RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8863
(442 letters)
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 690 bits (1784), Expect = 0.0
Identities = 235/444 (52%), Positives = 318/444 (71%), Gaps = 18/444 (4%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFK 60
MLKRVMGK SF LQD SG +IQLY+S + +G+ FK D+GDIIG +GTLFK
Sbjct: 64 MLKRVMGKASFATLQDGSG-----RIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFK 118
Query: 61 TNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQI 120
T TGELS+K + L L+TKSLRPLP+KF L++ E +YR RY+DLI+N +R+ F+KR++I
Sbjct: 119 TKTGELSVKATELTLLTKSLRPLPDKFHGLTDVETRYRQRYVDLIVNPESRETFRKRSKI 178
Query: 121 ISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLIIG 180
IS+IR F++ F+EVETP+L GGA A+PFITHHN+L++ ++LRIAPELYLKRLI+G
Sbjct: 179 ISAIRRFLDNRGFLEVETPMLQPIAGGAAARPFITHHNALDIDLYLRIAPELYLKRLIVG 238
Query: 181 GFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTTK 240
GF +++EI +NFRNEGI RHNPEFTM+EFY AY +Y +M TE++I+ + +GTTK
Sbjct: 239 GFERVYEIGRNFRNEGIDTRHNPEFTMLEFYQAYADYNDMMDLTEELIRHLAQAVLGTTK 298
Query: 241 IDYQGRLLDFSKSFEKLTIIEAIKKYTP-QYNEIDLQNKLFLKSELK-KINPKFNQKKIL 298
+ YQG +DF F++LT+++AIK+YT ++++ + L EL ++ + K++
Sbjct: 299 VTYQGTEIDFGPPFKRLTMVDAIKEYTGVDFDDMTDEEARALAKELGIEVEKSWGLGKLI 358
Query: 299 NNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELFIIGNE 358
N LFEE E KL PT+IT+YP EISPLA++ E+ +TERFELFI G E
Sbjct: 359 N---------ELFEEFVEPKLIQPTFITDYPVEISPLAKRHR-EDPGLTERFELFIGGRE 408
Query: 359 IANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDR 418
IAN FSELNDP +Q RF+ Q++ K + E + + D D++ ALEYGMPP G GIG+DR
Sbjct: 409 IANAFSELNDPIDQRERFEAQVEAKEAGDDE-AMFMDEDFLRALEYGMPPTGGLGIGIDR 467
Query: 419 LIMLLTNSKNIRDVILFPHLRNEN 442
L+MLLT+S +IRDVILFP +R E
Sbjct: 468 LVMLLTDSPSIRDVILFPLMRPEK 491
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 598 bits (1543), Expect = 0.0
Identities = 231/445 (51%), Positives = 312/445 (70%), Gaps = 16/445 (3%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTD-FKNYDIGDIIGAKGTLF 59
M R MGK SF LQD SG KIQLY++ + +G+ ++ FK D+GDIIG +G LF
Sbjct: 71 MTIRNMGKASFADLQDGSG-----KIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLF 125
Query: 60 KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQ 119
KT TGELS+ V L+L++KSLRPLP KF L+++EI+YR RY+DLI+N +R+ F KR++
Sbjct: 126 KTKTGELSVSVEELRLLSKSLRPLPEKFHGLTDKEIRYRQRYLDLIVNPESRQTFIKRSK 185
Query: 120 IISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLII 179
II +IR F++ F+EVETP+L PGGA A+PFITHHN+L+M ++LRIAPELYLKRLI+
Sbjct: 186 IIRAIREFLDDRGFLEVETPMLQPIPGGAAARPFITHHNALDMDLYLRIAPELYLKRLIV 245
Query: 180 GGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTT 239
GGF ++FEI +NFRNEGI HNPEFTM+EFY AY +Y LM TE++IK++ + GTT
Sbjct: 246 GGFERVFEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKELAKEVNGTT 305
Query: 240 KIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKINPKFNQKKILN 299
K+ Y G+ +DFSK F+++T+++A+K+Y + DL + K KK ++
Sbjct: 306 KVTYGGQEIDFSKPFKRITMVDALKEYLGV-DFDDLFDDEEAKELAKKH-----GIEVEK 359
Query: 300 NLKKDI--LQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELFIIGN 357
+ L LFEE E KL PT++T++P EISPLA++ + N +TERFELFI G
Sbjct: 360 YGTWGLGHLLNELFEELVEAKLIQPTFVTDHPVEISPLAKR-HRSNPGLTERFELFIGGK 418
Query: 358 EIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVD 417
EIAN +SELNDP +Q RF+ Q++ K + E + D D++ ALEYGMPP G GIG+D
Sbjct: 419 EIANAYSELNDPVDQRERFEAQVEEKEAGDDE-AMELDEDFVEALEYGMPPTGGLGIGID 477
Query: 418 RLIMLLTNSKNIRDVILFPHLRNEN 442
RL+MLLTNS +IRDVILFP +R E
Sbjct: 478 RLVMLLTNSPSIRDVILFPAMRPEK 502
>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 = 524 bits (1352), Expect = 0.0
Identities = 225/448 (50%), Positives = 304/448 (67%), Gaps = 24/448 (5%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYT-DFKNYDIGDIIGAKGTLF 59
M +R MGK +FI LQD SG +IQLY++ + + ++ Y D D+GDIIG G F
Sbjct: 63 MARRSMGKATFITLQDESG-----QIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPF 117
Query: 60 KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQ 119
KT TGELS+ V+ L+++TK+LRPLP+KF L++QE +YR RY+DLI+N ++R+ F R++
Sbjct: 118 KTKTGELSVHVTELQILTKALRPLPDKFHGLTDQETRYRQRYLDLIVNPDSRQTFLVRSK 177
Query: 120 IISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLII 179
II +IR F++ F+EVETP+L PGGA A+PFITHHN+L+M ++LRIAPELYLKRLI+
Sbjct: 178 IIKAIRRFLDDRGFIEVETPMLQVIPGGANARPFITHHNALDMDLYLRIAPELYLKRLIV 237
Query: 180 GGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTT 239
GGF K++EI +NFRNEG+ HNPEFTMIEFY AY +Y LM TE + K + + +GTT
Sbjct: 238 GGFEKVYEIGRNFRNEGVDTTHNPEFTMIEFYQAYADYEDLMDLTENLFKFLAQELLGTT 297
Query: 240 KIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYN-----EIDLQNKLFLKSELKKINPKFNQ 294
KI Y +DF K F+++T++EAIKKY + D + L ++ + +
Sbjct: 298 KITYGELEIDFKKPFKRITMVEAIKKYDMETGIDFDDLKDFETAKALAKKIGIEVAEKSL 357
Query: 295 KK--ILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFEL 352
ILN LFE+ E L PT+IT+YP EISPLA++ N N T+RFEL
Sbjct: 358 TLGHILNE---------LFEQFLEHTLIQPTFITHYPAEISPLAKR-NPSNPEFTDRFEL 407
Query: 353 FIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGC 412
FI G EIAN FSELNDP +Q RF+ Q+ + E + + + D D++ ALEYGMPP G
Sbjct: 408 FIAGKEIANAFSELNDPLDQRERFEQQVA-EKEAGDDEAQFVDEDFVEALEYGMPPTGGL 466
Query: 413 GIGVDRLIMLLTNSKNIRDVILFPHLRN 440
GIG+DRL+MLLT+SK+IRDVILFP +R
Sbjct: 467 GIGIDRLVMLLTDSKSIRDVILFPAMRP 494
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 489 bits (1262), Expect = e-170
Identities = 197/446 (44%), Positives = 283/446 (63%), Gaps = 20/446 (4%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNY----DIGDIIGAKG 56
M KR GK++F L+D G KIQLY + + + +F+ D GDI+G G
Sbjct: 118 MAKRAFGKLAFYDLRDDGG-----KIQLYADKKRLDLDE-EEFEKLHSLVDRGDIVGVTG 171
Query: 57 TLFKTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKK 116
T KT GELSI +S +++TK L LP+K+ L++QE +YR RY+DLI N R +F+
Sbjct: 172 TPGKTKKGELSIFPTSFEVLTKCLLMLPDKYHGLTDQETRYRQRYLDLIANPEVRDIFRT 231
Query: 117 RTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKR 176
R +IIS IR F++ F+EVETP+L+ GGA A+PF+THHN LNM ++LRIA EL+LKR
Sbjct: 232 RAKIISYIRRFLDDRGFLEVETPMLNMIAGGAAARPFVTHHNDLNMDLYLRIATELHLKR 291
Query: 177 LIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCI 236
L++GGF +++EI + FRNEGIS RHNPEFT EFY AY +Y +M+ TE+M+ ++ +
Sbjct: 292 LVVGGFERVYEIGRQFRNEGISTRHNPEFTTCEFYQAYADYNDMMELTEEMVSGMVKELT 351
Query: 237 GTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQN---KLFLKSELKKINPKFN 293
G+ KI Y G +DF+ F ++++I +++ T DL++ +L + +K + K
Sbjct: 352 GSYKIKYHGIEIDFTPPFRRISMISLVEEATGIDFPADLKSDEANAYLIAACEKFDVKCP 411
Query: 294 QKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELF 353
+ L + LFEE E L PT++ ++P E+SPLA K + +TERFELF
Sbjct: 412 PPQTTGRLLNE-----LFEEFLEETLVQPTFVLDHPVEMSPLA-KPHRSKPGLTERFELF 465
Query: 354 IIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCG 413
I G E+AN FSEL DP +Q RF+ Q+ N + E + D D+ ALEYG+PP G G
Sbjct: 466 INGRELANAFSELTDPVDQRERFEEQVKQHNAGDDE-AMALDEDFCTALEYGLPPTGGWG 524
Query: 414 IGVDRLIMLLTNSKNIRDVILFPHLR 439
+G+DRL+MLLT+S +IRDVI FP ++
Sbjct: 525 LGIDRLVMLLTDSASIRDVIAFPAMK 550
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 484 bits (1246), Expect = e-169
Identities = 233/440 (52%), Positives = 316/440 (71%), Gaps = 13/440 (2%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTD-FKNYDIGDIIGAKGTLF 59
M +R+MGK SF+ LQD G +IQLY++ + + + +Y D FK +D+GDIIGA+GTLF
Sbjct: 75 MTRRIMGKASFVTLQDVGG-----RIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLF 129
Query: 60 KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQ 119
KT TGELSI + L+L+TK+LRPLP+KF L +QE++YR RY+DLI N+ +R+ F R++
Sbjct: 130 KTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSK 189
Query: 120 IISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLII 179
I+++IR FM FMEVETP++ PGGA A+PFITHHN+L++ M+LRIAPELYLKRL++
Sbjct: 190 ILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVV 249
Query: 180 GGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTT 239
GGF ++FEIN+NFRNEGIS RHNPEFTM+E Y AY +Y L++ TE + + + + +GTT
Sbjct: 250 GGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTT 309
Query: 240 KIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKINPKFNQKKILN 299
K+ Y + DF K FEKLT+ EAIKKY P+ + DL N K+ + I + L
Sbjct: 310 KVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLG 369
Query: 300 NLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELFIIGNEI 359
+ +I F+E E L PT+IT YP E+SPLAR++++ N IT+RFE FI G EI
Sbjct: 370 RIVTEI-----FDEVAEAHLIQPTFITEYPAEVSPLARRNDV-NPEITDRFEFFIGGREI 423
Query: 360 ANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDRL 419
NGFSELND E+Q+ RF+ Q++ K + E + +YD DY+ ALEYG+PP +G GIG+DR+
Sbjct: 424 GNGFSELNDAEDQAERFQEQVNAKAAGDDE-AMFYDEDYVTALEYGLPPTAGLGIGIDRM 482
Query: 420 IMLLTNSKNIRDVILFPHLR 439
IML TNS IRDVILFP +R
Sbjct: 483 IMLFTNSHTIRDVILFPAMR 502
>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 = 463 bits (1193), Expect = e-163
Identities = 168/334 (50%), Positives = 224/334 (67%), Gaps = 7/334 (2%)
Query: 107 NENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFL 166
NE R+ F R++IIS IR F++ F+EVETP+L GGA A+PFITHHN+L+M ++L
Sbjct: 1 NEEVRQTFIVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGAAARPFITHHNALDMDLYL 60
Query: 167 RIAPELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEK 226
RIAPELYLKRLI+GGF +++EI +NFRNEGI HNPEFTMIEFY AY +Y +M TE
Sbjct: 61 RIAPELYLKRLIVGGFERVYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYNDMMDLTED 120
Query: 227 MIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKS-EL 285
+ ++ G TKI+Y G+ LDF+ F+++T+++A+K+ T ID + EL
Sbjct: 121 LFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALKEKTG----IDFPELDLEQPEEL 176
Query: 286 KKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNN 345
K+ K ++KI L LFEE E L PT+I ++P EISPLA++ N
Sbjct: 177 AKLLAKLIKEKIEKPRTLGKLLDKLFEEFVEPTLIQPTFIIDHPVEISPLAKRHR-SNPG 235
Query: 346 ITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYG 405
+TERFELFI G EIAN ++ELNDP +Q RF+ Q K + E + D D++ ALEYG
Sbjct: 236 LTERFELFICGKEIANAYTELNDPFDQRERFEEQAKQKEAGDDE-AMMMDEDFVTALEYG 294
Query: 406 MPPASGCGIGVDRLIMLLTNSKNIRDVILFPHLR 439
MPP G GIG+DRL+MLLT+S +IRDVILFP +R
Sbjct: 295 MPPTGGLGIGIDRLVMLLTDSNSIRDVILFPAMR 328
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 384 bits (988), Expect = e-123
Identities = 161/455 (35%), Positives = 252/455 (55%), Gaps = 46/455 (10%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNY-DIGDIIGAKGTLF 59
+ R G + F L+D SG ++Q+ + + + DF+ D+GD++ GT+
Sbjct: 661 LRIRDYGGVLFADLRDWSG-----ELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMG 715
Query: 60 KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQ 119
+ G LS+ V+S +L K LRPLP+K++ L++ E + R RY+DL +N R + + R+
Sbjct: 716 TSRNGTLSLLVTSWRLAGKCLRPLPDKWKGLTDPEARVRQRYLDLAVNPEARDLLRARSA 775
Query: 120 IISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLII 179
++ ++R + F+EVETPIL GGA A+PF+TH N+ +M ++LRIAPELYLKRL +
Sbjct: 776 VVRAVRETLVARGFLEVETPILQQVHGGANARPFVTHINAYDMDLYLRIAPELYLKRLCV 835
Query: 180 GGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTT 239
GG ++FE+ +NFRNEG+ HNPEFT++E Y A+ +Y + T ++I+ G
Sbjct: 836 GGVERVFELGRNFRNEGVDATHNPEFTLLEAYQAHADYDTMRDLTRELIQNAAQAAHGAP 895
Query: 240 KI---DYQGRL--LDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKI------ 288
+ D G L +D S + +T+ +A+ + + EID L +EL+K+
Sbjct: 896 VVMRPDGDGVLEPVDISGPWPVVTVHDAVSEALGE--EIDPDTPL---AELRKLCDAAGI 950
Query: 289 --NPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNI 346
++ ++ L + L E+ T PT+ T++PT +SPL R + +
Sbjct: 951 PYRTDWDAGAVVLELYEH-----LVEDRTTF----PTFYTDFPTSVSPLTRPHR-SDPGL 1000
Query: 347 TERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEING-----ELSSYYDTDYIHA 401
ER++L G E+ +SEL DP EQ R Q L G EL D D++ A
Sbjct: 1001 AERWDLVAWGVELGTAYSELTDPVEQRRRLTEQ-SLL-AAGGDPEAMEL----DEDFLQA 1054
Query: 402 LEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
LEY MPP G G+GVDRL+MLLT ++IR+ + FP
Sbjct: 1055 LEYAMPPTGGLGMGVDRLVMLLTG-RSIRETLPFP 1088
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 339 bits (873), Expect = e-114
Identities = 111/356 (31%), Positives = 183/356 (51%), Gaps = 18/356 (5%)
Query: 92 NQEIKYRHRYIDLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAK 151
++E + ++RY+DL + K R++II +IR F+++ F+EVETPIL A+
Sbjct: 1 SEETRLKYRYLDLRRPKMQA-NLKLRSKIIKAIREFLDERGFLEVETPILTKSTPEGGAR 59
Query: 152 PFITHHNSLNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNEGI-SPRHNPEFTMIEF 210
F+ + +L +P+LY + L++ GF+++F+I FR+E + + RH PEFT ++
Sbjct: 60 DFLVPSKFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFTQLDL 119
Query: 211 YAAYTNYIWLMKFTEKMIKKIIMDCIGTTKIDYQGRLLDFS-KSFEKLTIIEAIKKYTPQ 269
++ +Y +M TE +IK + +G + LL F ++T EAI++Y
Sbjct: 120 EMSFVDYEDVMDLTEDLIKYVFKKVLGKREE---LELLGIELPEFPRITYAEAIERYGS- 175
Query: 270 YNEIDLQNKLFLKSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKL-----WNPTY 324
++ DL+ L LK + + D L E E L NP +
Sbjct: 176 -DKPDLRFGLELKDVTEIFKGSEFKVFAEAGDVVDKALGALRSELGEENLGDKDKDNPVF 234
Query: 325 ITNYPTEISPLARKSNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKN 384
+T++P P + + + ERF+L + G EI G ++DPEEQ RF+
Sbjct: 235 VTDFPLFEHPFYMPKDEDPPGLAERFDLVLNGGEIGGGSIRIHDPEEQRKRFEEL----- 289
Query: 385 EINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFPHLRN 440
++ E + Y+ AL+YGMPP G G+G+DRL+MLLT ++IR+VI FP R
Sbjct: 290 GLDPEEAEEKFGFYLDALKYGMPPHGGIGLGLDRLVMLLTGLESIREVIAFPKTRK 345
>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 = 283 bits (727), Expect = 5e-94
Identities = 124/327 (37%), Positives = 183/327 (55%), Gaps = 60/327 (18%)
Query: 114 FKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPELY 173
FK R++II +IR FM+ F+EVETP+L GGA A+PF+ +N+L + +LRI+P+L+
Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLF 60
Query: 174 LKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIM 233
KRL++GG +++FEIN+NFRNE + RH PEFTM++ A+ +Y +++ TE++++ +
Sbjct: 61 KKRLMVGGLDRVFEINRNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLAR 120
Query: 234 DCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKINPKFN 293
+ +G T + Y L DF F +LT EA+++Y
Sbjct: 121 EVLGVTAVTYGFELEDFGLPFPRLTYREALERYGQ------------------------- 155
Query: 294 QKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEI-SPLARKSNIENNNITERFEL 352
P ++T+YP E+ SPLA + N I + F+L
Sbjct: 156 ----------------------------PLFLTDYPAEMHSPLASP-HDVNPEIADAFDL 186
Query: 353 FIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGC 412
FI G E+ NG S L+DP+ Q+ F+ Q IN E Y Y+ ALEYG+PP G
Sbjct: 187 FINGVEVGNGSSRLHDPDIQAEVFQEQG-----INKEAGMEYFEFYLKALEYGLPPHGGL 241
Query: 413 GIGVDRLIMLLTNSKNIRDVILFPHLR 439
GIG+DRLIML+TNS IR+VI FP +R
Sbjct: 242 GIGIDRLIMLMTNSPTIREVIAFPKMR 268
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 294 bits (754), Expect = 3e-93
Identities = 157/462 (33%), Positives = 257/462 (55%), Gaps = 40/462 (8%)
Query: 4 RVMGKISFIMLQDTSGPDSNG-KIQLYISNEIIGKNLYTDF-----KNYDIGDIIGAKGT 57
R +GKI F+ ++ SNG ++Q+ +G++ + + +GDIIGA G
Sbjct: 120 RDIGKIIFVTIR------SNGNELQVVGQ---VGEHFTREDLKKLKVSLRVGDIIGADGV 170
Query: 58 LFKTNTGELSIKVSSLKLIT------KSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTR 111
+ GELS+ S + +++ + + P F L + ++KYR+R+ D++ N
Sbjct: 171 PCRMQRGELSVAASRMLILSPYVCTDQVVCPNLRGFTVLQDNDVKYRYRFTDMMTNPCVI 230
Query: 112 KVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPE 171
+ KKR ++ ++R + + +F+EVETP+LH GA AK F+THHN+ M +FLR+APE
Sbjct: 231 ETIKKRHVMLQALRDYFNERNFVEVETPVLHTVASGANAKSFVTHHNANAMDLFLRVAPE 290
Query: 172 LYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKI 231
L+LK+ I+GG +I+EI K FRNE HNPEFT EFYAAY Y LM TE + +++
Sbjct: 291 LHLKQCIVGGMERIYEIGKVFRNEDADRSHNPEFTSCEFYAAYHTYEDLMPMTEDIFRQL 350
Query: 232 IMDCIGTTKIDYQ-------GRLLDFSKSFEKLTIIEAIKKYT----PQYNEIDLQNKL- 279
M GTT + +D K F ++++ + I++ + P NE++ +
Sbjct: 351 AMRVNGTTVVQIYPENAHGNPVTVDLGKPFRRVSVYDEIQRMSGVEFPPPNELNTPKGIA 410
Query: 280 FLKSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKS 339
++ + + N + + + ++ + + E PT++ ++P +SPLA K
Sbjct: 411 YMSVVMLRYNIPLPPVRTAAKMFEKLIDFFITDRVVE-----PTFVMDHPLFMSPLA-KE 464
Query: 340 NIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYI 399
+ + ERFELF+ G E N +SELNDP EQ RF+ Q+ + + E + D ++
Sbjct: 465 QVSRPGLAERFELFVNGIEYCNAYSELNDPHEQYHRFQQQL-VDRQGGDEEAMPLDETFL 523
Query: 400 HALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFPHLRNE 441
+L+ G+PP +G G+G+DR +MLLTNS NIRD I+FP LR +
Sbjct: 524 KSLQVGLPPTAGWGMGIDRALMLLTNSSNIRDGIIFPLLRQD 565
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 275 bits (705), Expect = 1e-86
Identities = 164/402 (40%), Positives = 237/402 (58%), Gaps = 13/402 (3%)
Query: 49 GDIIGAKGTLFKTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINE 108
GDI+G G K+ GELSI +++ L LP K+ L + EI+YR RY+DL+INE
Sbjct: 189 GDIVGIVGFPGKSKKGELSIFPKETIILSPCLHMLPMKY-GLKDTEIRYRQRYLDLMINE 247
Query: 109 NTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRI 168
+TR F RT+II+ +R+F+ F+EVETP ++ GGA A+PFITHHN L++ ++LRI
Sbjct: 248 STRSTFITRTKIINYLRNFLNDRGFIEVETPTMNLVAGGANARPFITHHNDLDLDLYLRI 307
Query: 169 APELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMI 228
A EL LK LI+GG +K++EI K FRNEGI HNPEFT EFY AY ++ L+K++E
Sbjct: 308 ATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADFYDLIKWSEDFF 367
Query: 229 KKIIMDCIGTTKIDY-------QGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFL 281
+++M GT KI Y +DF+ + K++I+E ++K T E + +
Sbjct: 368 SQLVMHLFGTYKILYNKDGPEKDPIEIDFTPPYPKVSIVEELEKLTNTKLEQPFDSPETI 427
Query: 282 KSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWN-PTYITNYPTEISPLARKSN 340
+ I K N+ ++ N L L E K N P +I +P +SPLA K +
Sbjct: 428 NKMINLI--KENKIEMPNPPTAAKLLDQLASHFIENKYPNKPFFIIEHPQIMSPLA-KYH 484
Query: 341 IENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIH 400
+TER E+FI G E+ N ++ELNDP +Q F Q + + + E + +D +
Sbjct: 485 RSKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFSAQQKDREKGDAE-AFQFDAAFCT 543
Query: 401 ALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFPHLRNEN 442
+LEYG+PP G G+G+DR+ M LTN I+DVILFP +R N
Sbjct: 544 SLEYGLPPTGGLGLGIDRITMFLTNKNCIKDVILFPTMRPAN 585
>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 = 230 bits (589), Expect = 8e-73
Identities = 106/317 (33%), Positives = 155/317 (48%), Gaps = 38/317 (11%)
Query: 127 FMEKNDFMEVETPILHNKPG-----GAIAKPFITHHNSLNMKMFLRIAPELYLKRLIIGG 181
F + +EVETP+L P A A F+ ++L+ +PE +KRL+ G
Sbjct: 1 FFAERGVLEVETPLLSPAPVTDPHLDAFATEFVGPDGQ-GRPLYLQTSPEYAMKRLLAAG 59
Query: 182 FNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTTKI 241
IF+I K FRN RHNPEFTM+E+Y +Y LM E ++++++
Sbjct: 60 SGPIFQICKVFRNGERGRRHNPEFTMLEWYRPGFDYHDLMDEVEALLQELLG-------- 111
Query: 242 DYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEID-LQNKLFLKSELKKINPKFNQKKILNN 300
D E+L+ EA +Y ID L L +EL+ + +
Sbjct: 112 -------DPFAPAERLSYQEAFLRYAG----IDPLTASL---AELQAAAAAHGIRASEED 157
Query: 301 LKKDILQLMLFEETTETKLWN--PTYITNYPTEISPLARKSNIENNNITERFELFIIGNE 358
+ D+L L LF E E L PT++ +YP + LAR S ++ + ERFEL+I G E
Sbjct: 158 DRDDLLDL-LFSEKVEPHLGFGRPTFLYDYPASQAALARIS-PDDPRVAERFELYIKGLE 215
Query: 359 IANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYY--DTDYIHALEYGMPPASGCGIGV 416
+ANGF EL D EQ RF+ L+ + Y D ++ ALE G+P SG +GV
Sbjct: 216 LANGFHELTDAAEQRRRFEADNALRKALGLPR---YPLDERFLAALEAGLPECSGVALGV 272
Query: 417 DRLIMLLTNSKNIRDVI 433
DRL+ML + +I DV+
Sbjct: 273 DRLLMLALGADSIDDVL 289
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 222 bits (567), Expect = 3e-69
Identities = 105/330 (31%), Positives = 157/330 (47%), Gaps = 38/330 (11%)
Query: 116 KRTQIISSIRHFMEKNDFMEVETPILHNKPGG-----AIAKPFITHHNSLNMKMFLRIAP 170
KR II++IR F + +EVETP L P F+ + ++L +P
Sbjct: 18 KRAAIIAAIRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSP 77
Query: 171 ELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKK 230
E ++KRL+ G IF++ K FRNE + HNPEFTM+E+Y +Y LM + +++
Sbjct: 78 EYHMKRLLAAGSGPIFQLGKVFRNEEMGRLHNPEFTMLEWYRVGCDYYRLMNEVDDLLQL 137
Query: 231 IIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDL--QNKLFLKSELKKI 288
+++C E+L+ EA +Y ID +K L+ K+
Sbjct: 138 -VLEC----------------VEAERLSYQEAFLRYL----GIDPLSADKTELREAAAKL 176
Query: 289 NPKFNQKKILNNLKKDILQLMLFEETTETKLW--NPTYITNYPTEISPLARKSNIENNNI 346
+ +LQL LF E E L PT++ ++P + LA+ S + +
Sbjct: 177 GLSAAT----DEDWDTLLQL-LFVEGVEPNLGKERPTFLYHFPASQAALAQIST-GDPRV 230
Query: 347 TERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGM 406
ERFEL+ G E+ANGF EL D EQ RF+ + D D++ AL M
Sbjct: 231 AERFELYYKGIELANGFHELTDAAEQRRRFEQDNKERARRGLPQYP-IDEDFLAALAR-M 288
Query: 407 PPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
PP SG +G DRL+ML +++I DVI FP
Sbjct: 289 PPCSGVALGFDRLVMLALGAESIDDVIAFP 318
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 199 bits (509), Expect = 8e-61
Identities = 106/335 (31%), Positives = 164/335 (48%), Gaps = 45/335 (13%)
Query: 112 KVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAI-AKPFITHHNSL----NMKMFL 166
KR +II+ IR F +EVETPIL I PF T ++L
Sbjct: 3 PNLLKRAKIIAEIRRFFADRGVLEVETPILSQATVTDIHLVPFETRFVGPGASQGKTLWL 62
Query: 167 RIAPELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEK 226
+PE ++KRL+ G IF+I K+FRNE HNPEFTM+E+Y + + LM +
Sbjct: 63 MTSPEYHMKRLLAAGSGPIFQICKSFRNEEAGRYHNPEFTMLEWYRPHYDMYRLMNEVDD 122
Query: 227 MIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELK 286
++++++ + E L+ +A +Y ID + K++L+
Sbjct: 123 LLQQVL-----------------DCEPAESLSYQQAFLRYL----GIDPLSA--DKTQLR 159
Query: 287 KINPKFNQKKILNNLKKD------ILQLMLFEETTETKLWN--PTYITNYPTEISPLARK 338
++ K L+N+ + +LQL LF E + PT++ ++P + LA K
Sbjct: 160 EVAAKLG----LSNIADEEEDRDTLLQL-LFTFGVEPNIGKEKPTFVYHFPASQAALA-K 213
Query: 339 SNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSY-YDTD 397
+ E++ + ERFE++ G E+ANGF EL D EQ RF+ D + L D +
Sbjct: 214 ISTEDHRVAERFEVYFKGIELANGFHELTDAREQRQRFEQ--DNRKRAARGLPQQPIDEN 271
Query: 398 YIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDV 432
I ALE G+P SG +GVDRLIML +++I +V
Sbjct: 272 LIAALEAGLPDCSGVALGVDRLIMLALGAESISEV 306
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 165 bits (421), Expect = 2e-46
Identities = 110/453 (24%), Positives = 195/453 (43%), Gaps = 64/453 (14%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTN 62
KR +GKI F++L+D SG IQ + + + L+ K + + G + +
Sbjct: 28 KRDLGKIIFLVLRDGSGF-----IQAVVPKNKVYEELF-KAKKLTLESSVVVTGIVKASP 81
Query: 63 T--GELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYR--HRYIDLIINENTRKVFKKRT 118
++V ++++ ++ P P K + E++ +R++DL + VFK R+
Sbjct: 82 KAPQGFELQVEKIEVLGEADPPYP--IDKKEHSELETLLDNRHLDLR-TPKIQAVFKIRS 138
Query: 119 QIISSIRHFMEKNDFMEVETPIL-HNKPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRL 177
I+ +IR F +N F EV TPI+ + G + F + + + +L +P+LY K
Sbjct: 139 SILRAIREFFYENGFTEVHTPIITASATEGG-GELFKV--DYFDKEAYLTQSPQLY-KEA 194
Query: 178 IIGGFNKIFEINKNFRNEGI-SPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCI 236
+ ++F I FR E + RH EF M++ A+ + +M E++IK + +
Sbjct: 195 LAAALERVFTIGPTFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVL 254
Query: 237 GTTKID-----YQGRLLD--FSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKIN 289
+ L S F ++T EAI+ + E ++ L +E
Sbjct: 255 EECADELEFLGRDNSELKRPESAPFPRITYKEAIEILEEKGFE-KVEWGDDLGTE----- 308
Query: 290 PKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITER 349
+++ + K P ++TNYP EI P + + +N
Sbjct: 309 ---HERYLGEEYFKP-----------------PVFVTNYPKEIKPFYMRPDPDNPGTVAS 348
Query: 350 FELFI-IGNEIANGFSELNDPEEQSVRFKNQ-IDLKNEINGELSSYYDTDYIHALEYGMP 407
F+L G EI G +D + R K + +D + SY Y+ +YGMP
Sbjct: 349 FDLLAPGGGEIIGGSQREHDYDLLVERIKEKGLDPE--------SYEW--YLDLRKYGMP 398
Query: 408 PASGCGIGVDRLIMLLTNSKNIRDVILFPHLRN 440
P +G G+G++RL+M + NIR+ I FP
Sbjct: 399 PHAGFGLGLERLVMYILGLDNIREAIPFPRDPG 431
>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 = 144 bits (367), Expect = 2e-42
Identities = 55/105 (52%), Positives = 71/105 (67%), Gaps = 6/105 (5%)
Query: 1 MLKRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNY-DIGDIIGAKGTLF 59
M KR GK+SF LQD +GKIQ+Y++ + +G+ + DFK D+GDIIG GT F
Sbjct: 9 MSKRGSGKLSFADLQD-----ESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPF 63
Query: 60 KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDL 104
KT TGELSI V L++KSLRPLP KF L++ E +YR RY+DL
Sbjct: 64 KTKTGELSIFVKEFTLLSKSLRPLPEKFHGLTDVETRYRQRYLDL 108
>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 = 147 bits (372), Expect = 1e-39
Identities = 112/446 (25%), Positives = 202/446 (45%), Gaps = 57/446 (12%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTNT 63
R +G + F++L+D G IQ+ + + KNL+ K ++ ++ +G +
Sbjct: 25 RDLGGLIFVLLRD-----REGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEK 79
Query: 64 --GELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYR--HRYIDLIINENTRKVFKKRTQ 119
G I + +++I ++ PLP + E+ R +R++DL + +F+ R+
Sbjct: 80 APGGFEIIPTKIEVINEAKEPLPLDPTEKVPAELDTRLDYRFLDLRRPTV-QAIFRIRSG 138
Query: 120 IISSIRHFMEKNDFMEVETPILHNKP--GGAIAKPFITHHNSLNMKMFLRIAPELYLKRL 177
++ S+R F+ + F+EV TP L GG P IT+ + FL +P+LY ++L
Sbjct: 139 VLESVREFLAEEGFIEVHTPKLVASATEGGTELFP-ITY---FEREAFLGQSPQLYKQQL 194
Query: 178 IIGGFNKIFEINKNFR-NEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCI 236
+ GF +++EI FR E + RH E T I+ A+ ++ +M E+++ ++ D
Sbjct: 195 MAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDIEMAFEDHHDVMDILEELVVRVFEDVP 254
Query: 237 G--TTKIDYQGRLLDFSKS-FEKLTIIEAIKKYTPQYNEIDLQNKLFLKSELKKINPKFN 293
+++ L+ + F +LT EAI+ + EI L
Sbjct: 255 ERCAHQLETLEFKLEKPEGKFVRLTYDEAIEMANAKGVEIGWGEDL----------STEA 304
Query: 294 QKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELF 353
+K + + +IT++PTEI P + +N I++ F+L
Sbjct: 305 EKALGEEMDGLY------------------FITDWPTEIRPFYTMPDEDNPEISKSFDLM 346
Query: 354 IIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCG 413
EI++G ++ + R K + L+ DY+ A YGMPP +G G
Sbjct: 347 YRDLEISSGAQRIHLHDLLVERIKAK---------GLNPEGFKDYLEAFSYGMPPHAGWG 397
Query: 414 IGVDRLIMLLTNSKNIRDVILFPHLR 439
+G +R +M L KNIR+ +LFP R
Sbjct: 398 LGAERFVMFLLGLKNIREAVLFPRDR 423
>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 = 136 bits (344), Expect = 2e-36
Identities = 96/363 (26%), Positives = 159/363 (43%), Gaps = 65/363 (17%)
Query: 92 NQEIKYRHRYIDLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKP--GGAI 149
N E +R++DL + +F+ R++++ + R F+ +N F EV TP + + GGA
Sbjct: 3 NLETLLDNRHLDLRTPKVQA-IFRIRSEVLRAFREFLRENGFTEVHTPKITSTDTEGGAE 61
Query: 150 AKPFITHHNSLNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNE-GISPRHNPEFTMI 208
+ +L +P+LY K ++I +++EI FR E + RH EF M+
Sbjct: 62 LFKV----SYFGKPAYLAQSPQLY-KEMLIAALERVYEIGPVFRAEKSNTRRHLSEFWML 116
Query: 209 EFYAAYTNYIW-LMKFTEKMIKKIIM----DCIGTTKIDYQ-GRLLDFSKS-FEKLTIIE 261
E A+ +M E++IK I C ++ Q R L F ++T E
Sbjct: 117 EAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRITYDE 176
Query: 262 AIKKYTPQYNEIDLQNKLFLKSELKKINPKF-------NQKKILNNLKKDILQLMLFEET 314
AI+ L+ + + K+ +++ + +K D
Sbjct: 177 AIE---------------LLREKGVEEEVKWGEDLSTEHERLLGEIVKGD---------- 211
Query: 315 TETKLWNPTYITNYPTEISPLARKSNIENNNITERFELFIIGN-EIANGFSELNDPEEQS 373
P ++T+YP EI P K + +N E F+L + G EI G ++D +E
Sbjct: 212 -------PVFVTDYPKEIKPFYMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELE 264
Query: 374 VRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVI 433
R K E + S+ Y+ +YGMPP G G+G++RL+M L NIR+ I
Sbjct: 265 ERIK-------EHGLDPESFEW--YLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIREAI 315
Query: 434 LFP 436
LFP
Sbjct: 316 LFP 318
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 135 bits (343), Expect = 2e-35
Identities = 109/458 (23%), Positives = 199/458 (43%), Gaps = 82/458 (17%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTNT 63
R +G I+F++L+D SG IQ+ + ++ + L+ K ++ GT+
Sbjct: 29 RDLGGIAFLILRDRSG-----IIQVVVKKKVD-EELFETIKKLKRESVVSVTGTVKANPK 82
Query: 64 --GELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYR--HRYIDLIINENTRKVFKKRTQ 119
G + + ++++ K+ PLP E+ R +R++DL R +FK R++
Sbjct: 83 APGGVEVIPEEIEVLNKAEEPLPLDISGKVLAELDTRLDNRFLDLR-RPRVRAIFKIRSE 141
Query: 120 IISSIRHFMEKNDFMEVETP--ILHNKPGGAIAKPFITHHNSLNMKMFLRIA-----PEL 172
++ + R F+ +N F E+ TP + GGA + F + A P+L
Sbjct: 142 VLRAFREFLYENGFTEIFTPKIVASGTEGGA---------ELFPIDYFEKEAYLAQSPQL 192
Query: 173 YLKRLIIGGFNKIFEINKNFRNEGI-SPRHNPEFTMIEFYAAYTN-YIWLMKFTEKMIKK 230
Y + ++ GF ++FEI FR E + RH E+T I+ + + + +M E +++
Sbjct: 193 YKQMMVGAGFERVFEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENLLRY 252
Query: 231 IIMDCIGTTKIDYQGRL--LDF-----SKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKS 283
+ + + L L ++T EAI EI LKS
Sbjct: 253 MY----EDVAENCEKELELLGIELPVPETPIPRITYDEAI--------EI-------LKS 293
Query: 284 ELKKINPKFN-----QKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARK 338
+ +I+ + ++ + +K++ F IT+YP+E P
Sbjct: 294 KGNEISWGDDLDTEGERLLGEYVKEEYGSDFYF-------------ITDYPSEKRPFYTM 340
Query: 339 SNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDY 398
+ ++ I++ F+L G EI +G ++ + K + L E S+ Y
Sbjct: 341 PDEDDPEISKSFDLLFRGLEITSGGQRIHRYDMLVESIKEK-GLNPE------SF--EFY 391
Query: 399 IHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
+ A +YGMPP G G+G++RL M L +NIR+ +LFP
Sbjct: 392 LEAFKYGMPPHGGFGLGLERLTMKLLGLENIREAVLFP 429
>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 = 113 bits (284), Expect = 2e-28
Identities = 82/330 (24%), Positives = 151/330 (45%), Gaps = 61/330 (18%)
Query: 114 FKKRTQIISSIRHFMEKNDFMEVETPIL-HNKPGGAIAKPFITHHNSLNMKMF--LRIAP 170
+ R+++I +IR+F+++ F+E+ETPIL + P GA + F+ + L+ F L +P
Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEGA--RDFLVP-SRLHPGKFYALPQSP 57
Query: 171 ELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKK 230
+L+ + L++ GF++ F+I + FR+E + PEFT I+ ++ + +M E ++K
Sbjct: 58 QLFKQLLMVSGFDRYFQIARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKY 117
Query: 231 IIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKK--YTPQYNEIDLQNKLFLKSELKKI 288
+ + +G ++ + F ++T EA+++ + +
Sbjct: 118 VFKEVLG----------VELTTPFPRMTYAEAMERYGFKFLW------------------ 149
Query: 289 NPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTY--ITNYPTEISPLARKSNIENNNI 346
I+ LFE E + T E L K +
Sbjct: 150 ----------------IVDFPLFEWDEEEGRLVSAHHPFTAPKEEDLDLLEKD--PEDAR 191
Query: 347 TERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGM 406
+ ++L + G E+ G ++DP+ Q F+ + E + + A +YG
Sbjct: 192 AQAYDLVLNGVELGGGSIRIHDPDIQEKVFEILGLSEEEAEEKFGFLLE-----AFKYGA 246
Query: 407 PPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
PP G +G+DRL+MLLT S++IRDVI FP
Sbjct: 247 PPHGGIALGLDRLVMLLTGSESIRDVIAFP 276
>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 = 115 bits (290), Expect = 4e-28
Identities = 105/457 (22%), Positives = 183/457 (40%), Gaps = 62/457 (13%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKT- 61
KR KI F+ L D S S G IQ I+ E L+ K+ G + G + ++
Sbjct: 28 KRSSKKIIFLELNDGS---SLGPIQAVINGED-NPYLFQLLKSLTTGSSVSVTGKVVESP 83
Query: 62 -NTGELSIKVSSLKLI---TKSLRPLPNKFQKL----SNQEIKYRHRYIDLIINENTRKV 113
+ ++V ++++ PL K L ++ R + ++
Sbjct: 84 GKGQPVELQVKKIEVVGEAEPDDYPLQKKEHSLEFLRDIAHLRLRTNTLGAVM------- 136
Query: 114 FKKRTQIISSIRHFMEKNDFMEVETPIL-HNKPGGAIAKPFITHHNSLNMKM-------F 165
+ R + +I + ++N F V PIL N GA + F +++ +
Sbjct: 137 -RVRNALSQAIHRYFQENGFTWVSPPILTSNDCEGA-GELFRVSTGNIDFSQDFFGKEAY 194
Query: 166 LRIAPELYLKRLIIGGFNKIFEINKNFRNEGI-SPRHNPEFTMIEFYAAYTNYIWLMKFT 224
L ++ +LYL+ + +K++ FR E + RH EF MIE A+ N L++
Sbjct: 195 LTVSGQLYLETYALA-LSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFANLNDLLQLA 253
Query: 225 EKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKL-FLKS 283
E +IK II + + + K+F+K I ++ I + + LK
Sbjct: 254 ETLIKYIIKAVLENCSQELK----FLEKNFDKDLIKRLENIINNKFARITYTDAIEILKE 309
Query: 284 ELKK--INPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNI 341
K + +L+ + + + E P ++TNYP +I K N
Sbjct: 310 SDKNFEYEDFWGD-----DLQTEHERFL-----AEEYFKPPVFVTNYPKDIKAFYMKLN- 358
Query: 342 ENNNITERFELFI--IGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYI 399
++ +L IG EI G +D ++ R K E+ + + Y+
Sbjct: 359 DDGKTVAAMDLLAPGIG-EIIGGSEREDDLDKLENRMK-------EMGLDTDALNW--YL 408
Query: 400 HALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
+YG P SG G+G +RL+ +T +NIRD I FP
Sbjct: 409 DLRKYGSVPHSGFGLGFERLLAYITGLENIRDAIPFP 445
>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 = 107 bits (269), Expect = 5e-25
Identities = 68/273 (24%), Positives = 131/273 (47%), Gaps = 30/273 (10%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIG------AKGT 57
R +G + FI L+D +G +Q+ + L +N D+ + G
Sbjct: 28 RDLGGLIFIDLRD-----RSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNI 82
Query: 58 LFKTNTGELSIKVSSLKLITKSLRPLPNKFQKLS-NQEIKYRHRYIDLIINENTRKVFKK 116
+TGE+ I S+ L+ KS P P +K +E++ ++RY+DL ++ K
Sbjct: 83 NRNLDTGEIEILAESITLLNKSKTP-PLIIEKTDAEEEVRLKYRYLDLR-RPEMQQRLKL 140
Query: 117 RTQIISSIRHFMEKNDFMEVETPIL-HNKPGGA--IAKPFITHHNSLNMKMFLRIAPELY 173
R ++ ++R+F+++ F+E+ETP+L + P GA P H L +P+L+
Sbjct: 141 RHKVTKAVRNFLDQQGFLEIETPMLTKSTPEGARDYLVPSRVHKGEF---YALPQSPQLF 197
Query: 174 LKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIM 233
+ L++ G ++ ++I + FR+E + PEFT I+ ++ +M+ EK++ + +
Sbjct: 198 KQLLMVSGVDRYYQIARCFRDEDLRADRQPEFTQIDMEMSFMTQEDVMELIEKLVSHVFL 257
Query: 234 DCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKY 266
+ G +D K F +T EA+++Y
Sbjct: 258 EVKG----------IDLKKPFPVMTYAEAMERY 280
Score = 67.1 bits (164), Expect = 6e-12
Identities = 40/127 (31%), Positives = 64/127 (50%), Gaps = 6/127 (4%)
Query: 310 LFEETTETKLWNPTYITNYPTEISPLARKSNIENNNITERFELFIIGNEIANGFSELNDP 369
+FE+ E +L + P + ++ E + E ++L + G E+ G ++DP
Sbjct: 431 MFEKDKEGRLCAAHHPFTMPKDEDLENLEAAPEEA-LAEAYDLVLNGVELGGGSIRIHDP 489
Query: 370 EEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNI 429
E Q F + + E E + + A +YG PP +G +G+DRL+MLLT + NI
Sbjct: 490 EVQKKVF-EILGIDPEEAREKFGFL----LEAFKYGTPPHAGFALGLDRLMMLLTGTDNI 544
Query: 430 RDVILFP 436
RDVI FP
Sbjct: 545 RDVIAFP 551
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 101 bits (254), Expect = 4e-23
Identities = 69/292 (23%), Positives = 136/292 (46%), Gaps = 63/292 (21%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFK-- 60
+R G + FI L+D G +Q+ + + + +I GT+
Sbjct: 27 RRDHGGLIFIDLRDREG-----IVQV-VFDPEDSPEAFEVASRLRNEFVIQVTGTVRARP 80
Query: 61 ---TN----TGELSIKVSSLKLITKSLRPLPNKFQ----KLSNQEIKYRHRYIDLIINEN 109
N TGE+ + ++++ S + LP FQ +++EI+ ++RY+DL E
Sbjct: 81 EGTINPNLPTGEIEVLAEEIEVLNAS-KTLP--FQIEDETNASEEIRLKYRYLDLRRPEM 137
Query: 110 TRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNK--PGGAIAKPFITHHNSLNMKMFL- 166
+ K R+++ +IR+F++ F+E+ETPIL K P GA + FL
Sbjct: 138 QKN-LKLRSKVTKAIRNFLDDQGFLEIETPIL-TKSTPEGA--------------RDFLV 181
Query: 167 --RI----------APELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAY 214
R+ +P+L+ + L++ GF++ ++I + FR+E + PEFT I+ ++
Sbjct: 182 PSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDLEMSF 241
Query: 215 TNYIWLMKFTEKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKY 266
+ +M+ EK+++ + + G ++ F ++T EA+++Y
Sbjct: 242 VDEEDVMELIEKLLRYVFKEVKG----------IELKTPFPRMTYAEAMRRY 283
Score = 69.5 bits (171), Expect = 1e-12
Identities = 42/150 (28%), Positives = 63/150 (42%), Gaps = 15/150 (10%)
Query: 295 KKILNNLKKDILQLM------LFEETTETKLWNPTY--ITNYPTEISPLARKSNIENNNI 346
K L + KD + + LFE E + + T P L +
Sbjct: 412 GKELGLIDKDQFKFLWVVDFPLFEWDEEEGRYVAAHHPFTM-PKPED-LELLEADPESVR 469
Query: 347 TERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEYGM 406
++L + G E+ G ++DPE Q F+ E + + A +YG
Sbjct: 470 ARAYDLVLNGYELGGGSIRIHDPEIQEKVFEILGISPEEAEEKFGFLLE-----AFKYGA 524
Query: 407 PPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
PP G G+DRL+MLLT +++IRDVI FP
Sbjct: 525 PPHGGIAFGLDRLVMLLTGAESIRDVIAFP 554
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 90.2 bits (224), Expect = 2e-19
Identities = 107/472 (22%), Positives = 191/472 (40%), Gaps = 82/472 (17%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTL----- 58
R GK +F++L+ + + +++S + K + K ++ +G +
Sbjct: 94 RGKGKSAFLVLRQSG---FTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKK 150
Query: 59 -FKTNTGELSIKVSSLKLITKSLRPLPNKFQKLS-------------------NQEIKYR 98
K T ++ I+V + ++K+L LP + + Q+ +
Sbjct: 151 PVKGTTQQVEIQVRKIYCVSKALATLPFNVEDAARSESEIEKALQTGEQLVRVGQDTRLN 210
Query: 99 HRYIDLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVETP--ILHNKPGGAIAKPFITH 156
+R +DL N + +F+ ++Q+ + R F+ F+E+ TP I GG+ F
Sbjct: 211 NRVLDLRTPAN-QAIFRIQSQVCNLFREFLLSKGFVEIHTPKLIAGASEGGSAV--FRLD 267
Query: 157 HNSLNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNE-GISPRHNPEFTMIEF-YAAY 214
+ L +P+L+ + I G F ++FEI FR E + RH EFT ++
Sbjct: 268 YK--GQPACLAQSPQLHKQMAICGDFRRVFEIGPVFRAEDSFTHRHLCEFTGLDLEMEIK 325
Query: 215 TNYIWLMKFTEKMIKKII----MDC---IGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYT 267
+Y ++ +++ I C + + Y L + +LT E I+
Sbjct: 326 EHYSEVLDVVDELFVAIFDGLNERCKKELEAIREQYPFEPLKYLPKTLRLTFAEGIQMLK 385
Query: 268 PQYNEIDLQNKLFLKSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYI-T 326
E+D L +SE K + QL+ + T+ YI
Sbjct: 386 EAGVEVDPLGDLNTESERK------------------LGQLVKEKYGTDF------YILH 421
Query: 327 NYPTEISPLARKSNIENNNITERFELFIIGNEIANGFSELNDPE--EQSVRFKNQIDLKN 384
YP + P ++ + F++FI G EI +G ++DPE E+ ID+K
Sbjct: 422 RYPLAVRPFYTMPCPDDPKYSNSFDVFIRGEEIISGAQRVHDPELLEKRAEECG-IDVK- 479
Query: 385 EINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
I + YI + YG PP G G+G++R++ML NIR LFP
Sbjct: 480 TI---------STYIDSFRYGAPPHGGFGVGLERVVMLFCGLNNIRKTSLFP 522
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 87.8 bits (218), Expect = 3e-19
Identities = 78/350 (22%), Positives = 140/350 (40%), Gaps = 61/350 (17%)
Query: 105 IINENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKM 164
I +E RKV K ++ I+ R F++ F+EV PI+ P + + L +K
Sbjct: 21 ISSEKYRKVLKVQSSILRYTREFLDGRGFVEVLPPII-----SPSTDPLMGLGSDLPVKQ 75
Query: 165 FLRIAP--ELYL-------KRLIIGGFNKIFEINKNFRNEG---ISPRHNPEFTMIEFYA 212
E YL K+L + KIF ++ NFR E + RH EFT ++
Sbjct: 76 ISIDFYGVEYYLADSMILHKQLALRMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEI 135
Query: 213 AYTNYIWLMKFTEKMIKKIIMDCIGTTK--IDYQGR-LLDFSKSFEKLTIIEAIKKYTPQ 269
+ +M E +IK ++ + + + +++ GR L + F+++T EA++
Sbjct: 136 EGADLDEVMDLIEDLIKYLVKELLEEHEDELEFFGRDLPHLKRPFKRITHKEAVE----- 190
Query: 270 YNEIDLQNKLFLKSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYP 329
L + +L+++ + + FEE P +I + P
Sbjct: 191 ----ILNEEGCRGIDLEELGSEGEKSLS-----------EHFEE--------PFWIIDIP 227
Query: 330 TEISPLARKSNIENNNITERFELFI---IGNEIANGFSELNDPEEQSVRFKNQIDLKNEI 386
+ + E + ++L + G E +G + EE R +
Sbjct: 228 KGSREFYDREDPERPGVLRNYDLLLPEGYG-EAVSGGEREYEYEEIVERIREH------- 279
Query: 387 NGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
G Y Y+ + G P++G GIGV+RL + ++IR+V FP
Sbjct: 280 -GVDPEKYK-WYLEMAKEGPLPSAGFGIGVERLTRYICGLRHIREVQPFP 327
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 88.6 bits (221), Expect = 8e-19
Identities = 62/221 (28%), Positives = 116/221 (52%), Gaps = 44/221 (19%)
Query: 63 TGELSIKVSSLKLITKSLRPLPNKFQKLSNQ----EIKYRHRYIDL---IINENTRKVFK 115
TGE+ + S L+++ KS + LP F + E++ ++RY+DL + +N K
Sbjct: 90 TGEIEVLASELEVLNKS-KTLP--FPIDDEEDVSEELRLKYRYLDLRRPEMQKN----LK 142
Query: 116 KRTQIISSIRHFMEKNDFMEVETPILHNK--PGGAIAKPFI----THHNSLNMKMF--LR 167
R+++ S+IR+F++ N F+E+ETPIL K P G A+ ++ H F L
Sbjct: 143 LRSKVTSAIRNFLDDNGFLEIETPIL-TKSTPEG--ARDYLVPSRVHPGK-----FYALP 194
Query: 168 IAPELYLKRLIIGGFNKIFEINKNFRNEGISPRHN--PEFTMIEFYAAYTNYIWLMKFTE 225
+P+L+ + L++ GF++ ++I + FR+E R + PEFT I+ ++ +M E
Sbjct: 195 QSPQLFKQLLMVAGFDRYYQIARCFRDE--DLRADRQPEFTQIDIEMSFVTQEDVMALME 252
Query: 226 KMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKY 266
+I+ + + +G +D F ++T EA+++Y
Sbjct: 253 GLIRHVFKEVLG----------VDLPTPFPRMTYAEAMRRY 283
Score = 68.2 bits (168), Expect = 3e-12
Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 401 ALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
AL+YG PP G G+DRL+MLL + +IRDVI FP
Sbjct: 521 ALKYGAPPHGGIAFGLDRLVMLLAGADSIRDVIAFP 556
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 85.6 bits (212), Expect = 8e-18
Identities = 69/306 (22%), Positives = 128/306 (41%), Gaps = 83/306 (27%)
Query: 2 LKRVMGKISFIMLQDTSG-------PDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGA 54
L R MG ++F+ ++D +G PD + + +N Y ++
Sbjct: 83 LHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRL---RNEY----------VVAV 129
Query: 55 KGTLF---------KTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQ------EIKYRH 99
+GT+ K TG + + S+ ++ + LP Q E++ R+
Sbjct: 130 EGTVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVTTADEQKDSIKEEVRLRY 189
Query: 100 RYIDL---IINENTRKVFKKRTQIISSIRHFME-KNDFMEVETPILHN------------ 143
R +DL +N N R R +++ IR ++E + F+E+ETPIL
Sbjct: 190 RVLDLRRPQMNANLRL----RHRVVKLIRRYLEDVHGFVEIETPILSRSTPEGARDYLVP 245
Query: 144 ---KPGGAIAKPFITHHNSLNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNEGISPR 200
+PG A P +P+L+ + L++ GF++ ++I + FR+E +
Sbjct: 246 SRVQPGTFYALP---------------QSPQLFKQMLMVSGFDRYYQIARCFRDEDLRAD 290
Query: 201 HNPEFTMIEFYAAYTNYIWLMKFTEKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTII 260
PEFT ++ A+T ++K E +I+++ + G + F +LT
Sbjct: 291 RQPEFTQLDMELAFTPLEDMLKLNEDLIRQVFKEIKG----------VQLPNPFPRLTYA 340
Query: 261 EAIKKY 266
EA+ KY
Sbjct: 341 EAMSKY 346
Score = 57.1 bits (138), Expect = 1e-08
Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 401 ALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
AL+ G PP G G+DRL+MLL +K+IRDVI FP
Sbjct: 584 ALDMGAPPHGGIAYGLDRLVMLLAGAKSIRDVIAFP 619
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 84.7 bits (209), Expect = 2e-17
Identities = 68/287 (23%), Positives = 126/287 (43%), Gaps = 44/287 (15%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFK--- 60
R G++ FI L+D NG IQ S E ++Y + + +G + K
Sbjct: 31 RDHGELLFIHLRD-----RNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLE 85
Query: 61 ------TNTGELSIKVSSLKLITKS-LRPLPNKFQKLS-----------NQEIKYRHRYI 102
TG++ + V L ++ S P + ++ N++++ ++RY+
Sbjct: 86 ETENPHIETGDIEVFVRELSILAASEALPFAISDKAMTAGAGSAGADAVNEDLRLQYRYL 145
Query: 103 DLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVETPIL-HNKPGGA--IAKPFITHHNS 159
D I + KR +II R F++ F+E+ETPIL + P GA P H
Sbjct: 146 D-IRRPAMQDHLAKRHRIIKCARDFLDSRGFLEIETPILTKSTPEGARDYLVPSRIHPKE 204
Query: 160 LNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNEGISPRHNPEFTMIEFYAAYTNYIW 219
L +P+L+ + L+I GF + F++ + FR+E + P PEFT ++ A++ + +
Sbjct: 205 FYA---LPQSPQLFKQLLMIAGFERYFQLARCFRDEDLRPNRQPEFTQLDIEASFIDEEF 261
Query: 220 LMKFTEKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKY 266
+ + E++ + M IG + + F ++ EA+
Sbjct: 262 IFELIEELTAR--MFAIGG---------IALPRPFPRMPYAEAMDTT 297
Score = 48.4 bits (115), Expect = 6e-06
Identities = 23/95 (24%), Positives = 49/95 (51%), Gaps = 13/95 (13%)
Query: 350 FELFIIGNEIANGFSELNDPEEQSVRFK----NQIDLKNEINGELSSYYDTDYIHALEYG 405
++L + G E+ G +ND + Q F ++ D++++ ++ A ++
Sbjct: 491 YDLVVNGEELGGGSIRINDKDIQLRIFAALGLSEEDIEDKFGF---------FLRAFDFA 541
Query: 406 MPPASGCGIGVDRLIMLLTNSKNIRDVILFPHLRN 440
PP G +G+DR++ ++ + +IR+VI FP R+
Sbjct: 542 APPHGGIALGLDRVVSMILQTPSIREVIAFPKNRS 576
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 79.4 bits (197), Expect = 6e-16
Identities = 110/483 (22%), Positives = 182/483 (37%), Gaps = 117/483 (24%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTN 62
KR GKI+F+ L+D S +Q+ N + + K G + GT+ ++
Sbjct: 28 KRDSGKIAFLQLRDGSCFKQ---LQVVKDNGE---EYFEEIKKLTTGSSVIVTGTVVESP 81
Query: 63 T--GELSIKVSSLKLITKSLR--PLPNK---FQKLSNQEIKY-RHRYIDLIINENTRK-- 112
++ + +++I + P+ K + L +EI + R R T K
Sbjct: 82 RAGQGYELQATKIEVIGEDPEDYPIQKKRHSIEFL--REIAHLRPR---------TNKFG 130
Query: 113 -VFKKRTQIISSIRHFMEKNDFMEVETPIL-HNKPGGAIAKPFITHHNSLNMKM------ 164
V + R + +I F +N F+ V+TPI+ + GA + F L+
Sbjct: 131 AVMRIRNTLAQAIHEFFNENGFVWVDTPIITASDCEGA-GELFRVTTLDLDFSKDFFGKE 189
Query: 165 -FLRIAPELYLKRLIIGGFNKIFEINKNFRNEGIS--PRHNPEFTMIEFYAAYTNYIWLM 221
+L ++ +LY + + K++ FR E S RH EF MIE A+ + M
Sbjct: 190 AYLTVSGQLYAEAYAMA-LGKVYTFGPTFRAEN-SNTRRHLAEFWMIEPEMAFADLEDNM 247
Query: 222 KFTEKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYT----PQ--YNE-ID 274
E+M+K ++ + D L+F IE ++ + P+ Y E I+
Sbjct: 248 DLAEEMLKYVVKYVLENCPDD-----LEFLNRRVDKGDIERLENFIESPFPRITYTEAIE 302
Query: 275 LQNKLFLKSELKKINPKF-NQKKILNNLKKDILQLMLFEET--TETKLWNPTYITNYPTE 331
+ L+K KF + ++L + E E P ++TNYP +
Sbjct: 303 I---------LQKSGKKFEFPVEWGDDLGSE-------HERYLAEEHFKKPVFVTNYPKD 346
Query: 332 ISPLARKSNIENN----------NITERFELFIIG--------NEIANGFSELNDPEEQS 373
I + N + I E IIG + + EL +E
Sbjct: 347 IKAFYMRLNPDGKTVAAMDLLAPGIGE-----IIGGSQREERLDVLEARIKELGLNKE-- 399
Query: 374 VRFKNQIDLKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVI 433
+ Y D YG P SG G+G +RL+ +T NIRDVI
Sbjct: 400 ---------------DYWWYLDLR-----RYGSVPHSGFGLGFERLVAYITGLDNIRDVI 439
Query: 434 LFP 436
FP
Sbjct: 440 PFP 442
>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 = 74.5 bits (183), Expect = 2e-15
Identities = 33/109 (30%), Positives = 46/109 (42%), Gaps = 10/109 (9%)
Query: 117 RTQIISSIRHFMEKNDFMEVETPILHNKPG----GAIAKPFITHHNSLNMKMFLRIAPEL 172
R++I +R FM + F EVETPI+ +P G K + ++LR E
Sbjct: 2 RSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEP 61
Query: 173 YLKRLIIG----GFNKIFEINKNFRNEGIS--PRHNPEFTMIEFYAAYT 215
L RL + ++ EI FRNEG R EFT +E
Sbjct: 62 GLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGE 110
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 76.6 bits (188), Expect = 5e-15
Identities = 101/471 (21%), Positives = 199/471 (42%), Gaps = 57/471 (12%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKN-------YDI-GDIIGAK 55
R GK++F++L+D G DS +Q + E DF D+ + +
Sbjct: 91 RKKGKMAFMVLRD--GSDS---VQAMAAVEGDVPKEMIDFIGQIPTESIVDVEATVCKVE 145
Query: 56 GTLFKTNTGELSIKVSSLKLITKSLRPLPNKFQKLSNQE----------IKYRHRYIDLI 105
+ T+ ++ +KV + +T+SLR LP + S +E + R++DL
Sbjct: 146 QPITSTSHSDIELKVKKIHTVTESLRTLPFTLEDASRKESDEGAKVNFDTRLNSRWMDLR 205
Query: 106 INENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMF 165
+ +F+ ++++ R F+ +DF E+ +P + N P A F + N +
Sbjct: 206 -TPASGAIFRLQSRVCQYFRQFLIDSDFCEIHSPKIINAPSEGGANVFKLEY--FNRFAY 262
Query: 166 LRIAPELYLKRLIIGGFNKIFEINKNFRNEGISP-RHNPEFTMIEFYAAYT-NYIWLMKF 223
L +P+LY + ++ G ++FE+ FR+E + RH EF ++ +Y ++
Sbjct: 263 LAQSPQLYKQMVLQGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDL 322
Query: 224 TEKMIKKIIMDCIGTTK-IDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLK 282
E + I TK + + F KLT E +K+ ++ +
Sbjct: 323 AESLFNYIFERLATHTKELKAVCQQYPFEPLVWKLT-PERMKELGVGVISEGVEPTDKYQ 381
Query: 283 SELKKINPKF------NQKKILNNLKKDILQLMLFEETTETKLWNPT---------YITN 327
+ + ++ + + ++LN + ++ + TT KL +I++
Sbjct: 382 ARVHNMDSRMLRINYMHCIELLNTVLEEKMAPTDDINTTNEKLLGKLVKERYGTDFFISD 441
Query: 328 -YPTEISPLARKSNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKN-QIDLKNE 385
+P+ P ++ T +++FI G EI++G ++DP+ R K +DL
Sbjct: 442 RFPSSARPFYTMECKDDERFTNSYDMFIRGEEISSGAQRIHDPDLLLARAKMLNVDL--- 498
Query: 386 INGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
+ +Y+ + G P G G+G++R++ML N+R LFP
Sbjct: 499 --TPIK-----EYVDSFRLGAWPHGGFGVGLERVVMLYLGLSNVRLASLFP 542
>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 = 57.6 bits (140), Expect = 9e-11
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTN 62
+R G + FI L+D S G +Q+ ++ E +G + + + ++G GT+ K
Sbjct: 11 RRDHGGLIFIDLRDGS-----GIVQVVVNKEELG-EFFEEAEKLRTESVVGVTGTVVKRP 64
Query: 63 -----TGELSIKVSSLKLITK 78
TGE+ ++ L++++K
Sbjct: 65 EGNLATGEIELQAEELEVLSK 85
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTN 62
+R GK++F+ L+D +G IQ+ + + K GD++ G + K
Sbjct: 11 RRSGGKVAFLTLRDGTG-----SIQVVLFK----EEAEKLAKKLKEGDVVLVTGKVKKRP 61
Query: 63 TGELSIKVSSLKLI 76
GEL + V ++++
Sbjct: 62 GGELELVVEEIEVL 75
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 50.4 bits (120), Expect = 1e-06
Identities = 65/278 (23%), Positives = 111/278 (39%), Gaps = 22/278 (7%)
Query: 160 LNMKMFLRIAPELYLKRLIIGGFNKIFEINKNFRNEGI-SPRHNPEFTMIEFYAAYTNYI 218
+ + FL ++ +L L+ L ++ FR E + RH EF MIE A+ +
Sbjct: 322 FSKQAFLTVSGQLSLENLC-SSMGDVYTFGPTFRAENSHTSRHLAEFWMIEPEIAFADLY 380
Query: 219 WLMKFTEKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNK 278
M+ E IK CIG + + F ++ E I + +I N
Sbjct: 381 DNMELAESYIKY----CIGYVLNNNFDDIYYFEENVETGLISRLKNILDEDFAKITYTNV 436
Query: 279 LFLKSELKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARK 338
+ L + P + ++ D LQ E P + NYP ++ K
Sbjct: 437 IDL------LQPYSDSFEVPVKWGMD-LQSEHERFVAEQIFKKPVIVYNYPKDLKAFYMK 489
Query: 339 SNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDY 398
N + + L E+ G E ++ +++ + ++N + SY+ Y
Sbjct: 490 LNEDQKTVAAMDVLVPKIGEVIGG-----SQREDNLERLDKMIKEKKLN--MESYW--WY 540
Query: 399 IHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
++G P +G G+G +RLIML+T NI+D I FP
Sbjct: 541 RQLRKFGSHPHAGFGLGFERLIMLVTGVDNIKDTIPFP 578
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 44.2 bits (104), Expect = 1e-04
Identities = 33/115 (28%), Positives = 50/115 (43%), Gaps = 9/115 (7%)
Query: 322 PTYITNYPTEISPLARKSNIENNNITERFELFIIGNEIANGFSELNDPEEQSVRFKNQID 381
P I +YP EI + N + + L E+ G + EE+ + ++D
Sbjct: 452 PVIIRDYPKEIKAFYMRENDDGKTVAAMDMLVPRVGELIGG----SQREERLEYLEARLD 507
Query: 382 LKNEINGELSSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
E+ SY+ Y+ YG P +G G+G +RL+ T NIRD I FP
Sbjct: 508 ---ELKLNKESYWW--YLDLRRYGSVPHAGFGLGFERLVQFATGIDNIRDAIPFP 557
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 42.9 bits (101), Expect = 2e-04
Identities = 42/145 (28%), Positives = 71/145 (48%), Gaps = 18/145 (12%)
Query: 79 SLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVET 138
SL KF++L ++ + R + + E+ K + I+ + F+++ F+E+++
Sbjct: 171 SLNSEKPKFKELESELVSRRKNDLKQMYEEDREDYLGKLERDIT--KFFVDR-GFLEIKS 227
Query: 139 PILHNKPGGAIAKPFITHHNSLNMKMF-------LR--IAPELY--LKRL--IIGGFNKI 185
PIL P I + I + L+ ++F LR +AP LY L++L I+ KI
Sbjct: 228 PIL--IPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPGLYNYLRKLDRILPDPIKI 285
Query: 186 FEINKNFRNEGISPRHNPEFTMIEF 210
FEI +R E H EFTM+ F
Sbjct: 286 FEIGPCYRKESDGKEHLEEFTMVNF 310
>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 = 40.6 bits (96), Expect = 2e-04
Identities = 25/114 (21%), Positives = 49/114 (42%), Gaps = 21/114 (18%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFK-- 60
+R G + FI L+D G +Q+ E + + +I G +
Sbjct: 26 RRDHGGLIFIDLRDRYG-----IVQVVFDPEE--APEFELAEKLRNESVIQVTGKVRARP 78
Query: 61 ---TN----TGELSIKVSSLKLITKSLRPLP---NKFQKLSNQEIKYRHRYIDL 104
N TGE+ + S L+++ K+ + LP + ++E++ ++RY+DL
Sbjct: 79 EGTVNPKLPTGEIEVVASELEVLNKA-KTLPFEIDDDVN-VSEELRLKYRYLDL 130
>gnl|CDD|188213 TIGR02367, PylS_Cterm, pyrrolysyl-tRNA synthetase, C-terminal
region. PylS is the enzyme responsible for charging the
pyrrolysine tRNA, PylT, by ligating a free molecule of
pyrrolysine. Pyrrolysine is encoded at an in-frame UAG
(amber) at least in several corrinoid-dependent
methyltransferases of the archaeal genera Methanosarcina
and Methanococcoides, such as trimethylamine
methyltransferase. This protein occurs as a fusion
protein in Methanosarcina but as split genes in
Desulfitobacterium hafniense and other bacteria [Protein
synthesis, tRNA aminoacylation].
Length = 242
Score = 42.1 bits (99), Expect = 3e-04
Identities = 38/138 (27%), Positives = 61/138 (44%), Gaps = 20/138 (14%)
Query: 87 FQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQIISSIRHFMEKNDFMEVETPILHNKPG 146
F+ L ++ I R R ++ + E R K + ++ + F++V+TPI+ P
Sbjct: 1 FKGLEHELISRRKRDLEQLRTEKRRPALGKLERELAK---ALVDRGFVQVKTPII--IPK 55
Query: 147 GAIAKPFITHHNSLNMKMF-------LR--IAPELY-----LKRLIIGGFNKIFEINKNF 192
+ K I + L ++F LR +AP LY L RL +IFEI +
Sbjct: 56 EYLEKMTIDEDHPLFSQVFWVDENKCLRPMLAPNLYNYLRKLDRLWPKPI-RIFEIGPCY 114
Query: 193 RNEGISPRHNPEFTMIEF 210
R E +H EFTM+
Sbjct: 115 RKESQGSQHLNEFTMLNL 132
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 40.4 bits (94), Expect = 0.001
Identities = 65/272 (23%), Positives = 98/272 (36%), Gaps = 56/272 (20%)
Query: 185 IFEINKNFRNEGI-SPRHNPEFTMIE---FYA----------AYTNYI--WLMKF----T 224
++ FR E + RH EF M+E +A AY Y+ WL+
Sbjct: 329 VYTFGPTFRAENSHTSRHLAEFWMVEPEIAFADLEDDMNCAEAYVKYMCKWLLDKCFDDM 388
Query: 225 EKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSE 284
E M K CI + + S F ++T EAI+ E + K F +
Sbjct: 389 ELMAKNFDSGCIDRLR-------MVASTPFGRITYTEAIELL----EEAVAKGKEFDNNV 437
Query: 285 LKKINPKFNQKKILNNLKKDILQLMLFEETTETKLWNPTYITNYPTEISPLARKSNIENN 344
I+ ++ L TE P + NYP I + N +
Sbjct: 438 EWGIDLASEHERYL----------------TEVLFQKPLIVYNYPKGIKAFYMRLNDDEK 481
Query: 345 NITERFELFIIGNEIANGFSELNDPEEQSVRFKNQIDLKNEINGELSSYYDTDYIHALEY 404
+ L E+ G + EE+ K +I+ E+ + Y Y+ Y
Sbjct: 482 TVAAMDVLVPKVGELIGG----SQREERYDVIKQRIE---EMGLPIEPY--EWYLDLRRY 532
Query: 405 GMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
G G G+G +R+I+ T NIRDVI FP
Sbjct: 533 GTVKHCGFGLGFERMILFATGIDNIRDVIPFP 564
>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 = 38.7 bits (91), Expect = 0.003
Identities = 34/113 (30%), Positives = 52/113 (46%), Gaps = 24/113 (21%)
Query: 117 RTQIISSIRHFM--EKNDFMEVETPILHNKPGGAIAKPFITHHNSLNMKMFLRIAPE--- 171
+ I S+ R E+ D +E+++PI+ + + K I S +LR PE
Sbjct: 35 KNNIKSAWRKSFVLEEEDMLEIDSPIITPEL---MFKTSIGPVESGGNLGYLR--PETAQ 89
Query: 172 ---LYLKRLIIGGFNK----IFEINKNFRNEGISPRHN----PEFTM--IEFY 211
+ K L+ K + +I K+FRNE ISPR+ EFT IEF+
Sbjct: 90 GIFVNFKNLLEFNRRKLPFGVAQIGKSFRNE-ISPRNGLFRVREFTQAEIEFF 141
>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 = 33.3 bits (77), Expect = 0.10
Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 24/114 (21%)
Query: 120 IISSIRHFMEKNDFMEVETPILHNKP-----GGA--IAKPFITH-HNSLNMKMFLRIAPE 171
+ + IR +++ + EV+TPIL K G + + + +++LR P
Sbjct: 5 LENFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLR--PT 62
Query: 172 ------LYLKRLIIGGFN---KIFEINKNFRNEGISPRHN----PEFTMIEFYA 212
K I+ K+++I FR E PR EFT ++
Sbjct: 63 AEVGITRLFKNEILSYRELPLKLYQIGPCFRYE-ARPRRGLGRVREFTQVDAEI 115
>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 = 33.4 bits (77), Expect = 0.16
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 184 KIFEINKNFRNEGISPRHNPEFTMIEFYAA-----YTNYIWLMK-FTEKM 227
+IF + FRN+ + H PEF +E +TN ++ F +KM
Sbjct: 152 RIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFLKKM 201
>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 = 32.5 bits (75), Expect = 0.29
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 184 KIFEINKNFRNEGISPRHNPEFTMIEFYAAYTN--YIWLMKFTEKMIKKI 231
+IF I + +RN+ I H PEF IE + L E+ K++
Sbjct: 82 RIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKEL 131
Score = 30.2 bits (69), Expect = 1.6
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 413 GIGVDRLIMLLTNSKNIRD 431
GIG++RL ML +IR
Sbjct: 193 GIGLERLAMLKYGIPDIRL 211
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 32.5 bits (75), Expect = 0.46
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 184 KIFEINKNFRNEGISPRHNPEFTMIE 209
K F I + FR + I H PEF +E
Sbjct: 352 KYFSIGRVFRPDTIDATHLPEFYQLE 377
Score = 30.2 bits (69), Expect = 2.7
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 413 GIGVDRLIMLLTNSKNIRDV 432
G+G++RL ML +IRD+
Sbjct: 458 GLGIERLAMLRLGLDDIRDL 477
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 32.0 bits (74), Expect = 0.66
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 403 EYGMPPASGCG--IGVDRLIMLL 423
++G PP G IGV+RL++LL
Sbjct: 289 QFGGPPTPAVGFAIGVERLLLLL 311
Score = 29.0 bits (66), Expect = 5.7
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 115 KKRTQIISSIRHFMEKNDFMEVETPIL 141
K + +IR E+ F E+ TPI
Sbjct: 19 AKWQYVEDTIREVFERYGFSEIRTPIF 45
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 31.4 bits (71), Expect = 1.1
Identities = 29/120 (24%), Positives = 50/120 (41%), Gaps = 19/120 (15%)
Query: 322 PTYITNYPTEISPLARKSNIENNNITERFELFI--IGNEIANGFSELNDPEEQSVRFKNQ 379
P I NYP E+ P + N ++ F+L + +G I +E +
Sbjct: 520 PVIIYNYPKELKPFYVRLN-DDGKTVAAFDLVVPKVGTVITGSQNE------------ER 566
Query: 380 IDLKNEINGEL---SSYYDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFP 436
+D+ N EL Y+ Y+ +G SG +G + +++ T ++RD I FP
Sbjct: 567 MDILNARIEELGLPREQYEW-YLDLRRHGTVKHSGFSLGFELMVLFATGLPDVRDAIPFP 625
>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 = 29.6 bits (67), Expect = 1.2
Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 4 RVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTNT 63
R +G I F++L+D G +Q+ + + K L+ + +I GT+
Sbjct: 25 RDLGGIKFVILRDR-----EGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK 79
Query: 64 GELSIKV--SSLKLITKSLRPLP 84
+++ +++++++ PLP
Sbjct: 80 APNGVEIIPEEIEVLSEAKTPLP 102
>gnl|CDD|129668 TIGR00578, ku70, ATP-dependent DNA helicase II, 70 kDa subunit
(ku70). Proteins in this family are involved in
non-homologous end joining, a process used for the
repair of double stranded DNA breaks. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). Cutoff does not
detect the putative ku70 homologs in yeast [DNA
metabolism, DNA replication, recombination, and repair].
Length = 584
Score = 31.0 bits (70), Expect = 1.4
Identities = 15/73 (20%), Positives = 35/73 (47%)
Query: 65 ELSIKVSSLKLITKSLRPLPNKFQKLSNQEIKYRHRYIDLIINENTRKVFKKRTQIISSI 124
++ + V L+ K+ +P P K + +N+ +K + R ++ KR+Q
Sbjct: 242 DVVMSVGIYNLVQKAGKPAPVKLYRETNEPVKTKTRTFNMDTGSLLLPSDTKRSQTYGGR 301
Query: 125 RHFMEKNDFMEVE 137
+ ++EK + E++
Sbjct: 302 QIYLEKEETEELK 314
>gnl|CDD|235754 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
Length = 529
Score = 31.1 bits (71), Expect = 1.4
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 403 EYGMP-PASGCGIGVDRLIMLLTNSKNIRD 431
EYG+ P G+GV+RL M+L ++++R+
Sbjct: 311 EYGIDVPVMNLGLGVERLAMILYGAEDVRE 340
>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 = 28.4 bits (64), Expect = 1.6
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIG---AKGTLF 59
R++ K+SF L+D +G IQL + + +L + G K
Sbjct: 12 PRIVKKLSFADLRDPNGD----IIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKS 67
Query: 60 KTNTGELSIKVSSLK 74
E + V ++
Sbjct: 68 SEKNDEWELVVDDIQ 82
>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 = 30.2 bits (69), Expect = 2.0
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 184 KIFEINKNFRNEGISPRHNPEFTMIEF 210
KIF I + FR + + H PEF +E
Sbjct: 104 KIFSIGRVFRRDQVDATHLPEFHQVEG 130
Score = 29.5 bits (67), Expect = 2.8
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 413 GIGVDRLIMLLTNSKNIRD 431
G+GV+RL ML +IRD
Sbjct: 215 GLGVERLAMLKYGIDDIRD 233
>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 = 30.1 bits (69), Expect = 2.5
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 403 EYGMPPASGCG--IGVDRLIMLL 423
E G PP G IG++RL++LL
Sbjct: 288 ELGGPPTPAVGFAIGIERLLLLL 310
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 29.9 bits (68), Expect = 2.8
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 184 KIFEINKNFRNEGISPRH----NPEFTMIEFYAAYTNYIWLMKFTEKMIK--KIIMDCIG 237
K+++I FR+E PR EF M + Y+ + + + EKM+ I +
Sbjct: 131 KLYQIQSKFRDE-KRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSRIFLRLP 189
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine 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 in the core domain.
Length = 298
Score = 29.4 bits (67), Expect = 3.2
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 117 RTQIISSIRHFMEKNDFMEVETPILHNK 144
R ++ +R K + EVETPI++NK
Sbjct: 33 RNELEDFLRELQRKRGYQEVETPIIYNK 60
>gnl|CDD|222843 PHA02030, PHA02030, hypothetical protein.
Length = 336
Score = 29.2 bits (65), Expect = 4.0
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 9/102 (8%)
Query: 225 EKMIKKIIMDCIGTTKIDYQGRLLDFSKSFEKLTIIEAIKKYTPQYNEIDLQNKLFLKSE 284
EK K+ D K+++ G+ F++ + II IK+ N +N +
Sbjct: 122 EKSKTKLAFD-----KMNWSGQHKHFAQMLGQAFIIP-IKRTKKGNNAGKERNDIDWGGI 175
Query: 285 LKKINPKFNQKKILNNLKKDILQLMLFEE-TTETKLWNPTYI 325
L +P + L D+LQL L++ T ET W+ +I
Sbjct: 176 LPPFDPVDGSPYNVPELDDDLLQLFLWDAPTKET--WDALHI 215
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 29.5 bits (66), Expect = 4.0
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 7/44 (15%)
Query: 394 YDTDYIHALEYGMPPASGCGIGVDRLIMLLTNSKNIRDVILFPH 437
YD+ IH L PA GC IG++RL+++ +D I+ P
Sbjct: 287 YDS-LIHQLGGPKTPAVGCAIGLERLLLI------AKDNIILPK 323
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 29.1 bits (66), Expect = 4.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 413 GIGVDRLIMLLTNSKNIRD 431
G+G++RL ML +IRD
Sbjct: 306 GLGLERLAMLKYGIPDIRD 324
Score = 29.1 bits (66), Expect = 5.1
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 184 KIFEINKNFRNEGISPRHNPEFTMIEF 210
KIF + +RN+ + H+PEF IE
Sbjct: 194 KIFSPGRVYRNDTVDATHSPEFHQIEG 220
>gnl|CDD|225304 COG2502, AsnA, Asparagine synthetase A [Amino acid transport and
metabolism].
Length = 330
Score = 28.6 bits (64), Expect = 6.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 406 MPPASGCGIGVDRLIMLLTNSKNIRDV 432
+P G GIG RL MLL K+I +V
Sbjct: 287 LPQTIGGGIGQSRLCMLLLQKKHIGEV 313
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 29.0 bits (66), Expect = 6.3
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 248 LDFSKSFEKLTIIEA-IKKYTPQYNEIDLQNKLFLKSELKKINPKFNQKKILNNLKKDIL 306
+ FS E +T E + Y + E +N KS LKK + K++ + +I
Sbjct: 76 VTFSIEVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIE 135
>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 = 26.8 bits (60), Expect = 6.7
Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 8/76 (10%)
Query: 3 KRVMGKISFIMLQDTSGPDSNGKIQLYISNEIIGKNLYTDFKNYDIGDIIGAKGTLFKTN 62
R KISFI L D S +Q+ + E+ G I +G L K+
Sbjct: 11 VRDSKKISFIELNDGS---CLKNLQVVVDKELTNFKEILKLS---TGSSIRVEGVLVKSP 64
Query: 63 TG--ELSIKVSSLKLI 76
++ ++++
Sbjct: 65 GAKQPFELQAEKIEVL 80
>gnl|CDD|129752 TIGR00669, asnA, aspartate--ammonia ligase, AsnA-type. This model
represents one of two non-homologous forms of
aspartate--ammonia ligase (asparagine synthetase) found
in E. coli. This type is also found in Haemophilus
influenzae, Treponema pallidum and Lactobacillus
delbrueckii, but appears to have a very limited
distribution. The fact that the protein from the H.
influenzae is more than 70 % identical to that from the
spirochete Treponema pallidum, but less than 65 %
identical to that from the closely related E. coli,
strongly suggests lateral transfer [Amino acid
biosynthesis, Aspartate family].
Length = 330
Score = 28.7 bits (64), Expect = 7.0
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 406 MPPASGCGIGVDRLIMLLTNSKNIRDV 432
+P G GIG RL MLL K+I +V
Sbjct: 287 LPQTIGGGIGQSRLAMLLLQLKHIGEV 313
>gnl|CDD|224935 COG2024, COG2024, Phenylalanyl-tRNA synthetase alpha subunit
(archaeal type) [Translation, ribosomal structure and
biogenesis].
Length = 536
Score = 28.6 bits (64), Expect = 8.2
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 403 EYGMP-PASGCGIGVDRLIMLLTNSKNIRDVI 433
EYG+ P G+GV+RL M+L + ++R ++
Sbjct: 318 EYGIDYPVMNLGLGVERLAMILHGADDVRSMV 349
>gnl|CDD|215458 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha
chain.
Length = 492
Score = 28.1 bits (63), Expect = 9.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 174 LKRLIIGGFN--KIFEINKNFRNEGISPRHNPEFTMIE 209
L +L GF + F I++ FRNE + H EF +E
Sbjct: 332 LYKLAQKGFKPKRYFSIDRVFRNEAVDRTHLAEFHQVE 369
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
0.319 0.138 0.395
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,084,905
Number of extensions: 2329376
Number of successful extensions: 2497
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2374
Number of HSP's successfully gapped: 150
Length of query: 442
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 342
Effective length of database: 6,502,202
Effective search space: 2223753084
Effective search space used: 2223753084
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 (21.7 bits)
S2: 61 (27.5 bits)