RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013865
(435 letters)
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 699 bits (1807), Expect = 0.0
Identities = 295/426 (69%), Positives = 338/426 (79%), Gaps = 17/426 (3%)
Query: 11 QEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQ 70
QE V+ S + ISKKAAKK AAK K R EA A AA+A +E+ PLA+NYGDVPL+
Sbjct: 3 QEAVEESGEKISKKAAKKAAAKAEKLRR----EATAKAAAASLEDEDDPLASNYGDVPLE 58
Query: 71 ELQSVNDPQTGKWSEAVNGREWTVVGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRE 130
ELQS V GREWT V L L EVLIRGRVHT R G K AF+V+R+
Sbjct: 59 ELQS-----------KVTGREWTDVSDLGEELAGSEVLIRGRVHTIRGKG-KSAFLVLRQ 106
Query: 131 RVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKL 190
TVQC+ V +VSK MV++ + LS ES+VDV GVVSVP +KG TQQVE+Q++K+
Sbjct: 107 SGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKGTTQQVEIQVRKI 166
Query: 191 YCVSRAAKT-PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFR 249
YCVS+A T P +EDA+RSE+EIEKA + G QL RV QDTRLNNRV+D+RT ANQ IFR
Sbjct: 167 YCVSKALATLPFNVEDAARSESEIEKALQTGEQLVRVGQDTRLNNRVLDLRTPANQAIFR 226
Query: 250 IQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMS 309
IQSQV N+FR+FLLS+ FVEIHTPKLIAG+SEGGSAVFRLDYKGQ ACLAQSPQLHKQM+
Sbjct: 227 IQSQVCNLFREFLLSKGFVEIHTPKLIAGASEGGSAVFRLDYKGQPACLAQSPQLHKQMA 286
Query: 310 ICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGL 369
ICGDF RVFE GPVFRAEDS+THRHLCEFTGLD+EMEIK+HYSEV+D+VD LFV IFDGL
Sbjct: 287 ICGDFRRVFEIGPVFRAEDSFTHRHLCEFTGLDLEMEIKEHYSEVLDVVDELFVAIFDGL 346
Query: 370 NNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPLGDLNTESERKLG 429
N CKKELEA+ +QYPFEPLKY PKTLRLTF EG+QMLK+AGVE+DPLGDLNTESERKLG
Sbjct: 347 NERCKKELEAIREQYPFEPLKYLPKTLRLTFAEGIQMLKEAGVEVDPLGDLNTESERKLG 406
Query: 430 QLVLEK 435
QLV EK
Sbjct: 407 QLVKEK 412
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 312 bits (800), Expect = e-101
Identities = 184/458 (40%), Positives = 258/458 (56%), Gaps = 67/458 (14%)
Query: 18 SQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDV----PLQELQ 73
S + + A K++ +E RK A A A A E+ L Y DV P+ +
Sbjct: 2 SSNHADAGAPAVEKKQSDKEARKAARLAEEKARA---AEKAALVEKYKDVFGAAPMVQ-- 56
Query: 74 SVNDPQTGKWSEAVNGREWTVVGALNG-SLKDQEVLIRGRVHTTRPVGNKLAFVVVRERV 132
S R + V L+ L D+ VLIR RV TTR G K+AF+V+R+
Sbjct: 57 ----------STTYKSRTFIPVAVLSKPELVDKTVLIRARVSTTRKKG-KMAFMVLRDGS 105
Query: 133 STVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQ-VEVQIKKLY 191
+VQ +A V+ D V KEM+ F+ + ESIVDV V + I + +E+++KK++
Sbjct: 106 DSVQAMAAVEGD-VPKEMIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIELKVKKIH 164
Query: 192 CVSRAAKT-PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRI 250
V+ + +T P T+EDASR E++ EG +VN DTRLN+R +D+RT A+ IFR+
Sbjct: 165 TVTESLRTLPFTLEDASRKESD------EGA---KVNFDTRLNSRWMDLRTPASGAIFRL 215
Query: 251 QSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMSI 310
QS+V FRQFL+ +F EIH+PK+I SEGG+ VF+L+Y + A LAQSPQL+KQM +
Sbjct: 216 QSRVCQYFRQFLIDSDFCEIHSPKIINAPSEGGANVFKLEYFNRFAYLAQSPQLYKQMVL 275
Query: 311 CGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLN 370
GD RVFE GPVFR+E+S THRHL EF GLDVEM I +HY EV+D+ + LF IF+ L
Sbjct: 276 QGDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDLAESLFNYIFERLA 335
Query: 371 NVCKKELEAVAKQYPFEPL-------------------------KYKPKT-------LRL 398
KEL+AV +QYPFEPL KY+ + LR+
Sbjct: 336 T-HTKELKAVCQQYPFEPLVWKLTPERMKELGVGVISEGVEPTDKYQARVHNMDSRMLRI 394
Query: 399 TFEEGVQMLKDAGVE-IDPLGDLNTESERKLGQLVLEK 435
+ +++L E + P D+NT +E+ LG+LV E+
Sbjct: 395 NYMHCIELLNTVLEEKMAPTDDINTTNEKLLGKLVKER 432
>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 = 281 bits (721), Expect = 3e-92
Identities = 96/213 (45%), Positives = 134/213 (62%), Gaps = 4/213 (1%)
Query: 225 RVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGS 284
N +T L+NR +D+RT Q IFRI+S+V FR+FL F E+HTPK+ + +EGG+
Sbjct: 1 DANLETLLDNRHLDLRTPKVQAIFRIRSEVLRAFREFLRENGFTEVHTPKITSTDTEGGA 60
Query: 285 AVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 344
+F++ Y G+ A LAQSPQL+K+M I RV+E GPVFRAE S T RHL EF L+ E
Sbjct: 61 ELFKVSYFGKPAYLAQSPQLYKEMLIAA-LERVYEIGPVFRAEKSNTRRHLSEFWMLEAE 119
Query: 345 MEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 404
M + Y+EVMD+++ L IF + C KELE V Q E LK R+T++E +
Sbjct: 120 MAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELV-NQLNRELLKPLEPFPRITYDEAI 178
Query: 405 QMLKDAGV--EIDPLGDLNTESERKLGQLVLEK 435
++L++ GV E+ DL+TE ER LG++V
Sbjct: 179 ELLREKGVEEEVKWGEDLSTEHERLLGEIVKGD 211
>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 = 270 bits (693), Expect = 8e-87
Identities = 122/327 (37%), Positives = 184/327 (56%), Gaps = 30/327 (9%)
Query: 105 QEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVD 164
QEV G VH R +G L FV++R+R +Q T VSK + ++ + L+ ES+V
Sbjct: 13 QEVTFMGWVHEIRDLG-GLIFVLLRDREGLIQ--ITAPAKKVSKNLFKWAKKLNLESVVA 69
Query: 165 VIGVVSVPDVEIKGAT-QQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQL 223
V G+V +IK E+ K+ ++ AK P+ ++ + AE+
Sbjct: 70 VRGIV-----KIKEKAPGGFEIIPTKIEVIN-EAKEPLPLDPTEKVPAEL---------- 113
Query: 224 PRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGG 283
DTRL+ R +D+R Q IFRI+S V R+FL E F+E+HTPKL+A ++EGG
Sbjct: 114 -----DTRLDYRFLDLRRPTVQAIFRIRSGVLESVREFLAEEGFIEVHTPKLVASATEGG 168
Query: 284 SAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDV 343
+ +F + Y + A L QSPQL+KQ + F RV+E GP+FRAE+ THRHL E T +D+
Sbjct: 169 TELFPITYFEREAFLGQSPQLYKQQLMAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDI 228
Query: 344 EMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEG 403
EM + H +VMDI++ L V +F+ + C +LE + + K+ RLT++E
Sbjct: 229 EMAFEDH-HDVMDILEELVVRVFEDVPERCAHQLETLEFKLEKPEGKFV----RLTYDEA 283
Query: 404 VQMLKDAGVEIDPLGDLNTESERKLGQ 430
++M GVEI DL+TE+E+ LG+
Sbjct: 284 IEMANAKGVEIGWGEDLSTEAEKALGE 310
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 268 bits (689), Expect = 6e-86
Identities = 121/331 (36%), Positives = 189/331 (57%), Gaps = 28/331 (8%)
Query: 105 QEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVD 164
+EV + G VH R +G +AF+++R+R +Q VK +E+ ++ L ES+V
Sbjct: 17 EEVTLAGWVHEIRDLG-GIAFLILRDRSGIIQV--VVKKKVD-EELFETIKKLKRESVVS 72
Query: 165 VIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLP 224
V G V A VEV +++ +++A + P+ ++ + + AE+
Sbjct: 73 VTGTV----KANPKAPGGVEVIPEEIEVLNKA-EEPLPLDISGKVLAEL----------- 116
Query: 225 RVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGS 284
DTRL+NR +D+R + IF+I+S+V FR+FL F EI TPK++A +EGG+
Sbjct: 117 ----DTRLDNRFLDLRRPRVRAIFKIRSEVLRAFREFLYENGFTEIFTPKIVASGTEGGA 172
Query: 285 AVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 344
+F +DY + A LAQSPQL+KQM + F RVFE GPVFRAE+ T RHL E+T +DVE
Sbjct: 173 ELFPIDYFEKEAYLAQSPQLYKQMMVGAGFERVFEIGPVFRAEEHNTSRHLNEYTSIDVE 232
Query: 345 MEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 404
M + +VMD+++ L +++ + C+KELE + + P R+T++E +
Sbjct: 233 MGFIDDHEDVMDLLENLLRYMYEDVAENCEKELELLGIELPVPETPIP----RITYDEAI 288
Query: 405 QMLKDAGVEIDPLGDLNTESERKLGQLVLEK 435
++LK G EI DL+TE ER LG+ V E+
Sbjct: 289 EILKSKGNEISWGDDLDTEGERLLGEYVKEE 319
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 260 bits (667), Expect = 1e-82
Identities = 109/327 (33%), Positives = 165/327 (50%), Gaps = 31/327 (9%)
Query: 105 QEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVD 164
QEV +RG VH R +G K+ F+V+R+ +Q V + V +E+ + + L+ ES V
Sbjct: 17 QEVTVRGWVHNKRDLG-KIIFLVLRDGSGFIQA--VVPKNKVYEELFKA-KKLTLESSVV 72
Query: 165 VIGVVSVPDVEIKGATQQVEVQIKKLYCVSRA-AKTPITIEDASRSEAEIEKASKEGVQL 223
V G+V A Q E+Q++K+ + A PI ++
Sbjct: 73 VTGIV----KASPKAPQGFELQVEKIEVLGEADPPYPIDKKE------------------ 110
Query: 224 PRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGG 283
+T L+NR +D+RT Q +F+I+S + R+F F E+HTP + A ++EGG
Sbjct: 111 -HSELETLLDNRHLDLRTPKIQAVFKIRSSILRAIREFFYENGFTEVHTPIITASATEGG 169
Query: 284 SAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDV 343
+F++DY + A L QSPQL+K+ RVF GP FRAE S T RHL EF LD
Sbjct: 170 GELFKVDYFDKEAYLTQSPQLYKEALAAA-LERVFTIGPTFRAEKSNTRRHLSEFWMLDP 228
Query: 344 EMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEG 403
EM ++VMD+ + L +F + C ELE + + R+T++E
Sbjct: 229 EMAFADL-NDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRITYKEA 287
Query: 404 VQMLKDAGVEIDPLG-DLNTESERKLG 429
+++L++ G E G DL TE ER LG
Sbjct: 288 IEILEEKGFEKVEWGDDLGTEHERYLG 314
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 152 bits (387), Expect = 1e-42
Identities = 61/196 (31%), Positives = 96/196 (48%), Gaps = 14/196 (7%)
Query: 227 NQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAV 286
+++TRL R +D+R Q +++S++ R+FL F+E+ TP L + EGG+
Sbjct: 1 SEETRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDERGFLEVETPILTKSTPEGGARD 60
Query: 287 FRLDYK--GQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 344
F + K + A L QSPQL+KQ+ + F RVF+ P FR ED T RH EFT LD+E
Sbjct: 61 FLVPSKFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFTQLDLE 120
Query: 345 MEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 404
M Y +VMD+ + L +F + ++ + F R+T+ E +
Sbjct: 121 MSFVD-YEDVMDLTEDLIKYVFKKVLGKREELELLGIELPEFP---------RITYAEAI 170
Query: 405 QMLKDAGVEIDPLGDL 420
+ + D L
Sbjct: 171 ERYG--SDKPDLRFGL 184
>gnl|CDD|239815 cd04320, AspRS_cyto_N, AspRS_cyto_N: N-terminal, anticodon
recognition domain of the type found in Saccharomyces
cerevisiae and human cytoplasmic 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 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.
Length = 102
Score = 142 bits (360), Expect = 2e-41
Identities = 53/102 (51%), Positives = 70/102 (68%), Gaps = 2/102 (1%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDV 165
EVLIR RVHT+R G KLAF+V+R++ T+Q + + VSK+MV++ SLS ESIVDV
Sbjct: 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDV 60
Query: 166 IGVVSVPDVEIKGATQQ-VEVQIKKLYCVSRAAKT-PITIED 205
G V P+ IK TQQ VE+ I+K+Y VS AA+ P +ED
Sbjct: 61 EGTVKKPEEPIKSCTQQDVELHIEKIYVVSEAAEPLPFQLED 102
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 133 bits (336), Expect = 7e-34
Identities = 86/308 (27%), Positives = 133/308 (43%), Gaps = 48/308 (15%)
Query: 96 GALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVR 155
G L S Q V + G VH R G L F+ +R+R VQ + S E
Sbjct: 7 GELRESHVGQTVTLSGWVHRRRDHG-GLIFIDLRDREGIVQVVFD---PEDSPEAFEVAS 62
Query: 156 SLSNESIVDVIGVVSV-PDVEI--KGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAE 212
L NE ++ V G V P+ I T ++EV +++ ++ + P IED
Sbjct: 63 RLRNEFVIQVTGTVRARPEGTINPNLPTGEIEVLAEEIEVLNASKTLPFQIEDE------ 116
Query: 213 IEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHT 272
+++ RL R +D+R Q +++S+V R FL + F+EI T
Sbjct: 117 -----------TNASEEIRLKYRYLDLRRPEMQKNLKLRSKVTKAIRNFLDDQGFLEIET 165
Query: 273 PKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQLHKQMSICGDFGRVFETGPVFR 325
P L + EG R D+ G+ L QSPQL KQ+ + F R ++ FR
Sbjct: 166 PILTKSTPEGA----R-DFLVPSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFR 220
Query: 326 AEDSYTHRHLCEFTGLDVEME-IKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQY 384
ED R EFT +D+EM + + +VM+++++L +F V EL+
Sbjct: 221 DEDLRADRQP-EFTQIDLEMSFVDEE--DVMELIEKLLRYVF---KEVKGIELKT----- 269
Query: 385 PFEPLKYK 392
PF + Y
Sbjct: 270 PFPRMTYA 277
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 131 bits (332), Expect = 8e-34
Identities = 92/356 (25%), Positives = 148/356 (41%), Gaps = 51/356 (14%)
Query: 93 TVVGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVR 152
++ L G QEV +RG V T R G K+AF+ +R+ Q E
Sbjct: 5 SIKDILKGKYVGQEVTVRGWVRTKRDSG-KIAFLQLRDGSCFKQLQVVKDNGE---EYFE 60
Query: 153 FVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKT-PITIEDASRSEA 211
++ L+ S V V G V VE A Q E+Q K+ + + PI + S
Sbjct: 61 EIKKLTTGSSVIVTGTV----VESPRAGQGYELQATKIEVIGEDPEDYPIQKKRHSI--- 113
Query: 212 EIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIH 271
+ + RT + RI++ + +F FV +
Sbjct: 114 -----------------EFLREIAHLRPRTNKFGAVMRIRNTLAQAIHEFFNENGFVWVD 156
Query: 272 TPKLIAGSSEGGSAVFRL---------DYKGQSACLAQSPQLHKQMSICGDFGRVFETGP 322
TP + A EG +FR+ D+ G+ A L S QL+ + G+V+ GP
Sbjct: 157 TPIITASDCEGAGELFRVTTLDLDFSKDFFGKEAYLTVSGQLYAEAYAMA-LGKVYTFGP 215
Query: 323 VFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDG-LNNVCKKELEAVA 381
FRAE+S T RHL EF ++ EM + MD+ + + + L N C +LE +
Sbjct: 216 TFRAENSNTRRHLAEFWMIEPEMAFADL-EDNMDLAEEMLKYVVKYVLEN-CPDDLEFLN 273
Query: 382 KQYP---FEPLK--YKPKTLRLTFEEGVQMLKDAGVEIDPL---G-DLNTESERKL 428
++ E L+ + R+T+ E +++L+ +G + + G DL +E ER L
Sbjct: 274 RRVDKGDIERLENFIESPFPRITYTEAIEILQKSGKKFEFPVEWGDDLGSEHERYL 329
>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 = 121 bits (305), Expect = 3e-30
Identities = 81/344 (23%), Positives = 146/344 (42%), Gaps = 44/344 (12%)
Query: 103 KDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESI 162
EV + G V T R K+ F+ + + S++ + V + + + ++SL+ S
Sbjct: 15 VGDEVTVSGWVRTKRSSK-KIIFLELNDG-SSLGPIQAVINGEDNPYLFQLLKSLTTGSS 72
Query: 163 VDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQ 222
V V G V VE G Q VE+Q+KK+ V A + Q
Sbjct: 73 VSVTGKV----VESPGKGQPVELQVKKIEVVGEAEPDDYPL------------------Q 110
Query: 223 LPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEG 282
+ + + + +RT + R+++ + ++ F + P L + EG
Sbjct: 111 KKEHSLEFLRDIAHLRLRTNTLGAVMRVRNALSQAIHRYFQENGFTWVSPPILTSNDCEG 170
Query: 283 GSAVFRL---------DYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHR 333
+FR+ D+ G+ A L S QL+ + +V+ GP FRAE S T R
Sbjct: 171 AGELFRVSTGNIDFSQDFFGKEAYLTVSGQLYLETYALA-LSKVYTFGPTFRAEKSNTSR 229
Query: 334 HLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKP 393
HL EF ++ EM ++++ + + L I + C +EL+ + K + + +K
Sbjct: 230 HLSEFWMIEPEMAFAN-LNDLLQLAETLIKYIIKAVLENCSQELKFLEKNFDKDLIKRLE 288
Query: 394 KTL-----RLTFEEGVQMLKDAG--VEIDPL--GDLNTESERKL 428
+ R+T+ + +++LK++ E + DL TE ER L
Sbjct: 289 NIINNKFARITYTDAIEILKESDKNFEYEDFWGDDLQTEHERFL 332
>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 = 117 bits (295), Expect = 2e-28
Identities = 79/308 (25%), Positives = 132/308 (42%), Gaps = 49/308 (15%)
Query: 95 VGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFV 154
G L Q V + G V+ R +G L F+ +R+R VQ PD+ + ++ + +
Sbjct: 6 CGQLRTEHLGQTVTLAGWVNRRRDLG-GLIFIDLRDRSGIVQ--VVCDPDADALKLAKGL 62
Query: 155 RSLSNESIVDVIGVVSVPDVEIKG---ATQQVEVQIKKLYCVSRAAKTPITIEDASRSEA 211
R NE +V V G VS T ++E+ + + ++++ P+ IE
Sbjct: 63 R---NEDVVQVKGKVSARPEGNINRNLDTGEIEILAESITLLNKSKTPPLIIEKTD---- 115
Query: 212 EIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIH 271
++ RL R +D+R Q +++ +V R FL + F+EI
Sbjct: 116 --------------AEEEVRLKYRYLDLRRPEMQQRLKLRHKVTKAVRNFLDQQGFLEIE 161
Query: 272 TPKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQLHKQMSICGDFGRVFETGPVF 324
TP L + EG DY KG+ L QSPQL KQ+ + R ++ F
Sbjct: 162 TPMLTKSTPEGAR-----DYLVPSRVHKGEFYALPQSPQLFKQLLMVSGVDRYYQIARCF 216
Query: 325 RAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQY 384
R ED R EFT +D+EM +VM+++++L +F E++ + +
Sbjct: 217 RDEDLRADRQ-PEFTQIDMEMSFMTQ-EDVMELIEKLVSHVF--------LEVKGIDLKK 266
Query: 385 PFEPLKYK 392
PF + Y
Sbjct: 267 PFPVMTYA 274
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 114 bits (289), Expect = 2e-27
Identities = 92/322 (28%), Positives = 140/322 (43%), Gaps = 67/322 (20%)
Query: 96 GALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVR 155
G L S Q V + G VH R G L F+ +R+R VQ PD+ + E+
Sbjct: 9 GELRESHVGQTVTLCGWVHRRRDHGG-LIFIDLRDREGIVQV--VFDPDAEAFEVAE--- 62
Query: 156 SLSNESIVDVIGVVSV-PDVEI--KGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAE 212
SL +E ++ V G V P+ + T ++EV +L ++++ P I+D E
Sbjct: 63 SLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVLASELEVLNKSKTLPFPIDD------E 116
Query: 213 IEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHT 272
+ V+++ RL R +D+R Q +++S+V + R FL F+EI T
Sbjct: 117 ED-----------VSEELRLKYRYLDLRRPEMQKNLKLRSKVTSAIRNFLDDNGFLEIET 165
Query: 273 PKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQLHKQMSICGDFGRVFETGPVFR 325
P L + EG A R DY G+ L QSPQL KQ+ + F R ++ FR
Sbjct: 166 PILTKSTPEG--A--R-DYLVPSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFR 220
Query: 326 AEDSYTHRHLCEFTGLDVEMEIKKHYS-----EVMDIVDRLFVTIFDGLNNVCKKELEAV 380
ED R EFT +D+EM S +VM +++ L +F V +L
Sbjct: 221 DEDLRADRQP-EFTQIDIEM------SFVTQEDVMALMEGLIRHVF---KEVLGVDLPT- 269
Query: 381 AKQYPFEPLKYKPKTLRLTFEE 402
PF R+T+ E
Sbjct: 270 ----PFP---------RMTYAE 278
>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 = 107 bits (268), Expect = 2e-26
Identities = 46/162 (28%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 248 FRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDY--KGQSACLAQSPQLH 305
F+++S++ R F+ F+E+ TP L + G+ F + Y G L SPQL
Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLF 60
Query: 306 KQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTI 365
K+ + G RVFE FR ED RH EFT +D+EM Y +V+++ +RL +
Sbjct: 61 KKRLMVGGLDRVFEINRNFRNEDL-RARHQPEFTMMDLEMAFAD-YEDVIELTERLVRHL 118
Query: 366 FDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQML 407
+ V + P RLT+ E ++
Sbjct: 119 AREVLGVTAVTYG----FELEDFGLPFP---RLTYREALERY 153
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 103 bits (260), Expect = 9e-25
Identities = 60/191 (31%), Positives = 91/191 (47%), Gaps = 15/191 (7%)
Query: 247 IFRIQSQVGNIFRQFLLSENFVEIHTP-------KLIAGSSEGGSAVFRLDYKGQSACLA 299
+ ++QS + R+FL FVE+ P L+ S+ +D+ G LA
Sbjct: 29 VLKVQSSILRYTREFLDGRGFVEVLPPIISPSTDPLMGLGSDLPVKQISIDFYGVEYYLA 88
Query: 300 QSPQLHKQMSICGDFGRVFETGPVFRAE--DSYTHRHLCEFTGLDVEMEIKKHYSEVMDI 357
S LHKQ+++ G++F P FR E D T RHL EFT LD+E+E EVMD+
Sbjct: 89 DSMILHKQLAL-RMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEIE-GADLDEVMDL 146
Query: 358 VDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPL 417
++ L + L + ELE + P K R+T +E V++L + G L
Sbjct: 147 IEDLIKYLVKELLEEHEDELEFFGRDLP----HLKRPFKRITHKEAVEILNEEGCRGIDL 202
Query: 418 GDLNTESERKL 428
+L +E E+ L
Sbjct: 203 EELGSEGEKSL 213
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 88.1 bits (218), Expect = 1e-18
Identities = 81/259 (31%), Positives = 115/259 (44%), Gaps = 25/259 (9%)
Query: 96 GALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVR 155
G L+ +EV + G V R G L F+ +R+R +Q A P++ ++
Sbjct: 10 GHLSLDDTGREVCLAGWVDAFRDHGELL-FIHLRDRNGFIQ--AVFSPEAAPADVYELAA 66
Query: 156 SLSNESIVDVIGVVSV-------PDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASR 208
SL E V + G V P +E T +EV +++L ++ + P I D
Sbjct: 67 SLRAEFCVALQGEVQKRLEETENPHIE----TGDIEVFVRELSILAASEALPFAISD--- 119
Query: 209 SEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFV 268
+A A G VN+D RL R +DIR A Q + ++ R FL S F+
Sbjct: 120 -KAMTAGAGSAGAD--AVNEDLRLQYRYLDIRRPAMQDHLAKRHRIIKCARDFLDSRGFL 176
Query: 269 EIHTPKLIAGSSEGGSAVF---RLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFR 325
EI TP L + EG R+ K A L QSPQL KQ+ + F R F+ FR
Sbjct: 177 EIETPILTKSTPEGARDYLVPSRIHPKEFYA-LPQSPQLFKQLLMIAGFERYFQLARCFR 235
Query: 326 AEDSYTHRHLCEFTGLDVE 344
ED +R EFT LD+E
Sbjct: 236 DEDLRPNRQ-PEFTQLDIE 253
>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 = 83.4 bits (207), Expect = 5e-18
Identities = 50/150 (33%), Positives = 73/150 (48%), Gaps = 18/150 (12%)
Query: 248 FRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVF----RLDYKGQSACLAQSPQ 303
R++S+V R FL + FVEI TP L S+ G+ F RL + G+ L QSPQ
Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTK-STPEGARDFLVPSRL-HPGKFYALPQSPQ 58
Query: 304 LHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEME-IKKHYSEVMDIVDRLF 362
L KQ+ + F R F+ FR ED R EFT +D+EM + + ++M +++ L
Sbjct: 59 LFKQLLMVSGFDRYFQIARCFRDEDLRADRQ-PEFTQIDIEMSFVDQE--DIMSLIEGLL 115
Query: 363 VTIFDGLNNVCKKELEAVAKQYPFEPLKYK 392
+F KE+ V PF + Y
Sbjct: 116 KYVF--------KEVLGVELTTPFPRMTYA 137
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 81.4 bits (201), Expect = 2e-16
Identities = 87/304 (28%), Positives = 121/304 (39%), Gaps = 56/304 (18%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDV 165
V + G V R +G L F+ VR+ VQ PD E R L NE +V V
Sbjct: 74 RVTLCGWVDLHRDMGG-LTFLDVRDHTGIVQ--VVTLPDE-FPEAHRTANRLRNEYVVAV 129
Query: 166 IGVV---SVPDVEIKGATQQVEV---QIKKLYCVSRAAKTPITIEDASRSEAEIEKASKE 219
G V K T VEV + L V+++ +T A+ +K
Sbjct: 130 EGTVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVT-------TADEQK---- 178
Query: 220 GVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLS-ENFVEIHTPKLIAG 278
+ ++ RL RV+D+R R++ +V + R++L FVEI TP L
Sbjct: 179 ----DSIKEEVRLRYRVLDLRRPQMNANLRLRHRVVKLIRRYLEDVHGFVEIETPILSRS 234
Query: 279 SSEGGSAVFRLDY-------KGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYT 331
+ EG DY G L QSPQL KQM + F R ++ FR ED
Sbjct: 235 TPEGA-----RDYLVPSRVQPGTFYALPQSPQLFKQMLMVSGFDRYYQIARCFRDEDLRA 289
Query: 332 HRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNN--VCK--KELEAVAKQYPFE 387
R EFT LD+E+ + D L LN + + KE++ V PF
Sbjct: 290 DRQ-PEFTQLDMELAF-------TPLEDML------KLNEDLIRQVFKEIKGVQLPNPFP 335
Query: 388 PLKY 391
L Y
Sbjct: 336 RLTY 339
>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 = 66.4 bits (163), Expect = 7e-14
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDV 165
EV + G VH+ R G L F+ +R+ VQ + E L ES+V V
Sbjct: 1 EVTLAGWVHSRRDHG-GLIFIDLRDGSGIVQVVV---NKEELGEFFEEAEKLRTESVVGV 56
Query: 166 IGVVSVPDVEIKGATQQVEVQIKKLYCVSR 195
G V V E AT ++E+Q ++L +S+
Sbjct: 57 TGTV-VKRPEGNLATGEIELQAEELEVLSK 85
>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 = 70.7 bits (174), Expect = 2e-13
Identities = 49/191 (25%), Positives = 84/191 (43%), Gaps = 29/191 (15%)
Query: 248 FRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSA--------VFRLDYKGQSAC 297
F ++S++ + R+FL F+E+ TP L IAG G +A +D
Sbjct: 8 FIVRSKIISYIRKFLDDRGFLEVETPMLQPIAG---GAAARPFITHHNALDMDLY----- 59
Query: 298 LAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDI 357
L +P+L+ + I G F RV+E G FR E H EFT ++ Y+++MD+
Sbjct: 60 LRIAPELYLKRLIVGGFERVYEIGRNFRNE-GIDLTHNPEFTMIEFYEAYAD-YNDMMDL 117
Query: 358 VDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPL 417
+ LF + + + K +Y + L + P R+T + ++ + G++ L
Sbjct: 118 TEDLFSGL---VKKINGKT----KIEYGGKELDFTPPFKRVTMVDALK--EKTGIDFPEL 168
Query: 418 GDLNTESERKL 428
E KL
Sbjct: 169 DLEQPEELAKL 179
>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 = 70.5 bits (173), Expect = 5e-13
Identities = 80/334 (23%), Positives = 137/334 (41%), Gaps = 57/334 (17%)
Query: 102 LKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNES 161
K+ EV I GR+ R K F+ +++ +Q V D + ++ F L +
Sbjct: 51 DKNIEVSIAGRIMARR-SMGKATFITLQDESGQIQLY--VNKDDLPEDFYEFDEYLLD-- 105
Query: 162 IVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGV 221
+ D+IGV P K T ++ V + +L +++A + D G+
Sbjct: 106 LGDIIGVTGYP---FKTKTGELSVHVTELQILTKALRPL---PDKFH-----------GL 148
Query: 222 QLPRVNQDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSS 280
+Q+TR R +D I ++ F ++S++ R+FL F+E+ TP L
Sbjct: 149 T----DQETRYRQRYLDLIVNPDSRQTFLVRSKIIKAIRRFLDDRGFIEVETPML---QV 201
Query: 281 EGGSAVFR--------LD---YKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDS 329
G A R LD Y L +P+L+ + I G F +V+E G FR E
Sbjct: 202 IPGGANARPFITHHNALDMDLY------LRIAPELYLKRLIVGGFEKVYEIGRNFRNE-G 254
Query: 330 YTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPL 389
H EFT ++ Y ++MD+ + LF + ++ L Y +
Sbjct: 255 VDTTHNPEFTMIEFYQAYAD-YEDLMDLTENLFKFL-------AQELLGTTKITYGELEI 306
Query: 390 KYKPKTLRLTFEEGVQML-KDAGVEIDPLGDLNT 422
+K R+T E ++ + G++ D L D T
Sbjct: 307 DFKKPFKRITMVEAIKKYDMETGIDFDDLKDFET 340
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 69.2 bits (170), Expect = 1e-12
Identities = 96/374 (25%), Positives = 160/374 (42%), Gaps = 60/374 (16%)
Query: 15 DSSSQSISKKAAKKE--AAKKAKEERRKEAEAAASAASALSIEEEGPLA--------NNY 64
+S+ + +SK A KK A + +E+ KE AA+AA+A A Y
Sbjct: 2 ESNGEPLSKNALKKRLKAKQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETMDPTQY 61
Query: 65 GDVPLQELQSV----NDPQTGKWSEAVNGREW-TVVGAL-NGS-LKDQEVLIRGRVHTTR 117
L++++++ +P K+ E G+L NG L+D V + GR+ R
Sbjct: 62 RANRLKKVEALRAKGVEPYPYKFDVTHTAPELQEKYGSLENGEELEDVSVSVAGRIMAKR 121
Query: 118 PVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIK 177
G KLAF +R+ +Q A K + + F + S D++GV P
Sbjct: 122 AFG-KLAFYDLRDDGGKIQLYADKK--RLDLDEEEFEKLHSLVDRGDIVGVTGTP----- 173
Query: 178 GATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPR-----VNQDTRL 232
G T++ E+ I + E +K + LP +Q+TR
Sbjct: 174 GKTKKGELSI----FPT-----------------SFEVLTKCLLMLPDKYHGLTDQETRY 212
Query: 233 NNRVIDIRTLAN---QGIFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSAVF 287
R +D+ +AN + IFR ++++ + R+FL F+E+ TP L IAG + V
Sbjct: 213 RQRYLDL--IANPEVRDIFRTRAKIISYIRRFLDDRGFLEVETPMLNMIAGGAAARPFVT 270
Query: 288 RLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEI 347
+ L + +LH + + G F RV+E G FR E T RH EFT +
Sbjct: 271 HHNDLNMDLYLRIATELHLKRLVVGGFERVYEIGRQFRNEGIST-RHNPEFTTCEFYQAY 329
Query: 348 KKHYSEVMDIVDRL 361
Y+++M++ + +
Sbjct: 330 AD-YNDMMELTEEM 342
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 61.1 bits (149), Expect = 4e-10
Identities = 52/205 (25%), Positives = 85/205 (41%), Gaps = 28/205 (13%)
Query: 228 QDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGS 284
++ R R +D I ++ F +S++ R+FL F+E+ TP L I G G +
Sbjct: 159 KEIRYRQRYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPG---GAA 215
Query: 285 A-VFRLDYKGQSACLAQ--SPQLHKQMSICGDFGRVFETGPVFRAED-SYTHRHLCEFTG 340
A F + L +P+L+ + I G F RVFE G FR E TH EFT
Sbjct: 216 ARPFITHHNALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTTHNP--EFTM 273
Query: 341 LD---VEMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLR 397
L+ + Y ++MD+ + L + K+ Y + + + R
Sbjct: 274 LEFYQAYAD----YEDLMDLTEELIKE-------LAKEVNGTTKVTYGGQEIDFSKPFKR 322
Query: 398 LTFEEGVQMLKDAGVEIDPLGDLNT 422
+T + ++ GV+ D L D
Sbjct: 323 ITMVDALKE--YLGVDFDDLFDDEE 345
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 55.8 bits (134), Expect = 2e-08
Identities = 38/142 (26%), Positives = 73/142 (51%), Gaps = 5/142 (3%)
Query: 227 NQDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTP--KLIAGSSEGG 283
+Q+ R R +D I ++ F ++S++ RQF+++ F+E+ TP ++I G +
Sbjct: 162 DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASAR 221
Query: 284 SAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDV 343
+ + L +P+L+ + + G F RVFE FR E + RH EFT +++
Sbjct: 222 PFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNE-GISVRHNPEFTMMEL 280
Query: 344 EMEIKKHYSEVMDIVDRLFVTI 365
M Y +++++ + LF T+
Sbjct: 281 YMAYAD-YHDLIELTESLFRTL 301
>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 = 51.8 bits (125), Expect = 4e-08
Identities = 40/148 (27%), Positives = 60/148 (40%), Gaps = 25/148 (16%)
Query: 96 GALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVR 155
G L S QEV + G V R G L F+ +R+R VQ + P+
Sbjct: 6 GELRESHVGQEVTLCGWVQRRRDHG-GLIFIDLRDRYGIVQVV--FDPEE--APEFELAE 60
Query: 156 SLSNESIVDVIGVVSV---PDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAE 212
L NES++ V G V V K T ++EV +L +++A P I+D
Sbjct: 61 KLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKAKTLPFEIDDDV----- 115
Query: 213 IEKASKEGVQLPRVNQDTRLNNRVIDIR 240
V+++ RL R +D+R
Sbjct: 116 ------------NVSEELRLKYRYLDLR 131
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 55.0 bits (132), Expect = 5e-08
Identities = 88/415 (21%), Positives = 152/415 (36%), Gaps = 75/415 (18%)
Query: 21 ISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQSVNDPQT 80
ISK +A K ++A R + + A+ +S I + YG +
Sbjct: 53 ISKASATKTVTQEASRAPRSKLDLPAAYSSFRGITPISEVRERYGYL------------- 99
Query: 81 GKWSEAVNGREWTVVGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLAT 140
A R V + GRV + R +G K+ FV +R + +Q +
Sbjct: 100 -----ASGDRAAQAT-----------VRVAGRVTSVRDIG-KIIFVTIRSNGNELQVVGQ 142
Query: 141 VKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKTP 200
V +++ + SL + D+IG VP R +
Sbjct: 143 VGEHFTREDLKKLKVSLR---VGDIIGADGVP---------------------CRMQRGE 178
Query: 201 ITIEDASRSEAEIEKASKEGVQLPRV-------NQDTRLNNRVIDIRTLANQGIF---RI 250
+++ ASR + V P + + D + R D+ T N + +
Sbjct: 179 LSVA-ASRMLILSPYVCTDQVVCPNLRGFTVLQDNDVKYRYRFTDMMT--NPCVIETIKK 235
Query: 251 QSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQM 308
+ + R + NFVE+ TP L +A + S V + L +P+LH +
Sbjct: 236 RHVMLQALRDYFNERNFVEVETPVLHTVASGANAKSFVTHHNANAMDLFLRVAPELHLKQ 295
Query: 309 SICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKH-YSEVMDIVDRLFVTIFD 367
I G R++E G VFR ED+ H EFT E H Y ++M + + +F +
Sbjct: 296 CIVGGMERIYEIGKVFRNEDA-DRSHNPEFT--SCEFYAAYHTYEDLMPMTEDIFRQLAM 352
Query: 368 GLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPLGDLNT 422
+N ++ + R++ + +Q + +GVE P +LNT
Sbjct: 353 RVNGTTVVQIYPENAHGNPVTVDLGKPFRRVSVYDEIQRM--SGVEFPPPNELNT 405
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 52.7 bits (126), Expect = 3e-07
Identities = 47/158 (29%), Positives = 79/158 (50%), Gaps = 14/158 (8%)
Query: 290 DYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKK 349
D+ G+ A L S QL + C V+ GP FRAE+S+T RHL EF ++ E+
Sbjct: 303 DFFGRQAFLTVSGQLQVETYACA-LSSVYTFGPTFRAENSHTSRHLAEFWMVEPEIAFAD 361
Query: 350 HYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQYP---FEPLKYKPKTL--RLTFEEGV 404
+ M+ + + L + C ++E +AK + + L+ T R+T+ E +
Sbjct: 362 LEDD-MNCAEAYVKYMCKWLLDKCFDDMELMAKNFDSGCIDRLRMVASTPFGRITYTEAI 420
Query: 405 QMLKDA---GVEID---PLG-DLNTESERKLGQLVLEK 435
++L++A G E D G DL +E ER L +++ +K
Sbjct: 421 ELLEEAVAKGKEFDNNVEWGIDLASEHERYLTEVLFQK 458
Score = 34.6 bits (79), Expect = 0.10
Identities = 49/194 (25%), Positives = 76/194 (39%), Gaps = 37/194 (19%)
Query: 102 LKDQEVLIRGRVHTTRPVGNK-LAFVVVRERVSTVQCLAT--VKPDSVSKEMVRFVRSLS 158
L Q+V I G V T R G AF+ V + C A V DS ++ V +
Sbjct: 48 LAGQKVRIGGWVKTGREQGKGTFAFLEVNDG----SCPANLQVMVDSSLYDLSTLVAT-- 101
Query: 159 NESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVS--RAAKTPITIEDASRSEAEIEKA 216
+ V V GV+ VP E KG Q++E+ ++K+ V K P
Sbjct: 102 -GTCVTVDGVLKVPP-EGKGTKQKIELSVEKVIDVGTVDPTKYP---------------- 143
Query: 217 SKEGVQLPRVNQDTRLNNRVIDIRTLAN--QGIFRIQSQVGNIFRQFLLSENFVEIHTPK 274
LP+ V+ +R+ N + RI++ + F +F+ IHTP
Sbjct: 144 ------LPKTKLTLEFLRDVLHLRSRTNSISAVARIRNALAFATHSFFQEHSFLYIHTPI 197
Query: 275 LIAGSSEGGSAVFR 288
+ EG +F+
Sbjct: 198 ITTSDCEGAGEMFQ 211
>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 = 50.6 bits (121), Expect = 3e-07
Identities = 24/121 (19%), Positives = 43/121 (35%), Gaps = 16/121 (13%)
Query: 258 FRQFLLSENFVEIHTPKLIAGSSEGGSA------VFRLDYKGQSACLAQSPQLHKQMS-- 309
R+F+ F E+ TP + + + + L + +
Sbjct: 9 LRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFV 68
Query: 310 --ICGDFGRVFETGPVFRAED-SYTHRHLCEFTGLDVEM-----EIKKHYSEVMDIVDRL 361
I R+ E GP FR E R + EFT L+ E+ E + E++++ + L
Sbjct: 69 SHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEFEELIELTEEL 128
Query: 362 F 362
Sbjct: 129 L 129
>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 = 47.3 bits (113), Expect = 7e-07
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 105 QEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVD 164
+EV + G VH R +G + FV++R+R VQ T V KE+ + VR LS ES++
Sbjct: 13 EEVTVAGWVHEIRDLG-GIKFVILRDREGIVQ--VTAPKKKVDKELFKTVRKLSRESVIS 69
Query: 165 VIGVV 169
V G V
Sbjct: 70 VTGTV 74
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 50.4 bits (120), Expect = 1e-06
Identities = 73/307 (23%), Positives = 125/307 (40%), Gaps = 63/307 (20%)
Query: 105 QEVLIRGRVHTTRPVGNKLAFVVVRER--VSTVQCLATVKPDSVSKEMVRFVRSLSNESI 162
+ + + G V T R + + F+ V + +S +QC+ T PD+ + V + S+
Sbjct: 108 KTLNVMGWVRTLR-AQSSVTFIEVNDGSCLSNMQCVMT--PDAEGYDQVESGLITTGASV 164
Query: 163 VDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKT-PITIEDASRSEAEIEKASKEGV 221
+ V G V V +G Q+VE+++ K+ V ++ + PI + SR
Sbjct: 165 L-VQGTV----VSSQGGKQKVELKVSKIVVVGKSDPSYPIQKKRVSR------------- 206
Query: 222 QLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTP-------- 273
+ R R RT + R+++ + +F FV + +P
Sbjct: 207 EFLRTKAHLR-------PRTNTFGAVARVRNALAYATHKFFQENGFVWVSSPIITASDCE 259
Query: 274 ---------KLIAGSSE-GGSAVFRL------------DYKGQSACLAQSPQLHKQMSIC 311
LI S+E GGS V + D+ G+ A L S QL+ + +
Sbjct: 260 GAGEQFCVTTLIPNSAENGGSLVDDIPKTKDGLIDWSQDFFGKPAFLTVSGQLNGE-TYA 318
Query: 312 GDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNN 371
V+ GP FRAE+S T RHL EF ++ E+ ++ L + L N
Sbjct: 319 TALSDVYTFGPTFRAENSNTSRHLAEFWMIEPELAFADLNDDMACATAYLQYVVKYILEN 378
Query: 372 VCKKELE 378
CK+++E
Sbjct: 379 -CKEDME 384
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 47.7 bits (113), Expect = 8e-06
Identities = 38/133 (28%), Positives = 54/133 (40%), Gaps = 25/133 (18%)
Query: 223 LPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEG 282
+PRVN+ + + DI N S N A SS
Sbjct: 269 IPRVNKKNKKGEKREDILNTCNANNNNGNSSSSN--------------------AVSSPA 308
Query: 283 GSAVFRLDYK----GQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEF 338
+ +DYK + A L S QL + ++C G V+ GP FRAE+S+T RHL EF
Sbjct: 309 YPDQYLIDYKKDFFSKQAFLTVSGQLSLE-NLCSSMGDVYTFGPTFRAENSHTSRHLAEF 367
Query: 339 TGLDVEMEIKKHY 351
++ E+ Y
Sbjct: 368 WMIEPEIAFADLY 380
Score = 28.5 bits (63), Expect = 9.1
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 247 IFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVF 287
+ RI++ + F S F+ IHTP + EGG +F
Sbjct: 214 VIRIRNALAIATHLFFQSRGFLYIHTPLITTSDCEGGGEMF 254
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 47.0 bits (113), Expect = 1e-05
Identities = 44/141 (31%), Positives = 66/141 (46%), Gaps = 32/141 (22%)
Query: 247 IFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSAVFR--------LD---YKG 293
FR +S++ + R+FL + F+E+ TP L IAG G +A R LD Y
Sbjct: 171 TFRKRSKIISAIRRFLDNRGFLEVETPMLQPIAG---GAAA--RPFITHHNALDIDLY-- 223
Query: 294 QSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIK---KH 350
L +P+L+ + I G F RV+E G FR E T RH EFT +E
Sbjct: 224 ----LRIAPELYLKRLIVGGFERVYEIGRNFRNEGIDT-RHNPEFT----MLEFYQAYAD 274
Query: 351 YSEVMDIVDRLFVTIFDGLNN 371
Y+++MD+ + L + +
Sbjct: 275 YNDMMDLTEELIRHLAQAVLG 295
>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 = 41.1 bits (97), Expect = 5e-05
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 12/85 (14%)
Query: 107 VLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVI 166
V + GRV + R G K+AF+ +R+ ++Q + +E + + L +V V
Sbjct: 1 VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLF------KEEAEKLAKKLKEGDVVLVT 54
Query: 167 GVVSVPDVEIKGATQQVEVQIKKLY 191
G V ++E+ ++++
Sbjct: 55 GKVKKRP------GGELELVVEEIE 73
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 41.7 bits (98), Expect = 5e-04
Identities = 55/242 (22%), Positives = 85/242 (35%), Gaps = 55/242 (22%)
Query: 130 ERVSTVQCLATVKPDSVSKEM----VRFVRSLSNES--IVDVIGVVSVPDVEIKGATQQV 183
E + V+ P K M VR + L N + G VP + + +
Sbjct: 88 EDKTQVKVKVVSAPTKKKKAMPKSVVRAPKPLENPVPAQAESSGSKPVPSIPVSTPEVKA 147
Query: 184 E------VQIKKL-YCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRV 236
Q +L +S K + E E E E S+ L ++ ++ R
Sbjct: 148 PAPALTPSQKDRLETLLSPKDKISLNSEKPKFKELESELVSRRKNDLKQMYEEDR----- 202
Query: 237 IDIRTLANQGIFRIQSQVGNIFR---QFLLSENFVEIHTPKLIAGSS----------EGG 283
+ +G + R +F + F+EI +P LI E
Sbjct: 203 --------------EDYLGKLERDITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELS 248
Query: 284 SAVFRLDYKGQSACLAQ--SPQL----HKQMSICGDFGRVFETGPVFRAEDSYTHRHLCE 337
+FR+D ++ CL +P L K I D ++FE GP +R E S HL E
Sbjct: 249 KQIFRVD---KNFCLRPMLAPGLYNYLRKLDRILPDPIKIFEIGPCYRKE-SDGKEHLEE 304
Query: 338 FT 339
FT
Sbjct: 305 FT 306
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 40.2 bits (94), Expect = 0.002
Identities = 30/111 (27%), Positives = 53/111 (47%), Gaps = 3/111 (2%)
Query: 274 KLIAGSSEGGSAV-FRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTH 332
KL G+S + F D+ + L S +LH + C G V+ GP FRA+ +
Sbjct: 349 KLKTGTSVKADKLSFSKDFFSRPTYLTVSGRLHLESYACA-LGNVYTFGPRFRADRIDSA 407
Query: 333 RHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFDGLNNVCKKELEAVAKQ 383
RHL E ++VEM + + M+ + F + + C ++++ V+K+
Sbjct: 408 RHLAEMWMVEVEMAFSE-LEDAMNCAEDYFKFLCKWVLENCSEDMKFVSKR 457
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 40.0 bits (93), Expect = 0.002
Identities = 70/324 (21%), Positives = 127/324 (39%), Gaps = 50/324 (15%)
Query: 27 KKEAAKKAKEERRKEAEAAASAA------SALSIEEEGPLANNYGDVPLQELQSVNDPQ- 79
KK + +A ++++KE EA S E++ N Y P + +++ P+
Sbjct: 61 KKVRSVQASKDKKKEEEAEVDPRLYYENRSKFIQEQKAKGINPY---PHKFERTITVPEF 117
Query: 80 TGKWSEAVNGREWTVVGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLA 139
K+ + +G L+D + + GR+ G KL F + + +Q LA
Sbjct: 118 VEKYQDLASGEH----------LEDTILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLA 167
Query: 140 TVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKT 199
+K F D++G+V P KG ++ + K+ +S
Sbjct: 168 NFAFHDHTKS--NFAECYDKIRRGDIVGIVGFPGKSKKG---ELSIFPKETIILSPCLHM 222
Query: 200 -PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLAN-QGIFRIQSQVGNI 257
P+ K G++ + + R R +D+ + + F ++++ N
Sbjct: 223 LPM----------------KYGLK----DTEIRYRQRYLDLMINESTRSTFITRTKIINY 262
Query: 258 FRQFLLSENFVEIHTP--KLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMSICGDFG 315
R FL F+E+ TP L+AG + + + L + +L +M I G
Sbjct: 263 LRNFLNDRGFIEVETPTMNLVAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGID 322
Query: 316 RVFETGPVFRAEDSYTHRHLCEFT 339
+V+E G VFR E + H EFT
Sbjct: 323 KVYEIGKVFRNE-GIDNTHNPEFT 345
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 39.9 bits (94), Expect = 0.003
Identities = 62/263 (23%), Positives = 99/263 (37%), Gaps = 53/263 (20%)
Query: 93 TVVGALNGSLKDQEVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLATVKPDSVSKEMVR 152
TV AL + +EV + GRV R G + F +R+ +Q L +
Sbjct: 641 TVAEAL-DAPTGEEVSVSGRVLRIRDYG-GVLFADLRDWSGELQVLLD-ASRLEQGSLAD 697
Query: 153 FVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAE 212
F ++ +V+V G + + T + V
Sbjct: 698 FRAAVDLGDLVEVTGTM----GTSRNGTLSLLVT-------------------------S 728
Query: 213 IEKASKEGVQLPR-----VNQDTRLNNRVID--IRTLANQGIFRIQSQVGNIFRQFLLSE 265
A K LP + + R+ R +D + A + R +S V R+ L++
Sbjct: 729 WRLAGKCLRPLPDKWKGLTDPEARVRQRYLDLAVNPEARD-LLRARSAVVRAVRETLVAR 787
Query: 266 NFVEIHTPKL--IAGSSEGGSA---VFRLDYKGQSACLAQSPQLH-KQMSICGDFGRVFE 319
F+E+ TP L + G G +A V ++ L +P+L+ K++ + G RVFE
Sbjct: 788 GFLEVETPILQQVHG---GANARPFVTHINAYDMDLYLRIAPELYLKRLCV-GGVERVFE 843
Query: 320 TGPVFRAED-SYTHRHLCEFTGL 341
G FR E TH EFT L
Sbjct: 844 LGRNFRNEGVDATHNP--EFTLL 864
>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 = 35.3 bits (82), Expect = 0.006
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 11/67 (16%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVRERVSTVQCLAT---VKPDSVSKEMVRFVRSLSNESI 162
V + G VH R KL F+V+R+ +QC+ + V +K SL+ ES
Sbjct: 1 RVKVFGWVHRLRSQK-KLMFLVLRDGTGFLQCVLSKKLVTEFYDAK-------SLTQESS 52
Query: 163 VDVIGVV 169
V+V G V
Sbjct: 53 VEVTGEV 59
>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 = 35.9 bits (83), Expect = 0.028
Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 21/103 (20%)
Query: 260 QFLLSENFVEIHTPKLIAGSSEG----------GSAVFRLDYKGQSACLAQ--SPQLH-- 305
+ L+ FV++ TP +I S VF +D ++ CL +P L+
Sbjct: 37 KALVDRGFVQVKTPIIIPKEYLEKMTIDEDHPLFSQVFWVD---ENKCLRPMLAPNLYNY 93
Query: 306 --KQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLD-VEM 345
K + R+FE GP +R E S +HL EFT L+ EM
Sbjct: 94 LRKLDRLWPKPIRIFEIGPCYRKE-SQGSQHLNEFTMLNLCEM 135
>gnl|CDD|225178 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA
synthetase (class II) [Translation, ribosomal structure
and biogenesis].
Length = 322
Score = 35.4 bits (82), Expect = 0.050
Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 9/117 (7%)
Query: 258 FRQFLLSENFVEIHTPKL-IAGSSEGGSAVFRLDY------KGQSACLAQSPQLHKQMSI 310
R+F +E+ TP L +A ++ F ++ KG+ L SP+ H + +
Sbjct: 26 IRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSPEYHMKRLL 85
Query: 311 CGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDRLFVTIFD 367
G +F+ G VFR E+ H EFT L+ + Y +M+ VD L + +
Sbjct: 86 AAGSGPIFQLGKVFRNEEM-GRLHNPEFTMLEW-YRVGCDYYRLMNEVDDLLQLVLE 140
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 34.4 bits (79), Expect = 0.11
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K + E + + +KK A+ EAA KA E +K+AEA A +A
Sbjct: 170 KAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAA 212
Score = 33.6 bits (77), Expect = 0.18
Identities = 18/43 (41%), Positives = 27/43 (62%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K + E + + + +KK A+ EA KKA E +K+A A A AA+A
Sbjct: 186 KAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAA 228
Score = 33.6 bits (77), Expect = 0.20
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K E +++ +KK A EA KKA E + A AA+ A A
Sbjct: 194 KAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKA 236
Score = 33.2 bits (76), Expect = 0.28
Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
KK A+ EAAKKA E +K+AEA A+A +A
Sbjct: 168 KKKAEAEAAKKAAAEAKKKAEAEAAAKAA 196
Score = 29.8 bits (67), Expect = 3.1
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
AAK A KA E+ A+AA AA+A
Sbjct: 225 AAAAKAAAEAKAAAEKAAAAKAAEKAAAA 253
Score = 29.4 bits (66), Expect = 3.7
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 9 KVQEEVDSSSQSISKK---AAKKEAAKKAKEERRKEAEAAASAASA 51
K + E + + +KK A K AA KA E + AE AA+A +A
Sbjct: 202 KAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEKAAAAKAA 247
Score = 29.4 bits (66), Expect = 3.8
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 4 ESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
E E K E+ ++Q K+A EAAK+A ++++ EAAA AA+A
Sbjct: 99 EQERLKQLEKERLAAQEQKKQAE--EAAKQAALKQKQAEEAAAKAAAA 144
Score = 28.6 bits (64), Expect = 6.5
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K E +++ + K A EA KKA+ E +A A A +
Sbjct: 162 KAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAE 204
Score = 28.6 bits (64), Expect = 6.6
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K E +++ + A EA KKA+ E +K+A A A +A
Sbjct: 178 KAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAA 220
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 34.1 bits (79), Expect = 0.12
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 7 PPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGD 66
EE + + ++S KK K+ K E++ E E A AA+ +++ A
Sbjct: 392 LLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAA----KKKAEAAAKKAK 447
Query: 67 VPLQELQSVND 77
P E + V+
Sbjct: 448 GPDGETKKVDP 458
Score = 33.4 bits (77), Expect = 0.25
Identities = 17/78 (21%), Positives = 26/78 (33%), Gaps = 1/78 (1%)
Query: 2 STESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLA 61
+ E + + + +K +K K KEE K A + A+A +
Sbjct: 394 AEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGET 453
Query: 62 NNYGDVPLQE-LQSVNDP 78
PL E L DP
Sbjct: 454 KKVDPDPLGEKLARTEDP 471
>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 = 33.3 bits (77), Expect = 0.23
Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 24/124 (19%)
Query: 261 FLLSENFVEIHTPKLI-AGSSEGGSAVFRLDYKGQSAC-----LAQSPQLH-KQMSICGD 313
F +E+ TP L A ++ F ++ G L SP+ K++ +
Sbjct: 1 FFAERGVLEVETPLLSPAPVTDPHLDAFATEFVGPDGQGRPLYLQTSPEYAMKRL-LAAG 59
Query: 314 FGRVFETGPVFRAEDSYTHRHLCEFT-------GLDVEMEIKKHYSEVMDIVDRLFVTIF 366
G +F+ VFR + RH EFT G D Y ++MD V+ L +
Sbjct: 60 SGPIFQICKVFRNGER-GRRHNPEFTMLEWYRPGFD--------YHDLMDEVEALLQELL 110
Query: 367 DGLN 370
Sbjct: 111 GDPF 114
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 33.4 bits (77), Expect = 0.26
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
+KAA++ KKA E R + + A +AA A
Sbjct: 465 EKAAREARHKKAAEARAAKDKDAVAAALA 493
>gnl|CDD|177680 PLN00048, PLN00048, photosystem I light harvesting chlorophyll a/b
binding protein 3; Provisional.
Length = 262
Score = 31.7 bits (72), Expect = 0.55
Identities = 28/98 (28%), Positives = 46/98 (46%), Gaps = 15/98 (15%)
Query: 14 VDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASA--------ASALSIEE-EGPLANNY 64
V ++ +++S AA+ +AKKA+ R EA A AS S+ +G L ++
Sbjct: 4 VQTARRALSSSAARSSSAKKARFVVRAEATPPAKQGADRQLWFASKQSLSYLDGTLPGDF 63
Query: 65 GDVPLQELQSVN-----DPQTGKWSEAVNGREWTVVGA 97
G PL +PQ + E +NGR + ++GA
Sbjct: 64 GFDPLGLSDPEGAGGFIEPQWLAYGEVINGR-FAMLGA 100
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 32.3 bits (73), Expect = 0.64
Identities = 21/75 (28%), Positives = 33/75 (44%)
Query: 2 STESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLA 61
E + +S++S SK A+K + + E +A+AS A + +EE P A
Sbjct: 139 QGEGLASSSDGKSKASAKSGSKSASKHGESNSSDESATDSGKASASVAGIVGADEEAPPA 198
Query: 62 NNYGDVPLQELQSVN 76
PL+EL N
Sbjct: 199 PKNTLTPLEELYETN 213
>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 = 29.6 bits (67), Expect = 0.72
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVR-ERVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVD 164
+V + G + + KL+F +R +Q ++T K D+ S ++S++ ES V
Sbjct: 1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVSTAKKDAFSL-----LKSITAESPVQ 55
Query: 165 VIGVVSVPDVEIKGATQQVEVQIK 188
V G + + + + + E+ +
Sbjct: 56 VRGKLQLKEAKSSEKNDEWELVVD 79
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 31.3 bits (71), Expect = 1.2
Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 9/93 (9%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSI----EEEGPLANN----YGDVPLQELQSV 75
KA KKE +E + K+ A S + E + + D +++
Sbjct: 575 KALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQADKIGDKVRIR 634
Query: 76 NDPQTGKWSEAVNGREWTV-VGALNGSLKDQEV 107
Q GK + + G +W V VG + + E+
Sbjct: 635 YFGQKGKIVQILGGNKWNVTVGGMRMKVHGSEL 667
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 31.1 bits (70), Expect = 1.3
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K + ++ +K A EA KKA+E + EA A A +A
Sbjct: 148 KAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAA 190
Score = 28.8 bits (64), Expect = 6.2
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 5 SEPPKVQEEVDSSSQSISKKAAKKEAAKKAKE-ERRKEAEAAASAASALSIEEE 57
+E K++ ++ ++ A +EA KA+ +K+AEA A AA+ + E
Sbjct: 158 AEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEA 211
Score = 28.8 bits (64), Expect = 6.9
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 4 ESEPPKVQEEVDSSSQSISK--KAAKKEAAKKAKEERRKEAEAAASAASALSIEE 56
E+E E+ + +++ +K K A+ A +KA E++K A A + +A + +
Sbjct: 197 EAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAAAAAKA 251
Score = 28.8 bits (64), Expect = 7.2
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 9 KVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
K EE + +++ + K + AK A E+ + EAEA A A
Sbjct: 178 KAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKK 220
Score = 28.4 bits (63), Expect = 8.6
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 22 SKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
+ + AK EA KAK E++ EA A AA+
Sbjct: 203 AAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAA 238
>gnl|CDD|192292 pfam09429, Wbp11, WW domain binding protein 11. The WW domain is
a small protein module with a triple-stranded
beta-sheet fold. This is a family of WW domain binding
proteins.
Length = 78
Score = 28.4 bits (64), Expect = 1.5
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
+K KK+ KK K ER+ EA + + ++ E
Sbjct: 11 RKEQKKKELKKNKAERQARREAKLAKKNPDRLQRE 45
>gnl|CDD|132854 cd07215, Pat17_PNPLA8_PNPLA9_like2, Patatin-like phospholipase of
bacteria. Patatin is a storage protein of the potato
tuber that shows Phospholipase A2 activity (PLA2; EC
3.1.1.4). Patatin catalyzes the nonspecific hydrolysis
of phospholipids, glycolipids, sulfolipids, and mono-
and diacylglycerols, thereby showing lipid acyl
hydrolase activity. The active site includes an oxyanion
hole with a conserved GGxR motif; it is found in almost
all the members of this family. The catalytic dyad is
formed by a serine and an aspartate. Patatin belongs to
the alpha-beta hydrolase family which is identified by a
characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Members of this family
have been found also in vertebrates. This family
includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
(iPLA2-beta) like phospholipases from human as well as
the Pat17 isozyme from Solanum cardiophyllum.
Length = 329
Score = 30.5 bits (69), Expect = 1.8
Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 171 VPDVEIKGATQQVEVQIKKLYCVSRAAK----TPITIEDASRSEAEIEKASKEGVQ 222
+ D+ + GA+Q V+ Q+K+++ + +EDA E++ AS E ++
Sbjct: 253 LIDIMMDGASQTVDYQLKQIFDAEGDQQQYLRIQPELEDAD---PEMDDASPENLE 305
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 30.1 bits (68), Expect = 1.9
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLAN 62
K A+ AA+ AK+E +A A AA + P A
Sbjct: 220 KALAEAAAAEAAKQEAAAKAAAQEQAALQAAATAAQPSAV 259
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 30.2 bits (68), Expect = 2.4
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
K A+ EA KKAKEE +K+AE A A +A
Sbjct: 133 KAKAEAEAEKKAKEEAKKQAEEEAKAKAA 161
Score = 29.8 bits (67), Expect = 3.1
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAA 49
K EA KKA+ E + +AEA A A
Sbjct: 164 AKKKAAEAKKKAEAEAKAKAEAKAKAK 190
Score = 29.4 bits (66), Expect = 3.6
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
+K AK+EA K+A+EE + +A A A +A
Sbjct: 141 EKKAKEEAKKQAEEEAKAKAAAEAKKKAA 169
Score = 29.0 bits (65), Expect = 4.6
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
KK A++EA KA E +K+A A A A
Sbjct: 149 KKQAEEEAKAKAAAEAKKKAAEAKKKAEA 177
Score = 28.6 bits (64), Expect = 7.5
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASA 51
K A + E A K EE++K+AE A + +A
Sbjct: 102 KAAKQAEQAAKQAEEKQKQAEEAKAKQAA 130
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 29.6 bits (67), Expect = 2.6
Identities = 11/54 (20%), Positives = 23/54 (42%)
Query: 4 ESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
E E + +EE + K A K ++ ++ +R++ E + E+E
Sbjct: 39 EEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDE 92
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
Length = 155
Score = 28.9 bits (65), Expect = 3.1
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 20 SISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
+ + K K A A E AEAAA+AA+
Sbjct: 121 ATTPKKKKAAAEAAAAEAAAPAAEAAAAAAAE 152
Score = 28.9 bits (65), Expect = 3.1
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 22 SKKAAKKEAAKKAKEERRKEAEAAASAASA 51
KK A EAA EA AAA+A
Sbjct: 125 KKKKAAAEAAAAEAAAPAAEAAAAAAAEEE 154
Score = 27.7 bits (62), Expect = 7.9
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
KK+ A A AA +AA+A + EE
Sbjct: 122 TTPKKKKAAAEAAAAEAAAPAAEAAAAAAAEEEA 155
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 29.8 bits (67), Expect = 3.2
Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 23 KKAAKKEAAKK--AKEERRKEAEAAASAA 49
+K AK+EA ++ A+E+RR+E E AA A
Sbjct: 259 EKLAKEEAERERQAEEQRRREEEKAAMEA 287
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 29.3 bits (66), Expect = 3.7
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 4 ESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
ES + E + ++ + +K A++ KE+RRKE E A L +
Sbjct: 256 ESAWEGFESEYEPINKP--VRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLA 307
>gnl|CDD|193531 cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein,
RocB. Peptidase M20 family, ArgE RocB (Arginine
utilization protein, RocB; arginine degradation protein,
RocB) subfamily. This group of proteins is possibly
related to acetylornithine deacetylase (ArgE) and may be
involved in the arginine and/or ornithine degradation
pathway. In Bacillus subtilis, RocB is one of the three
genes found in the rocABC operon, which is sigma L
dependent and induced by arginine. The function of
members of this family is as yet unknown, although they
are predicted as deacetylases.
Length = 535
Score = 29.5 bits (67), Expect = 3.8
Identities = 10/61 (16%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 356 DIVDRLFVTIFDGLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKD-AGVEI 414
+++++L + N + E + K LT+EE + K G +
Sbjct: 304 EVMEKLKKIATEAFENTINEAYEKYCRLSNKPGDSLPWKVKVLTYEELYEEAKKKGGEKF 363
Query: 415 D 415
+
Sbjct: 364 E 364
>gnl|CDD|132590 TIGR03551, F420_cofH, 7,8-didemethyl-8-hydroxy-5-deazariboflavin
synthase, CofH subunit. This enzyme, together with
CofG, complete the biosynthesis of
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the
chromophore of coenzyme F420. The chromophore is also
used in cyanobacteria DNA photolyases [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 343
Score = 29.2 bits (66), Expect = 3.9
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 377 LEAVAKQYP------FEPL--KYKPKTLRLTFEEGVQMLKDAGV 412
L AV ++ P F P+ Y + L+ EE ++ LK+AG+
Sbjct: 109 LRAVKEEVPGMHIHAFSPMEVYYGARNSGLSVEEALKRLKEAGL 152
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 29.4 bits (67), Expect = 4.0
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 13 EVDSSSQS--ISKKAAKKEAAKKAK 35
+VDSS + I+ A KEAAKKA
Sbjct: 571 DVDSSELAFKIAASMALKEAAKKAG 595
>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 = 28.3 bits (64), Expect = 4.6
Identities = 24/139 (17%), Positives = 50/139 (35%), Gaps = 40/139 (28%)
Query: 256 NIFRQFLLSENFVEIHTP-----KLIAGSSE----GGSAVFRL-DYKGQSACL------- 298
N R+ L + E+ TP +L GS +++ D G+ L
Sbjct: 7 NFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLRPTAEVG 66
Query: 299 -----AQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTH-----RHLCEFTGLDVE---- 344
++++ + ++++ GP FR E R EFT +D E
Sbjct: 67 ITRLFKNEILSYRELPL-----KLYQIGPCFRYEARPRRGLGRVR---EFTQVDAEIFGT 118
Query: 345 -MEIKKHYSEVMDIVDRLF 362
+ ++ E++ + + +
Sbjct: 119 PEQSEEELEELLKLAEEIL 137
>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
Length = 430
Score = 29.2 bits (65), Expect = 4.6
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 13/94 (13%)
Query: 10 VQEEVDSSSQSISKKAAKKEAAKKAK------------EERRKEAEAAASAASALSIEEE 57
V EE + +++ + AAK +AA AK E+ + +A AAA A +A + +
Sbjct: 195 VTEEEKAKAKAKAAAAAKAKAAALAKQKASQGNGDSGDEDAKAKAIAAAKAKAAAAARAK 254
Query: 58 GPLANNYGD-VPLQELQSVNDPQTGKWSEAVNGR 90
A + P QE SVN P K+ E + +
Sbjct: 255 TKGAEGKKEEEPKQEEPSVNQPYLNKYVEVIKEK 288
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.3 bits (65), Expect = 4.9
Identities = 19/74 (25%), Positives = 28/74 (37%)
Query: 16 SSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQSV 75
S+S + SK + K+ KK KEE ++ + + E P QEL
Sbjct: 51 STSSNDSKAESTKKPNKKIKEEATSPLKSTKRQREKPASDTEEPERVTAKKSKTQELSRP 110
Query: 76 NDPQTGKWSEAVNG 89
N P G+ G
Sbjct: 111 NSPSEGEGEGEGEG 124
>gnl|CDD|237110 PRK12472, PRK12472, hypothetical protein; Provisional.
Length = 508
Score = 29.1 bits (65), Expect = 5.1
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 3 TESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
T+ + +E ++Q ++ A + + AK E +R A A AA A
Sbjct: 253 TDEAKARAEERQQKAAQQAAEAATQLDTAKADAEAKRAAAAATKEAAKA 301
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 29.1 bits (66), Expect = 5.1
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 7 PPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASAL 52
+++E + S+Q+ + A ++E ++ +EE E AA+ AL
Sbjct: 285 DEELKEVL--SAQAQAAAAEEEEEEEEEEEEEEPSEEEAAAGLGAL 328
>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 = 27.1 bits (61), Expect = 5.2
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 12/87 (13%)
Query: 106 EVLIRGRVHTTRPVGNKLAFVVVRE--RVSTVQCLATVKPDSVSKEMVRFVRSLSNESIV 163
EV + G V + R K++F+ + + + +Q + V + + + + LS S +
Sbjct: 1 EVTVNGWVRSVRDSK-KISFIELNDGSCLKNLQVV--VDKELTNFK---EILKLSTGSSI 54
Query: 164 DVIGVVSVPDVEIKGATQQVEVQIKKL 190
V GV+ V+ GA Q E+Q +K+
Sbjct: 55 RVEGVL----VKSPGAKQPFELQAEKI 77
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 29.1 bits (65), Expect = 5.2
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 16 SSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
++ ++S K A K AAK AK+ ++ +A AA A
Sbjct: 231 AAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKA 266
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases
H1, and dsRNA dependent adenosine deaminases.
Length = 68
Score = 26.9 bits (60), Expect = 5.3
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 22 SKKAAKKEAAKKA 34
SKK AK+ AA+ A
Sbjct: 52 SKKEAKQNAAEAA 64
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.3 bits (65), Expect = 5.4
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 11 QEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
+ E ++++ K EAA+K KEE +K+A+AA A +E
Sbjct: 1349 KAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADE 1395
Score = 29.0 bits (64), Expect = 6.7
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 4 ESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
++E K +E ++ KKA +AAKK EE +K AEAA + A A + E E
Sbjct: 1310 KAEEAKKADEAKKKAEEAKKKA---DAAKKKAEEAKKAAEAAKAEAEAAADEAE 1360
Score = 29.0 bits (64), Expect = 6.8
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 2 STESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEE 56
+TE K +E + + + +EA KKA++ R+ AE A A A EE
Sbjct: 1092 ATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARK--AEEARKAEDARKAEE 1144
Score = 29.0 bits (64), Expect = 7.4
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 4 ESEPPKVQEEVDSSSQSISKKA---AKKEAAKKAKEERRKEAEAAASAASALSIEEE 57
++E K +E ++ KKA K AAKK +E +K+AE A A EE
Sbjct: 1386 KAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEE 1442
Score = 29.0 bits (64), Expect = 7.5
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 6 EPPKVQEEVDSSSQSISKKAAKK---EAAKKAKEERRKEAEAAASAASALSIEE 56
E K EE + + K AA K + AKK EE++K EA A A +E
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448
Score = 28.6 bits (63), Expect = 9.4
Identities = 22/58 (37%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 4 ESEPPKVQEEVDSSSQSISKKAA----KKEAAKKAKEERRKEAEAAASAASALSIEEE 57
E+E K EE+ + + KAA K E KK EE +K E AA AL E E
Sbjct: 1642 EAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAE 1699
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 28.6 bits (64), Expect = 5.5
Identities = 13/38 (34%), Positives = 16/38 (42%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLA 61
K A EA KK E R + +A +A EE A
Sbjct: 129 KKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAA 166
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 28.8 bits (65), Expect = 5.6
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 8 PKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEA 42
PK + + + SKK K A KK KE+ + +
Sbjct: 378 PKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKV 412
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 29.2 bits (65), Expect = 6.0
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 3 TESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
+ ++ ++ ++ KK AKK AKKA ++ +AAA A
Sbjct: 974 VRKTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVA 1022
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA
targets. Exemplified by Staufen, which is involved in
localisation of at least five different mRNAs in the
early Drosophila embryo. Also by interferon-induced
protein kinase in humans, which is part of the cellular
response to dsRNA.
Length = 66
Score = 26.5 bits (59), Expect = 6.3
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 22 SKKAAKKEAAKKA 34
SKK AK+ AA+KA
Sbjct: 50 SKKEAKQLAAEKA 62
>gnl|CDD|240242 PTZ00046, PTZ00046, rifin; Provisional.
Length = 358
Score = 28.8 bits (65), Expect = 6.6
Identities = 15/58 (25%), Positives = 23/58 (39%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQSVNDPQT 80
KKAA A K A + EAA AA ++ E + ++L+S+
Sbjct: 166 KKAALAAAIKAAIKAGAAAGEAAGIAAGKKAVIEGLKSIFGISTLGGKDLKSIITATN 223
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 27.1 bits (60), Expect = 6.9
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 22 SKKAAKKEAAKKAKEERRKEAEAAASAASAL 52
+KA +KE KK +EE+ +E E A + AL
Sbjct: 75 EEKAEEKEEEKKKEEEKEEEEEEALAGLGAL 105
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 28.8 bits (64), Expect = 7.4
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 17 SSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQSV 75
+++ K AAKK AAK A + ++A +A A ++ LA G P+ + +
Sbjct: 879 AAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLKPSAALAAVIGAEPVARPEVI 937
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 28.6 bits (65), Expect = 9.1
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 2 STESEPPKVQE------EVDSSSQSISKKAAKKEAAKKAKEER-RKEAEAAASAASA 51
E+ P V+E E + ++ AK A KKA + RK + ++
Sbjct: 799 GRETRAPTVEEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKD 855
>gnl|CDD|215039 PLN00041, PLN00041, photosystem I reaction center subunit II;
Provisional.
Length = 196
Score = 27.6 bits (61), Expect = 9.1
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 282 GGSAVFR-----LDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPV 323
GG+A+ R L + CLA +L + I F RVF G V
Sbjct: 103 GGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEV 149
>gnl|CDD|214371 CHL00122, secA, preprotein translocase subunit SecA; Validated.
Length = 870
Score = 28.4 bits (64), Expect = 9.6
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 197 AKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGN 256
A+TP+ I S++ + + E + N ++ + ++ L QGI I+
Sbjct: 213 ARTPLIISGQSKTNIDKYIVADELAKYLEKNVHYEVDEKNKNV-ILTEQGILFIE----- 266
Query: 257 IFRQFLLSENFVEIHTP 273
+ L E+ + P
Sbjct: 267 ---KILKIEDLYSANDP 280
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 28.0 bits (63), Expect = 9.6
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 7 PPKVQEEVDSSSQSISKK------AAKKEAAKKAKEERRKEAEAAASAASALSIEE 56
P+V +VD + + +K ++E A++ KEE++KE A A LS EE
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLA--KLSPEE 307
>gnl|CDD|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 28.2 bits (63), Expect = 9.7
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 16 SSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQS 74
I KA+ + AKE + + + S ++++EE +AN L + Q
Sbjct: 478 GLVGWIGIKASTASSESDAKEALLNQLTSERQSISGVNLDEE--MAN------LIQFQQ 528
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called
The RES complex, pre-mRNA retention and splicing
complex. Subunits of this complex are not essential for
viability of yeasts but they are required for efficient
splicing in vitro and in vivo. Furthermore,
inactivation of this complex causes pre-mRNA leakage
from the nucleus. Bud13 contains a unique,
phylogenetically conserved C-terminal region of unknown
function.
Length = 141
Score = 27.3 bits (61), Expect = 10.0
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 16/80 (20%)
Query: 15 DSSSQSISKKAAKKEAAKKAKEERRKEAEAAASA------------ASALSIEEEGPLAN 62
D S + I + ++E ++ +E+ RKE + L + PLA
Sbjct: 6 DKSGRIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLAR 65
Query: 63 NYGDV----PLQELQSVNDP 78
D L+E + +DP
Sbjct: 66 YADDEDYDEELKEQERWDDP 85
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.1 bits (63), Expect = 10.0
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGD 66
KA + AA +A R + AEA + + E L ++ G
Sbjct: 249 KAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLISSTGG 291
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
0.314 0.130 0.358
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,403,148
Number of extensions: 2095727
Number of successful extensions: 3597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3224
Number of HSP's successfully gapped: 218
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (27.0 bits)