RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022115
(302 letters)
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 482 bits (1242), Expect = e-171
Identities = 195/298 (65%), Positives = 230/298 (77%), Gaps = 2/298 (0%)
Query: 3 AIHSSLSFYMKPLFLSNSSLFPRKFTVPKEYLLNPRSLCALSSASNQNGGRSGARSLSPS 62
AI SS + + + SL +PR +SA+ GGRSG + PS
Sbjct: 2 AIASSAT-RVSASAIRRPSLPLSSRCSFLLSASSPRGGRCAASAA-AGGGRSGGTTAPPS 59
Query: 63 PVSDDLQKIDVNPPKGTRDFPPEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIR 122
D KIDVNPPKGTRDFPPEDMRLRNWLF +F+EVSRLFGFEEVD PVLESE L+IR
Sbjct: 60 VQEDGKPKIDVNPPKGTRDFPPEDMRLRNWLFDHFREVSRLFGFEEVDAPVLESEELYIR 119
Query: 123 KAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERM 182
KAGEEI DQLY FED+G RRVALRPELTPSLARLV+QKGKS+SLPLKWFA+GQCWRYERM
Sbjct: 120 KAGEEITDQLYNFEDKGGRRVALRPELTPSLARLVLQKGKSLSLPLKWFAIGQCWRYERM 179
Query: 183 TRGRRREHYQWNMDIIGVPAVTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLR 242
TRGRRREHYQWNMDIIGVP V AEAEL+++I+TFFKR+GIT+SDVG ++SSRKVLQ VL+
Sbjct: 180 TRGRRREHYQWNMDIIGVPGVEAEAELLAAIVTFFKRVGITSSDVGIKVSSRKVLQAVLK 239
Query: 243 CHSIPEHLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIKSLTELEG 300
+ IPE F VC+I+DK+EKLP + I+ +L + G+SE AIE +L VLS+KSL +LE
Sbjct: 240 SYGIPEESFAPVCVIVDKLEKLPREEIEKELDTLGVSEEAIEGILDVLSLKSLDDLEA 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 = 201 bits (514), Expect = 3e-62
Identities = 79/239 (33%), Positives = 125/239 (52%), Gaps = 20/239 (8%)
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 YQWNMDIIGVPAVTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSIPEHL 250
+Q+ +++IG + A+AE+I+ K +GI D I+S +L+ L E L
Sbjct: 121 HQFGVEVIGSDSPLADAEIIALAAEILKALGIK--DFTLEINSLGILEGRLE---YREAL 175
Query: 251 FGKVCIIIDKI--------EKLPLDVI--KNDLKSAGMSEAAIEELLRVLSIKSLTELE 299
+ +DK+ EK PL ++ KN+ + EA ++L L +S E
Sbjct: 176 LRYLDKHLDKLGEDSVRRLEKNPLRILDSKNEKIQELLKEA--PKILDFLDEESRAHFE 232
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 200 bits (511), Expect = 2e-61
Identities = 77/227 (33%), Positives = 122/227 (53%), Gaps = 12/227 (5%)
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 RREHYQWNMDIIGVPAVTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSI 246
R+ YQ+ +++IG + A+AE+I+ + + +GI I+SR +L+ L I
Sbjct: 121 YRQFYQFGVEVIGSDSPDADAEVIALAVEILEALGI--GGFTLEINSRGILEGRLEYLGI 178
Query: 247 PEHLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIK 293
+ + +DK++K+ + D K LRVL K
Sbjct: 179 DQRE--ALLRYLDKLDKIGKLELDEDSK----RRLKT-NPLRVLDSK 218
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 195 bits (499), Expect = 1e-59
Identities = 69/244 (28%), Positives = 113/244 (46%), Gaps = 23/244 (9%)
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 RREHYQWNMDIIGVPAVTAEAELISSIITFFKRIGITA--------SDVGFRISSRKVLQ 238
R+ +Q+ +++IG + A+AE+I+ K +G+ D R + RK L
Sbjct: 118 YRQFHQFGVEVIGSDSPLADAEVIALAADILKALGLKGLKLLINSLGDFEIRANYRKALV 177
Query: 239 EVLRCHSIPEHLFGKVCIIIDKIEKLPLDVI--KNDLKSAGMSEAAIEELLRVLSIKSLT 296
L + ++E PL ++ K+ + +A +LL L +S
Sbjct: 178 GFLEKG---LDELDEDS--KRRLETNPLRILDKKDKEDQELLKDA--PKLLDYLDEESKE 230
Query: 297 ELEG 300
E
Sbjct: 231 HFEE 234
>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 = 190 bits (485), Expect = 2e-59
Identities = 68/204 (33%), Positives = 117/204 (57%), Gaps = 8/204 (3%)
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 RPELTPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTA 205
RP+LT +AR V + S+ LPLK + +G +RYER +GR RE YQ ++IIG + A
Sbjct: 61 RPDLTAPVARAVAENLLSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSDSPLA 120
Query: 206 EAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSIPEHLFGKVCIIIDKIEKLP 265
+AE+I+ + + +G+ D +I+ R +L + E + +IDK++K
Sbjct: 121 DAEVIALAVEILEALGLK--DFQIKINHRGILDGIAGLLEDRE---EYIERLIDKLDKEA 175
Query: 266 ---LDVIKNDLKSAGMSEAAIEEL 286
L+ + + L++ G+ +L
Sbjct: 176 LAHLEKLLDYLEALGVDIKYSIDL 199
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 140 bits (355), Expect = 1e-38
Identities = 72/225 (32%), Positives = 124/225 (55%), Gaps = 6/225 (2%)
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 MDIIGVPAVTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSIPEHLFGKV 254
+DI+GV +V AEAEL+S F+R+ + +V + ++RK+L +L+ IP L V
Sbjct: 127 VDIVGVESVMAEAELMSMAFELFRRLNL---EVTIQYNNRKLLNGILQAIGIPTELTSDV 183
Query: 255 CIIIDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIKSLTELE 299
+ +DKIEK+ +D ++ DL G+SE + + + +
Sbjct: 184 ILSLDKIEKIGIDGVRKDLLERGISEEMADTICNTVLSCLQLSIA 228
>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 = 114 bits (288), Expect = 3e-31
Identities = 46/157 (29%), Positives = 77/157 (49%), Gaps = 11/157 (7%)
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 -AVTAEAELISSIITFFKRIGITASDVGFRISSRKVL 237
+ EL+ + +G+ +++ L
Sbjct: 121 QSEEELEELLKLAEEILQDLGL---PYRVVLATTGDL 154
>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 = 110 bits (276), Expect = 4e-28
Identities = 58/250 (23%), Positives = 100/250 (40%), Gaps = 47/250 (18%)
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 VPAVTAEAELISSIITFFKRIGITA---------------SDVGFRISSRKVLQEVLRCH 244
A+AE+I+ +I K +G+ + G +R+ L+E L
Sbjct: 120 AGGPAADAEVIALLIEALKALGLKDFKIELGHVGLVRALLEEAGLPEEAREALREALARK 179
Query: 245 SIPE----------------------HLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAA 282
+ L G ++++ L +EAA
Sbjct: 180 DLVALEELVAELGLSPEVRERLLALPRLRGDGEEVLEEARALAGSE---------TAEAA 230
Query: 283 IEELLRVLSI 292
++EL VL +
Sbjct: 231 LDELEAVLEL 240
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 100 bits (252), Expect = 2e-24
Identities = 44/161 (27%), Positives = 75/161 (46%), Gaps = 7/161 (4%)
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 NMDIIGVPAVTAEAELISSIITFFKRIG-----ITASDVGF 229
++++G + A+AE+I+ + K +G + G
Sbjct: 122 GIELLGDDSAAADAEVIALALAALKALGLADLKLELGHAGI 162
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 96.1 bits (239), Expect = 4e-22
Identities = 61/207 (29%), Positives = 101/207 (48%), Gaps = 8/207 (3%)
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-VTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSIPEHLFGKV 254
DI GV + + E+I + + I +V +++ RK+L +L +P F +
Sbjct: 446 DIAGVYEPMGPDFEIIKVLTELLDELDIGTYEV--KLNHRKLLDGMLEICGVPPEKFRTI 503
Query: 255 CIIIDKIEKLPLDVIKNDL-KSAGMSE 280
C IDK++K + +K ++ + G+S
Sbjct: 504 CSSIDKLDKQSFEQVKKEMVEEKGLSN 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 = 85.7 bits (213), Expect = 3e-19
Identities = 58/224 (25%), Positives = 90/224 (40%), Gaps = 36/224 (16%)
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 IGVPAVTAEAELISSIITFFKRIGITASDVGFRISSRKVLQEVLRCHSIPEHLFGKVCII 257
IG + A+AE+IS ++ + +G+ G + L I L
Sbjct: 119 IGHAGIEADAEVISLLLEALESLGVK----GVTLD--------LGHVGIVRAL------- 159
Query: 258 IDKIEKLPLDVIKNDLKSAGMSEAAIEELLRVLSIKSLTELEGW 301
L++ G+SEA E L L K L ELE
Sbjct: 160 ---------------LEALGLSEAQEEALRDALQRKDLPELEEL 188
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 83.0 bits (205), Expect = 7e-18
Identities = 42/155 (27%), Positives = 77/155 (49%), Gaps = 6/155 (3%)
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 REHYQWNMDIIGVPAVTAEAELISSIITFFKRIGI 222
R+ +Q ++ IG A+ E+I + F + +
Sbjct: 123 RQFHQLGIEFIGSIDARADTEVIHLAMQIFNELQV 157
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 80.3 bits (199), Expect = 5e-17
Identities = 41/149 (27%), Positives = 73/149 (48%), Gaps = 1/149 (0%)
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 NMDIIGVPAVTAEAELISSIITFFKRIGI 222
+++IG + A+AE+I ++ K +G+
Sbjct: 125 GVELIGDAGLEADAEVILLLLEALKALGL 153
>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 = 39/133 (29%), Positives = 57/133 (42%), Gaps = 11/133 (8%)
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----GVPAVTAEAEL 209
RL + + LPL+ +G +R E RG RR ++ + EL
Sbjct: 64 VRLFVSHIRK--LPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEFEEL 121
Query: 210 ISSIITFFKRIGI 222
I + +GI
Sbjct: 122 IELTEELLRALGI 134
>gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 373
Score = 49.2 bits (118), Expect = 1e-06
Identities = 32/130 (24%), Positives = 57/130 (43%), Gaps = 11/130 (8%)
Query: 105 GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSV 164
G VD P+L+ F+ +GE+IR +++ D + LRP+ T + R I
Sbjct: 22 GAVRVDPPILQPAEPFLDLSGEDIRRRIFVTSDENGEELCLRPDFTIPVCRRHIATA--G 79
Query: 165 SLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPA-VTAEAELISSIITFFKRIG-- 221
P ++ +G+ +R R R E Q ++ G A+AE+++ + +G
Sbjct: 80 GEPARYAYLGEVFRQR---RDRASEFLQAGIESFGRADPAAADAEVLALALEALAALGPG 136
Query: 222 ---ITASDVG 228
+ DVG
Sbjct: 137 DLEVRLGDVG 146
>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 = 46.6 bits (111), Expect = 4e-06
Identities = 33/108 (30%), Positives = 52/108 (48%), Gaps = 11/108 (10%)
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---GRRREHYQWNMDIIGVPA 202
+ S +LPL+ +G C+R+E R R RE Q + G P
Sbjct: 79 GEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE 126
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 41.5 bits (98), Expect = 3e-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|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 = 41.3 bits (97), Expect = 4e-04
Identities = 44/172 (25%), Positives = 68/172 (39%), Gaps = 20/172 (11%)
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--RRREHYQWNMDIIGVPAVTAEAELISSIITFFKRI 220
+RYE + TR R RE A AE +++ + +K
Sbjct: 130 QWVNVFRYETKHTRPFLRTREFTWQEAHTAHATAEEAEEQVL-RALDIYKEF 180
>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|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 36.7 bits (85), Expect = 0.011
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 = 35.7 bits (83), Expect = 0.025
Identities = 35/138 (25%), Positives = 62/138 (44%), Gaps = 22/138 (15%)
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 VIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTAE----AELISS 212
+ + K P+K F+ G+ +R + + E +Q I G+ V + A+L +
Sbjct: 185 LAENAKI---PIKIFSPGRVYRNDTVDATHSPEFHQ----IEGL--VVDKNISFADLKGT 235
Query: 213 IITFFKRIGITASDVGFR 230
+ F K+ V FR
Sbjct: 236 LEEFAKKFFGEDVKVRFR 253
>gnl|CDD|183411 PRK12293, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 281
Score = 34.6 bits (80), Expect = 0.043
Identities = 48/205 (23%), Positives = 87/205 (42%), Gaps = 55/205 (26%)
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 SVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTAEAELISSIITFFKRIGI 222
S + KWF + +RY E YQ ++IG + +E+++ F+ + +
Sbjct: 92 S-TEHKKWFYIQPVFRYP------SNEIYQIGAELIGEEDL---SEILNIAAEIFEELEL 141
Query: 223 TASDVGFRISSRKVLQEVLRCHSIPEHLFGKVCIIIDKIEKLPLDVIKNDLKSAGMSEAA 282
+IS+ K IP+ ++ +I L ++V K
Sbjct: 142 EPI---LQISNIK----------IPK--------LVAEILGLDIEVFKK---------GQ 171
Query: 283 IEELL--------RVLSIKSLTELE 299
IE+LL +++ IK+L +L+
Sbjct: 172 IEKLLAQNVPWLNKLVRIKTLEDLD 196
>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 = 33.3 bits (77), Expect = 0.11
Identities = 31/136 (22%), Positives = 60/136 (44%), Gaps = 16/136 (11%)
Query: 104 FGFEEVDFPVLESE-----ALFIRK--AGEEIRDQLYCFEDRGNRRVALRPELTPSLARL 156
GF EV+ P +E++ AL I + +++D Y R+ LR + AR
Sbjct: 17 MGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYI---NDPARLLLRTHTSAVQARA 73
Query: 157 VIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTAEAELISSIITF 216
+ + P++ F++G+ +R + + E +Q ++ + V A+L ++ F
Sbjct: 74 LAKLKP----PIRIFSIGRVYRNDEIDATHLPEFHQ--IEGLVVDKGLTFADLKGTLEEF 127
Query: 217 FKRIGITASDVGFRIS 232
K + + V FR S
Sbjct: 128 AKELFGPITKVRFRPS 143
>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 = 0.14
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 = 0.16
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 = 0.19
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 3/99 (3%)
Query: 84 PEDMRLRNWLFHNFQEVSRLFGFEEVDFPVLESEALFIRKAGEEI-RDQLYCFEDRGNRR 142
P+ +RN L + R +G++EV PVL L+ + ++ ++ E +R
Sbjct: 217 PKGATIRNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWDNYKEDMFLTES-DDRE 275
Query: 143 VALRPELTPSLARLVIQKGKSV-SLPLKWFAVGQCWRYE 180
AL+P P + +S LPL+ G +RYE
Sbjct: 276 YALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYE 314
>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 = 31.3 bits (71), Expect = 0.49
Identities = 25/118 (21%), Positives = 45/118 (38%), Gaps = 1/118 (0%)
Query: 105 GFEEVDFPVLESEALFIRKAGEEIRDQLYCFEDRGNRRVALRPELTPSLARLVIQKGKSV 164
GF +V P++ + + K + L+ + LRP L P+L + + +
Sbjct: 43 GFVQVKTPIIIPKEY-LEKMTIDEDHPLFSQVFWVDENKCLRPMLAPNLYNYLRKLDRLW 101
Query: 165 SLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTAEAELISSIITFFKRIGI 222
P++ F +G C+R E E N+ +G P L + +GI
Sbjct: 102 PKPIRIFEIGPCYRKESQGSQHLNEFTMLNLCEMGSPLECRRERLEDLARWVLEHLGI 159
>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 = 29.9 bits (67), Expect = 1.0
Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 19/102 (18%)
Query: 203 VTAEAELISSIITFFKRI--GITASDVGFRISSRKVLQEVLRCHSIPEHLFGKVCIIIDK 260
V L+ I+ I G+ +G I+ VL+ V+ G V ++
Sbjct: 35 VGGGDMLLDCIVALLANIVGGLLRVIIGLVITLSGVLEIVI----------GTVLGLVAT 84
Query: 261 IEKLPLDVIK-------NDLKSAGMSEAAIEELLRVLSIKSL 295
+ L LD++ ND IEE L L ++L
Sbjct: 85 LAALALDLVGGSVGGICNDFLDFDAILELIEESLHSLLAQAL 126
>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 = 1.6
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|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 30.1 bits (68), Expect = 1.8
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|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 29.7 bits (68), Expect = 1.9
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|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 = 2.2
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|225674 COG3132, COG3132, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 28.6 bits (64), Expect = 2.9
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|177954 PLN02320, PLN02320, seryl-tRNA synthetase.
Length = 502
Score = 29.1 bits (65), Expect = 3.1
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 16/79 (20%)
Query: 166 LPLKWFAVGQCWRYE-----RMTRGRRREHY--QWNMDIIGVPA---------VTAEAEL 209
LPLK+ A C+R E TRG R H + M +I P + E +L
Sbjct: 312 LPLKYVAFSHCFRTEAGAAGAATRGLYRVHQFSKVEMFVICRPEESESFHEELIQIEEDL 371
Query: 210 ISSIITFFKRIGITASDVG 228
+S+ FK + + +D+G
Sbjct: 372 FTSLGLHFKTLDMATADLG 390
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 29.1 bits (65), Expect = 3.9
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 = 6.1
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|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 27.7 bits (62), Expect = 7.5
Identities = 33/148 (22%), Positives = 63/148 (42%), Gaps = 31/148 (20%)
Query: 105 GFEEVDFPVLESEALFIRKAGE--EIRDQLYCFEDRGNRRVALRPELTPSLARL----VI 158
G++E+ P L +E + G+ + + ++ ED + L P L L ++
Sbjct: 191 GYQEIYPPYLVNEES-LDGTGQLPKFEEDIFKLEDT---DLYLIPTAEVPLTNLHRNEIL 246
Query: 159 QKGKSVSLPLKWFAVGQCWRYE-----RMTRGRRREHYQWN---MDIIGVPAVTAEA--E 208
++ LP+K+ A C+R E + T+G R H Q+N + P +AE E
Sbjct: 247 EEE---ELPIKYTAHSPCFRSEAGSYGKDTKGLIRVH-QFNKVELVKFCKPEESAEELEE 302
Query: 209 LISSIITF-------FKRIGITASDVGF 229
+ S ++ + + + D+GF
Sbjct: 303 MTSDAEQILQELELPYRVVNLCSGDLGF 330
>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 = 7.7
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|183048 PRK11239, PRK11239, hypothetical protein; Provisional.
Length = 215
Score = 27.0 bits (60), Expect = 9.5
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|193568 cd08022, M28_PSMA_like, M28 Zn-peptidase prostate-specific membrane
antigen. Peptidase M28 family; prostate-specific
membrane antigen (PSMA, also called glutamate
carboxypeptidase II or GCP-II)-like subfamily. PSMA is a
homodimeric type II transmembrane protein containing
three distinct domains: protease-like, apical or
protease-associated (PA) and helical domains. The
protease-like domain is a large extracellular portion
(ectodomain). PSMA is over-expressed predominantly in
prostate cancer (PCa) as well as neovasculature of most
solid tumors, but not in the vasculature of the normal
tissues. PSMA is considered a biomarker for PCa and
possibly for use as an imaging and therapeutic target.
The extracellular domain of PSMA possesses two unique
enzymatic functions: N-acetylated, alpha-linked acidic
dipeptidase (NAALADase) which cleaves terminal glutamate
from the neurodipeptide N-acetyl-aspartyl-glutamate
(NAAG), and folate hydrolase (FOLH) which cleaves the
terminal glutamates from gamma-linked polyglutamates
(carboxypeptidase). A mutation in this gene may be
associated with impaired intestinal absorption of
dietary folates, resulting in low blood folate levels
and consequent hyperhomocysteinemia. Expression of this
protein in the brain may be involved in a number of
pathological conditions associated with glutamate
excitotoxicity. This gene likely arose from a
duplication event of a nearby chromosomal region.
Alternative splicing gives rise to multiple transcript
variants.
Length = 286
Score = 27.2 bits (61), Expect = 9.8
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 16/80 (20%)
Query: 150 TPSLARLVIQKGKSVSLPLKWFAVGQCWRYERMTRGRRREHYQWNMDIIGVPAVTAEAEL 209
+P L +L+ + K V P K ++ + IG
Sbjct: 169 SPLLHKLIREAAKKVPDPDKGG----------SSQYLYDSWEKSTDPRIGNLGSG----- 213
Query: 210 ISSIITFFKRIGITASDVGF 229
S F + +GI + D+G+
Sbjct: 214 -SDYTVFLQHLGIPSLDLGY 232
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 0.414
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,046,602
Number of extensions: 1606942
Number of successful extensions: 1464
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1428
Number of HSP's successfully gapped: 54
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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: 59 (26.4 bits)