RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014856
(417 letters)
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 662 bits (1710), Expect = 0.0
Identities = 284/425 (66%), Positives = 326/425 (76%), Gaps = 33/425 (7%)
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 ELQSVNDPQTGKWSEAVSGREWTEVGALNGSLKDQEVLIRGR-----------------R 113
ELQS V+GREWT+V L L EVLIRGR
Sbjct: 59 ELQS-----------KVTGREWTDVSDLGEELAGSEVLIRGRVHTIRGKGKSAFLVLRQS 107
Query: 114 VSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLY 173
TVQC+ V +VSK MV++ + LS ES+VDV GVVSVP +KG TQQVE+Q++K+Y
Sbjct: 108 GFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKGTTQQVEIQVRKIY 167
Query: 174 CVSRAAKT-PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRI 232
CVS+A T P +EDA+RSE+EIEKA + G QL RV QDTRLNNRV+D+RT ANQ IFRI
Sbjct: 168 CVSKALATLPFNVEDAARSESEIEKALQTGEQLVRVGQDTRLNNRVLDLRTPANQAIFRI 227
Query: 233 QSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMSI 292
QSQV N+FR+FLLS+ FVEIHTPKLIAG+SEGGSAVFRLDYKGQ ACLAQSPQLHKQM+I
Sbjct: 228 QSQVCNLFREFLLSKGFVEIHTPKLIAGASEGGSAVFRLDYKGQPACLAQSPQLHKQMAI 287
Query: 293 CGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDSLN 352
CGDF RVFE GPVFRAEDS+THRHLCEFTGLD+EMEIK+HYSEV+D+VD LFV IFD LN
Sbjct: 288 CGDFRRVFEIGPVFRAEDSFTHRHLCEFTGLDLEMEIKEHYSEVLDVVDELFVAIFDGLN 347
Query: 353 NVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPLGDLNTESERKLGQ 412
CKKELEA+ +QYPFEPLKY PKTLRLTF EG+QMLK+AGVE+DPLGDLNTESERKLGQ
Sbjct: 348 ERCKKELEAIREQYPFEPLKYLPKTLRLTFAEGIQMLKEAGVEVDPLGDLNTESERKLGQ 407
Query: 413 LVLEK 417
LV EK
Sbjct: 408 LVKEK 412
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 287 bits (736), Expect = 4e-92
Identities = 175/457 (38%), Positives = 245/457 (53%), Gaps = 83/457 (18%)
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 SVNDPQTGKWSEAVSGREWTEVGALNG-SLKDQEVLIRGRRVST---------------- 116
S R + V L+ L D+ VLIR R +T
Sbjct: 57 ----------STTYKSRTFIPVAVLSKPELVDKTVLIRARVSTTRKKGKMAFMVLRDGSD 106
Query: 117 -VQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQ-VEVQIKKLYC 174
VQ +A V+ D V KEM+ F+ + ESIVDV V + I + +E+++KK++
Sbjct: 107 SVQAMAAVEGD-VPKEMIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIELKVKKIHT 165
Query: 175 VSRAAKT-PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQ 233
V+ + +T P T+EDASR E++ EG +VN DTRLN+R +D+RT A+ IFR+Q
Sbjct: 166 VTESLRTLPFTLEDASRKESD------EGA---KVNFDTRLNSRWMDLRTPASGAIFRLQ 216
Query: 234 SQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMSIC 293
S+V FRQFL+ +F EIH+PK+I SEGG+ VF+L+Y + A LAQSPQL+KQM +
Sbjct: 217 SRVCQYFRQFLIDSDFCEIHSPKIINAPSEGGANVFKLEYFNRFAYLAQSPQLYKQMVLQ 276
Query: 294 GDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDSLNN 353
GD RVFE GPVFR+E+S THRHL EF GLDVEM I +HY EV+D+ + LF IF+ L
Sbjct: 277 GDVPRVFEVGPVFRSENSNTHRHLTEFVGLDVEMRINEHYYEVLDLAESLFNYIFERLAT 336
Query: 354 VCKKELEAVAKQYPFEPL-------------------------KYKPKT-------LRLT 381
KEL+AV +QYPFEPL KY+ + LR+
Sbjct: 337 -HTKELKAVCQQYPFEPLVWKLTPERMKELGVGVISEGVEPTDKYQARVHNMDSRMLRIN 395
Query: 382 FEEGVQMLKDAGVE-IDPLGDLNTESERKLGQLVLEK 417
+ +++L E + P D+NT +E+ LG+LV E+
Sbjct: 396 YMHCIELLNTVLEEKMAPTDDINTTNEKLLGKLVKER 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 = 277 bits (712), Expect = 3e-91
Identities = 96/213 (45%), Positives = 134/213 (62%), Gaps = 4/213 (1%)
Query: 207 RVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGS 266
N +T L+NR +D+RT Q IFRI+S+V FR+FL F E+HTPK+ + +EGG+
Sbjct: 1 DANLETLLDNRHLDLRTPKVQAIFRIRSEVLRAFREFLRENGFTEVHTPKITSTDTEGGA 60
Query: 267 AVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 326
+F++ Y G+ A LAQSPQL+K+M I RV+E GPVFRAE S T RHL EF L+ E
Sbjct: 61 ELFKVSYFGKPAYLAQSPQLYKEMLIAA-LERVYEIGPVFRAEKSNTRRHLSEFWMLEAE 119
Query: 327 MEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 386
M + Y+EVMD+++ L IF + C KELE V Q E LK R+T++E +
Sbjct: 120 MAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELV-NQLNRELLKPLEPFPRITYDEAI 178
Query: 387 QMLKDAGV--EIDPLGDLNTESERKLGQLVLEK 417
++L++ GV E+ DL+TE ER LG++V
Sbjct: 179 ELLREKGVEEEVKWGEDLSTEHERLLGEIVKGD 211
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 250 bits (640), Expect = 7e-79
Identities = 112/311 (36%), Positives = 175/311 (56%), Gaps = 28/311 (9%)
Query: 107 VLIRGRRVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVE 166
+++R R +Q VK +E+ ++ L ES+V V G V A VE
Sbjct: 37 LILRDRS-GIIQV--VVKKKVD-EELFETIKKLKRESVVSVTGTV----KANPKAPGGVE 88
Query: 167 VQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLAN 226
V +++ +++A + P+ ++ + + AE+ DTRL+NR +D+R
Sbjct: 89 VIPEEIEVLNKA-EEPLPLDISGKVLAEL---------------DTRLDNRFLDLRRPRV 132
Query: 227 QGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQL 286
+ IF+I+S+V FR+FL F EI TPK++A +EGG+ +F +DY + A LAQSPQL
Sbjct: 133 RAIFKIRSEVLRAFREFLYENGFTEIFTPKIVASGTEGGAELFPIDYFEKEAYLAQSPQL 192
Query: 287 HKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVT 346
+KQM + F RVFE GPVFRAE+ T RHL E+T +DVEM + +VMD+++ L
Sbjct: 193 YKQMMVGAGFERVFEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENLLRY 252
Query: 347 IFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPLGDLNTES 406
+++ + C+KELE + + P R+T++E +++LK G EI DL+TE
Sbjct: 253 MYEDVAENCEKELELLGIELPVPETPIP----RITYDEAIEILKSKGNEISWGDDLDTEG 308
Query: 407 ERKLGQLVLEK 417
ER LG+ V E+
Sbjct: 309 ERLLGEYVKEE 319
>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 = 241 bits (617), Expect = 1e-75
Identities = 114/326 (34%), Positives = 172/326 (52%), Gaps = 46/326 (14%)
Query: 105 QEVLIRGR-----------------RVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDV 147
QEV G R +Q T VSK + ++ + L+ ES+V V
Sbjct: 13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQ--ITAPAKKVSKNLFKWAKKLNLESVVAV 70
Query: 148 IGVVSVPDVEIKGAT-QQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLP 206
G+V +IK E+ K+ ++ AK P+ ++ + AE+
Sbjct: 71 RGIV-----KIKEKAPGGFEIIPTKIEVIN-EAKEPLPLDPTEKVPAEL----------- 113
Query: 207 RVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGS 266
DTRL+ R +D+R Q IFRI+S V R+FL E F+E+HTPKL+A ++EGG+
Sbjct: 114 ----DTRLDYRFLDLRRPTVQAIFRIRSGVLESVREFLAEEGFIEVHTPKLVASATEGGT 169
Query: 267 AVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 326
+F + Y + A L QSPQL+KQ + F RV+E GP+FRAE+ THRHL E T +D+E
Sbjct: 170 ELFPITYFEREAFLGQSPQLYKQQLMAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDIE 229
Query: 327 MEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 386
M + H +VMDI++ L V +F+ + C +LE + + K+ RLT++E +
Sbjct: 230 MAFEDH-HDVMDILEELVVRVFEDVPERCAHQLETLEFKLEKPEGKFV----RLTYDEAI 284
Query: 387 QMLKDAGVEIDPLGDLNTESERKLGQ 412
+M GVEI DL+TE+E+ LG+
Sbjct: 285 EMANAKGVEIGWGEDLSTEAEKALGE 310
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 233 bits (597), Expect = 1e-72
Identities = 96/299 (32%), Positives = 146/299 (48%), Gaps = 30/299 (10%)
Query: 115 STVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYC 174
+Q V + V +E+ + + L+ ES V V G+V A Q E+Q++K+
Sbjct: 44 GFIQA--VVPKNKVYEELFKA-KKLTLESSVVVTGIV----KASPKAPQGFELQVEKIEV 96
Query: 175 VSRA-AKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQ 233
+ A PI ++ +T L+NR +D+RT Q +F+I+
Sbjct: 97 LGEADPPYPIDKKE-------------------HSELETLLDNRHLDLRTPKIQAVFKIR 137
Query: 234 SQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDYKGQSACLAQSPQLHKQMSIC 293
S + R+F F E+HTP + A ++EGG +F++DY + A L QSPQL+K+
Sbjct: 138 SSILRAIREFFYENGFTEVHTPIITASATEGGGELFKVDYFDKEAYLTQSPQLYKEALAA 197
Query: 294 GDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDSLNN 353
RVF GP FRAE S T RHL EF LD EM ++VMD+ + L +F +
Sbjct: 198 A-LERVFTIGPTFRAEKSNTRRHLSEFWMLDPEMAFADL-NDVMDLAEELIKYLFKKVLE 255
Query: 354 VCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPLG-DLNTESERKLG 411
C ELE + + R+T++E +++L++ G E G DL TE ER LG
Sbjct: 256 ECADELEFLGRDNSELKRPESAPFPRITYKEAIEILEEKGFEKVEWGDDLGTEHERYLG 314
>gnl|CDD|215753 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N).
Length = 345
Score = 151 bits (384), Expect = 2e-42
Identities = 61/196 (31%), Positives = 96/196 (48%), Gaps = 14/196 (7%)
Query: 209 NQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAV 268
+++TRL R +D+R Q +++S++ R+FL F+E+ TP L + EGG+
Sbjct: 1 SEETRLKYRYLDLRRPKMQANLKLRSKIIKAIREFLDERGFLEVETPILTKSTPEGGARD 60
Query: 269 FRLDYK--GQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 326
F + K + A L QSPQL+KQ+ + F RVF+ P FR ED T RH EFT LD+E
Sbjct: 61 FLVPSKFYAKEAYLPQSPQLYKQLLMVAGFDRVFQIAPCFRDEDLRTDRHPPEFTQLDLE 120
Query: 327 MEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGV 386
M Y +VMD+ + L +F + ++ + F R+T+ E +
Sbjct: 121 MSFVD-YEDVMDLTEDLIKYVFKKVLGKREELELLGIELPEFP---------RITYAEAI 170
Query: 387 QMLKDAGVEIDPLGDL 402
+ + D L
Sbjct: 171 ERYG--SDKPDLRFGL 184
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 114 bits (288), Expect = 5e-28
Identities = 86/351 (24%), Positives = 137/351 (39%), Gaps = 67/351 (19%)
Query: 97 ALNGSLKDQEVLIRG----RRVS-------------TVQCLATVKPDSVSKEMVRFVRSL 139
L G QEV +RG +R S Q E ++ L
Sbjct: 9 ILKGKYVGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGE---EYFEEIKKL 65
Query: 140 SNESIVDVIGVVSVPDVEIKGATQQVEVQIKKLYCVSRAAKT-PITIEDASRSEAEIEKA 198
+ S V V G V VE A Q E+Q K+ + + PI + S
Sbjct: 66 TTGSSVIVTGTV----VESPRAGQGYELQATKIEVIGEDPEDYPIQKKRHSI-------- 113
Query: 199 SKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLI 258
+ + RT + RI++ + +F FV + TP +
Sbjct: 114 ------------EFLREIAHLRPRTNKFGAVMRIRNTLAQAIHEFFNENGFVWVDTPIIT 161
Query: 259 AGSSEGGSAVFRL---------DYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAE 309
A EG +FR+ D+ G+ A L S QL+ + G+V+ GP FRAE
Sbjct: 162 ASDCEGAGELFRVTTLDLDFSKDFFGKEAYLTVSGQLYAEAYAMA-LGKVYTFGPTFRAE 220
Query: 310 DSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDS-LNNVCKKELEAVAKQYP- 367
+S T RHL EF ++ EM + MD+ + + + L N C +LE + ++
Sbjct: 221 NSNTRRHLAEFWMIEPEMAFADL-EDNMDLAEEMLKYVVKYVLEN-CPDDLEFLNRRVDK 278
Query: 368 --FEPLK--YKPKTLRLTFEEGVQMLKDAGVEIDPL---G-DLNTESERKL 410
E L+ + R+T+ E +++L+ +G + + G DL +E ER L
Sbjct: 279 GDIERLENFIESPFPRITYTEAIEILQKSGKKFEFPVEWGDDLGSEHERYL 329
>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 = 104 bits (261), Expect = 3e-27
Identities = 42/102 (41%), Positives = 55/102 (53%), Gaps = 20/102 (19%)
Query: 106 EVLIRGR------------------RVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDV 147
EVLIR R + T+Q + + VSK+MV++ SLS ESIVDV
Sbjct: 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDV 60
Query: 148 IGVVSVPDVEIKGATQQ-VEVQIKKLYCVSRAAKT-PITIED 187
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 = 111 bits (279), Expect = 2e-26
Identities = 70/260 (26%), Positives = 111/260 (42%), Gaps = 44/260 (16%)
Query: 126 DSVSKEMVRFVRSLSNESIVDVIGVVSV-PDVEI--KGATQQVEVQIKKLYCVSRAAKTP 182
S E L NE ++ V G V P+ I T ++EV +++ ++ + P
Sbjct: 51 PEDSPEAFEVASRLRNEFVIQVTGTVRARPEGTINPNLPTGEIEVLAEEIEVLNASKTLP 110
Query: 183 ITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQ 242
IED +++ RL R +D+R Q +++S+V R
Sbjct: 111 FQIEDE-----------------TNASEEIRLKYRYLDLRRPEMQKNLKLRSKVTKAIRN 153
Query: 243 FLLSENFVEIHTPKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQLHKQMSICGD 295
FL + F+EI TP L + EG R D+ G+ L QSPQL KQ+ +
Sbjct: 154 FLDDQGFLEIETPILTKSTPEGA----R-DFLVPSRVHPGKFYALPQSPQLFKQLLMVAG 208
Query: 296 FGRVFETGPVFRAEDSYTHRHLCEFTGLDVEME-IKKHYSEVMDIVDCLFVTIFDSLNNV 354
F R ++ FR ED R EFT +D+EM + + +VM++++ L +F V
Sbjct: 209 FDRYYQIARCFRDEDLRADRQP-EFTQIDLEMSFVDEE--DVMELIEKLLRYVF---KEV 262
Query: 355 CKKELEAVAKQYPFEPLKYK 374
EL+ PF + Y
Sbjct: 263 KGIELKT-----PFPRMTYA 277
>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 = 105 bits (264), Expect = 6e-26
Identities = 45/162 (27%), Positives = 71/162 (43%), Gaps = 11/162 (6%)
Query: 230 FRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDY--KGQSACLAQSPQLH 287
F+++S++ R F+ F+E+ TP L + G+ F + Y G L SPQL
Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLF 60
Query: 288 KQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTI 347
K+ + G RVFE FR ED RH EFT +D+EM Y +V+++ + L +
Sbjct: 61 KKRLMVGGLDRVFEINRNFRNEDL-RARHQPEFTMMDLEMAFAD-YEDVIELTERLVRHL 118
Query: 348 FDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQML 389
+ V + P RLT+ E ++
Sbjct: 119 AREVLGVTAVTYG----FELEDFGLPFP---RLTYREALERY 153
>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 = 108 bits (271), Expect = 1e-25
Identities = 74/318 (23%), Positives = 134/318 (42%), Gaps = 45/318 (14%)
Query: 111 GRRVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIK 170
G + +Q V + + + ++SL+ S V V G V VE G Q VE+Q+K
Sbjct: 42 GSSLGPIQA---VINGEDNPYLFQLLKSLTTGSSVSVTGKV----VESPGKGQPVELQVK 94
Query: 171 KLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIF 230
K+ V A + Q + + + + +RT +
Sbjct: 95 KIEVVGEAEPDDYPL------------------QKKEHSLEFLRDIAHLRLRTNTLGAVM 136
Query: 231 RIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRL---------DYKGQSACLA 281
R+++ + ++ F + P L + EG +FR+ D+ G+ A L
Sbjct: 137 RVRNALSQAIHRYFQENGFTWVSPPILTSNDCEGAGELFRVSTGNIDFSQDFFGKEAYLT 196
Query: 282 QSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVD 341
S QL+ + +V+ GP FRAE S T RHL EF ++ EM ++++ + +
Sbjct: 197 VSGQLYLETYALA-LSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFAN-LNDLLQLAE 254
Query: 342 CLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTL-----RLTFEEGVQMLKDAG--V 394
L I ++ C +EL+ + K + + +K + R+T+ + +++LK++
Sbjct: 255 TLIKYIIKAVLENCSQELKFLEKNFDKDLIKRLENIINNKFARITYTDAIEILKESDKNF 314
Query: 395 EIDPL--GDLNTESERKL 410
E + DL TE ER L
Sbjct: 315 EYEDFWGDDLQTEHERFL 332
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 100 bits (252), Expect = 8e-24
Identities = 60/191 (31%), Positives = 91/191 (47%), Gaps = 15/191 (7%)
Query: 229 IFRIQSQVGNIFRQFLLSENFVEIHTP-------KLIAGSSEGGSAVFRLDYKGQSACLA 281
+ ++QS + R+FL FVE+ P L+ S+ +D+ G LA
Sbjct: 29 VLKVQSSILRYTREFLDGRGFVEVLPPIISPSTDPLMGLGSDLPVKQISIDFYGVEYYLA 88
Query: 282 QSPQLHKQMSICGDFGRVFETGPVFRAE--DSYTHRHLCEFTGLDVEMEIKKHYSEVMDI 339
S LHKQ+++ G++F P FR E D T RHL EFT LD+E+E EVMD+
Sbjct: 89 DSMILHKQLAL-RMLGKIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEIE-GADLDEVMDL 146
Query: 340 VDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPL 399
++ L + L + ELE + P K R+T +E V++L + G L
Sbjct: 147 IEDLIKYLVKELLEEHEDELEFFGRDLP----HLKRPFKRITHKEAVEILNEEGCRGIDL 202
Query: 400 GDLNTESERKL 410
+L +E E+ L
Sbjct: 203 EELGSEGEKSL 213
>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 = 96.7 bits (241), Expect = 1e-21
Identities = 68/277 (24%), Positives = 115/277 (41%), Gaps = 48/277 (17%)
Query: 108 LIRGRRVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKG---ATQQ 164
+ R VQ PD+ + ++ + +R NE +V V G VS T +
Sbjct: 36 IDLRDRSGIVQ--VVCDPDADALKLAKGLR---NEDVVQVKGKVSARPEGNINRNLDTGE 90
Query: 165 VEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTL 224
+E+ + + ++++ P+ IE ++ RL R +D+R
Sbjct: 91 IEILAESITLLNKSKTPPLIIEKTD------------------AEEEVRLKYRYLDLRRP 132
Query: 225 ANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDY-------KGQS 277
Q +++ +V R FL + F+EI TP L + EG DY KG+
Sbjct: 133 EMQQRLKLRHKVTKAVRNFLDQQGFLEIETPMLTKSTPEGAR-----DYLVPSRVHKGEF 187
Query: 278 ACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVM 337
L QSPQL KQ+ + R ++ FR ED R EFT +D+EM +VM
Sbjct: 188 YALPQSPQLFKQLLMVSGVDRYYQIARCFRDEDLRADRQ-PEFTQIDMEMSFMTQ-EDVM 245
Query: 338 DIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYK 374
++++ L +F E++ + + PF + Y
Sbjct: 246 ELIEKLVSHVF--------LEVKGIDLKKPFPVMTYA 274
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 96.3 bits (241), Expect = 2e-21
Identities = 78/283 (27%), Positives = 123/283 (43%), Gaps = 66/283 (23%)
Query: 117 VQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSV-PDVEI--KGATQQVEVQIKKLY 173
VQ PD+ + E+ SL +E ++ V G V P+ + T ++EV +L
Sbjct: 47 VQV--VFDPDAEAFEVAE---SLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVLASELE 101
Query: 174 CVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQ 233
++++ P I+D E + V+++ RL R +D+R Q +++
Sbjct: 102 VLNKSKTLPFPIDD------EED-----------VSEELRLKYRYLDLRRPEMQKNLKLR 144
Query: 234 SQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQL 286
S+V + R FL F+EI TP L + EG A R DY G+ L QSPQL
Sbjct: 145 SKVTSAIRNFLDDNGFLEIETPILTKSTPEG--A--R-DYLVPSRVHPGKFYALPQSPQL 199
Query: 287 HKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYS-----EVMDIVD 341
KQ+ + F R ++ FR ED R EFT +D+EM S +VM +++
Sbjct: 200 FKQLLMVAGFDRYYQIARCFRDEDLRADRQP-EFTQIDIEM------SFVTQEDVMALME 252
Query: 342 CLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEE 384
L +F + V +L PF R+T+ E
Sbjct: 253 GLIRHVFKEVLGV---DLPT-----PFP---------RMTYAE 278
>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 = 81.9 bits (203), Expect = 2e-17
Identities = 50/150 (33%), Positives = 73/150 (48%), Gaps = 18/150 (12%)
Query: 230 FRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVF----RLDYKGQSACLAQSPQ 285
R++S+V R FL + FVEI TP L S+ G+ F RL + G+ L QSPQ
Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTK-STPEGARDFLVPSRL-HPGKFYALPQSPQ 58
Query: 286 LHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEME-IKKHYSEVMDIVDCLF 344
L KQ+ + F R F+ FR ED R EFT +D+EM + + ++M +++ L
Sbjct: 59 LFKQLLMVSGFDRYFQIARCFRDEDLRADRQ-PEFTQIDIEMSFVDQE--DIMSLIEGLL 115
Query: 345 VTIFDSLNNVCKKELEAVAKQYPFEPLKYK 374
+F + V EL PF + Y
Sbjct: 116 KYVFKEVLGV---EL-----TTPFPRMTYA 137
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 78.1 bits (192), Expect = 2e-15
Identities = 68/216 (31%), Positives = 95/216 (43%), Gaps = 22/216 (10%)
Query: 121 ATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSV-------PDVEIKGATQQVEVQIKKLY 173
A P++ ++ SL E V + G V P +E T +EV +++L
Sbjct: 50 AVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETENPHIE----TGDIEVFVRELS 105
Query: 174 CVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQ 233
++ + P I D +A A G VN+D RL R +DIR A Q +
Sbjct: 106 ILAASEALPFAISD----KAMTAGAGSAGAD--AVNEDLRLQYRYLDIRRPAMQDHLAKR 159
Query: 234 SQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVF---RLDYKGQSACLAQSPQLHKQM 290
++ R FL S F+EI TP L + EG R+ K A L QSPQL KQ+
Sbjct: 160 HRIIKCARDFLDSRGFLEIETPILTKSTPEGARDYLVPSRIHPKEFYA-LPQSPQLFKQL 218
Query: 291 SICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVE 326
+ F R F+ FR ED +R EFT LD+E
Sbjct: 219 LMIAGFERYFQLARCFRDEDLRPNRQ-PEFTQLDIE 253
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 76.0 bits (187), Expect = 8e-15
Identities = 76/267 (28%), Positives = 106/267 (39%), Gaps = 53/267 (19%)
Query: 125 PDSVSKEMVRFVRSLSNESIVDVIGVV---SVPDVEIKGATQQVEV---QIKKLYCVSRA 178
PD E R L NE +V V G V K T VEV + L V+++
Sbjct: 108 PDE-FPEAHRTANRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKS 166
Query: 179 AKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGN 238
+T A+ +K + ++ RL RV+D+R R++ +V
Sbjct: 167 LPFLVT-------TADEQK--------DSIKEEVRLRYRVLDLRRPQMNANLRLRHRVVK 211
Query: 239 IFRQFLLS-ENFVEIHTPKLIAGSSEGGSAVFRLDY-------KGQSACLAQSPQLHKQM 290
+ R++L FVEI TP L + EG DY G L QSPQL KQM
Sbjct: 212 LIRRYLEDVHGFVEIETPILSRSTPEGA-----RDYLVPSRVQPGTFYALPQSPQLFKQM 266
Query: 291 SICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDS 350
+ F R ++ FR ED R EFT LD+E+ + D L
Sbjct: 267 LMVSGFDRYYQIARCFRDEDLRADRQ-PEFTQLDMELAF-------TPLEDML------K 312
Query: 351 LNN--VCK--KELEAVAKQYPFEPLKY 373
LN + + KE++ V PF L Y
Sbjct: 313 LNEDLIRQVFKEIKGVQLPNPFPRLTY 339
>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 = 68.4 bits (168), Expect = 1e-12
Identities = 49/191 (25%), Positives = 84/191 (43%), Gaps = 29/191 (15%)
Query: 230 FRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSA--------VFRLDYKGQSAC 279
F ++S++ + R+FL F+E+ TP L IAG G +A +D
Sbjct: 8 FIVRSKIISYIRKFLDDRGFLEVETPMLQPIAG---GAAARPFITHHNALDMDLY----- 59
Query: 280 LAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDI 339
L +P+L+ + I G F RV+E G FR E H EFT ++ Y+++MD+
Sbjct: 60 LRIAPELYLKRLIVGGFERVYEIGRNFRNE-GIDLTHNPEFTMIEFYEAYAD-YNDMMDL 117
Query: 340 VDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEIDPL 399
+ LF + + + K +Y + L + P R+T + ++ + G++ L
Sbjct: 118 TEDLFSGL---VKKINGKT----KIEYGGKELDFTPPFKRVTMVDALK--EKTGIDFPEL 168
Query: 400 GDLNTESERKL 410
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 = 60.5 bits (147), Expect = 6e-10
Identities = 55/209 (26%), Positives = 88/209 (42%), Gaps = 31/209 (14%)
Query: 209 NQDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSA 267
+Q+TR R +D I ++ F ++S++ R+FL F+E+ TP L G A
Sbjct: 150 DQETRYRQRYLDLIVNPDSRQTFLVRSKIIKAIRRFLDDRGFIEVETPML---QVIPGGA 206
Query: 268 VFR--------LD---YKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRH 316
R LD Y L +P+L+ + I G F +V+E G FR E H
Sbjct: 207 NARPFITHHNALDMDLY------LRIAPELYLKRLIVGGFEKVYEIGRNFRNE-GVDTTH 259
Query: 317 LCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPK 376
EFT ++ Y ++MD+ + LF + L K Y + +K
Sbjct: 260 NPEFTMIEFYQAYAD-YEDLMDLTENLFKFLAQELLGTTK-------ITYGELEIDFKKP 311
Query: 377 TLRLTFEEGVQML-KDAGVEIDPLGDLNT 404
R+T E ++ + G++ D L D T
Sbjct: 312 FKRITMVEAIKKYDMETGIDFDDLKDFET 340
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 59.1 bits (144), Expect = 2e-09
Identities = 52/205 (25%), Positives = 85/205 (41%), Gaps = 28/205 (13%)
Query: 210 QDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGS 266
++ R R +D I ++ F +S++ R+FL F+E+ TP L I G G +
Sbjct: 159 KEIRYRQRYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPG---GAA 215
Query: 267 A-VFRLDYKGQSACLAQ--SPQLHKQMSICGDFGRVFETGPVFRAED-SYTHRHLCEFTG 322
A F + L +P+L+ + I G F RVFE G FR E TH EFT
Sbjct: 216 ARPFITHHNALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTTHNP--EFTM 273
Query: 323 LD---VEMEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLR 379
L+ + Y ++MD+ + L + +N Y + + + R
Sbjct: 274 LEFYQAYAD----YEDLMDLTEELIKELAKEVNG-------TTKVTYGGQEIDFSKPFKR 322
Query: 380 LTFEEGVQMLKDAGVEIDPLGDLNT 404
+T + ++ GV+ D L D
Sbjct: 323 ITMVDALKE--YLGVDFDDLFDDEE 345
>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
Length = 505
Score = 56.6 bits (136), Expect = 1e-08
Identities = 47/181 (25%), Positives = 86/181 (47%), Gaps = 14/181 (7%)
Query: 209 NQDTRLNNRVID-IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTP--KLIAGSSEGG 265
+Q+ R R +D I ++ F ++S++ RQF+++ F+E+ TP ++I G +
Sbjct: 162 DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASAR 221
Query: 266 SAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDV 325
+ + L +P+L+ + + G F RVFE FR E + RH EFT +++
Sbjct: 222 PFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNE-GISVRHNPEFTMMEL 280
Query: 326 EMEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQY--PFEPL-------KYKPK 376
M Y +++++ + LF T+ + K + PFE L KY+P+
Sbjct: 281 YMAYAD-YHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPE 339
Query: 377 T 377
T
Sbjct: 340 T 340
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 53.8 bits (129), Expect = 8e-08
Identities = 52/161 (32%), Positives = 85/161 (52%), Gaps = 20/161 (12%)
Query: 272 DYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKK 331
D+ G+ A L S QL + C V+ GP FRAE+S+T RHL EF VE EI
Sbjct: 303 DFFGRQAFLTVSGQLQVETYACA-LSSVYTFGPTFRAENSHTSRHLAEF--WMVEPEIA- 358
Query: 332 HYSEVMDIVDC--LFVT-IFDSLNNVCKKELEAVAKQYP---FEPLKYKPKTL--RLTFE 383
++++ D ++C +V + L + C ++E +AK + + L+ T R+T+
Sbjct: 359 -FADLEDDMNCAEAYVKYMCKWLLDKCFDDMELMAKNFDSGCIDRLRMVASTPFGRITYT 417
Query: 384 EGVQMLKDA---GVEID---PLG-DLNTESERKLGQLVLEK 417
E +++L++A G E D G DL +E ER L +++ +K
Sbjct: 418 EAIELLEEAVAKGKEFDNNVEWGIDLASEHERYLTEVLFQK 458
Score = 32.7 bits (74), Expect = 0.46
Identities = 31/130 (23%), Positives = 51/130 (39%), Gaps = 27/130 (20%)
Query: 145 VDVIGVVSVPDVEIKGATQQVEVQIKKLYCVS--RAAKTPITIEDASRSEAEIEKASKEG 202
V V GV+ VP E KG Q++E+ ++K+ V K P
Sbjct: 105 VTVDGVLKVPP-EGKGTKQKIELSVEKVIDVGTVDPTKYP-------------------- 143
Query: 203 VQLPRVNQDTRLNNRVIDIRTLAN--QGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAG 260
LP+ V+ +R+ N + RI++ + F +F+ IHTP +
Sbjct: 144 --LPKTKLTLEFLRDVLHLRSRTNSISAVARIRNALAFATHSFFQEHSFLYIHTPIITTS 201
Query: 261 SSEGGSAVFR 270
EG +F+
Sbjct: 202 DCEGAGEMFQ 211
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 53.8 bits (130), Expect = 1e-07
Identities = 87/376 (23%), Positives = 149/376 (39%), Gaps = 90/376 (23%)
Query: 15 DSSSQSISKKAAKKE--AAKKAKEERRKEAE---------------AAASAASALSIEEE 57
+S+ + +SK A KK A + +E+ KE +AA+ + +
Sbjct: 2 ESNGEPLSKNALKKRLKAKQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETMDPTQ- 60
Query: 58 GPLANNYGDVPLQELQSV----NDPQTGKWSEAVSGREWTEV-GAL-NGS-LKDQEVLIR 110
Y L++++++ +P K+ + E E G+L NG L+D V +
Sbjct: 61 ------YRANRLKKVEALRAKGVEPYPYKFDVTHTAPELQEKYGSLENGEELEDVSVSVA 114
Query: 111 GR----RVS-------------TVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSV 153
GR R +Q A K + + F + S D++GV
Sbjct: 115 GRIMAKRAFGKLAFYDLRDDGGKIQLYADKK--RLDLDEEEFEKLHSLVDRGDIVGVTGT 172
Query: 154 PDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPR-----V 208
P G T++ E+ I + E +K + LP
Sbjct: 173 P-----GKTKKGELSI----FPT-----------------SFEVLTKCLLMLPDKYHGLT 206
Query: 209 NQDTRLNNRVIDIRTLAN---QGIFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSE 263
+Q+TR R +D+ +AN + IFR ++++ + R+FL F+E+ TP L IAG +
Sbjct: 207 DQETRYRQRYLDL--IANPEVRDIFRTRAKIISYIRRFLDDRGFLEVETPMLNMIAGGAA 264
Query: 264 GGSAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGL 323
V + L + +LH + + G F RV+E G FR E T RH EFT
Sbjct: 265 ARPFVTHHNDLNMDLYLRIATELHLKRLVVGGFERVYEIGRQFRNEGIST-RHNPEFTTC 323
Query: 324 DVEMEIKKHYSEVMDI 339
+ Y+++M++
Sbjct: 324 EFYQAYAD-YNDMMEL 338
>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 = 50.2 bits (120), Expect = 4e-07
Identities = 21/99 (21%), Positives = 34/99 (34%), Gaps = 11/99 (11%)
Query: 240 FRQFLLSENFVEIHTPKLIAGSSEGGSA------VFRLDYKGQSACLAQSPQLHKQMS-- 291
R+F+ F E+ TP + + + + L + +
Sbjct: 9 LRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLEPGLVRLFV 68
Query: 292 --ICGDFGRVFETGPVFRAED-SYTHRHLCEFTGLDVEM 327
I R+ E GP FR E R + EFT L+ E+
Sbjct: 69 SHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEV 107
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 48.1 bits (114), Expect = 6e-06
Identities = 49/202 (24%), Positives = 84/202 (41%), Gaps = 13/202 (6%)
Query: 209 NQDTRLNNRVIDIRTLANQGIF---RIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSE 263
+ D + R D+ T N + + + + R + NFVE+ TP L +A +
Sbjct: 211 DNDVKYRYRFTDMMT--NPCVIETIKKRHVMLQALRDYFNERNFVEVETPVLHTVASGAN 268
Query: 264 GGSAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGL 323
S V + L +P+LH + I G R++E G VFR ED+ H EFT
Sbjct: 269 AKSFVTHHNANAMDLFLRVAPELHLKQCIVGGMERIYEIGKVFRNEDA-DRSHNPEFT-- 325
Query: 324 DVEMEIKKH-YSEVMDIVDCLFVTIFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTF 382
E H Y ++M + + +F + +N ++ + R++
Sbjct: 326 SCEFYAAYHTYEDLMPMTEDIFRQLAMRVNGTTVVQIYPENAHGNPVTVDLGKPFRRVSV 385
Query: 383 EEGVQMLKDAGVEIDPLGDLNT 404
+ +Q + +GVE P +LNT
Sbjct: 386 YDEIQRM--SGVEFPPPNELNT 405
>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: 205 LPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEG 264
+PRVN+ + + DI N S N A SS
Sbjct: 269 IPRVNKKNKKGEKREDILNTCNANNNNGNSSSSN--------------------AVSSPA 308
Query: 265 GSAVFRLDYK----GQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEF 320
+ +DYK + A L S QL + ++C G V+ GP FRAE+S+T RHL EF
Sbjct: 309 YPDQYLIDYKKDFFSKQAFLTVSGQLSLE-NLCSSMGDVYTFGPTFRAENSHTSRHLAEF 367
Query: 321 TGLDVEMEIKKHY 333
++ E+ Y
Sbjct: 368 WMIEPEIAFADLY 380
Score = 28.5 bits (63), Expect = 9.0
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 229 IFRIQSQVGNIFRQFLLSENFVEIHTPKLIAGSSEGGSAVF 269
+ RI++ + F S F+ IHTP + EGG +F
Sbjct: 214 VIRIRNALAIATHLFFQSRGFLYIHTPLITTSDCEGGGEMF 254
>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 = 42.9 bits (102), Expect = 1e-05
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 113 RVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEIKGATQQVEVQIKKL 172
VQ + E L ES+V V G V V E AT ++E+Q ++L
Sbjct: 25 GSGIVQVVV---NKEELGEFFEEAEKLRTESVVGVTGTV-VKRPEGNLATGEIELQAEEL 80
Query: 173 YCVSR 177
+S+
Sbjct: 81 EVLSK 85
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 46.2 bits (111), Expect = 2e-05
Identities = 44/141 (31%), Positives = 67/141 (47%), Gaps = 32/141 (22%)
Query: 229 IFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEGGSAVFR--------LD---YKG 275
FR +S++ + R+FL + F+E+ TP L IAG G +A R LD Y
Sbjct: 171 TFRKRSKIISAIRRFLDNRGFLEVETPMLQPIAG---GAAA--RPFITHHNALDIDLY-- 223
Query: 276 QSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIK---KH 332
L +P+L+ + I G F RV+E G FR E T RH EFT +E
Sbjct: 224 ----LRIAPELYLKRLIVGGFERVYEIGRNFRNEGIDT-RHNPEFT----MLEFYQAYAD 274
Query: 333 YSEVMDIVDCLFVTIFDSLNN 353
Y+++MD+ + L + ++
Sbjct: 275 YNDMMDLTEELIRHLAQAVLG 295
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 45.3 bits (107), Expect = 4e-05
Identities = 90/434 (20%), Positives = 160/434 (36%), Gaps = 108/434 (24%)
Query: 43 EAAASAASALSIEEEGPLANNYGD----VPLQELQSVNDPQTGKWSEAVSGREWTEVGAL 98
+ S SA +G G+ + + +++ D + + ++ W
Sbjct: 62 ASLQSPESAKVEAAKGAFGEAVGEFRKKLRIADVKGGEDEGLARVGKTLNVMGWVRTLRA 121
Query: 99 NGSLKDQEVLIRGRRVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVVSVPDVEI 158
S+ EV G +S +QC+ T PD+ + V + S++ V G V V
Sbjct: 122 QSSVTFIEV-NDGSCLSNMQCVMT--PDAEGYDQVESGLITTGASVL-VQGTV----VSS 173
Query: 159 KGATQQVEVQIKKLYCVSRAAKT-PITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNR 217
+G Q+VE+++ K+ V ++ + PI + SR + R R
Sbjct: 174 QGGKQKVELKVSKIVVVGKSDPSYPIQKKRVSR-------------EFLRTKAHLR---- 216
Query: 218 VIDIRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTP-----------------KLIAG 260
RT + R+++ + +F FV + +P LI
Sbjct: 217 ---PRTNTFGAVARVRNALAYATHKFFQENGFVWVSSPIITASDCEGAGEQFCVTTLIPN 273
Query: 261 SSE-GGSAVFRL------------DYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFR 307
S+E GGS V + D+ G+ A L S QL+ + + V+ GP FR
Sbjct: 274 SAENGGSLVDDIPKTKDGLIDWSQDFFGKPAFLTVSGQLNGE-TYATALSDVYTFGPTFR 332
Query: 308 AEDSYTHRHLCEF---------TGLDVEMEIKKHY------------SEVMDIVDCLFVT 346
AE+S T RHL EF L+ +M Y E M+ +
Sbjct: 333 AENSNTSRHLAEFWMIEPELAFADLNDDMACATAYLQYVVKYILENCKEDMEFFNTWIEK 392
Query: 347 -IFDSLNNVCKKELEAVAKQYPFEPLKYKPKTLRLTFEEGVQMLKDAGVEID-PLG---D 401
I D L++V +K ++L++ + +++L A + + P+ D
Sbjct: 393 GIIDRLSDVVEKNF------------------VQLSYTDAIELLLKAKKKFEFPVKWGLD 434
Query: 402 LNTESERKLGQLVL 415
L +E ER + +
Sbjct: 435 LQSEHERYITEEAF 448
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 43.3 bits (102), Expect = 2e-04
Identities = 34/106 (32%), Positives = 50/106 (47%), Gaps = 10/106 (9%)
Query: 256 KLIAGSSEGGSAV-FRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTH 314
KL G+S + F D+ + L S +LH + C G V+ GP FRA+ +
Sbjct: 349 KLKTGTSVKADKLSFSKDFFSRPTYLTVSGRLHLESYACA-LGNVYTFGPRFRADRIDSA 407
Query: 315 RHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDSLNNVCKKELE 360
RHL E ++VEM +SE+ D ++C D +CK LE
Sbjct: 408 RHLAEMWMVEVEMA----FSELEDAMNC----AEDYFKFLCKWVLE 445
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 40.2 bits (94), Expect = 0.001
Identities = 54/239 (22%), Positives = 84/239 (35%), Gaps = 55/239 (23%)
Query: 115 STVQCLATVKPDSVSKEM----VRFVRSLSNES--IVDVIGVVSVPDVEIKGATQQVE-- 166
+ V+ P K M VR + L N + G VP + + +
Sbjct: 91 TQVKVKVVSAPTKKKKAMPKSVVRAPKPLENPVPAQAESSGSKPVPSIPVSTPEVKAPAP 150
Query: 167 ----VQIKKL-YCVSRAAKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDI 221
Q +L +S K + E E E E S+ L ++ ++ R
Sbjct: 151 ALTPSQKDRLETLLSPKDKISLNSEKPKFKELESELVSRRKNDLKQMYEEDR-------- 202
Query: 222 RTLANQGIFRIQSQVGNIFR---QFLLSENFVEIHTPKLIAGSS----------EGGSAV 268
+ +G + R +F + F+EI +P LI E +
Sbjct: 203 -----------EDYLGKLERDITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELSKQI 251
Query: 269 FRLDYKGQSACLAQ--SPQL----HKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFT 321
FR+D ++ CL +P L K I D ++FE GP +R E S HL EFT
Sbjct: 252 FRVD---KNFCLRPMLAPGLYNYLRKLDRILPDPIKIFEIGPCYRKE-SDGKEHLEEFT 306
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 38.8 bits (90), Expect = 0.005
Identities = 31/116 (26%), Positives = 53/116 (45%), Gaps = 4/116 (3%)
Query: 209 NQDTRLNNRVIDIRTLAN-QGIFRIQSQVGNIFRQFLLSENFVEIHTP--KLIAGSSEGG 265
+ + R R +D+ + + F ++++ N R FL F+E+ TP L+AG +
Sbjct: 231 DTEIRYRQRYLDLMINESTRSTFITRTKIINYLRNFLNDRGFIEVETPTMNLVAGGANAR 290
Query: 266 SAVFRLDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFT 321
+ + L + +L +M I G +V+E G VFR E + H EFT
Sbjct: 291 PFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNE-GIDNTHNPEFT 345
>gnl|CDD|235095 PRK02983, lysS, lysyl-tRNA synthetase; Provisional.
Length = 1094
Score = 38.4 bits (90), Expect = 0.008
Identities = 37/124 (29%), Positives = 59/124 (47%), Gaps = 16/124 (12%)
Query: 209 NQDTRLNNRVID--IRTLANQGIFRIQSQVGNIFRQFLLSENFVEIHTPKL--IAGSSEG 264
+ + R+ R +D + A + R +S V R+ L++ F+E+ TP L + G G
Sbjct: 748 DPEARVRQRYLDLAVNPEARD-LLRARSAVVRAVRETLVARGFLEVETPILQQVHG---G 803
Query: 265 GSA---VFRLDYKGQSACLAQSPQLH-KQMSICGDFGRVFETGPVFRAED-SYTHRHLCE 319
+A V ++ L +P+L+ K++ + G RVFE G FR E TH E
Sbjct: 804 ANARPFVTHINAYDMDLYLRIAPELYLKRLCV-GGVERVFELGRNFRNEGVDATHNP--E 860
Query: 320 FTGL 323
FT L
Sbjct: 861 FTLL 864
>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 = 35.2 bits (82), Expect = 0.018
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 20/90 (22%)
Query: 136 VRSLSNESIVDVIGVVSV---PDVEIKGATQQVEVQIKKLYCVSRAAKTPITIEDASRSE 192
L NES++ V G V V K T ++EV +L +++A P I+D
Sbjct: 59 AEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKAKTLPFEIDDDV--- 115
Query: 193 AEIEKASKEGVQLPRVNQDTRLNNRVIDIR 222
V+++ RL R +D+R
Sbjct: 116 --------------NVSEELRLKYRYLDLR 131
>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 = 0.027
Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 21/103 (20%)
Query: 242 QFLLSENFVEIHTPKLIAGSSEG----------GSAVFRLDYKGQSACLAQ--SPQLH-- 287
+ L+ FV++ TP +I S VF +D ++ CL +P L+
Sbjct: 37 KALVDRGFVQVKTPIIIPKEYLEKMTIDEDHPLFSQVFWVD---ENKCLRPMLAPNLYNY 93
Query: 288 --KQMSICGDFGRVFETGPVFRAEDSYTHRHLCEFTGLD-VEM 327
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 = 34.6 bits (80), Expect = 0.082
Identities = 31/117 (26%), Positives = 52/117 (44%), Gaps = 9/117 (7%)
Query: 240 FRQFLLSENFVEIHTPKL-IAGSSEGGSAVFRLDY------KGQSACLAQSPQLHKQMSI 292
R+F +E+ TP L +A ++ F ++ KG+ L SP+ H + +
Sbjct: 26 IRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSPEYHMKRLL 85
Query: 293 CGDFGRVFETGPVFRAEDSYTHRHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFD 349
G +F+ G VFR E+ H EFT L+ + Y +M+ VD L + +
Sbjct: 86 AAGSGPIFQLGKVFRNEEM-GRLHNPEFTMLEW-YRVGCDYYRLMNEVDDLLQLVLE 140
>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 = 0.13
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 = 33.0 bits (76), Expect = 0.27
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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 34.0 bits (78), Expect = 0.14
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 = 33.2 bits (76), Expect = 0.23
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 = 33.2 bits (76), Expect = 0.26
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 = 32.5 bits (74), Expect = 0.36
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 = 29.4 bits (66), Expect = 3.8
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 = 29.0 bits (65), Expect = 4.7
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASA 51
A K AA KA E + AE AA+A +A
Sbjct: 220 AAEAKAAAAKAAAEAKAAAEKAAAAKAA 247
Score = 29.0 bits (65), Expect = 5.0
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 = 28.2 bits (63), Expect = 8.0
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 = 28.2 bits (63), Expect = 8.2
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|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|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 = 32.0 bits (72), Expect = 0.67
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|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 = 30.6 bits (70), Expect = 1.2
Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 24/124 (19%)
Query: 243 FLLSENFVEIHTPKLI-AGSSEGGSAVFRLDYKGQSAC-----LAQSPQLH-KQMSICGD 295
F +E+ TP L A ++ F ++ G L SP+ K++ +
Sbjct: 1 FFAERGVLEVETPLLSPAPVTDPHLDAFATEFVGPDGQGRPLYLQTSPEYAMKRL-LAAG 59
Query: 296 FGRVFETGPVFRAEDSYTHRHLCEFT-------GLDVEMEIKKHYSEVMDIVDCLFVTIF 348
G +F+ VFR + RH EFT G D Y ++MD V+ L +
Sbjct: 60 SGPIFQICKVFRNGER-GRRHNPEFTMLEWYRPGFD--------YHDLMDEVEALLQELL 110
Query: 349 DSLN 352
Sbjct: 111 GDPF 114
>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|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 30.3 bits (68), Expect = 1.7
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 = 28.4 bits (63), Expect = 8.3
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 = 28.0 bits (62), Expect = 9.2
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 = 28.0 bits (62), Expect = 9.4
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
>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: 153 VPDVEIKGATQQVEVQIKKLYCVSRAAK----TPITIEDASRSEAEIEKASKEGVQ 204
+ 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 = 29.7 bits (67), Expect = 2.5
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|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 = 30.2 bits (68), Expect = 2.6
Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 9/93 (9%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSI----EEEGPLANN----YGDVPLQELQSV 75
KA KKE +E + K+ A S + E + + D +++
Sbjct: 575 KALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQADKIGDKVRIR 634
Query: 76 NDPQTGKWSEAVSGREWTE-VGALNGSLKDQEV 107
Q GK + + G +W VG + + E+
Sbjct: 635 YFGQKGKIVQILGGNKWNVTVGGMRMKVHGSEL 667
>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 = 28.4 bits (64), Expect = 2.6
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 107 VLIRGRRVSTVQCLATVKPDSVSKEMVRFVRSLSNESIVDVIGVV 151
V++R R VQ T V KE+ + VR LS ES++ V G V
Sbjct: 33 VILRDRE-GIVQ--VTAPKKKVDKELFKTVRKLSRESVISVTGTV 74
>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 = 29.8 bits (67), Expect = 2.8
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 = 29.4 bits (66), Expect = 3.6
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 23 KKAAKKEAAKKAKEERRKEAEAAASAA 49
K EA KKA+ E + +AEA A A
Sbjct: 164 AKKKAAEAKKKAEAEAKAKAEAKAKAK 190
Score = 29.0 bits (65), Expect = 4.3
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 = 28.6 bits (64), Expect = 5.4
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 = 28.3 bits (63), Expect = 8.7
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|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
Length = 430
Score = 29.9 bits (67), Expect = 2.8
Identities = 28/99 (28%), Positives = 45/99 (45%), Gaps = 13/99 (13%)
Query: 10 VQEEVDSSSQSISKKAAKKEAAKKAK------------EERRKEAEAAASAASALSIEEE 57
V EE + +++ + AAK +AA AK E+ + +A AAA A +A + +
Sbjct: 195 VTEEEKAKAKAKAAAAAKAKAAALAKQKASQGNGDSGDEDAKAKAIAAAKAKAAAAARAK 254
Query: 58 GPLANNYGD-VPLQELQSVNDPQTGKWSEAVSGREWTEV 95
A + P QE SVN P K+ E + + +V
Sbjct: 255 TKGAEGKKEEEPKQEEPSVNQPYLNKYVEVIKEKLGEDV 293
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 29.8 bits (67), Expect = 3.1
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|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|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 = 29.2 bits (66), Expect = 3.2
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|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 29.8 bits (68), Expect = 3.6
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|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 = 29.6 bits (67), Expect = 3.6
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 359 LEAVAKQYP------FEPL--KYKPKTLRLTFEEGVQMLKDAGV 394
L AV ++ P F P+ Y + L+ EE ++ LK+AG+
Sbjct: 109 LRAVKEEVPGMHIHAFSPMEVYYGARNSGLSVEEALKRLKEAGL 152
>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 = 4.0
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|204181 pfam09251, PhageP22-tail, Salmonella phage P22 tail-spike. Members
of this family of viral domains adopt a structure
consisting of a single-stranded right-handed beta-helix,
which in turn is made of parallel beta-strands and short
turns. They are required for recognition of the
0-antigenic repeating units of the cell surface, and for
subsequent infection of the bacterial cell.
Length = 549
Score = 29.4 bits (66), Expect = 4.1
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 88 SGREWTEVGALNGSLKDQEVLIRGR---RVSTVQCLATVKPDSVSKEMVRFVRSLSNESI 144
SG WTE+ A++GS D L R R + + TV PD K++ F L S+
Sbjct: 473 SGSAWTELTAISGSTPDAVSLKVNRGDYRAAEIPFSPTVLPDEAVKDISCFSLYLEANSL 532
>gnl|CDD|237110 PRK12472, PRK12472, hypothetical protein; Provisional.
Length = 508
Score = 29.1 bits (65), Expect = 4.8
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|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 29.1 bits (65), Expect = 4.8
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|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 29.1 bits (66), Expect = 4.9
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|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 = 5.0
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 NDPQTGKWSEAVSG 89
N P G+ G
Sbjct: 111 NSPSEGEGEGEGEG 124
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 29.1 bits (66), Expect = 5.1
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 8 PKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEA 42
PK + + + SKK K A KK KE+ + +
Sbjct: 378 PKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKV 412
>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 = 26.5 bits (59), Expect = 5.4
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 22 SKKAAKKEAAKKA 34
SKK AK+ AA+ A
Sbjct: 52 SKKEAKQNAAEAA 64
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 28.2 bits (63), Expect = 5.6
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|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 29.2 bits (65), Expect = 5.6
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 3 TESEPPKVQEEVDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASA 51
+ ++ ++ ++ KK AKK AKKA ++ +AAA A
Sbjct: 974 VRKTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVA 1022
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 6.2
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 = 28.6 bits (63), Expect = 8.0
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 = 28.6 bits (63), Expect = 8.1
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 = 28.6 bits (63), Expect = 8.8
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 = 28.6 bits (63), Expect = 8.9
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
>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 = 6.4
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 = 28.4 bits (64), Expect = 6.8
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|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 28.8 bits (64), Expect = 7.2
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|227434 COG5103, CDC39, Cell division control protein, negative regulator of
transcription [Cell division and chromosome partitioning
/ Transcription].
Length = 2005
Score = 28.8 bits (64), Expect = 7.4
Identities = 20/108 (18%), Positives = 35/108 (32%)
Query: 14 VDSSSQSISKKAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGDVPLQELQ 73
V S+SIS + + + AA+ LS+ L + G Q+
Sbjct: 1168 VSKVSESISAEIEHMIVERVRHRKTTPNLPFVDPAAANLSLNLPSSLELSIGKATPQQFS 1227
Query: 74 SVNDPQTGKWSEAVSGREWTEVGALNGSLKDQEVLIRGRRVSTVQCLA 121
D S + E + A++ D + +TV+ A
Sbjct: 1228 LYEDFDRLSLSTIMGHIEKIAINAIDTDSADSTDALNNNLNNTVENEA 1275
>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 = 8.1
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|215039 PLN00041, PLN00041, photosystem I reaction center subunit II;
Provisional.
Length = 196
Score = 28.0 bits (62), Expect = 8.2
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 264 GGSAVFR-----LDYKGQSACLAQSPQLHKQMSICGDFGRVFETGPV 305
GG+A+ R L + CLA +L + I F RVF G V
Sbjct: 103 GGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEV 149
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 28.6 bits (65), Expect = 8.4
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|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 28.2 bits (63), Expect = 9.2
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|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 28.1 bits (64), Expect = 9.7
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 315 RHLCEFTGLDVEMEIKKHYSEVMDIVDCLFVTIFDS---LNNVCKKELEAVAKQY 366
R L L+ E+EI+K E+ + L I S L + KKEL+A AK++
Sbjct: 432 RRL---AKLE-EIEIRKEQDELRKEIAEL-EAILASERKLRKLIKKELKADAKKF 481
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.1 bits (63), Expect = 9.9
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 24 KAAKKEAAKKAKEERRKEAEAAASAASALSIEEEGPLANNYGD 66
KA + AA +A R + AEA + + E L ++ G
Sbjct: 249 KAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLISSTGG 291
>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 = 9.9
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|214371 CHL00122, secA, preprotein translocase subunit SecA; Validated.
Length = 870
Score = 28.4 bits (64), Expect = 9.9
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 179 AKTPITIEDASRSEAEIEKASKEGVQLPRVNQDTRLNNRVIDIRTLANQGIFRIQSQVGN 238
A+TP+ I S++ + + E + N ++ + ++ L QGI I+
Sbjct: 213 ARTPLIISGQSKTNIDKYIVADELAKYLEKNVHYEVDEKNKNV-ILTEQGILFIE----- 266
Query: 239 IFRQFLLSENFVEIHTP 255
+ L E+ + P
Sbjct: 267 ---KILKIEDLYSANDP 280
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
0.313 0.130 0.355
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: 20,329,658
Number of extensions: 1968409
Number of successful extensions: 3517
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3164
Number of HSP's successfully gapped: 222
Length of query: 417
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 318
Effective length of database: 6,546,556
Effective search space: 2081804808
Effective search space used: 2081804808
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)