RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024194
(271 letters)
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 407 bits (1049), Expect = e-142
Identities = 173/299 (57%), Positives = 200/299 (66%), Gaps = 39/299 (13%)
Query: 2 PAIHSSLSFYMKPLFLSNSSLFPRKFTVPKEYLLNPRSLCALSSASNQNGGRSGARSLSP 61
S+ + L LS+ F + P+ CA S+A GGRSG + P
Sbjct: 7 ATRVSASAIRRPSLPLSSRCSFLLSASSPR------GGRCAASAA--AGGGRSGGTTAPP 58
Query: 62 SPVSDDLQKIDVNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFI 121
S D KIDVNPPKGTRDFPPEDMRLRNWLF +F+EVSRLFGFEEVD PVLESE L+I
Sbjct: 59 SVQEDGKPKIDVNPPKGTRDFPPEDMRLRNWLFDHFREVSRLFGFEEVDAPVLESEELYI 118
Query: 122 RKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYER 181
RKAGEEI DQLY FED+G RRVALRPELTPSLARLV+QKGKS+SLPLKWFA+GQCWRYER
Sbjct: 119 RKAGEEITDQLYNFEDKGGRRVALRPELTPSLARLVLQKGKSLSLPLKWFAIGQCWRYER 178
Query: 182 MTRGRRREHYQWNMDIIGVPAVT-------------------------------VLQEVL 210
MTRGRRREHYQWNMDIIGVP V VLQ VL
Sbjct: 179 MTRGRRREHYQWNMDIIGVPGVEAEAELLAAIVTFFKRVGITSSDVGIKVSSRKVLQAVL 238
Query: 211 RCHSIPEHLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIKSLTELEG 269
+ + IPE F VC+I+DK+EKLP + I+ +L + G+SE AIE +L VLS+KSL +LE
Sbjct: 239 KSYGIPEESFAPVCVIVDKLEKLPREEIEKELDTLGVSEEAIEGILDVLSLKSLDDLEA 297
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 169 bits (430), Expect = 3e-50
Identities = 51/131 (38%), Positives = 79/131 (60%), Gaps = 3/131 (2%)
Query: 74 NPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEE---IRD 130
P+GTRDF PE+M ++ +EV L+GF+E+ P+ E LF RK GEE +
Sbjct: 1 QAPRGTRDFLPEEMIKWQYIEETIREVFELYGFKEIRTPIFEYTELFARKVGEETDIVEK 60
Query: 131 QLYCFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREH 190
++Y F+D+G R + LRPE T +AR VI+ + P K + +G +RYER +GR R+
Sbjct: 61 EMYTFKDKGGRSLTLRPEGTAPVARAVIENKLLLPKPFKLYYIGPMFRYERPQKGRYRQF 120
Query: 191 YQWNMDIIGVP 201
+Q+ +++IG
Sbjct: 121 HQFGVEVIGSD 131
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 167 bits (424), Expect = 5e-49
Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 35/223 (15%)
Query: 70 KIDVNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEE-- 127
+ + P+GTRDF PEDM LR ++ ++V +GF E+ P+ E LF RK+GEE
Sbjct: 1 MMKIQRPRGTRDFLPEDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETD 60
Query: 128 -IRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGR 186
+ ++Y F+D+G R +ALRPELT +AR V + + PLK + G +RYER +GR
Sbjct: 61 VVEKEMYTFKDKGGRSLALRPELTAPVARAVAENKLDLPKPLKLYYFGPVFRYERPQKGR 120
Query: 187 RREHYQWNMDIIGVP-----------AVTVLQEV-----------LRC-HSIPEHLFG-- 221
R+ YQ+ +++IG AV +L+ + E+L
Sbjct: 121 YRQFYQFGVEVIGSDSPDADAEVIALAVEILEALGIGGFTLEINSRGILEGRLEYLGIDQ 180
Query: 222 --KVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIK 262
+ +DK++K+ + D K LRVL K
Sbjct: 181 REALLRYLDKLDKIGKLELDEDSK----RRLKT-NPLRVLDSK 218
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 158 bits (403), Expect = 1e-47
Identities = 60/183 (32%), Positives = 98/183 (53%), Gaps = 14/183 (7%)
Query: 86 DMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVAL 145
+ LR ++ +EV +G+EE+D PV E LF+RK+G+E+ ++Y F+D+G R +AL
Sbjct: 1 EAALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVSKEMYRFKDKGGRDLAL 60
Query: 146 RPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTV 205
RP+LT +AR V + S+ LPLK + +G +RYER +GR RE YQ ++IIG +
Sbjct: 61 RPDLTAPVARAVAENLLSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSDSPLA 120
Query: 206 LQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEEL-LRVLSIKSL 264
EV+ + ++ +E L L + + G+ + L R I+ L
Sbjct: 121 DAEVIA-------------LAVEILEALGLKDFQIKINHRGILDGIAGLLEDREEYIERL 167
Query: 265 TEL 267
+
Sbjct: 168 IDK 170
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 160 bits (407), Expect = 1e-46
Identities = 57/184 (30%), Positives = 90/184 (48%), Gaps = 21/184 (11%)
Query: 70 KIDVNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIR 129
+ + P+GTRD PE+ ++ +EV +GF E+ P+ E LF RK GEE
Sbjct: 1 MMKIQAPRGTRDILPEESAKWQYVEDTIREVFERYGFSEIRTPIFEYTELFKRKVGEETD 60
Query: 130 D---QLYCFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGR 186
++Y F+D+G R + LRPE T + R VI+ P K + +G +RYER +GR
Sbjct: 61 IVEKEMYTFQDKGGRSLTLRPEGTAPVVRAVIEHKL---QPFKLYYIGPMFRYERPQKGR 117
Query: 187 RREHYQWNMDIIGVPAVTVLQEVLRCHSIPEHLFGKVCIIIDKI-EKLPLDVIKNDLKSA 245
R+ +Q+ +++IG + L + E V + I + L L +K + S
Sbjct: 118 YRQFHQFGVEVIGSD--SPLADA-------E-----VIALAADILKALGLKGLKLLINSL 163
Query: 246 GMSE 249
G E
Sbjct: 164 GDFE 167
>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 = 103 bits (259), Expect = 3e-27
Identities = 45/131 (34%), Positives = 72/131 (54%), Gaps = 8/131 (6%)
Query: 89 LRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEE--IRDQLYCFEDRGNRRVALR 146
LRN L + +E+ + +G++EVD P+LE + L+ + +++Y F+DRG + LR
Sbjct: 1 LRNALENFIRELLKRYGYQEVDTPILEPKELWEGSGHWDDYFEEEMYKFKDRGGEELYLR 60
Query: 147 PELTPSLARLVIQKGKSVS-LPLKWFAVGQCWRYE---RMTRGRRREHYQWNMDIIGVP- 201
P + RL + S LPLK + +G C+RYE R GR RE Q + +I G P
Sbjct: 61 PTAEVGITRLFKNEILSYRELPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFGTPE 120
Query: 202 -AVTVLQEVLR 211
+ L+E+L+
Sbjct: 121 QSEEELEELLK 131
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 104 bits (262), Expect = 7e-26
Identities = 62/222 (27%), Positives = 105/222 (47%), Gaps = 31/222 (13%)
Query: 77 KGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRK--AGEEIRDQLYC 134
KGT+D+ PE+ LRN + ++V +G + ++ P L L K G+EI ++Y
Sbjct: 8 KGTKDYLPEEQVLRNKIKRALEDVFERYGCKPLETPTLNMYELMSSKYGGGDEILKEIYT 67
Query: 135 FEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWN 194
D+G R +ALR +LT A+ V+ ++ LP K + +G+ +R + +GR RE Q +
Sbjct: 68 LTDQGKRDLALRYDLTIPFAK-VVAMNPNIRLPFKRYEIGKVFRDGPIKQGRFREFIQCD 126
Query: 195 MDIIGVP---------------------AVTV-------LQEVLRCHSIPEHLFGKVCII 226
+DI+GV VT+ L +L+ IP L V +
Sbjct: 127 VDIVGVESVMAEAELMSMAFELFRRLNLEVTIQYNNRKLLNGILQAIGIPTELTSDVILS 186
Query: 227 IDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIKSLTELE 268
+DKIEK+ +D ++ DL G+SE + + + +
Sbjct: 187 LDKIEKIGIDGVRKDLLERGISEEMADTICNTVLSCLQLSIA 228
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase,
regulatory subunit. Apparant second copies of
histidyl-tRNA synthetase, found in Bacillus subtilis,
Synechocystis sp., Aquifex aeolicus, and others, are in
fact a regulatory subunit of ATP
phosphoribosyltransferase, and usually encoded by a gene
adjacent to that encoding the catalytic subunit [Amino
acid biosynthesis, Histidine family].
Length = 313
Score = 97.7 bits (244), Expect = 7e-24
Identities = 54/202 (26%), Positives = 87/202 (43%), Gaps = 24/202 (11%)
Query: 80 RDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRG 139
RD PE+ + + Q+V R +G++E+ P LE +G + L+ D+
Sbjct: 1 RDLLPEEAARKEEIERQLQDVFRSWGYQEIITPTLEYLDTLSAGSGIL-NEDLFKLFDQL 59
Query: 140 NRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIG 199
R + LRP++T +ARLV + + LPL+ G +R GR RE Q +++IG
Sbjct: 60 GRVLGLRPDMTAPIARLVSTRLRDRPLPLRLCYAGNVFRTNESGGGRSREFTQAGVELIG 119
Query: 200 VPAVTVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIKND----------LKSAGMSE 249
EV+ ++I+ ++ L L K + L+ AG+ E
Sbjct: 120 AGGPAADAEVI-------------ALLIEALKALGLKDFKIELGHVGLVRALLEEAGLPE 166
Query: 250 AAIEELLRVLSIKSLTELEGWF 271
A E L L+ K L LE
Sbjct: 167 EAREALREALARKDLVALEELV 188
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 86.7 bits (215), Expect = 2e-19
Identities = 37/130 (28%), Positives = 62/130 (47%), Gaps = 2/130 (1%)
Query: 74 NPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLY 133
P+G RD P + R + + + R +G+E V+ P LE + AGE++R +L+
Sbjct: 4 QLPEGIRDVLPLEARRKEEIRDQLLALFRAWGYERVETPTLEPADPLLDGAGEDLRRRLF 63
Query: 134 CFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQW 193
ED R+ LRP+ T +AR+ PL+ G+ +R GRR E Q
Sbjct: 64 KLEDETGGRLGLRPDFTIPVARIHATLLA--GTPLRLSYAGKVFRAREGRHGRRAEFLQA 121
Query: 194 NMDIIGVPAV 203
++++G +
Sbjct: 122 GIELLGDDSA 131
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 82.2 bits (203), Expect = 1e-17
Identities = 58/206 (28%), Positives = 89/206 (43%), Gaps = 37/206 (17%)
Query: 76 PKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYCF 135
PKGTRDF E M +R F V + G +D PV E + K GE+ + +Y
Sbjct: 330 PKGTRDFAKEQMAIREKAFSIITSVFKRHGATALDTPVFELRETLMGKYGEDSK-LIYDL 388
Query: 136 EDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNM 195
D+G +LR +LT AR V G + K + + + +R + ++GR RE YQ +
Sbjct: 389 ADQGGELCSLRYDLTVPFARYVAMNGIT---SFKRYQIAKVYRRDNPSKGRYREFYQCDF 445
Query: 196 DIIGVPA--------VTVLQEVLR-----------------------CHSIPEHLFGKVC 224
DI GV + VL E+L C +P F +C
Sbjct: 446 DIAGVYEPMGPDFEIIKVLTELLDELDIGTYEVKLNHRKLLDGMLEIC-GVPPEKFRTIC 504
Query: 225 IIIDKIEKLPLDVIKNDL-KSAGMSE 249
IDK++K + +K ++ + G+S
Sbjct: 505 SSIDKLDKQSFEQVKKEMVEEKGLSN 530
>gnl|CDD|222097 pfam13393, tRNA-synt_His, Histidyl-tRNA synthetase. This is a
family of class II aminoacyl-tRNA synthetase-like and
ATP phosphoribosyltransferase regulatory subunits.
Length = 308
Score = 79.5 bits (197), Expect = 3e-17
Identities = 53/203 (26%), Positives = 85/203 (41%), Gaps = 25/203 (12%)
Query: 78 GTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYCFED 137
G RD P + R L ++ R +G+E V P+LE + AG ++ DQ + D
Sbjct: 1 GIRDLLPPEARRIEELRRRLLDLFRSWGYELVIPPLLEYLESLLTGAGADL-DQTFKLVD 59
Query: 138 RGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDI 197
+ R + LR ++TP +AR+ + PL+ G R G RE Q ++
Sbjct: 60 QSGRLLGLRADITPQVARIDAHRLNR-PRPLRLCYAGPVLRTRPDGLGGSREPLQIGAEL 118
Query: 198 IGVPAVTVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIKNDL----------KSAGM 247
IG + EV+ ++++ +E L + + DL ++ G+
Sbjct: 119 IGHAGIEADAEVIS-------------LLLEALESLGVKGVTLDLGHVGIVRALLEALGL 165
Query: 248 SEAAIEELLRVLSIKSLTELEGW 270
SEA E L L K L ELE
Sbjct: 166 SEAQEEALRDALQRKDLPELEEL 188
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 77.6 bits (191), Expect = 3e-16
Identities = 38/132 (28%), Positives = 68/132 (51%), Gaps = 6/132 (4%)
Query: 73 VNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEE---IR 129
+ +GT+D P+++ ++ + L + E+ P+ E+ +L+ R GE +
Sbjct: 4 IQAIRGTKDILPDEINYWQFIHDKALTLLSLANYSEIRTPIFENSSLYDRGIGETTDIVN 63
Query: 130 DQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSV--SLPLKWFAVGQCWRYERMTRGRR 187
++Y F DR NR + LRPE T + R I+ +L W++ G +RYER GR+
Sbjct: 64 KEMYRFTDRSNRDITLRPEGTAGIVRAFIENKMDYHSNLQRLWYS-GPMFRYERPQSGRQ 122
Query: 188 REHYQWNMDIIG 199
R+ +Q ++ IG
Sbjct: 123 RQFHQLGIEFIG 134
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 71.4 bits (176), Expect = 3e-14
Identities = 52/205 (25%), Positives = 89/205 (43%), Gaps = 24/205 (11%)
Query: 75 PPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYC 134
P+G RD PE+ R + ++ R +G+EEV P LE + G + + +
Sbjct: 5 LPEGIRDLLPEEARKIEEIRRRLLDLFRRWGYEEVITPTLEYLDTLLAGGGAILDLRTFK 64
Query: 135 FEDRG-NRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQW 193
D+ R + LRP++T +AR+ + + PL+ G +R + GR RE Q
Sbjct: 65 LVDQLSGRTLGLRPDMTAQIARIAATRLANRPGPLRLCYAGNVFRAQERGLGRSREFLQS 124
Query: 194 NMDIIGVPAVTVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIKND----------LK 243
+++IG + EV+ ++++ ++ L L D L+
Sbjct: 125 GVELIGDAGLEADAEVIL-------------LLLEALKALGLPNFTLDLGHVGLFRALLE 171
Query: 244 SAGMSEAAIEELLRVLSIKSLTELE 268
+AG+SE E L R L+ K LE
Sbjct: 172 AAGLSEELEEVLRRALANKDYVALE 196
>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 = 51.3 bits (123), Expect = 8e-08
Identities = 34/105 (32%), Positives = 49/105 (46%), Gaps = 7/105 (6%)
Query: 97 FQEVSRLF---GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSL 153
Q++ R GF+EV+ P++E E L KAG E +D L + LRP L P L
Sbjct: 6 EQKLRRFMAELGFQEVETPIVEREPLL-EKAGHEPKDLLP-VGAENEEDLYLRPTLEPGL 63
Query: 154 ARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDII 198
RL + + LPL+ +G +R E RG RR ++
Sbjct: 64 VRLFVSHIRK--LPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGE 106
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 47.8 bits (114), Expect = 1e-06
Identities = 35/125 (28%), Positives = 57/125 (45%), Gaps = 12/125 (9%)
Query: 105 GFEEVDFPVLESEALFIRKAG--EEIRDQLYCFEDRG----NRRVALRPELTPSLARLVI 158
G++E+ FP L LF K G + R ++Y FED+G + + LRP + ++
Sbjct: 20 GYQEILFPFLAPTVLF-FKGGHLDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFS 78
Query: 159 QKGKSV-SLPLKWFAVGQCWRYERMTR---GRRREHYQWNMDIIGVPAVTVLQEVLRCHS 214
+ S +LPL+ +G C+R+E R R RE Q + G P +E
Sbjct: 79 GEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE-EAEEERREWLE 137
Query: 215 IPEHL 219
+ E +
Sbjct: 138 LAEEI 142
>gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 373
Score = 47.6 bits (114), Expect = 2e-06
Identities = 25/95 (26%), Positives = 43/95 (45%), Gaps = 5/95 (5%)
Query: 105 GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSV 164
G VD P+L+ F+ +GE+IR +++ D + LRP+ T + R I
Sbjct: 22 GAVRVDPPILQPAEPFLDLSGEDIRRRIFVTSDENGEELCLRPDFTIPVCRRHIATA--G 79
Query: 165 SLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIG 199
P ++ +G+ +R R R E Q ++ G
Sbjct: 80 GEPARYAYLGEVFRQR---RDRASEFLQAGIESFG 111
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 41.8 bits (99), Expect = 2e-04
Identities = 33/97 (34%), Positives = 45/97 (46%), Gaps = 17/97 (17%)
Query: 104 FGFEEVDFPVLESEALF-----IRKAGEEIRDQLYCFEDRGNRRVALRP---ELTPSLAR 155
G +EV FP L L+ G E L+ +DRG+R +ALRP E+ + R
Sbjct: 64 IGAQEVLFPTLIPAELWKESGRWEGFGPE----LFRVKDRGDRPLALRPTSEEVITDMFR 119
Query: 156 LVIQKGKSVSLPLKWFAVGQCWRYE-RMTRG--RRRE 189
I+ K LPLK + + +R E R G R RE
Sbjct: 120 KWIRSYK--DLPLKLYQIQSKFRDEKRPRFGLLRGRE 154
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 39.1 bits (92), Expect = 0.001
Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 12/94 (12%)
Query: 96 NFQEVSRLFGFEEVDFPVLES-----EALFIRK--AGEEIRDQLYCFEDRG--NRRVALR 146
+++ GFEEV+ P +ES +AL I + +++D Y + +RR+ LR
Sbjct: 25 EIRDIFLSMGFEEVEGPEVESDFYNFDALNIPQDHPARDMQDTFYLKKPLKEEDRRLLLR 84
Query: 147 PELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYE 180
TP AR + +K K P+K F++G+ +R +
Sbjct: 85 THTTPVQARTLAKKNK---PPIKIFSIGRVFRRD 115
>gnl|CDD|232961 TIGR00408, proS_fam_I, prolyl-tRNA synthetase, family I.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent families. This family includes the archaeal
enzyme, the Pro-specific domain of a human
multifunctional tRNA ligase, and the enzyme from the
spirochete Borrelia burgdorferi. The other family
includes enzymes from Escherichia coli, Bacillus
subtilis, Synechocystis PCC6803, and one of the two
prolyL-tRNA synthetases of Saccharomyces cerevisiae
[Protein synthesis, tRNA aminoacylation].
Length = 472
Score = 38.2 bits (89), Expect = 0.004
Identities = 40/143 (27%), Positives = 59/143 (41%), Gaps = 19/143 (13%)
Query: 65 SDDLQK---IDVNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFI 121
L+K ID P KG + P ++ + + + G EEV FP+L E+ +
Sbjct: 13 HQILEKAEIIDYYPVKGCYVWLPYGFKIWKNIQKILRNILDEIGHEEVYFPMLIPES-EL 71
Query: 122 RKAGEEIR---DQLYCFEDRG----NRRVALRPELTPSLARLVIQKGKSVS---LPLKWF 171
K + I+ ++Y G + +ALRP T A + K S LPLK
Sbjct: 72 AKEKDHIKGFEPEVYWITHGGLSKLDEPLALRP--TSETAMYPMFKKWVKSYTDLPLKIN 129
Query: 172 AVGQCWRYE-RMTRG--RRREHY 191
+RYE + TR R RE
Sbjct: 130 QWVNVFRYETKHTRPFLRTREFT 152
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 36.7 bits (85), Expect = 0.009
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 98 QEVSRLF---GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLA 154
+++++ F GF E+ P+L A +I + G + +L R ++ LRP L P L
Sbjct: 211 RDITKFFVDRGFLEIKSPIL-IPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPGLY 269
Query: 155 RLVIQKGKSVSLPLKWFAVGQCWRYE 180
+ + + + P+K F +G C+R E
Sbjct: 270 NYLRKLDRILPDPIKIFEIGPCYRKE 295
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 34.1 bits (79), Expect = 0.067
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 104 FGFEEVDFPVLESE-----ALFIRK--AGEEIRDQLYCFEDRGNRRVALRPELTPSLARL 156
GF EV+ P +E++ AL I + +++D Y +D + + LR +P AR
Sbjct: 127 MGFTEVEGPEIETDFYNFDALNIPQDHPARDMQDTFY-LKDDREKLL-LRTHTSPVQART 184
Query: 157 VIQKGKSVSLPLKWFAVGQCWRYE 180
+ + K P+K F+ G+ +R +
Sbjct: 185 LAENAKI---PIKIFSPGRVYRND 205
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 33.5 bits (77), Expect = 0.12
Identities = 26/107 (24%), Positives = 47/107 (43%), Gaps = 10/107 (9%)
Query: 76 PKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALF-IRKAGEEIRDQLYC 134
PKG +RN L ++ +G+ EV+ P++ L+ I + +++++
Sbjct: 197 PKGAT--------IRNLLEDFVRQKQIKYGYMEVETPIMYDLELWEISGHWDNYKERMFP 248
Query: 135 FEDRGNRRVALRPELTPSLARLVIQKGKSV-SLPLKWFAVGQCWRYE 180
F + NR L+P P + +S LPL+ +G RYE
Sbjct: 249 FTELDNREFMLKPMNCPGHFLIFKSSLRSYRDLPLRIAELGYSHRYE 295
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 32.9 bits (76), Expect = 0.15
Identities = 31/120 (25%), Positives = 53/120 (44%), Gaps = 17/120 (14%)
Query: 76 PKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALF-IRKAGEEIRDQLYC 134
PKG +RN L +E+ R G++EV+ P++ ++ L+ + R+ ++
Sbjct: 27 PKGAI--------IRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFP 78
Query: 135 FEDRGNRRVALRPELTPSLARLVIQKGKSV-SLPLKWFAVGQCWRYER------MTRGRR 187
FE + L+P P + K +S LPL+ G RYE+ +TR R
Sbjct: 79 FE-EEDEEYGLKPMNCPGHCLIFKSKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRG 137
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 33.0 bits (76), Expect = 0.15
Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 3/105 (2%)
Query: 78 GTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEI-RDQLYCFE 136
G + P+ +RN L + R +G++EV PVL L+ + ++ ++ E
Sbjct: 211 GLPFWHPKGATIRNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWDNYKEDMFLTE 270
Query: 137 DRGNRRVALRPELTPSLARLVIQKGKSV-SLPLKWFAVGQCWRYE 180
+R AL+P P + +S LPL+ G +RYE
Sbjct: 271 S-DDREYALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYE 314
>gnl|CDD|146478 pfam03866, HAP, Hydrophobic abundant protein (HAP). Expression of
HAP is thought to be developmentally regulated and
possibly involved in spherule cell wall formation.
Length = 167
Score = 31.0 bits (70), Expect = 0.34
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 15/75 (20%)
Query: 197 IIGVPAVTVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIK-------NDLKSAGMSE 249
IIG+ V L VL E + G V ++ + L LD++ ND
Sbjct: 60 IIGL--VITLSGVL------EIVIGTVLGLVATLAALALDLVGGSVGGICNDFLDFDAIL 111
Query: 250 AAIEELLRVLSIKSL 264
IEE L L ++L
Sbjct: 112 ELIEESLHSLLAQAL 126
>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 = 30.2 bits (68), Expect = 1.0
Identities = 31/147 (21%), Positives = 56/147 (38%), Gaps = 13/147 (8%)
Query: 105 GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSV 164
GF +V P++ + + K + L+ + LRP L P+L + + +
Sbjct: 43 GFVQVKTPIIIPKEY-LEKMTIDEDHPLFSQVFWVDENKCLRPMLAPNLYNYLRKLDRLW 101
Query: 165 SLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPA-------VTVLQEVLRCHSIPE 217
P++ F +G C+R E E N+ +G P + + VL I E
Sbjct: 102 PKPIRIFEIGPCYRKESQGSQHLNEFTMLNLCEMGSPLECRRERLEDLARWVLEHLGIRE 161
Query: 218 -HLFGKVCIIIDKIEKLPLDVIKNDLK 243
L ++ +DV+ DL+
Sbjct: 162 FELVTDSSVVYGDT----VDVMHGDLE 184
>gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 281
Score = 30.0 bits (68), Expect = 1.1
Identities = 44/181 (24%), Positives = 77/181 (42%), Gaps = 38/181 (20%)
Query: 105 GFEEVDFPVLE-SEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQK-GK 162
GFEE+ P + I E IR F D N +++LR + T + R+V ++ G+
Sbjct: 37 GFEEIVTPFFSYHQHQSIADEKELIR-----FSDEKNHQISLRADSTLDVVRIVTKRLGR 91
Query: 163 SVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIG----VPAVTVLQEVLRCHSIPEH 218
S + KWF + +RY E YQ ++IG + + E+ +
Sbjct: 92 S-TEHKKWFYIQPVFRYP------SNEIYQIGAELIGEEDLSEILNIAAEIFEELELEPI 144
Query: 219 L---FGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELL--------RVLSIKSLTEL 267
L K+ ++ +I L ++V K IE+LL +++ IK+L +L
Sbjct: 145 LQISNIKIPKLVAEILGLDIEVFKK---------GQIEKLLAQNVPWLNKLVRIKTLEDL 195
Query: 268 E 268
+
Sbjct: 196 D 196
>gnl|CDD|238402 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II
core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain. This
subfamily contains the core domain of ProRS from
prokaryotes and from the mitochondria of eukaryotes.
Length = 255
Score = 29.9 bits (68), Expect = 1.2
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 11/93 (11%)
Query: 105 GFEEVDFPVLESEALFIRKAG--EEIRDQLYCFEDRGNRRVALRP---ELTPSLARLVIQ 159
G +E+ P+L+ L+ +++G + +L +DR + L P E+ L I+
Sbjct: 49 GAQEILMPILQPAELW-KESGRWDAYGPELLRLKDRHGKEFLLGPTHEEVITDLVANEIK 107
Query: 160 KGKSVSLPLKWFAVGQCWRYERMTRG---RRRE 189
K LPL + + +R E R R RE
Sbjct: 108 SYK--QLPLNLYQIQTKFRDEIRPRFGLMRGRE 138
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 29.7 bits (68), Expect = 1.5
Identities = 22/114 (19%), Positives = 47/114 (41%), Gaps = 10/114 (8%)
Query: 82 FPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAG--EEIRDQLYCFEDRG 139
+ P+ +R + ++ G+E V P + L+ + +G + ++ ++ +
Sbjct: 201 WHPKGAIIRREIEDYLRKEHLKRGYEFVYTPHIGKSDLW-KTSGHLDNYKENMFPPMEID 259
Query: 140 NRRVALRPELTPSLARLVIQKGKSV-SLPLKWFAVGQCWRYER------MTRGR 186
L+P P + + +S LPL+ G +RYE+ +TR R
Sbjct: 260 EEEYYLKPMNCPGHILIYKSRLRSYRDLPLRLAEFGTVYRYEKSGVLHGLTRVR 313
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 30.1 bits (68), Expect = 1.6
Identities = 27/104 (25%), Positives = 54/104 (51%), Gaps = 9/104 (8%)
Query: 82 FPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAG--EEIRDQLYCFEDRG 139
+ P+ +RN L +E+ + + ++EV P + ++ L+ ++G + +D +Y F +
Sbjct: 269 YLPKGQIIRNELEAFLREIQKEYNYQEVRTPFMMNQELW-ERSGHWDHYKDNMY-FSEVD 326
Query: 140 NRRVALRPELTPSLARLVIQKGKSVS---LPLKWFAVGQCWRYE 180
N+ AL+P P +++ K K S LP++ GQ R+E
Sbjct: 327 NKSFALKPMNCP--GHMLMFKNKLHSYRELPIRMCEFGQVHRHE 368
>gnl|CDD|200600 cd10978, CE4_Sll1306_like, Putative catalytic domain of
Synechocystis sp. Sll1306 protein and other bacterial
homologs. The family contains Synechocystis sp. Sll1306
protein and uncharacterized bacterial polysaccharide
deacetylases. Although their biological function remains
unknown, they show very high sequence homology to the
catalytic domain of bacterial PuuE (purine utilization
E) allantoinases. PuuE allantoinase specifically
catalyzes the hydrolysis of (S)-allantoin into allantoic
acid. It functions as a homotetramer. Its monomer is
composed of a 7-stranded barrel with detectable sequence
similarity to the 6-stranded barrel NodB homology domain
of polysaccharide deacetylase-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. PuuE allantoinase
appears to be metal-independent and acts on a small
substrate molecule, which is distinct from the common
feature of polysaccharide deacetylases that are normally
metal ion dependent and recognize multimeric substrates.
Length = 271
Score = 29.3 bits (66), Expect = 2.0
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 148 ELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYE-RMTRGRRREHYQWNMDII 198
E P LA+ ++Q+G + A G+ W+ + M+R + R Q +D I
Sbjct: 79 EKHPDLAKEIVQRGHEAA------AHGRDWQNQFSMSREQERAFIQDGVDSI 124
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino acid
at the 2'-OH group, like class I aaRSs. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 28.7 bits (65), Expect = 2.6
Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 104 FGFEEVDFPVLESE-----ALFIRK--AGEEIRDQLYCFEDRGNRRVALRPELTPSLARL 156
GF EV+ P +E++ AL I + +++D Y R+ LR + AR
Sbjct: 17 MGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYI---NDPARLLLRTHTSAVQARA 73
Query: 157 VIQKGKSVSLPLKWFAVGQCWRYE 180
+ + P++ F++G+ +R +
Sbjct: 74 LAKLKP----PIRIFSIGRVYRND 93
>gnl|CDD|225674 COG3132, COG3132, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 28.6 bits (64), Expect = 3.0
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 21 SLFPRKFTVPKEYLLNPRSLCALSSASNQNGGRSGARSLSPSPVSDDLQ 69
L ++ T P++Y P +L L +A NQ R +LS S V + L
Sbjct: 15 CLLEKQVTTPEQY---PLTLNGLVTACNQKTNRDPVMNLSESEVQEQLD 60
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 29.1 bits (65), Expect = 3.3
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 36 NPRSLCALSSASNQNGGRSGARSLSPSPVSDDLQKIDVNPPKGTRDFPPEDMRLRNWLFH 95
NP SASNQN R P + +DV+ + E R +++
Sbjct: 98 NPDPSTDHGSASNQNMER-------SPPPRIPYRPLDVSDALSYLEKVKEQFSNRPEIYN 150
Query: 96 NFQEVSRLFGFEEVDFP 112
NF ++ + F + +D P
Sbjct: 151 NFLDIMKDFKSQAIDTP 167
>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
Every known example of the phenylalanyl-tRNA synthetase,
except the monomeric form of mitochondrial, is an alpha
2 beta 2 heterotetramer. The beta subunits break into
two subfamilies that are considerably different in
sequence, length, and pattern of gaps. This model
represents the subfamily that includes the beta subunit
from eukaryotic cytosol, the Archaea, and spirochetes
[Protein synthesis, tRNA aminoacylation].
Length = 551
Score = 28.2 bits (63), Expect = 4.8
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 1/81 (1%)
Query: 96 NFQEVSRLFGFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLAR 155
+E+ GF+EV L SE + ++ E + + + +R L P L
Sbjct: 370 IIREIMVGLGFQEVIPLTLTSEEVNFKRMRIEDNNDVKVANPKTLEYTIVRTSLLPGLLE 429
Query: 156 LVIQKGKSVSLPLKWFAVGQC 176
+ + K LP K F +G
Sbjct: 430 TL-SENKHHELPQKIFEIGDV 449
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 27.7 bits (62), Expect = 6.0
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 17/85 (20%)
Query: 104 FGFEEVDFPVLESE-----ALFIRK--AGEEIRDQLYCFEDRGNRRVALRPELTP-SLAR 155
GF E P +E++ AL I + +++D Y R+ LR T L
Sbjct: 88 LGFTEETGPEVETDFWNFDALNIPQDHPARDMQDTFYI-----KDRLLLRTHTTAVQLRT 142
Query: 156 LVIQKGKSVSLPLKWFAVGQCWRYE 180
+ Q+ P++ F+ G+ +R +
Sbjct: 143 MEEQEKP----PIRIFSPGRVFRND 163
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 27.2 bits (61), Expect = 8.3
Identities = 13/40 (32%), Positives = 27/40 (67%), Gaps = 5/40 (12%)
Query: 197 IIGVPAVTVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLD 236
+ G+ +VT + ++R H+I E L + ++I+KI++L L+
Sbjct: 105 VEGLTSVT--ERLIR-HAIQEGL--PMVLVINKIDRLILE 139
>gnl|CDD|183048 PRK11239, PRK11239, hypothetical protein; Provisional.
Length = 215
Score = 27.0 bits (60), Expect = 9.1
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 22 LFPRKFTVPKEYLLNPRSLCALSSASNQNGGRSGARSLSPSPVSDDL 68
L ++ T P++Y P S+ + +A NQ R +LS S V + L
Sbjct: 16 LLEKQVTTPEQY---PLSVNGVVTACNQKTNREPVMNLSESEVQEQL 59
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 27.0 bits (61), Expect = 9.2
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 147 PELTPSLARLVIQKGKSVSLP 167
PE P L RL I K K+ ++P
Sbjct: 43 PEGNPRL-RLAIDKAKAANMP 62
>gnl|CDD|220874 pfam10778, DehI, Halocarboxylic acid dehydrogenase DehI. Haloacid
dehalogenases catalyze the removal of halides from
organic haloacids. DehI can process both L- and
D-substrates. A crucial aspartate residue is predicted
to activate a water molecule for nucleophilic attack of
the substrate chiral centre resulting in an inversion of
the configuration of either L- or D-substrates in
contrast to D-only enzymes.
Length = 159
Score = 26.6 bits (59), Expect = 9.6
Identities = 11/38 (28%), Positives = 13/38 (34%)
Query: 224 CIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSI 261
I L +AG S A IEE+ VL
Sbjct: 42 RSEAQVINSFSFPNPTRRLSAAGYSPAEIEEIRAVLDT 79
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
0.322 0.138 0.420
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,485,138
Number of extensions: 1440906
Number of successful extensions: 1232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1205
Number of HSP's successfully gapped: 60
Length of query: 271
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 176
Effective length of database: 6,723,972
Effective search space: 1183419072
Effective search space used: 1183419072
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)