Coenzyme transport and metabolism].
Length = 360
Score = 28.4 bits (64), Expect = 7.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 266 AIKSGAK----GLPFLKVLDAGGVEGIPALVSSL 295
A+ GA G PFL L AGG G+ ++ +
Sbjct: 291 ALALGADAVGIGRPFLYGLAAGGEAGVERVLEII 324
>gnl|CDD|212548 cd11710, GINS_A_psf1, Alpha-helical domain of GINS complex protein
Psf1. Psf1 is a component of the GINS tetrameric
protein complex. Psf1 is mainly expressed in highly
proliferative tissues, such as blastocysts, adult bone
marrow, and testis, in which the stem cell system is
active. Loss of Psf1 causes embryonic lethality. GINS is
a complex of four subunits (Sld5, Psf1, Psf2 and Psf3)
that is involved in both initiation and elongation
stages of eukaryotic chromosome replication. Besides
being essential for the maintenance of genomic
integrity, GINS plays a central role in coordinating DNA
replication with cell cycle checkpoints and is involved
in cell growth. The eukaryotic GINS subunits are
homologous and homologs are also found in the archaea;
the complex is not found in bacteria. The four subunits
of the complex consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 129
Score = 27.2 bits (61), Expect = 9.3
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 153 QLDMELAFTPLDDMLRLNEDLIRKIFLEIKD 183
+L EL + D + NEDL+R++ EI+D
Sbjct: 6 KLVKELKRSENDTLPPYNEDLVRQVLEEIRD 36
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
0.321 0.139 0.404
Gapped
Lambda K H
0.267 0.0854 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,064,968
Number of extensions: 2454465
Number of successful extensions: 2343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2243
Number of HSP's successfully gapped: 81
Length of query: 452
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 352
Effective length of database: 6,502,202
Effective search space: 2288775104
Effective search space used: 2288775104
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 (21.9 bits)
S2: 61 (27.0 bits)