RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3762
(595 letters)
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 966 bits (2499), Expect = 0.0
Identities = 330/591 (55%), Positives = 437/591 (73%), Gaps = 14/591 (2%)
Query: 1 MRTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIA 60
MRTHYCG + E + Q ++LCGWVHR+R+HGG+IFIDLRD G+VQ+VFDP D + +++A
Sbjct: 3 MRTHYCGELRESHVGQTVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDP-DAEAFEVA 61
Query: 61 KIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQI-DEKNILE 119
+ +R+E+ +Q+ G V +RP T N NL +G IE+L EL++LN S TLPF I DE+++ E
Sbjct: 62 ESLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVLASELEVLNKSKTLPFPIDDEEDVSE 121
Query: 120 VTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLV 179
LKYR L LR MQKNL+LR KVT +R FLD F+EIETPIL+KSTPEGARDYLV
Sbjct: 122 ELRLKYRYLDLRRPEMQKNLKLRSKVTSAIRNFLDDNGFLEIETPILTKSTPEGARDYLV 181
Query: 180 PSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSF 239
PSR++PG+F+ALPQSPQLFKQLLMVA FDRYYQI +CFRDEDLR+DRQPEFTQID E SF
Sbjct: 182 PSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDIEMSF 241
Query: 240 MNEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDKPDMCIKLIFTDLTN 299
+ +E++ L E +IR +F + L + LP PFP + ++ A++ YGSDKPD+ L D+T+
Sbjct: 242 VTQEDVMALMEGLIRHVFKEVLGVDLPTPFPRMTYAEAMRRYGSDKPDLRFGLELVDVTD 301
Query: 300 IMKDSDFKLFSKIANMKNGRIIGLKIPGG-FSISRNEINYYTQFVKTYGAKGLTYIKIHK 358
+ KDS FK+F+ AN GR+ +++PGG +SR +I+ T+F K YGAKGL YIK+
Sbjct: 302 LFKDSGFKVFAGAAN-DGGRVKAIRVPGGAAQLSRKQIDELTEFAKIYGAKGLAYIKV-- 358
Query: 359 ISKEFDGLKSPIIKYFNNLILEKIINKTEAQNGDIIFLGGDEKNIVNNFMSALRIKIGYS 418
DGLK PI K+ + L ++ +T A++GD+IF G D+ +VN+ + ALR+K+G
Sbjct: 359 ---NEDGLKGPIAKFLSEEELAALLERTGAKDGDLIFFGADKAKVVNDALGALRLKLGK- 414
Query: 419 DFGKRNNILNNKWHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIIT-NPEKIF 477
+ I +K+ LWV++FPMF+YD+ W+A HHPFT PKD D + T +P K
Sbjct: 415 ---ELGLIDEDKFAFLWVVDFPMFEYDEEEGRWVAAHHPFTMPKDEDLDELETTDPGKAR 471
Query: 478 SKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGG 537
+ AYDL++NG+E+GGGSIRIH EIQ+K+F++L I + + +FGFLL++LKYGAPPHGG
Sbjct: 472 AYAYDLVLNGYELGGGSIRIHRPEIQEKVFEILGISEEEAEEKFGFLLDALKYGAPPHGG 531
Query: 538 IAFGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAPSIVDEKQLNELNI 588
IAFGLDRL+ ++ G+ SIRDVIAFPKTQSAQ LLT APS VDEKQL EL I
Sbjct: 532 IAFGLDRLVMLLAGADSIRDVIAFPKTQSAQDLLTGAPSPVDEKQLRELGI 582
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 889 bits (2300), Expect = 0.0
Identities = 326/594 (54%), Positives = 439/594 (73%), Gaps = 12/594 (2%)
Query: 1 MRTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIK-IYKI 59
MRTHYCG + E + Q ++L GWVHR+R+HGG+IFIDLRD G+VQ+VFDP D +++
Sbjct: 1 MRTHYCGELRESHVGQTVTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDPEDSPEAFEV 60
Query: 60 AKIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQI-DEKNIL 118
A +RNEF +Q+ G V +RP T N NL +G IE+L E+++LN+S TLPFQI DE N
Sbjct: 61 ASRLRNEFVIQVTGTVRARPEGTINPNLPTGEIEVLAEEIEVLNASKTLPFQIEDETNAS 120
Query: 119 EVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYL 178
E LKYR L LR MQKNL+LR KVT +R FLD + F+EIETPIL+KSTPEGARD+L
Sbjct: 121 EEIRLKYRYLDLRRPEMQKNLKLRSKVTKAIRNFLDDQGFLEIETPILTKSTPEGARDFL 180
Query: 179 VPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETS 238
VPSR++PG+F+ALPQSPQLFKQLLMVA FDRYYQI +CFRDEDLR+DRQPEFTQID E S
Sbjct: 181 VPSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDLEMS 240
Query: 239 FMNEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDKPDMCIKLIFTDLT 298
F++EE++ L E+++R +F + I+L PFP + ++ A++ YGSDKPD+ L D+T
Sbjct: 241 FVDEEDVMELIEKLLRYVFKEVKGIELKTPFPRMTYAEAMRRYGSDKPDLRFPLELIDVT 300
Query: 299 NIMKDSDFKLFSKIANMKNGRIIGLKIPGGFSISRNEINYYTQFVKTYGAKGLTYIKIHK 358
++ KDS+FK+FS GR+ + +PGG S+SR +I+ T+F K YGAKGL YIK+ +
Sbjct: 301 DLFKDSEFKVFSNALA-NGGRVKAIVVPGGASLSRKQIDELTEFAKIYGAKGLAYIKVEE 359
Query: 359 ISKEFDGLKSPIIKYFNNLILEKIINKTEAQNGDIIFLGGDEKNIVNNFMSALRIKIGYS 418
DGLK PI K+ + ILE++I + A++GDIIF D+K +VN + ALR+K+G
Sbjct: 360 -----DGLKGPIAKFLSEEILEELIERLGAEDGDIIFFVADKKKVVNKALGALRLKLGK- 413
Query: 419 DFGKRNNILNNKWHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFS 478
+ I +++ LWV++FP+F++D+ ++A HHPFT PK + + +PE + +
Sbjct: 414 ---ELGLIDKDQFKFLWVVDFPLFEWDEEEGRYVAAHHPFTMPKPEDLELLEADPESVRA 470
Query: 479 KAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGI 538
+AYDL++NG+E+GGGSIRIHD EIQ+K+F++L I + + +FGFLL + KYGAPPHGGI
Sbjct: 471 RAYDLVLNGYELGGGSIRIHDPEIQEKVFEILGISPEEAEEKFGFLLEAFKYGAPPHGGI 530
Query: 539 AFGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAPSIVDEKQLNELNILYKK 592
AFGLDRL+ ++TG++SIRDVIAFPKTQ A LLTNAPS VDEKQL EL+I +
Sbjct: 531 AFGLDRLVMLLTGAESIRDVIAFPKTQQAADLLTNAPSEVDEKQLKELSIKVRP 584
>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 = 738 bits (1907), Expect = 0.0
Identities = 305/591 (51%), Positives = 415/591 (70%), Gaps = 13/591 (2%)
Query: 1 MRTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIA 60
MRTHYCG + + L Q ++L GWV+R+R+ GG+IFIDLRD +G+VQ+V DP D K+A
Sbjct: 1 MRTHYCGQLRTEHLGQTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDP-DADALKLA 59
Query: 61 KIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQIDEKNILEV 120
K +RNE +Q+ GKV +RP N NL +G IEIL + +LN S T P I++ + E
Sbjct: 60 KGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEILAESITLLNKSKTPPLIIEKTDAEEE 119
Query: 121 TNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVP 180
LKYR L LR MQ+ L+LR+KVT VR FLD + F+EIETP+L+KSTPEGARDYLVP
Sbjct: 120 VRLKYRYLDLRRPEMQQRLKLRHKVTKAVRNFLDQQGFLEIETPMLTKSTPEGARDYLVP 179
Query: 181 SRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFM 240
SR++ GEF+ALPQSPQLFKQLLMV+ DRYYQI +CFRDEDLR+DRQPEFTQID E SFM
Sbjct: 180 SRVHKGEFYALPQSPQLFKQLLMVSGVDRYYQIARCFRDEDLRADRQPEFTQIDMEMSFM 239
Query: 241 NEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDKPDMCIKLIFTDLTNI 300
+E++ L E+++ +F + I L PFPV+ ++ A++ YGSDKPD+ L D+T++
Sbjct: 240 TQEDVMELIEKLVSHVFLEVKGIDLKKPFPVMTYAEAMERYGSDKPDLRFPLELIDVTDL 299
Query: 301 MKDSDFKLFSKIANMKNGRIIGLKIPGGFS-ISRNEINYYTQFVKTYGAKGLTYIKIHKI 359
KDS+FK+FS + N GR+ +++PGG++ +SR I +F K YGAKGL Y+K++
Sbjct: 300 FKDSEFKVFSNLIN-DGGRVKAIRVPGGWAELSRKSIKELRKFAKEYGAKGLAYLKVN-- 356
Query: 360 SKEFDGLKSPIIKYFNNLILEKIINKTEAQNGDIIFLGGDEKNIVNNFMSALRIKIGYSD 419
DG+ SPI K+ + + ++ +T+AQNGDI+ G K IV + + ALR+K+G
Sbjct: 357 ---EDGINSPIKKFLDEKKGKILLERTDAQNGDILLFGAGSKKIVLDALGALRLKLGKD- 412
Query: 420 FGKRNNILNNKWHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSK 479
+ + + LWV++FPMF+ DK A HHPFT PKD + + PE+ ++
Sbjct: 413 ---LGLVDPDLFSFLWVVDFPMFEKDK-EGRLCAAHHPFTMPKDEDLENLEAAPEEALAE 468
Query: 480 AYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIA 539
AYDL++NG E+GGGSIRIHD E+QKK+F++L ID + + +FGFLL + KYG PPH G A
Sbjct: 469 AYDLVLNGVELGGGSIRIHDPEVQKKVFEILGIDPEEAREKFGFLLEAFKYGTPPHAGFA 528
Query: 540 FGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAPSIVDEKQLNELNILY 590
GLDRL+ ++TG+ +IRDVIAFPKT +A CL+T APS +DEKQL EL+I Y
Sbjct: 529 LGLDRLMMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFIDEKQLEELSIKY 579
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 614 bits (1584), Expect = 0.0
Identities = 259/601 (43%), Positives = 395/601 (65%), Gaps = 28/601 (4%)
Query: 2 RTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDI-KIYKIA 60
R+H CG ++ + ++LCGWV R+ GG+ F+D+RD+TG+VQ+V P++ + ++ A
Sbjct: 59 RSHLCGALSVNDVGSRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTA 118
Query: 61 KIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNS-SITLPFQI----DEK 115
+RNE+ + + G V SRP ++ N + +G++E++ + ILN + +LPF + ++K
Sbjct: 119 NRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVTTADEQK 178
Query: 116 N-ILEVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFL-DSKKFIEIETPILSKSTPEG 173
+ I E L+YRVL LR M NLRLR++V +R++L D F+EIETPILS+STPEG
Sbjct: 179 DSIKEEVRLRYRVLDLRRPQMNANLRLRHRVVKLIRRYLEDVHGFVEIETPILSRSTPEG 238
Query: 174 ARDYLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQI 233
ARDYLVPSR+ PG F+ALPQSPQLFKQ+LMV+ FDRYYQI +CFRDEDLR+DRQPEFTQ+
Sbjct: 239 ARDYLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDRYYQIARCFRDEDLRADRQPEFTQL 298
Query: 234 DCETSFMNEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDKPDMCIKLI 293
D E +F E++ L E++IR +F + ++LPNPFP + ++ A+ YGSDKPD+ L
Sbjct: 299 DMELAFTPLEDMLKLNEDLIRQVFKEIKGVQLPNPFPRLTYAEAMSKYGSDKPDLRYGLE 358
Query: 294 FTDLTNIMKDSDFKLFSKIANMKNGRIIGLKIPGGFSISRNEI----NYYTQFVKTYGAK 349
D++++ +S FK+F+ G + + +P G IS N + Y + +K+ GAK
Sbjct: 359 LVDVSDVFAESSFKVFAGALE-SGGVVKAICVPDGKKISNNTALKKGDIYNEAIKS-GAK 416
Query: 350 GLTYIKIHKISKEFDGLKSPIIKYFNNLILEKIINKTEAQNGDIIFLGGDEKNIVNNFMS 409
GL ++K+ E +G+K+ +++ + E+++ A GD+I + VN +
Sbjct: 417 GLAFLKVLD-DGELEGIKA-LVESLSPEQAEQLLAACGAGPGDLILFAAGPTSSVNKTLD 474
Query: 410 ALRIKIGYSDFGKRNNILNNKWHP-LWVINFPMFKYDKINNNWIARHHPFTAPK-DGYED 467
LR I K ++++ H LWV +FPMF++++ A HHPFTAP + D
Sbjct: 475 RLRQFI-----AKTLDLIDPSRHSILWVTDFPMFEWNEDEQRLEALHHPFTAPNPEDMGD 529
Query: 468 FIITNPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNS 527
+++ + AYD++ NG EIGGGS+RI+ ++Q+K+ + + + + +++FG+LL +
Sbjct: 530 --LSSARAL---AYDMVYNGVEIGGGSLRIYRRDVQQKVLEAIGLSPEEAESKFGYLLEA 584
Query: 528 LKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAPSIVDEKQLNELN 587
L GAPPHGGIA+GLDRL+ ++ G+KSIRDVIAFPKT +AQC LT APS VD+KQL +L+
Sbjct: 585 LDMGAPPHGGIAYGLDRLVMLLAGAKSIRDVIAFPKTTTAQCALTRAPSEVDDKQLQDLS 644
Query: 588 I 588
I
Sbjct: 645 I 645
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 542 bits (1398), Expect = 0.0
Identities = 259/606 (42%), Positives = 382/606 (63%), Gaps = 35/606 (5%)
Query: 5 YCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDI--KIYKIAKI 62
+CG+++ + + L GWV R+HG ++FI LRD G +Q VF P +Y++A
Sbjct: 8 FCGHLSLDDTGREVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAAS 67
Query: 63 IRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQIDEKNIL---- 118
+R EFC+ + G+V R +T N ++ +G+IE+ REL IL +S LPF I +K +
Sbjct: 68 LRAEFCVALQGEVQKRLEETENPHIETGDIEVFVRELSILAASEALPFAISDKAMTAGAG 127
Query: 119 --------EVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKST 170
E L+YR L +R MQ +L R+++ R FLDS+ F+EIETPIL+KST
Sbjct: 128 SAGADAVNEDLRLQYRYLDIRRPAMQDHLAKRHRIIKCARDFLDSRGFLEIETPILTKST 187
Query: 171 PEGARDYLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEF 230
PEGARDYLVPSRI+P EF+ALPQSPQLFKQLLM+A F+RY+Q+ +CFRDEDLR +RQPEF
Sbjct: 188 PEGARDYLVPSRIHPKEFYALPQSPQLFKQLLMIAGFERYFQLARCFRDEDLRPNRQPEF 247
Query: 231 TQIDCETSFMNEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDKPDMCI 290
TQ+D E SF++EE I L EE+ +F I LP PFP + ++ A+ GSD+PD+
Sbjct: 248 TQLDIEASFIDEEFIFELIEELTARMF-AIGGIALPRPFPRMPYAEAMDTTGSDRPDLRF 306
Query: 291 KLIFTDLTNIMKDSDFKLFSKIANMKNGRIIGLKIPG-GFSISRNEIN--YYTQFVKTYG 347
L F D T+I +++ + +F +I + GRI G+ I G +S+N + Y + ++G
Sbjct: 307 DLKFADATDIFENTRYGIFKQILQ-RGGRIKGINIKGQSEKLSKNVLQNEYAKEIAPSFG 365
Query: 348 AKGLTYIKIHKISKEFDGLKSPIIKYFNNLILEKIINKTEAQNGDIIFLGGDEK-NIVNN 406
AKG+T+++ E GL S I+++F+ E + + A++GD+I + D IV +
Sbjct: 366 AKGMTWMRA-----EAGGLDSNIVQFFSADEKEALKRRFHAEDGDVIIMIADASCAIVLS 420
Query: 407 FMSALRIKIGYSDFGKRNNILNNKWHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYE 466
+ LR+ + + I +HPLW+ +FP+F+ + + HHPFTAP E
Sbjct: 421 ALGQLRLHLA----DRLGLIPEGVFHPLWITDFPLFEATD-DGGVTSSHHPFTAPDR--E 473
Query: 467 DFIITNPEKIF---SKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGF 523
DF + E++ S+AYDL++NG E+GGGSIRI+D +IQ +IF L + + ++ +FGF
Sbjct: 474 DFDPGDIEELLDLRSRAYDLVVNGEELGGGSIRINDKDIQLRIFAALGLSEEDIEDKFGF 533
Query: 524 LLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAPSIVDEKQL 583
L + + APPHGGIA GLDR+++++ + SIR+VIAFPK +SA C LT APS V ++QL
Sbjct: 534 FLRAFDFAAPPHGGIALGLDRVVSMILQTPSIREVIAFPKNRSAACPLTGAPSEVAQEQL 593
Query: 584 NELNIL 589
EL +L
Sbjct: 594 AELGLL 599
>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 = 272 bits (697), Expect = 2e-87
Identities = 89/144 (61%), Positives = 120/144 (83%)
Query: 139 LRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVPSRINPGEFFALPQSPQLF 198
LRLR +V +R FLD + F+EIETPIL+KSTPEGARD+LVPSR++PG+F+ALPQSPQLF
Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEGARDFLVPSRLHPGKFYALPQSPQLF 60
Query: 199 KQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNLFEEMIRVIFY 258
KQLLMV+ FDRY+QI +CFRDEDLR+DRQPEFTQID E SF+++E+I +L E +++ +F
Sbjct: 61 KQLLMVSGFDRYFQIARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKYVFK 120
Query: 259 KTLNIKLPNPFPVIEWSTAIKLYG 282
+ L ++L PFP + ++ A++ YG
Sbjct: 121 EVLGVELTTPFPRMTYAEAMERYG 144
Score = 234 bits (599), Expect = 8e-73
Identities = 74/136 (54%), Positives = 107/136 (78%)
Query: 431 WHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIINGWEI 490
+ LW+++FP+F++D+ ++ HHPFTAPK+ D + +PE ++AYDL++NG E+
Sbjct: 145 FKFLWIVDFPLFEWDEEEGRLVSAHHPFTAPKEEDLDLLEKDPEDARAQAYDLVLNGVEL 204
Query: 491 GGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMT 550
GGGSIRIHD +IQ+K+F++L + + + +FGFLL + KYGAPPHGGIA GLDRL+ ++T
Sbjct: 205 GGGSIRIHDPDIQEKVFEILGLSEEEAEEKFGFLLEAFKYGAPPHGGIALGLDRLVMLLT 264
Query: 551 GSKSIRDVIAFPKTQS 566
GS+SIRDVIAFPKTQ+
Sbjct: 265 GSESIRDVIAFPKTQN 280
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 241 bits (617), Expect = 1e-74
Identities = 109/209 (52%), Positives = 145/209 (69%), Gaps = 21/209 (10%)
Query: 121 TNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEG-ARDYLV 179
T LKYR L LR MQ NL+LR K+ +R+FLD + F+E+ETPIL+KSTPEG ARD+LV
Sbjct: 4 TRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDERGFLEVETPILTKSTPEGGARDFLV 63
Query: 180 PSRINPGEFFA----LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQP-EFTQID 234
PS +F+A LPQSPQL+KQLLMVA FDR +QI CFRDEDLR+DR P EFTQ+D
Sbjct: 64 PS-----KFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFTQLD 118
Query: 235 CETSFMNEEEIRNLFEEMIRVIF---------YKTLNIKLPNPFPVIEWSTAIKLYGSDK 285
E SF++ E++ +L E++I+ +F + L I+LP FP I ++ AI+ YGSDK
Sbjct: 119 LEMSFVDYEDVMDLTEDLIKYVFKKVLGKREELELLGIELP-EFPRITYAEAIERYGSDK 177
Query: 286 PDMCIKLIFTDLTNIMKDSDFKLFSKIAN 314
PD+ L D+T I K S+FK+F++ +
Sbjct: 178 PDLRFGLELKDVTEIFKGSEFKVFAEAGD 206
Score = 186 bits (474), Expect = 9e-54
Identities = 75/189 (39%), Positives = 111/189 (58%), Gaps = 31/189 (16%)
Query: 384 NKTEAQNGDIIFLGGDEK------NIVNNFMSALRIKIGYSDFGKRNNILNNKWHPLWVI 437
E ++ IF G + K ++V+ + ALR ++G + N +K +P++V
Sbjct: 182 FGLELKDVTEIFKGSEFKVFAEAGDVVDKALGALRSELG-----EENLGDKDKDNPVFVT 236
Query: 438 NFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIINGWEIGGGSIRI 497
+FP+F+ HPF PKD ++ +DL++NG EIGGGSIRI
Sbjct: 237 DFPLFE------------HPFYMPKDEDP--------PGLAERFDLVLNGGEIGGGSIRI 276
Query: 498 HDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRD 557
HD E Q+K F+ L +D + + +FGF L++LKYG PPHGGI GLDRL+ ++TG +SIR+
Sbjct: 277 HDPEEQRKRFEELGLDPEEAEEKFGFYLDALKYGMPPHGGIGLGLDRLVMLLTGLESIRE 336
Query: 558 VIAFPKTQS 566
VIAFPKT+
Sbjct: 337 VIAFPKTRK 345
>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 = 190 bits (485), Expect = 4e-58
Identities = 68/135 (50%), Positives = 95/135 (70%), Gaps = 1/135 (0%)
Query: 2 RTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAK 61
RTHYCG + E + Q ++LCGWV R+R+HGG+IFIDLRD G+VQ+VFDP + +++A+
Sbjct: 1 RTHYCGELRESHVGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAE 60
Query: 62 IIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQIDEK-NILEV 120
+RNE +Q+ GKV +RP T N L +G IE++ EL++LN + TLPF+ID+ N+ E
Sbjct: 61 KLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKAKTLPFEIDDDVNVSEE 120
Query: 121 TNLKYRVLYLRYKHM 135
LKYR L LR M
Sbjct: 121 LRLKYRYLDLRRPKM 135
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 181 bits (463), Expect = 3e-51
Identities = 92/310 (29%), Positives = 153/310 (49%), Gaps = 51/310 (16%)
Query: 1 MRTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIK-IYKI 59
M+ H +T +L + ++L GWVH R+ GGI F+ LRD +G++Q+V + +++
Sbjct: 2 MKRHLTSELTPELDGEEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFET 61
Query: 60 AKIIRNEFCLQIIGKVCSRPNKTNNTNLIS-GNIEILCRELKILNSSIT-LPFQIDEK-- 115
K ++ E + + G V N + G +E++ E+++LN + LP I K
Sbjct: 62 IKKLKRESVVSVTGTV--------KANPKAPGGVEVIPEEIEVLNKAEEPLPLDISGKVL 113
Query: 116 NILEVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETP-ILSKSTPEGA 174
L+ T L R L LR ++ ++R +V R+FL F EI TP I++ T GA
Sbjct: 114 AELD-TRLDNRFLDLRRPRVRAIFKIRSEVLRAFREFLYENGFTEIFTPKIVASGTEGGA 172
Query: 175 RDYLVPSRINPGEFFA---------LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSD 225
E F L QSPQL+KQ+++ A F+R ++I FR E+ +
Sbjct: 173 ------------ELFPIDYFEKEAYLAQSPQLYKQMMVGAGFERVFEIGPVFRAEEHNTS 220
Query: 226 RQ-PEFTQIDCETSFMN-EEEIRNLFEEMIRVIF----------YKTLNIKLP---NPFP 270
R E+T ID E F++ E++ +L E ++R ++ + L I+LP P P
Sbjct: 221 RHLNEYTSIDVEMGFIDDHEDVMDLLENLLRYMYEDVAENCEKELELLGIELPVPETPIP 280
Query: 271 VIEWSTAIKL 280
I + AI++
Sbjct: 281 RITYDEAIEI 290
Score = 88.7 bits (221), Expect = 9e-19
Identities = 40/109 (36%), Positives = 57/109 (52%), Gaps = 18/109 (16%)
Query: 457 PF-TAPKDGYEDFIITNPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKV--LNID 513
PF T P + +PE SK++DL+ G EI G RIH ++ + K LN +
Sbjct: 336 PFYTMPDED-------DPE--ISKSFDLLFRGLEITSGGQRIHRYDMLVESIKEKGLNPE 386
Query: 514 NKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
+ F F L + KYG PPHGG GL+RL + G ++IR+ + FP
Sbjct: 387 S------FEFYLEAFKYGMPPHGGFGLGLERLTMKLLGLENIREAVLFP 429
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 177 bits (452), Expect = 1e-49
Identities = 85/304 (27%), Positives = 139/304 (45%), Gaps = 33/304 (10%)
Query: 1 MRTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDI--KIYK 58
M+ Y +I + Q +++ GWVH KR+ G IIF+ LRD +G +Q V N + +++K
Sbjct: 2 MKRTYIKDIKPHVGGQEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFK 61
Query: 59 IAKIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSS-ITLPFQIDEKNI 117
K+ E + + G V + E+ ++++L + P E +
Sbjct: 62 AKKLTL-ESSVVVTGIV----KASPKA---PQGFELQVEKIEVLGEADPPYPIDKKEHSE 113
Query: 118 LEVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDY 177
LE T L R L LR +Q ++R + +R+F F E+ TPI++ S EG +
Sbjct: 114 LE-TLLDNRHLDLRTPKIQAVFKIRSSILRAIREFFYENGFTEVHTPIITASATEGGGE- 171
Query: 178 LVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDCE 236
L E + L QSPQL+K+ L A +R + I FR E + R EF +D E
Sbjct: 172 LFKVDYFDKEAY-LTQSPQLYKEALAAA-LERVFTIGPTFRAEKSNTRRHLSEFWMLDPE 229
Query: 237 TSFMNEEEIRNLFEEMIRVIF-------------YKTLNIKLPN----PFPVIEWSTAIK 279
+F + ++ +L EE+I+ +F N +L PFP I + AI+
Sbjct: 230 MAFADLNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRITYKEAIE 289
Query: 280 LYGS 283
+
Sbjct: 290 ILEE 293
Score = 78.0 bits (193), Expect = 3e-15
Identities = 38/136 (27%), Positives = 60/136 (44%), Gaps = 31/136 (22%)
Query: 433 PLWVINFPMFK---YDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIINGW- 488
P++V N+P Y + + + NP ++DL+ G
Sbjct: 321 PVFVTNYPKEIKPFYMRPDPD---------------------NPG--TVASFDLLAPGGG 357
Query: 489 EIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITI 548
EI GGS R HD ++ + K +D + + L+ KYG PPH G GL+RL+
Sbjct: 358 EIIGGSQREHDYDLLVERIKEKGLD----PESYEWYLDLRKYGMPPHAGFGLGLERLVMY 413
Query: 549 MTGSKSIRDVIAFPKT 564
+ G +IR+ I FP+
Sbjct: 414 ILGLDNIREAIPFPRD 429
>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 = 163 bits (415), Expect = 3e-46
Identities = 57/155 (36%), Positives = 86/155 (55%), Gaps = 12/155 (7%)
Query: 139 LRLRYKVTMEVRKFLDSKKFIEIETPILSKSTP-EGARDYLVPSRINPGEFFALPQSPQL 197
++R K+ +R F+D + F+E+ETP+L K T GAR +LV G + L SPQL
Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYN-ALGLDYYLRISPQL 59
Query: 198 FKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNLFEEMIRVIF 257
FK+ LMV DR ++I + FR+EDLR+ QPEFT +D E +F + E++ L E ++R +
Sbjct: 60 FKKRLMVGGLDRVFEINRNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLA 119
Query: 258 ----------YKTLNIKLPNPFPVIEWSTAIKLYG 282
Y PFP + + A++ YG
Sbjct: 120 REVLGVTAVTYGFELEDFGLPFPRLTYREALERYG 154
Score = 135 bits (342), Expect = 4e-36
Identities = 54/132 (40%), Positives = 76/132 (57%), Gaps = 20/132 (15%)
Query: 433 PLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIINGWEIGG 492
PL++ ++P H P +P D NPE + A+DL ING E+G
Sbjct: 156 PLFLTDYPAEM-----------HSPLASPHD-------VNPE--IADAFDLFINGVEVGN 195
Query: 493 GSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGS 552
GS R+HD +IQ ++F+ I+ + F F L +L+YG PPHGG+ G+DRLI +MT S
Sbjct: 196 GSSRLHDPDIQAEVFQEQGINKEAGMEYFEFYLKALEYGLPPHGGLGIGIDRLIMLMTNS 255
Query: 553 KSIRDVIAFPKT 564
+IR+VIAFPK
Sbjct: 256 PTIREVIAFPKM 267
>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 = 158 bits (400), Expect = 2e-42
Identities = 98/295 (33%), Positives = 146/295 (49%), Gaps = 27/295 (9%)
Query: 4 HYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDI--KIYKIAK 61
Y +I ++ Q ++ GWVH R+ GG+IF+ LRD GL+QI + ++K AK
Sbjct: 1 VYSADIKPEMDGQEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAK 60
Query: 62 IIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSS-ITLPFQIDEKNILEV 120
+ E + + G V K G EI+ +++++N + LP EK E+
Sbjct: 61 KLNLESVVAVRGIV-KIKEKA------PGGFEIIPTKIEVINEAKEPLPLDPTEKVPAEL 113
Query: 121 -TNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLV 179
T L YR L LR +Q R+R V VR+FL + FIE+ TP L S EG + L
Sbjct: 114 DTRLDYRFLDLRRPTVQAIFRIRSGVLESVREFLAEEGFIEVHTPKLVASATEGGTE-LF 172
Query: 180 PSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDCETS 238
P E F L QSPQL+KQ LM A F+R Y+I FR E+ + R E T ID E +
Sbjct: 173 PITYFEREAF-LGQSPQLYKQQLMAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDIEMA 231
Query: 239 FMNEEEIRNLFEEMIRVIF----------YKTLNIKLP---NPFPVIEWSTAIKL 280
F + ++ ++ EE++ +F +TL KL F + + AI++
Sbjct: 232 FEDHHDVMDILEELVVRVFEDVPERCAHQLETLEFKLEKPEGKFVRLTYDEAIEM 286
Score = 69.5 bits (170), Expect = 1e-12
Identities = 40/117 (34%), Positives = 57/117 (48%), Gaps = 18/117 (15%)
Query: 450 NWIARHHPF-TAPKDGYEDFIITNPEKIFSKAYDLIINGWEIGGGSIRIHD-AEIQKKI- 506
+W PF T P ED NPE SK++DL+ EI G+ RIH + ++I
Sbjct: 320 DWPTEIRPFYTMP---DED----NPE--ISKSFDLMYRDLEISSGAQRIHLHDLLVERIK 370
Query: 507 FKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPK 563
K LN + F L + YG PPH G G +R + + G K+IR+ + FP+
Sbjct: 371 AKGLNPEG------FKDYLEAFSYGMPPHAGWGLGAERFVMFLLGLKNIREAVLFPR 421
>gnl|CDD|239766 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal, anticodon
recognition domain of class 2b aminoacyl-tRNA
synthetases (aaRSs). This domain is a beta-barrel domain
(OB fold) involved in binding the tRNA anticodon
stem-loop. Class 2b aaRSs include the homodimeric
aspartyl-, asparaginyl-, and lysyl-tRNA synthetases
(AspRS, AsnRS, and LysRS). 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
protein synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Included in this group
are archeal and archeal-like AspRSs which are
non-discriminating and can charge both tRNAAsp and
tRNAAsn. E. coli cells have two isoforms of LysRSs (LysS
and LysU) encoded by two distinct genes, which are
differentially regulated. The cytoplasmic and the
mitochondrial isoforms of human LysRS are encoded by a
single gene. Yeast cytoplasmic and mitochondrial LysRSs
participate in mitochondrial import of cytoplasmic
tRNAlysCUU. In addition to their housekeeping role,
human LysRS may function as a signaling molecule that
activates immune cells. Tomato LysRS may participate in
a process possibly connected to conditions of
oxidative-stress conditions or heavy metal uptake. It is
known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging. AsnRS is immunodominant antigen of the
filarial nematode Brugia malayai and is of interest as a
target for anti-parasitic drug design. Human AsnRS has
been shown to be a pro-inflammatory chemokine which
interacts with CCR3 chemokine receptors on T cells,
immature dendritic cells and macrophages.
Length = 85
Score = 105 bits (264), Expect = 2e-27
Identities = 34/87 (39%), Positives = 55/87 (63%), Gaps = 5/87 (5%)
Query: 18 ISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKI-YKIAKIIRNEFCLQIIGKVC 76
++L GWVH +R+HGG+IFIDLRD +G+VQ+V + ++ ++ A+ +R E + + G V
Sbjct: 2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVV 61
Query: 77 SRPNKTNNTNLISGNIEILCRELKILN 103
RP T G IE+ EL++L+
Sbjct: 62 KRPEGNLAT----GEIELQAEELEVLS 84
>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 = 99.2 bits (248), Expect = 9e-23
Identities = 55/182 (30%), Positives = 84/182 (46%), Gaps = 29/182 (15%)
Query: 121 TNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVP 180
T L R L LR +Q R+R +V R+FL F E+ TP ++ + EG
Sbjct: 6 TLLDNRHLDLRTPKVQAIFRIRSEVLRAFREFLRENGFTEVHTPKITSTDTEG------G 59
Query: 181 SRINPGEFFA----LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDC 235
+ + +F L QSPQL+K++L+ A +R Y+I FR E + R EF ++
Sbjct: 60 AELFKVSYFGKPAYLAQSPQLYKEMLIAA-LERVYEIGPVFRAEKSNTRRHLSEFWMLEA 118
Query: 236 ETSFMN-EEEIRNLFEEMIRVIF----------------YKTLNIKLPNPFPVIEWSTAI 278
E +F+ E+ +L EE+I+ IF +K PFP I + AI
Sbjct: 119 EMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRITYDEAI 178
Query: 279 KL 280
+L
Sbjct: 179 EL 180
Score = 83.8 bits (208), Expect = 1e-17
Identities = 40/109 (36%), Positives = 58/109 (53%), Gaps = 13/109 (11%)
Query: 457 PFTAPKDGYEDFIITNPEKIFSKAYDLIINGW-EIGGGSIRIHDAEIQKKIFKVLNIDNK 515
PF D NPE +++DL++ G EI GGS RIHD + ++ K +D +
Sbjct: 224 PFYMKPDD------DNPET--VESFDLLMPGVGEIVGGSQRIHDYDELEERIKEHGLDPE 275
Query: 516 IVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPKT 564
F + L+ KYG PPHGG GL+RL+ + G +IR+ I FP+
Sbjct: 276 S----FEWYLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIREAILFPRD 320
>gnl|CDD|145868 pfam02938, GAD, GAD domain. This domain is found in some members
of the GatB and aspartyl tRNA synthetases.
Length = 94
Score = 90.0 bits (224), Expect = 7e-22
Identities = 32/93 (34%), Positives = 52/93 (55%), Gaps = 5/93 (5%)
Query: 316 KNGRIIGLKIPGGFSISRNEINYYTQFVKTYGAKGLTYIKIHKISKEFDGLKSPIIKYFN 375
K G + L +PGG +SR +I+ +F K +GAKGL +IK+ G PI K+
Sbjct: 7 KGGSVKALCVPGGAGLSRKQIDELERFAKEFGAKGLAWIKVEGG-----GHTGPIAKFLT 61
Query: 376 NLILEKIINKTEAQNGDIIFLGGDEKNIVNNFM 408
+E+++ + AQNGDI+ D++ +VN +
Sbjct: 62 EEEVEELLERVGAQNGDILLFVADKEKVVNKAL 94
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 97.1 bits (243), Expect = 2e-21
Identities = 69/307 (22%), Positives = 128/307 (41%), Gaps = 48/307 (15%)
Query: 9 ITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQI-VFDPNDIKIYKIAKIIRNEF 67
+ K + Q +++ GWV KR+ G I F+ LRD + Q+ V N + ++ K +
Sbjct: 10 LKGKYVGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGS 69
Query: 68 CLQIIGKVCSRPNKTNNTNLISGNIEILCRELKIL-NSSITLPFQIDEKNI---LEVTNL 123
+ + G V P E+ +++++ P Q +I E+
Sbjct: 70 SVIVTGTVVESPRA-------GQGYELQATKIEVIGEDPEDYPIQKKRHSIEFLREI--- 119
Query: 124 KYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARD-YLVPSR 182
L R +R+R + + +F + F+ ++TPI++ S EGA + + V +
Sbjct: 120 --AHLRPRTNKFGAVMRIRNTLAQAIHEFFNENGFVWVDTPIITASDCEGAGELFRVTTL 177
Query: 183 --INPGEFFA----LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDC 235
+FF L S QL+ + +A + Y FR E+ + R EF I+
Sbjct: 178 DLDFSKDFFGKEAYLTVSGQLYAEAYAMA-LGKVYTFGPTFRAENSNTRRHLAEFWMIEP 236
Query: 236 ETSFMNEEEIRNLFEEMIRVIFYKTLN-----------------IK-----LPNPFPVIE 273
E +F + E+ +L EEM++ + L I+ + +PFP I
Sbjct: 237 EMAFADLEDNMDLAEEMLKYVVKYVLENCPDDLEFLNRRVDKGDIERLENFIESPFPRIT 296
Query: 274 WSTAIKL 280
++ AI++
Sbjct: 297 YTEAIEI 303
Score = 60.5 bits (148), Expect = 9e-10
Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 5/86 (5%)
Query: 480 AYDLIINGW-EIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGI 538
A DL+ G EI GGS R ++ + K L ++ K + + L+ +YG+ PH G
Sbjct: 363 AMDLLAPGIGEIIGGSQREERLDVLEARIKELGLN----KEDYWWYLDLRRYGSVPHSGF 418
Query: 539 AFGLDRLITIMTGSKSIRDVIAFPKT 564
G +RL+ +TG +IRDVI FP+T
Sbjct: 419 GLGFERLVAYITGLDNIRDVIPFPRT 444
>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 = 96.7 bits (241), Expect = 3e-21
Identities = 78/307 (25%), Positives = 138/307 (44%), Gaps = 45/307 (14%)
Query: 5 YCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDI---------K 55
N + + +S+ G + +R+ G FI L+D +G +Q+ + +D+
Sbjct: 43 DLSNEELEDKNIEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEY 102
Query: 56 IYKIAKIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSI-TLPFQIDE 114
+ + II V P KT +G + + EL+IL ++ LP D+
Sbjct: 103 LLDLGDII----------GVTGYPFKTK-----TGELSVHVTELQILTKALRPLP---DK 144
Query: 115 KNILEVTNLKYRVLYLRY---KHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTP 171
+ L +YR YL ++ +R K+ +R+FLD + FIE+ETP+L P
Sbjct: 145 FHGLTDQETRYRQRYLDLIVNPDSRQTFLVRSKIIKAIRRFLDDRGFIEVETPMLQ-VIP 203
Query: 172 EGA--RDYLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPE 229
GA R ++ + + L +P+L+ + L+V F++ Y+I + FR+E + + PE
Sbjct: 204 GGANARPFITHHNALDMDLY-LRIAPELYLKRLIVGGFEKVYEIGRNFRNEGVDTTHNPE 262
Query: 230 FTQIDCETSFMNEEEIRNLFEEMIR----------VIFYKTLNIKLPNPFPVIEWSTAIK 279
FT I+ ++ + E++ +L E + + I Y L I PF I AIK
Sbjct: 263 FTMIEFYQAYADYEDLMDLTENLFKFLAQELLGTTKITYGELEIDFKKPFKRITMVEAIK 322
Query: 280 LYGSDKP 286
Y +
Sbjct: 323 KYDMETG 329
Score = 63.5 bits (155), Expect = 1e-10
Identities = 35/95 (36%), Positives = 55/95 (57%), Gaps = 6/95 (6%)
Query: 472 NPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFL----LNS 527
NPE F+ ++L I G EI ++D Q++ F+ + + + F+ + +
Sbjct: 398 NPE--FTDRFELFIAGKEIANAFSELNDPLDQRERFEQQVAEKEAGDDEAQFVDEDFVEA 455
Query: 528 LKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
L+YG PP GG+ G+DRL+ ++T SKSIRDVI FP
Sbjct: 456 LEYGMPPTGGLGIGIDRLVMLLTDSKSIRDVILFP 490
>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 = 95.1 bits (237), Expect = 8e-21
Identities = 69/302 (22%), Positives = 125/302 (41%), Gaps = 41/302 (13%)
Query: 12 KLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGL--VQIVFD-PNDIKIYKIAKIIRNEFC 68
K + +++ GWV KR+ IIF++L D + L +Q V + ++ ++++ K +
Sbjct: 13 KFVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSS 72
Query: 69 LQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQIDEKNILEVTNLKYRVL 128
+ + GKV P K L IE++ P Q E ++ + ++ + L
Sbjct: 73 VSVTGKVVESPGKGQPVELQVKKIEVVG-----EAEPDDYPLQKKEHSLEFLRDIAH--L 125
Query: 129 YLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVPSRINPG-- 186
LR + +R+R ++ + ++ F + PIL+ + EGA + S N
Sbjct: 126 RLRTNTLGAVMRVRNALSQAIHRYFQENGFTWVSPPILTSNDCEGAGELFRVSTGNIDFS 185
Query: 187 -EFFA----LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDCETSFM 240
+FF L S QL+ + +A + Y FR E + R EF I+ E +F
Sbjct: 186 QDFFGKEAYLTVSGQLYLETYALA-LSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFA 244
Query: 241 NEEEIRNLFEEMIRVIFYKTLN------------------IKLPN----PFPVIEWSTAI 278
N ++ L E +I+ I L +L N F I ++ AI
Sbjct: 245 NLNDLLQLAETLIKYIIKAVLENCSQELKFLEKNFDKDLIKRLENIINNKFARITYTDAI 304
Query: 279 KL 280
++
Sbjct: 305 EI 306
Score = 65.1 bits (159), Expect = 4e-11
Identities = 32/87 (36%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 479 KAYDLIINGW-EIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGG 537
A DL+ G EI GGS R D + + K + +D + L+ KYG+ PH G
Sbjct: 365 AAMDLLAPGIGEIIGGSEREDDLDKLENRMKEMGLDTD----ALNWYLDLRKYGSVPHSG 420
Query: 538 IAFGLDRLITIMTGSKSIRDVIAFPKT 564
G +RL+ +TG ++IRD I FP+T
Sbjct: 421 FGLGFERLLAYITGLENIRDAIPFPRT 447
>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 = 89.9 bits (223), Expect = 1e-20
Identities = 39/145 (26%), Positives = 63/145 (43%), Gaps = 14/145 (9%)
Query: 141 LRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARD----YLVPSRINPGEFFALPQSPQ 196
+R K+ ++R+F+ F E+ETPI+ + L+P E L + +
Sbjct: 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLE 60
Query: 197 LFKQLLMVAN----FDRYYQITKCFRDEDLRSD--RQPEFTQIDCETSFMNEEEIRNLFE 250
L V++ R +I FR+E R R EFTQ++ E F + E + FE
Sbjct: 61 PGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEV-FGEDGEEASEFE 119
Query: 251 EMIRVI--FYKTLNIKLPNPFPVIE 273
E+I + + L IKL V +
Sbjct: 120 ELIELTEELLRALGIKLD-IVFVEK 143
Score = 43.6 bits (103), Expect = 1e-04
Identities = 25/119 (21%), Positives = 36/119 (30%), Gaps = 39/119 (32%)
Query: 427 LNNKWHPLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIIN 486
L K ++V P G+E + +PE
Sbjct: 132 LGIKLDIVFVEKTPGEFSP-------------GGAGPGFE-IEVDHPEG----------R 167
Query: 487 GWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRL 545
G EIG G R + ++ FL +L+Y PP G GL+RL
Sbjct: 168 GLEIGSGGYRQDEQARAADLY---------------FLDEALEYRYPPTIGFGLGLERL 211
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 94.6 bits (236), Expect = 2e-20
Identities = 80/323 (24%), Positives = 140/323 (43%), Gaps = 67/323 (20%)
Query: 2 RTHYCGNITEKLLDQ----------VISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDP 51
RTH ++ EK D+ +S+ G + RN G F DL+D +G +Q+ +
Sbjct: 38 RTHTSADLREKYADKTKEELEALNIEVSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNK 97
Query: 52 NDIKIYKIAKIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQ 111
+++ + + IIG V KT +G + + EL++L+ S+ P
Sbjct: 98 DEVGEEVFEALFKKLDLGDIIG-VEGPLFKTK-----TGELSVSVEELRLLSKSL-RPLP 150
Query: 112 IDEKNILEVTNLKYRVLYLRYKHMQKNL------RLRYKVTMEVRKFLDSKKFIEIETPI 165
+ + ++YR RY + N R K+ +R+FLD + F+E+ETP+
Sbjct: 151 EKFHGLTDK-EIRYRQ---RYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPM 206
Query: 166 LSKSTPEGARD--------------YLVPSRINPGEFFALPQSPQLF-KQLLMVANFDRY 210
L + P GA YL RI P +L+ K+L+ V F+R
Sbjct: 207 L-QPIPGGAAARPFITHHNALDMDLYL---RIAP----------ELYLKRLI-VGGFERV 251
Query: 211 YQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNLFEEMIRVI---FYKTLNIKLPN 267
++I + FR+E + + PEFT ++ ++ + E++ +L EE+I+ + T +
Sbjct: 252 FEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKELAKEVNGTTKVTYGG 311
Query: 268 -------PFPVIEWSTAIKLYGS 283
PF I A+K Y
Sbjct: 312 QEIDFSKPFKRITMVDALKEYLG 334
Score = 65.3 bits (160), Expect = 4e-11
Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 12/99 (12%)
Query: 471 TNPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIF------KVL-NIDNKIVKTQFGF 523
+NP ++ ++L I G EI ++D Q++ F K + + + F
Sbjct: 403 SNPG--LTERFELFIGGKEIANAYSELNDPVDQRERFEAQVEEKEAGDDEAMELDEDF-- 458
Query: 524 LLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
+ +L+YG PP GG+ G+DRL+ ++T S SIRDVI FP
Sbjct: 459 -VEALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFP 496
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 94.8 bits (236), Expect = 2e-20
Identities = 83/284 (29%), Positives = 123/284 (43%), Gaps = 46/284 (16%)
Query: 7 GNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIV--FDPNDI--KIYKIAKI 62
++ E+L + + G VH R G F+ LR VQ V + + K AK
Sbjct: 73 SDLGEELAGSEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQ 132
Query: 63 IRNEFCLQIIGKVCSRPNKTNNTNLISG---NIEILCRELKILNSSI-TLPFQID----- 113
+ E + + G V S P K + G +EI R++ ++ ++ TLPF ++
Sbjct: 133 LSRESVVDVEGVV-SVPKKP-----VKGTTQQVEIQVRKIYCVSKALATLPFNVEDAARS 186
Query: 114 EKNI-------------LEVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIE 160
E I + T L RVL LR Q R++ +V R+FL SK F+E
Sbjct: 187 ESEIEKALQTGEQLVRVGQDTRLNNRVLDLRTPANQAIFRIQSQVCNLFREFLLSKGFVE 246
Query: 161 IETPILSKSTPEGAR-----DYLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITK 215
I TP L EG DY G+ L QSPQL KQ+ + +F R ++I
Sbjct: 247 IHTPKLIAGASEGGSAVFRLDYK-------GQPACLAQSPQLHKQMAICGDFRRVFEIGP 299
Query: 216 CFRDEDLRSDRQ-PEFTQIDCETSFMNE-EEIRNLFEEMIRVIF 257
FR ED + R EFT +D E E+ ++ +E+ IF
Sbjct: 300 VFRAEDSFTHRHLCEFTGLDLEMEIKEHYSEVLDVVDELFVAIF 343
Score = 71.3 bits (175), Expect = 5e-13
Identities = 33/87 (37%), Positives = 52/87 (59%), Gaps = 4/87 (4%)
Query: 477 FSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHG 536
+S ++D+ I G EI G+ R+HD E+ +K + ID K + T ++S +YGAPPHG
Sbjct: 441 YSNSFDVFIRGEEIISGAQRVHDPELLEKRAEECGIDVKTIST----YIDSFRYGAPPHG 496
Query: 537 GIAFGLDRLITIMTGSKSIRDVIAFPK 563
G GL+R++ + G +IR FP+
Sbjct: 497 GFGVGLERVVMLFCGLNNIRKTSLFPR 523
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 88.5 bits (220), Expect = 2e-18
Identities = 73/266 (27%), Positives = 117/266 (43%), Gaps = 49/266 (18%)
Query: 11 EKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIA--KIIRNEFC 68
E+L D +S+ G + KR G + F DLRD G +Q+ D + + + K+
Sbjct: 104 EELEDVSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDR 163
Query: 69 LQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSI-TLPFQIDEKNILEVTNLKYRV 127
I+G V P KT G + I ++L + LP D+ + L +YR
Sbjct: 164 GDIVG-VTGTPGKTKK-----GELSIFPTSFEVLTKCLLMLP---DKYHGLTDQETRYR- 213
Query: 128 LYLRYKHMQKN------LRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGA------- 174
RY + N R R K+ +R+FLD + F+E+ETP+L GA
Sbjct: 214 --QRYLDLIANPEVRDIFRTRAKIISYIRRFLDDRGFLEVETPML-NMIAGGAAARPFVT 270
Query: 175 ------RD-YLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ 227
D YL RI + +L + L+V F+R Y+I + FR+E + +
Sbjct: 271 HHNDLNMDLYL---RI----------ATELHLKRLVVGGFERVYEIGRQFRNEGISTRHN 317
Query: 228 PEFTQIDCETSFMNEEEIRNLFEEMI 253
PEFT + ++ + ++ L EEM+
Sbjct: 318 PEFTTCEFYQAYADYNDMMELTEEMV 343
Score = 56.2 bits (136), Expect = 3e-08
Identities = 22/38 (57%), Positives = 28/38 (73%)
Query: 525 LNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
+L+YG PP GG G+DRL+ ++T S SIRDVIAFP
Sbjct: 510 CTALEYGLPPTGGWGLGIDRLVMLLTDSASIRDVIAFP 547
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 84.0 bits (209), Expect = 5e-17
Identities = 79/293 (26%), Positives = 131/293 (44%), Gaps = 72/293 (24%)
Query: 2 RTHYCGNITEK----------LLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDP 51
RTH + K L+ +S+ G V KR G F L+D +G +Q+
Sbjct: 31 RTHTAAELRAKYDDKEKEELEELEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSK 90
Query: 52 NDI-----KIYKIAKIIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSI 106
+D+ + +K + IIG V KT +G + + EL +L S+
Sbjct: 91 DDVGEEALEAFKKLDL------GDIIG-VEGTLFKTK-----TGELSVKATELTLLTKSL 138
Query: 107 T-LPFQIDEK-NILEVTNLKYRVLYLRY------KHMQKNLRLRYKVTMEVRKFLDSKKF 158
LP +K + L +YR RY ++ R R K+ +R+FLD++ F
Sbjct: 139 RPLP----DKFHGLTDVETRYR---QRYVDLIVNPESRETFRKRSKIISAIRRFLDNRGF 191
Query: 159 IEIETPILSKSTPEG--AR---------D---YLVPSRINPGEFFALPQSPQLF-KQLLM 203
+E+ETP+L G AR D YL RI +P+L+ K+L+
Sbjct: 192 LEVETPMLQ-PIAGGAAARPFITHHNALDIDLYL---RI----------APELYLKRLI- 236
Query: 204 VANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNLFEEMIRVI 256
V F+R Y+I + FR+E + + PEFT ++ ++ + ++ +L EE+IR +
Sbjct: 237 VGGFERVYEIGRNFRNEGIDTRHNPEFTMLEFYQAYADYNDMMDLTEELIRHL 289
Score = 65.5 bits (161), Expect = 3e-11
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 24/95 (25%)
Query: 482 DLIINGWEIGGGSIRIHDAEIQKKIFK--------------VLNIDNKIVKTQFGFLLNS 527
+L I G EI ++D Q++ F+ ++ D FL +
Sbjct: 401 ELFIGGREIANAFSELNDPIDQRERFEAQVEAKEAGDDEAMFMDED---------FL-RA 450
Query: 528 LKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
L+YG PP GG+ G+DRL+ ++T S SIRDVI FP
Sbjct: 451 LEYGMPPTGGLGIGIDRLVMLLTDSPSIRDVILFP 485
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 78.2 bits (192), Expect = 3e-15
Identities = 66/283 (23%), Positives = 132/283 (46%), Gaps = 25/283 (8%)
Query: 14 LDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAKIIRNEFCLQIIG 73
L+ +S+ G + +R G F+ L+D G +Q+ + + + ++F +G
Sbjct: 64 LNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLP----EGVYNDQFKKWDLG 119
Query: 74 KVCSRPNKTNNTNLISGNIEILCRELKILNSSI-TLPFQIDEKNILEVTNLKYRVLYLRY 132
+ T +G + I C EL++L ++ LP D+ + L+ ++YR YL
Sbjct: 120 DIIGARGTLFKTQ--TGELSIHCTELRLLTKALRPLP---DKFHGLQDQEVRYRQRYLDL 174
Query: 133 ---KHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVPSRINPGEF- 188
++ +R K+ +R+F+ ++ F+E+ETP++ + P GA + N +
Sbjct: 175 IANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMM-QVIPGGASARPFITHHNALDLD 233
Query: 189 FALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNL 248
L +P+L+ + L+V F+R ++I + FR+E + PEFT ++ ++ + ++ L
Sbjct: 234 MYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIEL 293
Query: 249 FEEMIRVIFYKTL-NIKLP---------NPFPVIEWSTAIKLY 281
E + R + + L K+ PF + AIK Y
Sbjct: 294 TESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKY 336
Score = 58.9 bits (142), Expect = 4e-09
Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 8/96 (8%)
Query: 472 NPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFL-----LN 526
NPE + ++ I G EIG G ++DAE Q + F+ ++ K +
Sbjct: 407 NPE--ITDRFEFFIGGREIGNGFSELNDAEDQAERFQE-QVNAKAAGDDEAMFYDEDYVT 463
Query: 527 SLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
+L+YG PP G+ G+DR+I + T S +IRDVI FP
Sbjct: 464 ALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFP 499
>gnl|CDD|239811 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal,
anticodon recognition domain of the type found in the
homodimeric non-discriminating (ND) Pyrococcus
kodakaraensis aspartyl-tRNA synthetase (AspRS). This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. P. kodakaraensis
AspRS is a class 2b aaRS. aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation 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. P. kodakaraensis
ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of
the enzymes in this group may be discriminating, based
on the presence of homologs of asparaginyl-tRNA
synthetase (AsnRS) in their completed genomes.
Length = 108
Score = 69.7 bits (171), Expect = 2e-14
Identities = 35/115 (30%), Positives = 59/115 (51%), Gaps = 10/115 (8%)
Query: 4 HYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVF--DPNDIKIYKIAK 61
HY IT +L + +++ GWVH R+ GGI F+ LRD G+VQ+ D +++K +
Sbjct: 1 HYSAEITPELDGEEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVR 60
Query: 62 IIRNEFCLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSIT-LPFQIDEK 115
+ E + + G V + P N +EI+ E+++L+ + T LP K
Sbjct: 61 KLSRESVISVTGTVKAEPKAPN-------GVEIIPEEIEVLSEAKTPLPLDPTGK 108
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This
family contains OB-fold domains that bind to nucleic
acids. The family includes the anti-codon binding domain
of lysyl, aspartyl, and asparaginyl -tRNA synthetases
(See pfam00152). Aminoacyl-tRNA synthetases catalyze the
addition of an amino acid to the appropriate tRNA
molecule EC:6.1.1.-. This family also includes part of
RecG helicase involved in DNA repair. Replication factor
A is a heterotrimeric complex, that contains a subunit
in this family. This domain is also found at the
C-terminus of bacterial DNA polymerase III alpha chain.
Length = 75
Score = 65.7 bits (161), Expect = 1e-13
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 18 ISLCGWVHRK-RNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAKIIRNEFCLQIIGKVC 76
+++ G V R+ G + F+ LRD TG +Q+V + K+AK ++ + + GKV
Sbjct: 1 VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKE--EAEKLAKKLKEGDVVLVTGKVK 58
Query: 77 SRPNKTNNTNLISGNIEILCRELKIL 102
RP G +E++ E+++L
Sbjct: 59 KRPG---------GELELVVEEIEVL 75
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 71.2 bits (175), Expect = 2e-13
Identities = 42/195 (21%), Positives = 77/195 (39%), Gaps = 22/195 (11%)
Query: 123 LKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARD-----Y 177
L+ ++ + +K L+++ + R+FLD + F+E+ PI+S ST
Sbjct: 14 LRMSWKHISSEKYRKVLKVQSSILRYTREFLDGRGFVEVLPPIISPSTDPLMGLGSDLPV 73
Query: 178 LVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQP---EFTQID 234
S G + L S L KQL + + + ++ FR E + D EFTQ+D
Sbjct: 74 KQISIDFYGVEYYLADSMILHKQL-ALRMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLD 132
Query: 235 CETSFMNEEEIRNLFEEMIRVIFYKTLNI-------------KLPNPFPVIEWSTAIKLY 281
E + +E+ +L E++I+ + + L L PF I A+++
Sbjct: 133 IEIEGADLDEVMDLIEDLIKYLVKELLEEHEDELEFFGRDLPHLKRPFKRITHKEAVEIL 192
Query: 282 GSDKPDMCIKLIFTD 296
+
Sbjct: 193 NEEGCRGIDLEELGS 207
Score = 35.8 bits (83), Expect = 0.056
Identities = 32/134 (23%), Positives = 57/134 (42%), Gaps = 28/134 (20%)
Query: 433 PLWVINFPMFKYDKINNNWIARHHPFTAPKDGYEDFIITNPEKIFSKAYDLII-NGW-EI 490
P W+I+ P +R F +D ++ N YDL++ G+ E
Sbjct: 220 PFWIIDIP----------KGSR--EFYDREDPERPGVLRN--------YDLLLPEGYGEA 259
Query: 491 GGGSIRIHDAE-IQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIM 549
G R ++ E I ++I + + + ++ + L K G P G G++RL +
Sbjct: 260 VSGGEREYEYEEIVERIRE-----HGVDPEKYKWYLEMAKEGPLPSAGFGIGVERLTRYI 314
Query: 550 TGSKSIRDVIAFPK 563
G + IR+V FP+
Sbjct: 315 CGLRHIREVQPFPR 328
>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 = 71.1 bits (175), Expect = 2e-13
Identities = 41/149 (27%), Positives = 69/149 (46%), Gaps = 29/149 (19%)
Query: 139 LRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGA-------------RD-YLVPSRIN 184
+R K+ +RKFLD + F+E+ETP+L GA D YL RI
Sbjct: 8 FIVRSKIISYIRKFLDDRGFLEVETPMLQ-PIAGGAAARPFITHHNALDMDLYL---RI- 62
Query: 185 PGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEE 244
+P+L+ + L+V F+R Y+I + FR+E + PEFT I+ ++ + +
Sbjct: 63 ---------APELYLKRLIVGGFERVYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYND 113
Query: 245 IRNLFEEMIRVIFYKTLNIKLPNPFPVIE 273
+ +L E++ + K K + E
Sbjct: 114 MMDLTEDLFSGLVKKING-KTKIEYGGKE 141
Score = 63.8 bits (156), Expect = 6e-11
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 6/87 (6%)
Query: 481 YDLIINGWEIGGGSIRIHDAEIQKKIFK--VLNIDNKIVKTQF---GFLLNSLKYGAPPH 535
++L I G EI ++D Q++ F+ + + F+ +L+YG PP
Sbjct: 240 FELFICGKEIANAYTELNDPFDQRERFEEQAKQKEAGDDEAMMMDEDFV-TALEYGMPPT 298
Query: 536 GGIAFGLDRLITIMTGSKSIRDVIAFP 562
GG+ G+DRL+ ++T S SIRDVI FP
Sbjct: 299 GGLGIGIDRLVMLLTDSNSIRDVILFP 325
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 70.0 bits (171), Expect = 1e-12
Identities = 70/263 (26%), Positives = 118/263 (44%), Gaps = 21/263 (7%)
Query: 11 EKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQ-IVFDPNDIKIYKIAKI--IRNEF 67
+L+D+ + + V R G + F+ LRD + VQ + D+ I I I E
Sbjct: 74 PELVDKTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTES 133
Query: 68 CLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSI-TLPFQIDEKNILEV------ 120
+ + VC +T+ +IE+ +++ + S+ TLPF +++ + E
Sbjct: 134 IVDVEATVCKVEQPITSTS--HSDIELKVKKIHTVTESLRTLPFTLEDASRKESDEGAKV 191
Query: 121 ---TNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDY 177
T L R + LR RL+ +V R+FL F EI +P + + EG +
Sbjct: 192 NFDTRLNSRWMDLRTPASGAIFRLQSRVCQYFRQFLIDSDFCEIHSPKIINAPSEGGANV 251
Query: 178 LVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQ-PEFTQIDCE 236
N F L QSPQL+KQ+++ + R +++ FR E+ + R EF +D E
Sbjct: 252 FKLEYFN--RFAYLAQSPQLYKQMVLQGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVE 309
Query: 237 TSFMNEE--EIRNLFEEMIRVIF 257
+NE E+ +L E + IF
Sbjct: 310 MR-INEHYYEVLDLAESLFNYIF 331
Score = 63.1 bits (153), Expect = 2e-10
Identities = 31/87 (35%), Positives = 50/87 (57%), Gaps = 4/87 (4%)
Query: 477 FSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHG 536
F+ +YD+ I G EI G+ RIHD ++ K+LN+D +K ++S + GA PHG
Sbjct: 461 FTNSYDMFIRGEEISSGAQRIHDPDLLLARAKMLNVDLTPIKE----YVDSFRLGAWPHG 516
Query: 537 GIAFGLDRLITIMTGSKSIRDVIAFPK 563
G GL+R++ + G ++R FP+
Sbjct: 517 GFGVGLERVVMLYLGLSNVRLASLFPR 543
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 69.3 bits (169), Expect = 3e-12
Identities = 37/145 (25%), Positives = 75/145 (51%), Gaps = 11/145 (7%)
Query: 117 ILEVTNLKYRVLYLRYKHMQKN------LRLRYKVTMEVRKFLDSKKFIEIETPIL-SKS 169
+L+ ++KYR R+ M N ++ R+ + +R + + + F+E+ETP+L + +
Sbjct: 208 VLQDNDVKYR---YRFTDMMTNPCVIETIKKRHVMLQALRDYFNERNFVEVETPVLHTVA 264
Query: 170 TPEGARDYLVPSRINPGEFFALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPE 229
+ A+ ++ N + F L +P+L + +V +R Y+I K FR+ED PE
Sbjct: 265 SGANAKSFVTHHNANAMDLF-LRVAPELHLKQCIVGGMERIYEIGKVFRNEDADRSHNPE 323
Query: 230 FTQIDCETSFMNEEEIRNLFEEMIR 254
FT + ++ E++ + E++ R
Sbjct: 324 FTSCEFYAAYHTYEDLMPMTEDIFR 348
Score = 47.3 bits (112), Expect = 2e-05
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 14/95 (14%)
Query: 477 FSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFG---------FLLNS 527
++ ++L +NG E ++D Q F+ ++V Q G L S
Sbjct: 471 LAERFELFVNGIEYCNAYSELNDPHEQYHRFQ-----QQLVDRQGGDEEAMPLDETFLKS 525
Query: 528 LKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
L+ G PP G G+DR + ++T S +IRD I FP
Sbjct: 526 LQVGLPPTAGWGMGIDRALMLLTNSSNIRDGIIFP 560
>gnl|CDD|239818 cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal,
anticodon recognition domain of the type found in human
and Saccharomyces cerevisiae cytoplasmic
asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai
AsnRs and, in various putative bacterial AsnRSs. This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. The enzymes in
this group are homodimeric class2b aminoacyl-tRNA
synthetases (aaRSs). 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. AsnRS is
immunodominant antigen of the filarial nematode B.
malayai and of interest as a target for anti-parasitic
drug design. Human AsnRS has been shown to be a
pro-inflammatory chemokine which interacts with CCR3
chemokine receptors on T cells, immature dendritic cells
and macrophages.
Length = 84
Score = 60.3 bits (147), Expect = 1e-11
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 18 ISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAKIIRNEFCLQIIGKVCS 77
+ + GWVHR R+ ++F+ LRD TG +Q V + + AK + E +++ G+V
Sbjct: 2 VKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEV-- 59
Query: 78 RPNKTNNTNLISGNIEILCRELKIL 102
+ G E+ L+I+
Sbjct: 60 --KEDPRAKQAPGGYELQVDYLEII 82
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 57.7 bits (140), Expect = 1e-08
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 2 RTHYCGNITEKLLDQVISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFD 50
TH + + +S+ G V R R++GG++F DLRD++G +Q++ D
Sbjct: 638 PTHTVAEALDAPTGEEVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLD 686
Score = 56.9 bits (138), Expect = 2e-08
Identities = 37/126 (29%), Positives = 66/126 (52%), Gaps = 18/126 (14%)
Query: 138 NLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEG---ARDYLVPSRINPGEFFA---- 190
LR R V VR+ L ++ F+E+ETPIL G AR ++ + IN A
Sbjct: 769 LLRARSAVVRAVRETLVARGFLEVETPIL--QQVHGGANARPFV--THIN-----AYDMD 819
Query: 191 --LPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEIRNL 248
L +P+L+ + L V +R +++ + FR+E + + PEFT ++ + + + +R+L
Sbjct: 820 LYLRIAPELYLKRLCVGGVERVFELGRNFRNEGVDATHNPEFTLLEAYQAHADYDTMRDL 879
Query: 249 FEEMIR 254
E+I+
Sbjct: 880 TRELIQ 885
Score = 53.4 bits (129), Expect = 3e-07
Identities = 18/38 (47%), Positives = 28/38 (73%), Gaps = 1/38 (2%)
Query: 525 LNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
L +L+Y PP GG+ G+DRL+ ++TG +SIR+ + FP
Sbjct: 1052 LQALEYAMPPTGGLGMGVDRLVMLLTG-RSIRETLPFP 1088
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 55.0 bits (133), Expect = 3e-08
Identities = 29/102 (28%), Positives = 46/102 (45%), Gaps = 9/102 (8%)
Query: 137 KNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARDYLVPSR---INPGEFFALP- 192
NL R + +R+F + +E+ETP LS + +L P + PG P
Sbjct: 14 DNLLKRAAIIAAIRRFFAERGVLEVETPALSVAP--VTDIHLHPFETEFLGPGGAKGKPL 71
Query: 193 ---QSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFT 231
SP+ + L+ A +Q+ K FR+E++ PEFT
Sbjct: 72 WLHTSPEYHMKRLLAAGSGPIFQLGKVFRNEEMGRLHNPEFT 113
Score = 50.8 bits (122), Expect = 9e-07
Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 13/90 (14%)
Query: 481 YDLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFG--------FLLNSLKYGA 532
++L G E+ G + DA Q++ F+ DNK + + G L +L
Sbjct: 234 FELYYKGIELANGFHELTDAAEQRRRFE---QDNK-ERARRGLPQYPIDEDFLAALAR-M 288
Query: 533 PPHGGIAFGLDRLITIMTGSKSIRDVIAFP 562
PP G+A G DRL+ + G++SI DVIAFP
Sbjct: 289 PPCSGVALGFDRLVMLALGAESIDDVIAFP 318
>gnl|CDD|239817 cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition domain
of lysyl-tRNA synthetases (LysRS). These enzymes are
homodimeric class 2b 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.
Included in this group are E. coli LysS and LysU. These
two isoforms of LysRS are encoded by distinct genes
which are differently regulated. Eukaryotes contain 2
sets of aaRSs, both of which encoded by the nuclear
genome. One set concerns with cytoplasmic protein
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Saccharomyces
cerevisiae cytoplasmic and mitochondrial LysRSs have
been shown to participate in the mitochondrial import of
the only nuclear-encoded tRNA of S. cerevisiae
(tRNAlysCUU). The gene for human LysRS encodes both the
cytoplasmic and the mitochondrial isoforms of LysRS. In
addition to their housekeeping role, human lysRS may
function as a signaling molecule that activates immune
cells and tomato LysRS may participate in a
root-specific process possibly connected to conditions
of oxidative-stress conditions or heavy metal uptake. It
is known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging.
Length = 108
Score = 50.6 bits (122), Expect = 6e-08
Identities = 32/117 (27%), Positives = 55/117 (47%), Gaps = 16/117 (13%)
Query: 18 ISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAKIIRNEFCLQ---IIGK 74
+S+ G + KR G + F DL+D +G +Q+ + +D+ + + L IIG
Sbjct: 2 VSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKL---LDLGDIIG- 57
Query: 75 VCSRPNKTNNTNLISGNIEILCRELKILNSSIT-LPFQIDEKNILEVTNLKYRVLYL 130
V P KT +G + I +E +L+ S+ LP ++ + L +YR YL
Sbjct: 58 VTGTPFKTK-----TGELSIFVKEFTLLSKSLRPLP---EKFHGLTDVETRYRQRYL 106
>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 = 53.3 bits (129), Expect = 1e-07
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 483 LIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFG-------FLLNSLKYGAPPH 535
L I G E+ G + DA Q++ F+ DN + K L +L+ G P
Sbjct: 209 LYIKGLELANGFHELTDAAEQRRRFE---ADNALRKALGLPRYPLDERFLAALEAGLPEC 265
Query: 536 GGIAFGLDRLITIMTGSKSIRDVIA 560
G+A G+DRL+ + G+ SI DV+A
Sbjct: 266 SGVALGVDRLLMLALGADSIDDVLA 290
Score = 49.5 bits (119), Expect = 2e-06
Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 152 FLDSKKFIEIETPILSKST-PEGARDYLVPSRINP---GEFFALPQSPQLF-KQLLMVAN 206
F + +E+ETP+LS + + D + P G L SP+ K+LL A
Sbjct: 1 FFAERGVLEVETPLLSPAPVTDPHLDAFATEFVGPDGQGRPLYLQTSPEYAMKRLL-AAG 59
Query: 207 FDRYYQITKCFRDEDLRSDR-QPEFT 231
+QI K FR+ + R R PEFT
Sbjct: 60 SGPIFQICKVFRNGE-RGRRHNPEFT 84
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 50.4 bits (120), Expect = 2e-06
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 489 EIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITI 548
E+ GGS R E + L ++ K + + L+ +YG+ PH G G +RL+
Sbjct: 488 ELIGGSQREERLEYLEARLDELKLN----KESYWWYLDLRRYGSVPHAGFGLGFERLVQF 543
Query: 549 MTGSKSIRDVIAFPKT 564
TG +IRD I FP+
Sbjct: 544 ATGIDNIRDAIPFPRV 559
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 49.2 bits (117), Expect = 4e-06
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 482 DLIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQ-FGF---LLNSLKYGAPPHGG 537
++ I G E+ ++D QK+ F D + + F F SL+YG PP GG
Sbjct: 495 EMFICGKEVLNAYTELNDPFKQKECFSAQQKDREKGDAEAFQFDAAFCTSLEYGLPPTGG 554
Query: 538 IAFGLDRLITIMTGSKSIRDVIAFPKTQSA 567
+ G+DR+ +T I+DVI FP + A
Sbjct: 555 LGLGIDRITMFLTNKNCIKDVILFPTMRPA 584
Score = 48.5 bits (115), Expect = 7e-06
Identities = 43/152 (28%), Positives = 75/152 (49%), Gaps = 12/152 (7%)
Query: 90 GNIEILCRELKILNSSI-TLPFQIDEKNILEVTNLKYRVLYLRY---KHMQKNLRLRYKV 145
G + I +E IL+ + LP + K+ T ++YR YL + + R K+
Sbjct: 204 GELSIFPKETIILSPCLHMLPMKYGLKD----TEIRYRQRYLDLMINESTRSTFITRTKI 259
Query: 146 TMEVRKFLDSKKFIEIETPILS-KSTPEGARDYLVPSRINPGEFFALPQSPQLFKQLLMV 204
+R FL+ + FIE+ETP ++ + AR ++ + + L + +L ++L+V
Sbjct: 260 INYLRNFLNDRGFIEVETPTMNLVAGGANARPFITHHNDLDLDLY-LRIATELPLKMLIV 318
Query: 205 ANFDRYYQITKCFRDEDLRSDRQPEFTQIDCE 236
D+ Y+I K FR+E + + PEFT CE
Sbjct: 319 GGIDKVYEIGKVFRNEGIDNTHNPEFTS--CE 348
>gnl|CDD|239814 cd04319, PhAsnRS_like_N, PhAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Pyrococcus
horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. The archeal
enzymes in this group are homodimeric class2b
aminoacyl-tRNA synthetases (aaRSs). 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.
Length = 103
Score = 45.2 bits (107), Expect = 5e-06
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 18 ISLCGWVHRKRNHGGIIFIDLRDYTGLVQIVFDPNDIK-IYKIAKIIRNEFCLQIIGKVC 76
++L GWV+RKR G FI LRD TG+VQ VF + + Y+ AK + E + + G V
Sbjct: 2 VTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVK 61
Query: 77 SRPNKTNNTNLISGNIEIL 95
+ P + +EI+
Sbjct: 62 ADPRAPGGAEVHGEKLEII 80
>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 = 46.4 bits (111), Expect = 5e-06
Identities = 32/147 (21%), Positives = 55/147 (37%), Gaps = 25/147 (17%)
Query: 141 LRYKVTMEVRKFLDSKKFIEIETPILSKS--------TPEGARDYLVPSRINPGEFFAL- 191
LR + +R+ L + E++TPIL + + + + GE L
Sbjct: 1 LRNALENFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLR 60
Query: 192 -----PQSPQLFKQLLMVANFD-RYYQITKCFRDEDLRSDRQP-----EFTQIDCETSFM 240
+ ++L + YQI CFR E R+ EFTQ+D E F
Sbjct: 61 PTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYE--ARPRRGLGRVREFTQVDAE-IFG 117
Query: 241 NEEEIRNLFEEMIRVI--FYKTLNIKL 265
E+ EE++++ + L +
Sbjct: 118 TPEQSEEELEELLKLAEEILQDLGLPY 144
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 48.0 bits (115), Expect = 7e-06
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 7/103 (6%)
Query: 135 MQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGAR------DYLVPSRINPGEF 188
NL R K+ E+R+F + +E+ETPILS++T ++ P
Sbjct: 1 SIPNLLKRAKIIAEIRRFFADRGVLEVETPILSQATVTDIHLVPFETRFVGPGASQGKTL 60
Query: 189 FALPQSPQLFKQLLMVANFDRYYQITKCFRDEDLRSDRQPEFT 231
+ L SP+ + L+ A +QI K FR+E+ PEFT
Sbjct: 61 W-LMTSPEYHMKRLLAAGSGPIFQICKSFRNEEAGRYHNPEFT 102
Score = 45.7 bits (109), Expect = 3e-05
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 20/93 (21%)
Query: 478 SKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLN------------IDNKIVKTQFGFLL 525
++ +++ G E+ G + DA Q++ F+ N ID L+
Sbjct: 222 AERFEVYFKGIELANGFHELTDAREQRQRFEQDNRKRAARGLPQQPIDE--------NLI 273
Query: 526 NSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDV 558
+L+ G P G+A G+DRLI + G++SI +V
Sbjct: 274 AALEAGLPDCSGVALGVDRLIMLALGAESISEV 306
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 46.9 bits (111), Expect = 2e-05
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 9/109 (8%)
Query: 458 FTAPKDGYEDFIITNPEKIFSKAYDLIING-WEIGGGSIRIHDAEIQKKIF--KVLNIDN 514
+ PKD ++ N ++ A D+++ E+ GGS R + E K+ K LN+++
Sbjct: 477 YNYPKDLKAFYMKLNEDQKTVAAMDVLVPKIGEVIGGSQREDNLERLDKMIKEKKLNMES 536
Query: 515 KIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPK 563
Q K+G+ PH G G +RLI ++TG +I+D I FP+
Sbjct: 537 YWWYRQL------RKFGSHPHAGFGLGFERLIMLVTGVDNIKDTIPFPR 579
Score = 45.4 bits (107), Expect = 7e-05
Identities = 50/207 (24%), Positives = 96/207 (46%), Gaps = 24/207 (11%)
Query: 12 KLLDQVISLCGWVHRKRNHGG--IIFIDLRDYTGL--VQIVFDPNDIKIYKIAKIIRNEF 67
K +DQ+I++CGW R GG F++L D + +QI+ D I+ Y+
Sbjct: 78 KYIDQIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIENYEKLLKCGVGC 136
Query: 68 CLQIIGKVCSRPNKTNNTN-LISGNIEILCRELKILNSSI------TLPFQIDEKN---- 116
C + GK+ P + N L+ N+E+ ++ I N I + + +KN
Sbjct: 137 CFRFTGKLIISPVQNENKKGLLKENVELALKDNSIHNFEIYGENLDPQKYPLSKKNHGKE 196
Query: 117 -ILEVTNLKYRVLYLRYKHMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGAR 175
+ EV +L+ R ++ +R+R + + F S+ F+ I TP+++ S EG
Sbjct: 197 FLREVAHLRPRSYFI-----SSVIRIRNALAIATHLFFQSRGFLYIHTPLITTSDCEGGG 251
Query: 176 D-YLVPSRINP-GEFFALPQSPQLFKQ 200
+ + V + + ++ A+P+ + K+
Sbjct: 252 EMFTVTTLLGEDADYRAIPRVNKKNKK 278
>gnl|CDD|239816 cd04321, ScAspRS_mt_like_N, ScAspRS_mt_like_N: N-terminal,
anticodon recognition domain of the type found in
Saccharomyces cerevisiae mitochondrial (mt)
aspartyl-tRNA synthetase (AspRS). This domain is a
beta-barrel domain (OB fold) involved in binding the
tRNA anticodon stem-loop. The enzymes in this fungal
group are homodimeric class2b aminoacyl-tRNA synthetases
(aaRSs). 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 protein synthesis,
whereas the other exclusively with mitochondrial protein
synthesis. Mutations in the gene for S. cerevisiae
mtAspRS result in a "petite" phenotype typical for a
mutation in a nuclear gene that results in a
non-functioning mitochondrial protein synthesis system.
Length = 86
Score = 41.5 bits (98), Expect = 6e-05
Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 18 ISLCGWVHRKRN-HGGIIFIDLRDYTG-LVQIVFDPNDIKIYKIAKIIRNEFCLQIIGKV 75
++L GW+ RK + F DLRD G ++Q+V + + K I E +Q+ GK+
Sbjct: 2 VTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLV-STAKKDAFSLLKSITAESPVQVRGKL 60
Query: 76 CSRPNKTNNTNLISGNIEILCRELKILNS 104
+ K++ N E++ +++ LN+
Sbjct: 61 QLKEAKSSEKN---DEWELVVDDIQTLNA 86
>gnl|CDD|239813 cd04318, EcAsnRS_like_N, EcAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia
coli asparaginyl-tRNA synthetase (AsnRS) and, in
Arabidopsis thaliana and Saccharomyces cerevisiae
mitochondrial (mt) AsnRS. This domain is a beta-barrel
domain (OB fold) involved in binding the tRNA anticodon
stem-loop. The enzymes in this group are homodimeric
class2b aminoacyl-tRNA synthetases (aaRSs). 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 protein synthesis,
whereas the other exclusively with mitochondrial
protein synthesis. S. cerevisiae mtAsnRS can charge
E.coli tRNA with asparagines. Mutations in the gene for
S. cerevisiae mtAsnRS has been found to induce a
"petite" phenotype typical for a mutation in a nuclear
gene that results in a non-functioning mitochondrial
protein synthesis system.
Length = 82
Score = 40.6 bits (96), Expect = 1e-04
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 18 ISLCGWVHRKRNHGGIIFIDLRDYTGL--VQIVFDPNDIKIYKIAKIIRNEFCLQIIGKV 75
+++ GWV R+ I FI+L D + L +Q+V D ++ +K + +++ G +
Sbjct: 2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDK-ELTNFKEILKLSTGSSIRVEGVL 60
Query: 76 CSRPNKTNNTNLISGNIEIL 95
P L + IE+L
Sbjct: 61 VKSPGAKQPFELQAEKIEVL 80
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 41.8 bits (98), Expect = 0.001
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 516 IVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPKT 564
+ + Q+ + L+ ++G H G + G + ++ TG +RD I FP++
Sbjct: 579 LPREQYEWYLDLRRHGTVKHSGFSLGFELMVLFATGLPDVRDAIPFPRS 627
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 41.1 bits (96), Expect = 0.002
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 489 EIGGGSIRIHDAEIQKKIFKVLNIDNKIVKTQFGFLLNSLKYGAPPHGGIAFGLDRLITI 548
E+ GGS R ++ K+ + + + + + + L+ +YG H G G +R+I
Sbjct: 495 ELIGGSQREERYDVIKQRIEEMGLPIE----PYEWYLDLRRYGTVKHCGFGLGFERMILF 550
Query: 549 MTGSKSIRDVIAFPK 563
TG +IRDVI FP+
Sbjct: 551 ATGIDNIRDVIPFPR 565
Score = 38.1 bits (88), Expect = 0.013
Identities = 42/183 (22%), Positives = 80/183 (43%), Gaps = 16/183 (8%)
Query: 12 KLLDQVISLCGWVH--RKRNHGGIIFIDLRDYT--GLVQIVFDPNDIKIYKIAKIIRNEF 67
L Q + + GWV R++ G F+++ D + +Q++ D + +Y ++ ++
Sbjct: 47 GLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSS---LYDLSTLVATGT 103
Query: 68 CLQIIGKVCSRPNKTNNTNLISGNIEILCRELKILNSSITLPFQIDEKNILEVTNLKYRV 127
C+ + G + P I ++E + + + LP K L + L+ V
Sbjct: 104 CVTVDGVLKVPPEGKGTKQKIELSVEKVIDVGTVDPTKYPLP-----KTKLTLEFLR-DV 157
Query: 128 LYLRYK--HMQKNLRLRYKVTMEVRKFLDSKKFIEIETPILSKSTPEGARD-YLVPSRIN 184
L+LR + + R+R + F F+ I TPI++ S EGA + + V + IN
Sbjct: 158 LHLRSRTNSISAVARIRNALAFATHSFFQEHSFLYIHTPIITTSDCEGAGEMFQVTTLIN 217
Query: 185 PGE 187
E
Sbjct: 218 YTE 220
>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 = 37.0 bits (86), Expect = 0.018
Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 8/51 (15%)
Query: 209 RYYQITKCFRDE-----DLRSDRQPEFTQIDCETSFMNEEEIRNLFEEMIR 254
R QI CFR E L R EF Q++ F EE E +
Sbjct: 90 RLDQIGPCFRHEPSGRRGL--MRVREFRQVEYVV-FGEPEEAEEERREWLE 137
>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 = 0.055
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 209 RYYQITKCFRDEDLRSDRQPEFTQIDCE 236
+ Y I FR E + R EF Q+ E
Sbjct: 84 KLYYIGPVFRYERPQKGRYREFYQVGVE 111
>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 = 34.4 bits (80), Expect = 0.14
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 9/60 (15%)
Query: 209 RYYQITKCFRDEDLRSDRQPEFTQIDCET----SFMNEEEIRNLFEEMIRVIFYKTLNIK 264
+ Y I FR E + R +F Q E S + + EI L E K L IK
Sbjct: 99 KLYYIGPMFRYERPQKGRYRQFHQFGVEVIGSDSPLADAEIIALAAE-----ILKALGIK 153
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 34.2 bits (79), Expect = 0.23
Identities = 42/175 (24%), Positives = 63/175 (36%), Gaps = 43/175 (24%)
Query: 137 KNLRLRYKVTMEVRKFLDSKKFIEIETPILSKST---PEGARD------YLVPSRINPGE 187
+NL Y VR L S + E++TP+L+ G D +L S
Sbjct: 223 RNLLEDY-----VRTKLRSYGYQEVKTPVLADLELWELSGHWDNYKEDMFLTES---DDR 274
Query: 188 FFAL-----PQSPQLFKQLLMV--ANFDRYYQITKCFRDE------DLRSDRQPEFTQID 234
+AL P +FK L R + +R E L R FTQ D
Sbjct: 275 EYALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVR--GFTQDD 332
Query: 235 ----CETSFMNEEEIRNLFEEMIRVIFYKTLNIKLPNPFPVIEWSTAIKLYGSDK 285
C + ++E + + E ++ V YK ++ ST K GSD+
Sbjct: 333 AHIFCTPDQI-KDEFKGILELILEV--YKDFGFT----DYEVKLSTRPKFIGSDE 380
>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 = 33.3 bits (77), Expect = 0.24
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 209 RYYQITKCFRDEDLRSDRQPEFTQIDCETSFMNEEEI--RNL---FEEMIRVIFYKTLNI 263
+ + I + FR + + + PEF Q++ + +E + +L EE +R F + +
Sbjct: 104 KIFSIGRVFRRDQVDATHLPEFHQVEG---LVVDENVSFADLKGVLEEFLRKFFGFEVKV 160
Query: 264 KL-PNPFPVIEWST 276
+ P+ FP E S
Sbjct: 161 RFRPSYFPFTEPSA 174
>gnl|CDD|235553 PRK05672, dnaE2, error-prone DNA polymerase; Validated.
Length = 1046
Score = 33.7 bits (78), Expect = 0.33
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 18 ISLCGWV-HRKR--NHGGIIFIDLRDYTGLVQIVFDPNDIKIYKIAKIIRNEFCLQIIGK 74
+ + G V HR+R G+ F+ L D TG+V +V P + + + L + G+
Sbjct: 956 VRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWERQR--REALGARLLLVRGR 1013
Query: 75 V 75
V
Sbjct: 1014 V 1014
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 33.0 bits (76), Expect = 0.43
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 209 RYYQITKCFRDEDLRSDRQP-----EFTQIDCETSFMNEEEIRNLFEEMIRVIFYKTLNI 263
+ YQI FRDE + R EF D + +EE+ +E+M+ Y + +
Sbjct: 131 KLYQIQSKFRDE--KRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKML--DAYSRIFL 186
Query: 264 KLPNPF-PVIEWSTAI 278
+LP F PV I
Sbjct: 187 RLPLIFGPVPADEGFI 202
>gnl|CDD|181225 PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional.
Length = 254
Score = 32.0 bits (73), Expect = 0.62
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 447 INNNWIARHHPFTA-PKDGYEDFIITNPEKIF 477
INN I R HPFT P+ + D I N +F
Sbjct: 91 INNAGIQRRHPFTEFPEQEWNDVIAVNQTAVF 122
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 32.2 bits (74), Expect = 0.76
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 209 RYYQITKCFRDEDLRSDRQPEFTQIDCET 237
+ Y FR E + R +F Q E
Sbjct: 103 KLYYFGPVFRYERPQKGRYRQFYQFGVEV 131
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 28.6 bits (64), Expect = 2.0
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 2 RTHYCGNITEKLLDQVI-----SLCGWVHRKR 28
RT YC NI +K+ + SLCG V R R
Sbjct: 5 RTIYCTNIDKKVTQSDVKLFFESLCGEVSRLR 36
>gnl|CDD|128624 smart00329, BPI2, BPI/LBP/CETP C-terminal domain. Bactericidal
permeability-increasing protein (BPI) /
Lipopolysaccharide-binding protein (LBP) / Cholesteryl
ester transfer protein (CETP) C-terminal domain.
Length = 202
Score = 30.4 bits (69), Expect = 2.2
Identities = 30/165 (18%), Positives = 57/165 (34%), Gaps = 31/165 (18%)
Query: 132 YKHMQKNLRLRYKVTME----VRKFLDSKKFIEIETPILSKSTPEG----ARDYLVPSRI 183
Q+ L+ +T + KFL + P +++ P+ L P R+
Sbjct: 18 LFVYQQAGALKLTITDDMLPKESKFLLTTCCFGTLVPEVAEQYPDSTLQLEISVLSPPRV 77
Query: 184 N--PGE-----------FFALPQSP--QLFKQLLMVANFDRYYQITKCFRDEDLRSDRQP 228
PG F LP S LF + + N F+ + L + +
Sbjct: 78 TLQPGGATVYIHASVKVFAILPDSSRASLF-LMSVDTNV----SAKSSFKTKKLLGELKL 132
Query: 229 EFTQIDCETSF---MNEEEIRNLFEEMIRVIFYKTLNIKLPNPFP 270
+ Q++ + S + E + +L ++ + +N KL P
Sbjct: 133 DKLQVELKHSNVGGFDAELLEDLLNYLVPAVLLPKVNEKLRRGVP 177
>gnl|CDD|224592 COG1678, COG1678, Putative transcriptional regulator
[Transcription].
Length = 194
Score = 29.9 bits (68), Expect = 2.8
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 25/93 (26%)
Query: 483 LIINGWEIGGGSIRIHDAEIQKKIFKVLNIDNKI------------VKTQFGFLLNSLKY 530
LIIN R + ++ + L ++ KI V+ GF+L+S Y
Sbjct: 47 LIIN---------RPSETLTLAELLEKLKLEIKILRLPKPVYLGGPVQRDRGFVLHSSDY 97
Query: 531 GAPPHGGIAFGLDRLITIMTGSKSIRDVIAFPK 563
GA + +T S + + IA K
Sbjct: 98 GAFQS-SLRVSDGLA---LTTSLDVLEAIAAGK 126
>gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated.
Length = 405
Score = 30.0 bits (68), Expect = 3.7
Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 537 GIAFGLDRLITIMTGSKSIRDVIAFPKTQSAQCLLTNAP-SIVDEKQLNELNILYKK 592
G A G +RLI +T KS D AF Q A N P + E+ LYKK
Sbjct: 248 GFAVGNERLIAALTRVKSYLDYGAFTPIQVAATAALNGPQDCIA-----EMRELYKK 299
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 29.7 bits (68), Expect = 4.7
Identities = 10/31 (32%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 209 RYYQITKCFRDEDLR--SDRQPEFTQIDCET 237
+ Y I FR E R R +F Q E
Sbjct: 100 KLYYIGPMFRYE--RPQKGRYRQFHQFGVEV 128
>gnl|CDD|163628 cd07385, MPP_YkuE_C, Bacillus subtilis YkuE and related proteins,
C-terminal metallophosphatase domain. YkuE is an
uncharacterized Bacillus subtilis protein with a
C-terminal metallophosphatase domain and an N-terminal
twin-arginine (RR) motif. An RR-signal peptide derived
from the Bacillus subtilis YkuE protein can direct
Tat-dependent secretion of agarase in Streptomyces
lividans. This is an indication that YkuE is transported
by the Bacillus subtilis Tat (Twin-arginine
translocation) pathway machinery. YkuE belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 29.2 bits (66), Expect = 5.1
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 379 LEKIINKTEAQNGDIIFLGGD 399
LE+++ K A D++ L GD
Sbjct: 21 LERLVEKINALKPDLVVLTGD 41
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 29.7 bits (67), Expect = 5.1
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 207 FDRYYQITKCFRDEDLRSDRQPEFTQIDCE----TSFMNEEEIRNLFEEMIR 254
F RY +I K FRD ++ R EF Q D + S M E E+ ++ E+ R
Sbjct: 100 FKRY-EIGKVFRDGPIKQGRFREFIQCDVDIVGVESVMAEAELMSMAFELFR 150
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 29.2 bits (66), Expect = 7.6
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 11/75 (14%)
Query: 452 IARHHPFTAPKDGYEDFIITNPEKIFSKAYDLIINGWEIGGGSIRIHDAEIQKKIFKVLN 511
+A + E N EK KA +L+ E+ ++Q KI K
Sbjct: 166 VAASLQLKEKDELQEVLETVNIEKRLKKALELLKKELEL---------LKLQNKITK--K 214
Query: 512 IDNKIVKTQFGFLLN 526
++ K+ KTQ + L
Sbjct: 215 VEEKMEKTQREYYLR 229
>gnl|CDD|216132 pfam00814, Peptidase_M22, Glycoprotease family. The Peptidase M22
proteins are part of the HSP70-actin superfamily. The
region represented here is an insert into the fold and
is not found in the rest of the family (beyond the
Peptidase M22 family). Included in this family are the
Rhizobial NodU proteins and the HypF regulator. This
region also contains the histidine dyad believed to
coordinate the metal ion and hence provide catalytic
activity. Interestingly the histidines are not well
conserved, and there is a lack of experimental evidence
to support peptidase activity as a general property of
this family. There also appear to be instances of this
domain outside of the HSP70-actin superfamily.
Length = 271
Score = 28.5 bits (64), Expect = 9.6
Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 18/83 (21%)
Query: 301 MKDSDFKLFSKI-------ANMKNGRIIGLKIPGGFSISRNEINYYTQFVKTYGAKGLTY 353
KD +++ + A K R++GL PGG +I + +F
Sbjct: 121 AKDGRYEILGETLDDAAGEAFDKVARLLGLPYPGGPAIEKLAKEGAFEF---------PR 171
Query: 354 IKIHKISKEFDGLKSPIIKYFNN 376
K S F GLK+ +++
Sbjct: 172 PKGMDFS--FSGLKTAVLRLIEK 192
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
0.323 0.141 0.422
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,273,115
Number of extensions: 3201829
Number of successful extensions: 3003
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2882
Number of HSP's successfully gapped: 134
Length of query: 595
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 493
Effective length of database: 6,413,494
Effective search space: 3161852542
Effective search space used: 3161852542
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 62 (27.8 bits)