RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046127
(345 letters)
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 498 bits (1282), Expect = e-174
Identities = 241/326 (73%), Positives = 273/326 (83%), Gaps = 11/326 (3%)
Query: 28 MAARINYSIQNSLWLL----NPLHSKATTHFRNRLKFRQNL-----FSLSKGAVFCSYAT 78
MAARIN S+ N+L L PL++K + RN +F + L FS K A++C+ +
Sbjct: 1 MAARINTSLHNALSFLKAFNTPLNTKPFSFCRNCFRFSKKLPYYSQFSSGKRALYCT--S 58
Query: 79 NTDKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEH 138
++ +S + AD FVLTTPLYYVNAPPHMGSAYTTIAAD+IARFQRLLGKKVIFITGTDEH
Sbjct: 59 SSQESTVDEADTFVLTTPLYYVNAPPHMGSAYTTIAADSIARFQRLLGKKVIFITGTDEH 118
Query: 139 GEKIAAAAADGGSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVL 198
GEKIA +AA G +P EHCD++SQ+Y+TLWKDLDIAYDKFIRTT+PKHEAIVKEFY+ V
Sbjct: 119 GEKIATSAAANGRNPPEHCDIISQSYRTLWKDLDIAYDKFIRTTDPKHEAIVKEFYARVF 178
Query: 199 ANGDIYKADYEGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKYQKLLE 258
ANGDIY+ADYEGLYCVNCEEYKDEKELLEN CCP+H PCVARKEDNYFFALSKYQK LE
Sbjct: 179 ANGDIYRADYEGLYCVNCEEYKDEKELLENNCCPVHQMPCVARKEDNYFFALSKYQKPLE 238
Query: 259 DTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVPNDNKQTIYVWFDALLG 318
D L +NP FVQPS+RLNEVQ WIKSGLRDFSISRA VDWGIPVP+D+KQTIYVWFDALLG
Sbjct: 239 DILAQNPRFVQPSYRLNEVQSWIKSGLRDFSISRALVDWGIPVPDDDKQTIYVWFDALLG 298
Query: 319 YISALSEDRDQPSLRTAVSSGWPASL 344
YISAL+ED Q +L TAVS GWPASL
Sbjct: 299 YISALTEDNKQQNLETAVSFGWPASL 324
>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
Length = 511
Score = 402 bits (1035), Expect = e-138
Identities = 135/256 (52%), Positives = 171/256 (66%), Gaps = 1/256 (0%)
Query: 90 PFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADG 149
F +TTP+YY N PH+G AYTT+AAD +ARF+RL G V F+TGTDEHG+KI A +
Sbjct: 2 KFYITTPIYYPNGKPHIGHAYTTLAADVLARFKRLRGYDVFFLTGTDEHGQKIQRKAEEA 61
Query: 150 GSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYE 209
G SP E D S A+K LW+ L+I+YD FIRTT+P+H+ V+E + +LANGDIY YE
Sbjct: 62 GISPQELADRNSAAFKRLWEALNISYDDFIRTTDPRHKEAVQEIFQRLLANGDIYLGKYE 121
Query: 210 GLYCVNCEEYKDEKELLE-NQCCPIHLKPCVARKEDNYFFALSKYQKLLEDTLTENPDFV 268
G YCV CEE+ E EL+E CP P +E++YFF LSKYQ L + NPDF+
Sbjct: 122 GWYCVRCEEFYTESELIEDGYRCPPTGAPVEWVEEESYFFRLSKYQDKLLELYEANPDFI 181
Query: 269 QPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVPNDNKQTIYVWFDALLGYISALSEDRD 328
QP+ R NEV ++KSGL+D SISR + DWGIPVP D K IYVWFDAL Y++AL D
Sbjct: 182 QPASRRNEVISFVKSGLKDLSISRTNFDWGIPVPGDPKHVIYVWFDALTNYLTALGYPDD 241
Query: 329 QPSLRTAVSSGWPASL 344
+ L + WPA +
Sbjct: 242 EELLAELFNKYWPADV 257
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 367 bits (944), Expect = e-123
Identities = 126/236 (53%), Positives = 163/236 (69%), Gaps = 1/236 (0%)
Query: 89 DPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAAD 148
F +TTP+YY N PH+G AYTTIAADA+AR++RL G V F+TGTDEHG+KI AA
Sbjct: 4 KTFYITTPIYYPNGKPHIGHAYTTIAADALARYKRLQGYDVFFLTGTDEHGQKIQQAAEK 63
Query: 149 GGSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADY 208
G +P E+ D +S +K LWK LDI+YDKFIRTT+ +H+ +V++ + + GDIYK +Y
Sbjct: 64 AGKTPQEYVDEISAGFKELWKKLDISYDKFIRTTDERHKKVVQKIFEKLYEQGDIYKGEY 123
Query: 209 EGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKYQKLLEDTLTENPDFV 268
EG YCV+CE + E +L++ CP + KE++YFF +SKYQ L + ENPDF+
Sbjct: 124 EGWYCVSCETFFTESQLVDGGKCPDCGREVELVKEESYFFRMSKYQDRLLEYYEENPDFI 183
Query: 269 QPSFRLNEV-QGWIKSGLRDFSISRASVDWGIPVPNDNKQTIYVWFDALLGYISAL 323
QP R NE+ +IK GL D SISR S DWGIPVP D K +YVW DALL YI+AL
Sbjct: 184 QPESRKNEMINNFIKPGLEDLSISRTSFDWGIPVPFDPKHVVYVWIDALLNYITAL 239
>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
synthetases. Methionine tRNA synthetase (MetRS)
catalytic core domain. This class I enzyme aminoacylates
the 2'-OH of the nucleotide at the 3' of the appropriate
tRNA. MetRS, which consists of the core domain and an
anti-codon binding domain, functions as a monomer.
However, in some species the anti-codon binding domain
is followed by an EMAP domain. In this case, MetRS
functions as a homodimer. The core domain is based on
the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. As a result of a deletion event, MetRS has a
significantly shorter core domain insertion than IleRS,
ValRS, and LeuR. Consequently, the MetRS insertion
lacks the editing function.
Length = 319
Score = 324 bits (833), Expect = e-110
Identities = 118/254 (46%), Positives = 156/254 (61%), Gaps = 17/254 (6%)
Query: 90 PFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADG 149
++TT L YVN PH+G Y T+ AD AR+QRL G V+F+TGTDEHG KI A +
Sbjct: 1 KVLITTALPYVNGVPHLGHLYGTVLADVFARYQRLRGYDVLFVTGTDEHGTKIEQKAEEE 60
Query: 150 GSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYE 209
G +P E CD + +K L+K L+I++D FIRTT P+H+ IV+EF+ + NG IY+ +YE
Sbjct: 61 GVTPQELCDKYHEIFKDLFKWLNISFDYFIRTTSPRHKEIVQEFFKKLYENGYIYEGEYE 120
Query: 210 GLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKYQKLLEDTLTENPDFVQ 269
GLYCV+CE + E R+E++YFF LSK+Q L + L +NPDF+
Sbjct: 121 GLYCVSCERFLPEW-----------------REEEHYFFRLSKFQDRLLEWLEKNPDFIW 163
Query: 270 PSFRLNEVQGWIKSGLRDFSISRASVDWGIPVPNDNKQTIYVWFDALLGYISALSEDRDQ 329
P NEV W+K GL+D SI+R DWGIPVP D + IYVWFDAL+GYISA ++
Sbjct: 164 PENARNEVLSWLKEGLKDLSITRDLFDWGIPVPLDPGKVIYVWFDALIGYISATGYYNEE 223
Query: 330 PSLRTAVSSGWPAS 343
GWP
Sbjct: 224 WGNSWWWKDGWPEL 237
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 319 bits (819), Expect = e-105
Identities = 118/269 (43%), Positives = 160/269 (59%), Gaps = 28/269 (10%)
Query: 85 TEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAA 144
+ ++TT L Y N PPH+G YT +AAD AR+ RL G +V F+TGTDEHG KI
Sbjct: 1 MKMMKKILVTTALPYPNGPPHLGHLYTYLAADVYARYLRLRGYEVFFLTGTDEHGTKIEL 60
Query: 145 AAADGGSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIY 204
A G +P E D + +K L+K L+I++D FIRTT P+H+ +V+EF+ + NGDIY
Sbjct: 61 KAEKEGITPQELVDKNHEEFKELFKALNISFDNFIRTTSPEHKELVQEFFLKLYENGDIY 120
Query: 205 KADYEGLYCVNCEEYKDEKELLE------------NQC-------CPIHLK--------- 236
+YEGLYCV+CE + ++ + +QC P L
Sbjct: 121 LREYEGLYCVSCERFLPDRYVEGTCPKCGGEDARGDQCENCGRTLDPTELINPVCVISGA 180
Query: 237 PCVARKEDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVD 296
R+E++YFF LSK+Q L + NPDF+ P+ R NEV ++K GL+D SI+R +D
Sbjct: 181 TPEVREEEHYFFRLSKFQDKLLEWYESNPDFIWPANRRNEVLNFLKEGLKDLSITRTDLD 240
Query: 297 WGIPVPNDNKQTIYVWFDALLGYISALSE 325
WGIPVP D + IYVWFDAL+GYISAL E
Sbjct: 241 WGIPVPGDPGKVIYVWFDALIGYISALGE 269
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 303 bits (778), Expect = e-101
Identities = 114/271 (42%), Positives = 155/271 (57%), Gaps = 32/271 (11%)
Query: 91 FVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGG 150
F++TT L YVN PPH+G YTTI AD AR+ RL G V+F+TGTDEHG KI AA G
Sbjct: 1 FLITTALPYVNGPPHIGHLYTTIPADVYARYLRLRGYDVLFVTGTDEHGTKIELAAEKEG 60
Query: 151 SSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEG 210
+P E D + +K L+K +I++D FIRTT +H+ +V+EF+ + GDIY+ +YEG
Sbjct: 61 VTPQELVDRYHEEFKELFKKFNISFDDFIRTTSERHKELVQEFFLKLYEKGDIYEGEYEG 120
Query: 211 LYCVNCEEYKDEKEL----------------------------LENQCCPIHLKPCVARK 242
YCV+ E + ++ + L N I ++
Sbjct: 121 WYCVSDERFLPDRYVEGTCPYCGSEDARGDQCEVCGRPLEPTELINPRSAISGSTPELKE 180
Query: 243 EDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNE-VQGWIKSGLRDFSISRASVDWGIPV 301
E++YFF LSK+Q L + + ENPD +P +NE V W+K GL+D SI+R +DWGIPV
Sbjct: 181 EEHYFFRLSKFQDKLLEWIKENPD--EPPSNVNEVVLSWLKEGLKDLSITR-DLDWGIPV 237
Query: 302 PNDNKQTIYVWFDALLGYISALSEDRDQPSL 332
P D + IYVWFDAL+GYISA P
Sbjct: 238 PGDPGKVIYVWFDALIGYISATKYLSGNPEK 268
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 285 bits (731), Expect = 2e-92
Identities = 104/267 (38%), Positives = 152/267 (56%), Gaps = 29/267 (10%)
Query: 91 FVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGG 150
++TT L Y N PH+G AYTTI AD AR++RL G +V+F+ GTDEHG KI A G
Sbjct: 1 ILITTALPYANGKPHLGHAYTTILADVYARYKRLRGYEVLFVCGTDEHGTKIELKAEQEG 60
Query: 151 SSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEG 210
+P E D + +K WK L+I++D+FIRTT+ +H+ IV++ + + NG IY+ + +
Sbjct: 61 LTPKELVDKYHEEFKDDWKWLNISFDRFIRTTDEEHKEIVQKIFQKLKENGYIYEKEIKQ 120
Query: 211 LYCVNCEEYK------------DEKELLENQC--CPIHLKPC--------------VARK 242
LYC CE + ++ + C C HL+P R
Sbjct: 121 LYCPECEMFLPDRYVEGTCPKCGSEDARGDHCEVCGRHLEPTELINPRCKICGAKPELRD 180
Query: 243 EDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNEV-QGWIKSGLRDFSISRASVDWGIPV 301
++YFF LS ++K LE+ + +NP+ P+ + Q W+K GL+D +I+R V WGIPV
Sbjct: 181 SEHYFFRLSAFEKELEEWIRKNPESGSPASNVKNKAQNWLKGGLKDLAITRDLVYWGIPV 240
Query: 302 PNDNKQTIYVWFDALLGYISALSEDRD 328
PND + +YVWFDAL+GYIS+L
Sbjct: 241 PNDPNKVVYVWFDALIGYISSLGILSG 267
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 210 bits (538), Expect = 2e-63
Identities = 88/267 (32%), Positives = 128/267 (47%), Gaps = 36/267 (13%)
Query: 91 FVLTTPLYYVNAPPHMGSAYTT-IAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADG 149
++T+ Y N P H+G + + AD AR+QRL G +V+F++G+DEHG I AA
Sbjct: 5 ILITSAWPYANGPLHLGHLAGSGLPADVFARYQRLKGNEVLFVSGSDEHGTPIELAAKKE 64
Query: 150 GSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYE 209
G +P E D + +K +K L I+YD F RTT P H +V+EF+ + NG IYK E
Sbjct: 65 GVTPQELADKYHEEHKEDFKKLGISYDLFTRTTSPNHHEVVQEFFLKLYENGYIYKKTIE 124
Query: 210 GLYCVNCE-------------------EYKDEKELLENQCCPIHLK---------PCVAR 241
YC + D+ + P L R
Sbjct: 125 QAYCPSDGRFLPDRYVEGTCPYCGYEGARGDQCDNCGALLDPTDLINPRSKISGSTPEFR 184
Query: 242 KEDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPV 301
+ +++F L + + L + + D P LN W+K GL+ +I+R +DWGIPV
Sbjct: 185 ETEHFFLDLPAFAERLRAWIESSGD--WPPNVLNFTLNWLKEGLKPRAITR-DLDWGIPV 241
Query: 302 P---NDNKQTIYVWFDALLGYISALSE 325
P + K YVWFDA++GYISA E
Sbjct: 242 PWPGFEGK-VFYVWFDAVIGYISASKE 267
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 159 bits (405), Expect = 7e-44
Identities = 69/272 (25%), Positives = 119/272 (43%), Gaps = 46/272 (16%)
Query: 90 PFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADG 149
++T L Y N P H+G I AD R+QR+ G +V+F+ D HG I A
Sbjct: 3 KILVTCALPYANGPIHLGHLVEYIQADIWVRYQRMRGHEVLFVCADDAHGTPIMLKAEKE 62
Query: 150 GSSPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYE 209
G +P E +K + I++D + T ++ + +E Y + NG IY+ E
Sbjct: 63 GITPEELIARYHAEHKRDFAGFGISFDNYGSTHSEENRELAQEIYLKLKENGYIYEKTIE 122
Query: 210 GLYCVNC-------------------EEYKDEKELLENQC--CPIHLKP----------C 238
LY ++Y D C C P
Sbjct: 123 QLYDPEKGMFLPDRFVKGTCPKCGAEDQYGD-------NCEVCGATYSPTELINPKSAIS 175
Query: 239 ----VARKEDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRAS 294
V ++ +++FF L ++++ L++ +T + + +QP+ N+++ W++ GL+D+ ISR
Sbjct: 176 GATPVLKESEHFFFKLPRFEEFLKEWITRSGE-LQPNVA-NKMKEWLEEGLQDWDISR-D 232
Query: 295 VDW-GIPVPNDNKQTIYVWFDALLGYISALSE 325
+ G +P + YVW DA +GYIS+
Sbjct: 233 APYFGFEIPGAPGKVFYVWLDAPIGYISSTKN 264
>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
isoleucyl, leucyl, valyl and methioninyl tRNA
synthetases. Catalytic core domain of isoleucyl,
leucyl, valyl and methioninyl tRNA synthetases. These
class I enzymes are all monomers. However, in some
species, MetRS functions as a homodimer, as a result of
an additional C-terminal domain. These enzymes
aminoacylate the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. Enzymes in
this subfamily share an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids. MetRS has a significantly shorter
insertion, which lacks the editing function.
Length = 312
Score = 140 bits (355), Expect = 3e-39
Identities = 70/249 (28%), Positives = 108/249 (43%), Gaps = 52/249 (20%)
Query: 90 PFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADG 149
F +TTP Y N H+G A T I AD IAR++R+ G +V F+ G D HG I A
Sbjct: 1 KFYVTTPPPYANGSLHLGHALTHIIADFIARYKRMRGYEVPFLPGWDTHGLPIELKAERK 60
Query: 150 G-------------SSPSEHCDVVSQAYKTLWKDLDIAYD--KFIRTTEPKHEAIVKEFY 194
G P E + +S +K ++ L I+YD TTEP++ V+ +
Sbjct: 61 GGRKKKTIWIEEFREDPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPEYSKAVELIF 120
Query: 195 SSVLANGDIYKADYEGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKYQ 254
S + G IY+ + R + +FF + K++
Sbjct: 121 SRLYEKGLIYRGTHPV------------------------------RITEQWFFDMPKFK 150
Query: 255 KLLEDTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVPNDNKQTIYVWFD 314
+ L L V + N ++ W++S L D++ISR WG P+P D VWFD
Sbjct: 151 EKLLKALRRGK-IVPEHVK-NRMEAWLESLL-DWAISRQRY-WGTPLPED---VFDVWFD 203
Query: 315 ALLGYISAL 323
+ +G + +L
Sbjct: 204 SGIGPLGSL 212
>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
Length = 801
Score = 122 bits (308), Expect = 1e-30
Identities = 75/266 (28%), Positives = 122/266 (45%), Gaps = 41/266 (15%)
Query: 93 LTTPLYYVNAPPHMGSAY-TTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGS 151
+T+ L YVN PH+G+ ++AD AR+ RL G I+I GTDE+G A +
Sbjct: 21 ITSALPYVNNVPHLGNIIGCVLSADVFARYCRLRGYNAIYICGTDEYGTATETKALEENC 80
Query: 152 SPSEHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEGL 211
+P E CD +K ++ DI++DKF RT+ P+ I + + ++ N + + + L
Sbjct: 81 TPKEICDKYHAIHKEVYDWFDISFDKFGRTSTPQQTEICQAIFKKLMENNWLSENTMQQL 140
Query: 212 YCVNCEE-----------------YKDEK--------------ELLENQCCPIHLKPCVA 240
YC C++ Y + EL++ +C P
Sbjct: 141 YCDTCQKFLADRLVEGTCPTEGCNYDSARGDQCEKCGKLLNPTELIDPKCKVCKNTP-RI 199
Query: 241 RKEDNYFFALSKYQKLLEDTLTENPDFVQPSFRLNEVQ---GWIKSGLRDFSISRASVDW 297
R D+ F L + L + + E V + N +Q W++ GL+ I+R + W
Sbjct: 200 RDTDHLFLELPLLKDKLVEYINETS--VAGGWSQNAIQTTNAWLRDGLKPRCITR-DLKW 256
Query: 298 GIPVPND--NKQTIYVWFDALLGYIS 321
G+PVP + + YVWFDA +GY+S
Sbjct: 257 GVPVPLEKYKDKVFYVWFDAPIGYVS 282
>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA
synthetases. Valine amino-acyl tRNA synthetase (ValRS)
catalytic core domain. This enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. ValRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements. This editing region
hydrolyzes mischarged cognate tRNAs and thus prevents
the incorporation of chemically similar amino acids.
Length = 382
Score = 67.7 bits (166), Expect = 1e-12
Identities = 66/297 (22%), Positives = 100/297 (33%), Gaps = 55/297 (18%)
Query: 89 DPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG-------EK 141
FV+ TP V HMG A D IAR++R+ G V++ GTD G EK
Sbjct: 1 PVFVIDTPPPNVTGSLHMGHALNNTIQDIIARYKRMKGYNVLWPPGTDHAGIATQVVVEK 60
Query: 142 IAAAAADGGSSPS-----EHCDVVSQAY----KTLWKDLDIAYD--KFIRTTEPKHEAIV 190
E C + + K L + D + T +P V
Sbjct: 61 KLGIEGKTRHDLGREEFLEKCWEWKEESGGKIREQLKRLGASVDWSREYFTMDPGLSRAV 120
Query: 191 KEFYSSVLANGDIYKADYEGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFAL 250
+E + + G IY+ + +C + E+ I K +
Sbjct: 121 QEAFVRLYEKGLIYRDNRLVNWCPKLRTAISDIEVCSRSGDVIEPLL----KPQWFVKVK 176
Query: 251 SKYQKLLEDTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVPNDNKQTIY 310
+K LE + FV P + W+++ +RD+ ISR WG +P
Sbjct: 177 DLAKKALEAVKEGDIKFV-PERMEKRYENWLEN-IRDWCISRQLW-WGHRIP-------- 225
Query: 311 VWFDALLGY-ISALSED--------------------RDQPSLRTAVSSG-WPASLT 345
W+ G+ + A ED +D+ L T SS WP S
Sbjct: 226 AWYCKDGGHWVVAREEDEAIDKAAPEACVPCGGEELKQDEDVLDTWFSSSLWPFSTL 282
>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
synthetases. Leucyl tRNA synthetase (LeuRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. In Aquifex
aeolicus, the gene encoding LeuRS is split in two, just
before the KMSKS motif. Consequently, LeuRS is a
heterodimer, which likely superimposes with the LeuRS
monomer found in most other organisms. LeuRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements and thus differs between
prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
editing region hydrolyzes mischarged cognate tRNAs and
thus prevents the incorporation of chemically similar
amino acids.
Length = 314
Score = 63.4 bits (155), Expect = 3e-11
Identities = 46/216 (21%), Positives = 74/216 (34%), Gaps = 41/216 (18%)
Query: 91 FVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGG 150
F + Y + H+G T D IAR++R+ G V+F G D G AA G
Sbjct: 2 FYILVMFPYPSGALHVGHVRTYTIGDIIARYKRMQGYNVLFPMGFDAFGLPAENAAIKIG 61
Query: 151 SSPSEHCDVVSQAYKTLWKDLDIAYD--KFIRTTEPKHEAIVKEFYSSVLANGDIYKADY 208
P + + + K K + +YD + T +P++ + + + G YK +
Sbjct: 62 RDPEDWTEYNIKKMKEQLKRMGFSYDWRREFTTCDPEYYKFTQWLFLKLYEKGLAYKKEA 121
Query: 209 EGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALS--KYQKLLEDTLTENPD 266
+C D +F S ++++ L L E D
Sbjct: 122 PVNWCKLL---------------------------DQWFLKYSETEWKEKLLKDL-EKLD 153
Query: 267 FVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVP 302
R + WI S R WG P+P
Sbjct: 154 GWPEEVR-AMQENWI-----GCSRQRY---WGTPIP 180
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 62.1 bits (152), Expect = 1e-10
Identities = 41/163 (25%), Positives = 70/163 (42%), Gaps = 23/163 (14%)
Query: 84 GTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG---- 139
E + + TP V+ H+G ++ D IAR+QR+ G V F G D++G
Sbjct: 33 PDERKPVYSIDTPPPTVSGSLHIGHVFSYTHTDFIARYQRMRGYNVFFPQGWDDNGLPTE 92
Query: 140 ---EKIAAAAADGGSSP------SEHCDVVSQAYKTLWKDLDIAYD--KFIRTTEPKHEA 188
EK D S E D + ++ LW+ L ++ D +T P++
Sbjct: 93 RKVEKYYGIRKDDISREEFIELCRELTDEDEKKFRELWRRLGLSVDWSLEYQTISPEYRR 152
Query: 189 IVKEFYSSVLANGDIYKADYEGLYCVNCE--------EYKDEK 223
I ++ + + G IY+A+ L+C CE EY++ +
Sbjct: 153 ISQKSFLDLYKKGLIYRAEAPVLWCPRCETAIAQAEVEYRERE 195
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 143
Score = 57.9 bits (140), Expect = 2e-10
Identities = 19/75 (25%), Positives = 27/75 (36%)
Query: 94 TTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSP 153
T N H+G T + D +A+ R LG KV I D+ G I A G +
Sbjct: 2 TFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANKKGENA 61
Query: 154 SEHCDVVSQAYKTLW 168
+ + K
Sbjct: 62 KAFVERWIERIKEDV 76
>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
Other tRNA synthetase sub-families are too dissimilar to
be included.
Length = 606
Score = 57.4 bits (139), Expect = 5e-09
Identities = 40/213 (18%), Positives = 69/213 (32%), Gaps = 37/213 (17%)
Query: 85 TEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAA 144
+ F + H+G A D + R++R+ G V+++ G D HG
Sbjct: 19 GKGKPSFTIHDGPPNATGLLHIGHALNKTLKDIVIRYKRMQGFDVLWVPGWDHHGLPTEQ 78
Query: 145 A-----AADGGSSPS------------EHCDVVSQAYKTLWKDLDIAYDKFIR---TTEP 184
G E + ++ +K L ++ D + R T +P
Sbjct: 79 KVEKKLGIKGKKDRHKLGREKFREKCREWKMEYADEIRSQFKRLGVSGD-WDREYFTLDP 137
Query: 185 KHEAIVKEFYSSVLANGDIYKADYEGLYCVNCE--------EYKDEKELLENQCCPIHLK 236
EA V + + G IY+ + EYKD K IH+
Sbjct: 138 GLEAAVWRVFVRLHDKGLIYRGKKPVNWSPALNTALSEAEVEYKDVKGPS------IHVA 191
Query: 237 PCVARKEDNYF-FALSKYQKLLEDT-LTENPDF 267
+A + + L +T + NP+F
Sbjct: 192 FPLADGKGASLVIWTTTPWTLPGNTAVAVNPEF 224
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 56.1 bits (136), Expect = 1e-08
Identities = 30/145 (20%), Positives = 54/145 (37%), Gaps = 7/145 (4%)
Query: 76 YATNTDKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGT 135
+ + D E F + Y + H+G D IAR++R+ G V+ G
Sbjct: 24 FEADEDSDKPEK---FYVLVMFPYPSGALHVGHVRNYTIGDVIARYKRMQGYNVLHPMGW 80
Query: 136 DEHGEKIAAAAADGGSSPSEHCDVVSQAYKTLWKDLDIAYD---KFIRTTEPKHEAIVKE 192
D G AA G+ P++ K K L + D +F T +P++ ++
Sbjct: 81 DAFGLPAENAAIKIGTDPAKWTYYNIAYMKKQLKSLGFSIDWRREFA-TCDPEYYKWIQW 139
Query: 193 FYSSVLANGDIYKADYEGLYCVNCE 217
+ + G Y+ + +C
Sbjct: 140 QFLKLYEKGLAYRKEAPVNWCPVDG 164
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 54.2 bits (131), Expect = 5e-08
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 83 SGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
E PF + TP V HMG A D +AR++R+ G V++ GTD G
Sbjct: 27 DPNEDKPPFSIDTPPPNVTGSLHMGHALNYTLQDILARYKRMRGYNVLWPPGTDHAG 83
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 52.4 bits (126), Expect = 2e-07
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 83 SGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG--- 139
G PF + P V H+G A D IAR++R+ G V+++ GTD G
Sbjct: 27 DGNSNKPPFCIDIPPPNVTGSLHIGHALNWSIQDIIARYKRMKGYNVLWLPGTDHAGIAT 86
Query: 140 ----EKIAAA 145
EK A
Sbjct: 87 QVKVEKKLGA 96
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 49.2 bits (118), Expect = 1e-06
Identities = 56/254 (22%), Positives = 86/254 (33%), Gaps = 73/254 (28%)
Query: 99 YVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKI--AAAAADGGSSPS-- 154
Y N PH G A I D I R++ + G V G D HG I G S
Sbjct: 11 YANGLPHYGHALNKILKDIINRYKTMQGYYVPRRPGWDCHGLPIELKVEKELGISGKKDI 70
Query: 155 ---------EHCDVVSQAYKTLWK----------DLDIAYDKFIRTTEPKHEAIVKEFYS 195
C + Y + D + Y +T +P++ V +
Sbjct: 71 EKMGIAEFNAKCREFALRYVDEQEEQFQRLGVWVDWENPY----KTMDPEYMESVWWVFK 126
Query: 196 SVLANGDIYKADYEGLYCVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKY-Q 254
+ G +Y+ YK + P + R +F ++K
Sbjct: 127 QLHEKGLLYRG------------YK-----------VVPW-PLIYRATPQWFIRVTKIKD 162
Query: 255 KLLE--DTLTENPDFVQPSFRLNEVQGWIKSGLRDFSISRASVDWGIPVP----NDNKQ- 307
+LLE D + P++V+ F W++ RD+ ISR WG P+P D +
Sbjct: 163 RLLEANDKVNWIPEWVKNRFG-----NWLE-NRRDWCISRQRY-WGTPIPVWYCEDCGEV 215
Query: 308 -------TIYVWFD 314
+ VWFD
Sbjct: 216 LVRRVPDVLDVWFD 229
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 46.2 bits (110), Expect = 1e-05
Identities = 38/112 (33%), Positives = 51/112 (45%), Gaps = 17/112 (15%)
Query: 105 HMGSAYTTIAADAIARFQRLLGKKVIF---ITGTDEHGEKIAAAAADGGSSPSEHCDVVS 161
H+G A T I D + R+ R LG KV + IT D +KI A + G S E +
Sbjct: 36 HIGHARTAIVFDVLRRYLRYLGYKVQYVQNITDID---DKIIKRARENGESVYEVSERFI 92
Query: 162 QAYKTLWKDLDIAY-DKFIRTTEPKHEAIVKEF--------YSSVLANGDIY 204
+AY K L++ D R TE H + EF Y+ V NGD+Y
Sbjct: 93 EAYFEDMKALNVLPPDLEPRATE--HIDEIIEFIEQLIEKGYAYVSDNGDVY 142
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 45.3 bits (108), Expect = 2e-05
Identities = 34/113 (30%), Positives = 49/113 (43%), Gaps = 9/113 (7%)
Query: 104 PHMGSAYTTIAADAIARFQRLLGKKVIF---ITGTDEHGEKIAAAAADGGSSPSEHCDVV 160
H+G A T + D + R+ R LG KV + IT D +KI A + G S E +
Sbjct: 36 AHIGHARTYVVFDVLRRYLRYLGYKVTYVRNITDID---DKIINRAREEGLSIREVAERY 92
Query: 161 SQAYKTLWKDLDIAY-DKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEGLY 212
A+ L++ D R TE H + EF ++ G Y AD +Y
Sbjct: 93 IAAFFEDMDALNVLPPDIEPRATE--HIDEIIEFIEKLIEKGYAYVADDGDVY 143
>gnl|CDD|216482 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
domain. This family includes only cysteinyl tRNA
synthetases.
Length = 301
Score = 44.6 bits (106), Expect = 3e-05
Identities = 31/108 (28%), Positives = 48/108 (44%), Gaps = 7/108 (6%)
Query: 104 PHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCDVVSQA 163
H+G A + +A D + R+ + LG V F+ + +KI A G S E A
Sbjct: 23 SHIGHARSAVAFDVLRRYLQALGYDVQFVQNFTDIDDKIIKRAQQQGESFRELAARFITA 82
Query: 164 YKTLWKDLDI-AYDKFIRTTE--PKH----EAIVKEFYSSVLANGDIY 204
Y L++ D R TE + E ++K+ Y+ V NGD+Y
Sbjct: 83 YTKDMDALNVLPPDLEPRVTEHIDEIIEFIERLIKKGYAYVSDNGDVY 130
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 44.0 bits (104), Expect = 9e-05
Identities = 38/179 (21%), Positives = 72/179 (40%), Gaps = 13/179 (7%)
Query: 99 YVNAPPHMG--SAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPS-- 154
Y + HMG YT D ++R+ R+ G V+ G D G AA G P+
Sbjct: 39 YPSGALHMGHVRNYT--ITDVLSRYYRMKGYNVLHPIGWDAFGLPAENAAIKRGIHPAKW 96
Query: 155 --EHCDVVSQAYKTLWKDLDIAYDKFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEGLY 212
E+ + + + L D +D+ I T +P++ + + + G Y + + +
Sbjct: 97 TYENIANMKKQLQALGFSYD--WDREIATCDPEYYKWTQWIFLELFEKGLAYVKEADVNW 154
Query: 213 CVNCEEYKDEKELLENQCCPIHLKPCVARKEDNYFFALSKY-QKLLED--TLTENPDFV 268
C N +++ + P ++ +F ++ Y ++LL D L P+ V
Sbjct: 155 CPNDGTVLANEQVDSDGRSWRGDTPVEKKELKQWFLKITAYAEELLNDLEELDHWPESV 213
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 42.9 bits (102), Expect = 2e-04
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)
Query: 104 PHMGSAYTTIAADAIARFQRLLGKKVIF-----ITGT 135
H+G T D IAR++R+ G V+F +TGT
Sbjct: 1 LHVGHGRTYTIGDVIARYKRMRGYNVLFPMAFHVTGT 37
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 42.1 bits (99), Expect = 4e-04
Identities = 22/55 (40%), Positives = 27/55 (49%)
Query: 88 ADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKI 142
+ F L Y N H+G A I D I R+Q L GKKV ++ G D HG I
Sbjct: 31 GESFTLHDGPPYANGDLHIGHALNKILKDFINRYQLLQGKKVHYVPGWDCHGLPI 85
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 40.7 bits (95), Expect = 0.001
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 76 YATNTDKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGT 135
+ N D+ G DPFV+ P V HMG A D + R+ R+ G+ ++I GT
Sbjct: 79 FKPNFDRGG----DPFVIPMPPPNVTGSLHMGHAMFVTLEDIMVRYNRMKGRPTLWIPGT 134
Query: 136 DEHG 139
D G
Sbjct: 135 DHAG 138
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 40.7 bits (96), Expect = 0.001
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 99 YVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
Y N H+G A I D I R++ + G V ++ G D HG
Sbjct: 59 YANGNIHIGHALNKILKDIIVRYKTMQGYDVPYVPGWDCHG 99
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 40.8 bits (96), Expect = 0.001
Identities = 16/55 (29%), Positives = 22/55 (40%)
Query: 85 TEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
+ F+ Y N H+G A I D I R++ + G V G D HG
Sbjct: 32 NKGKPEFIFHDGPPYANGSIHLGHALNKILKDIILRYKTMQGFNVTRKPGWDTHG 86
>gnl|CDD|173899 cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA
synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding.
Length = 213
Score = 38.7 bits (91), Expect = 0.002
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 104 PHMGSAYTTIAADAIARFQRLLGKKVIF---ITGTDEHGEKIAAAAADGGSSPSEHCDVV 160
H+G A T + D + R+ LG KV + IT D +KI A + G S E D
Sbjct: 34 AHIGHARTYVVFDVLRRYLEDLGYKVRYVQNITDID---DKIIKRAREEGLSWKEVADYY 90
Query: 161 SQAYKTLWKDLDIAY-DKFIRT 181
++ + K L++ D R
Sbjct: 91 TKEFFEDMKALNVLPPDVVPRV 112
>gnl|CDD|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
cytosolic family. The leucyl-tRNA synthetases belong to
two families so broadly different that they are
represented by separate models. This model includes both
archaeal and cytosolic eukaryotic leucyl-tRNA
synthetases; the eubacterial and mitochondrial forms
differ so substantially that some other tRNA ligases
score higher by this model than does any eubacterial
LeuS [Protein synthesis, tRNA aminoacylation].
Length = 938
Score = 39.0 bits (91), Expect = 0.003
Identities = 39/173 (22%), Positives = 67/173 (38%), Gaps = 31/173 (17%)
Query: 88 ADP-----FVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIF-----ITGTDE 137
ADP F LT Y+N H G T + ARF+R+ GK V+F +TGT
Sbjct: 19 ADPDDREKFFLTMAYPYLNGVMHAGHCRTFTIPEVSARFERMKGKNVLFPLGFHVTGTPI 78
Query: 138 HG--EKIAAAAADGG-----------------SSPSEHCDVVSQAYKTLWKDLDIAYD-- 176
G E I + P + S+ ++ K + + D
Sbjct: 79 LGLAELIKRRDELTIKNYTEVHAIPREELLKFTDPEYIVEYFSREAESACKSMGYSIDWR 138
Query: 177 KFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEGLYCVNCEEYKDEKELLENQ 229
+ +TT+P ++ ++ + + G I K ++ YC ++ +LL +
Sbjct: 139 RSFKTTDPYYDRFIEWQMNKLKELGLIVKGEHPVRYCPKDGNPVEDHDLLSGE 191
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 38.8 bits (91), Expect = 0.004
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 89 DPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIA 143
FV+ P V H+G A T D++ R+ R+ G + +++ GTD G IA
Sbjct: 60 KKFVIVLPPPNVTGYLHIGHALTGAIQDSLIRYHRMKGDETLWVPGTDHAG--IA 112
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 38.6 bits (91), Expect = 0.005
Identities = 14/41 (34%), Positives = 18/41 (43%)
Query: 99 YVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
N PH G T D + R++ + G KV G D HG
Sbjct: 51 TANGLPHYGHLLTRTIKDVVPRYKTMKGYKVERRAGWDTHG 91
Score = 28.6 bits (65), Expect = 6.0
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 9/31 (29%)
Query: 280 WIKSG--------LRDFSISRASVDWGIPVP 302
IK G RD++ISR WG P+P
Sbjct: 430 HIKDGRFGKWLENARDWNISRNRY-WGTPLP 459
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 37.8 bits (89), Expect = 0.007
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 12/61 (19%)
Query: 82 KSGTEPADPFVLTTPLYYVNAPP------HMGSAYTTIAADAIARFQRLLGKKVIFITGT 135
K PF + P PP HMG A D + R++R+ G +++ GT
Sbjct: 29 KPDDNSKKPFSIVIP------PPNVTGSLHMGHALNNTLQDILIRYKRMQGYNTLWLPGT 82
Query: 136 D 136
D
Sbjct: 83 D 83
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 36.0 bits (83), Expect = 0.029
Identities = 36/147 (24%), Positives = 61/147 (41%), Gaps = 13/147 (8%)
Query: 2 IKTGKKATPVKHSEEQT---LSLQKEFEEMAARINYSIQNSLWLLNPLHSKATTHFRNRL 58
+K +K K +Q ++ K+ E+ + + + +N ++P T + +
Sbjct: 36 LKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRDVEDENPEDFIDPD----TPFGQKKR 91
Query: 59 KFRQNLFSLSKGAVFCSYATNTDKSGTEPAD------PFVLTTPLYYVNAPPHMGSAYTT 112
Q S AV S+ +KSG AD PFV+ P V H+G A T
Sbjct: 92 LSSQMAKQYSPSAVEKSWYAWWEKSGYFGADAKSSKPPFVIVLPPPNVTGALHIGHALTA 151
Query: 113 IAADAIARFQRLLGKKVIFITGTDEHG 139
D I R++R+ G +++ G D G
Sbjct: 152 AIEDTIIRWKRMSGYNALWVPGVDHAG 178
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 35.4 bits (82), Expect = 0.046
Identities = 17/69 (24%), Positives = 27/69 (39%)
Query: 78 TNTDKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDE 137
+P + F P Y+N H+G A++ + A + RL G V+
Sbjct: 34 AEAGDEPPKPGEKFFGNFPYPYMNGLLHLGHAFSLSKLEFAAAYHRLRGANVLLPFAFHC 93
Query: 138 HGEKIAAAA 146
G I A+A
Sbjct: 94 TGMPIKASA 102
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 33.4 bits (77), Expect = 0.12
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 117 AIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCDVVSQA 163
A+AR G VI ITG E E++A A + + + DV
Sbjct: 20 ALARKFLEAGNTVI-ITGRRE--ERLAEAKKELPNIHTIVLDVGDAE 63
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 33.2 bits (77), Expect = 0.19
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 104 PHMGSAYTTIAADAIARFQRLLGKKVIF---ITGTDEHGEKIAAAAADGGSSPSEHCDVV 160
H+G A + + D + R+ R LG KV + IT D +KI A + G S E +
Sbjct: 37 AHIGHARSFVVFDVLRRYLRYLGYKVTYVRNITDID---DKIIKRANEEGESIKELTERY 93
Query: 161 SQAYKTLWKDLD 172
A+ +D+D
Sbjct: 94 IAAF---HEDMD 102
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 33.2 bits (75), Expect = 0.25
Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 105 HMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCDVVSQAY 164
H+G A + D IAR+ R G + ++ + +KI A AA+ G + E + ++
Sbjct: 263 HLGHARVMVVFDMIARWLRECGYPLTYVRNITDIDDKIIARAAENGETIGE---LTARFI 319
Query: 165 KTLWKDLDIAYDKFIRTTEPKH-----------EAIVKEFYSSVLANGDIYKADYE 209
+ + +D D A EPK E +++ + ANGD+Y A E
Sbjct: 320 QAMHEDAD-ALGVLRPDIEPKATENIPQMIAMIETLIQNGKAYPAANGDVYYAVRE 374
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 33.1 bits (77), Expect = 0.25
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 105 HMGSAYTTIAADAIARFQRLLGKKV 129
HMG D IAR++R+ G V
Sbjct: 48 HMGHVRNYTIGDVIARYKRMQGYNV 72
>gnl|CDD|173777 cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain found in Ribonuclease M5:
(RNase M5) and other small primase-like proteins from
bacteria and archaea. RNase M5 catalyzes the maturation
of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM
domain has two conserved motifs, one of which centers at
a conserved glutamate and the other one at two conserved
aspartates (DxD). The conserved glutamate may act as a
general base in nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function.
Length = 81
Score = 30.3 bits (69), Expect = 0.32
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 107 GSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAA 144
GS + I + + VI +T D GEKI
Sbjct: 30 GSIINKETIELIKKA----YRGVIILTDPDRKGEKIRK 63
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 32.7 bits (74), Expect = 0.35
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 90 PFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
PF + P V H+G A T D + R++R+ G +++ GTD G
Sbjct: 49 PFSIVLPPPNVTGSLHLGHALTATLQDVLIRWKRMSGFNTLWLPGTDHAG 98
>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
Length = 961
Score = 32.2 bits (74), Expect = 0.48
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 99 YVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHG 139
Y N H+G A I D I R +++LG ++ G D HG
Sbjct: 64 YANGNIHIGHALNKILKDVIVRSKQMLGFDANYVPGWDCHG 104
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 30.8 bits (71), Expect = 1.1
Identities = 37/167 (22%), Positives = 54/167 (32%), Gaps = 61/167 (36%)
Query: 99 YVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCD 158
Y N H+G A I D I + + + G ++ G D HG I E
Sbjct: 59 YANGDIHIGHALNKILKDIIVKSKTMSGFDAPYVPGWDCHGLPI------------EL-- 104
Query: 159 VVSQAYKTLWKDLDIA--------Y---------DKFIR------------TTEPKHEA- 188
V + K L A Y + F R T + K+EA
Sbjct: 105 KVEKKLGKKGKKLSAAEFRKKCREYALEQVDIQREDFKRLGVLGDWDNPYLTMDFKYEAN 164
Query: 189 IVKEFYSSVLANGDIYKADYEGL----YCVNCE--------EYKDEK 223
I++ + G +YK GL +C +C EY D+
Sbjct: 165 IIRAL-GKMAKKGYLYK----GLKPVYWCPDCGSALAEAEVEYHDKT 206
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 30.4 bits (69), Expect = 1.2
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 1/60 (1%)
Query: 117 AIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCDVVSQAYKTLWKDLDIAYD 176
A+ + G +VI +DE E AD E D+ + T D+ D
Sbjct: 149 LAAQLAKAAGARVIVTDRSDEKLELAKELGADHVIDYKEE-DLEEELRLTGGGGADVVID 207
>gnl|CDD|107263 cd06268, PBP1_ABC_transporter_LIVBP_like, Periplasmic binding
domain of ATP-binding cassette transporter-like systems
that belong to the type I periplasmic binding fold
protein superfamily. Periplasmic binding domain of
ATP-binding cassette transporter-like systems that
belong to the type I periplasmic binding fold protein
superfamily. They are mostly present in archaea and
eubacteria, and are primarily involved in scavenging
solutes from the environment. ABC-type transporters
couple ATP hydrolysis with the uptake and efflux of a
wide range of substrates across bacterial membranes,
including amino acids, peptides, lipids and sterols, and
various drugs. These systems are comprised of
transmembrane domains, nucleotide binding domains, and
in most bacterial uptake systems, periplasmic binding
proteins (PBPs) which transfer the ligand to the
extracellular gate of the transmembrane domains. These
PBPs bind their substrates selectively and with high
affinity. Members of this group include ABC-type
Leucine-Isoleucine-Valine-Binding Proteins (LIVBP),
which are homologous to the aliphatic amidase
transcriptional repressor, AmiC, of Pseudomonas
aeruginosa. The uncharacterized periplasmic components
of various ABC-type transport systems are included in
this group.
Length = 298
Score = 30.1 bits (68), Expect = 1.7
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 15/83 (18%)
Query: 68 SKGAVFCSYATNTDKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARF--QRLL 125
G S + + T +P+V T + A A+A + ++
Sbjct: 88 EAGVPLISPGATSP-ALTGKGNPYVFRT------------APSDAQQAAALADYLAEKGK 134
Query: 126 GKKVIFITGTDEHGEKIAAAAAD 148
KKV I +G +AAA +
Sbjct: 135 VKKVAIIYDDYAYGRGLAAAFRE 157
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 29.8 bits (67), Expect = 2.5
Identities = 28/104 (26%), Positives = 45/104 (43%), Gaps = 10/104 (9%)
Query: 93 LTTPLYYV--------NAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAA 144
+ P +YV A H+G A D +AR++R+ G V+ G D G
Sbjct: 107 TSKPKFYVLDMFPYPSGAGLHVGHPEGYTATDILARYKRMQGYNVLHPMGWDAFGLPAEQ 166
Query: 145 AAADGGSSPSEHCDVVSQAYKTLWKDLDIAYD--KFIRTTEPKH 186
A + G+ P +++ K L +YD + I TTEP++
Sbjct: 167 YAIETGTHPKITTLKNIARFRSQLKSLGFSYDWDREISTTEPEY 210
>gnl|CDD|184261 PRK13705, PRK13705, plasmid-partitioning protein SopA; Provisional.
Length = 388
Score = 29.6 bits (66), Expect = 2.5
Identities = 29/108 (26%), Positives = 39/108 (36%), Gaps = 21/108 (19%)
Query: 81 DKSGTEPADPFVLTTPLYYVNAPPHMGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGE 140
D GT + P+ V A H G Y T + +A+ L G +V+ + G D G
Sbjct: 92 DVFGTRLRRAEDVFPPVIGVAA--HKGGVYKTSVSVHLAQDLALKGLRVLLVEGNDPQG- 148
Query: 141 KIAAAAADGGSSPSEHC--------------DVVSQAYK-TLWKDLDI 173
A+ G P H D + A K T W LDI
Sbjct: 149 ---TASMYHGWVPDLHIHAEDTLLPFYLGEKDDATYAIKPTCWPGLDI 193
>gnl|CDD|143453 cd07135, ALDH_F14-YMR110C, Saccharomyces cerevisiae aldehyde
dehydrogenase family 14 and related proteins. Aldehyde
dehydrogenase family 14 (ALDH14), isolated mainly from
the mitochondrial outer membrane of Saccharomyces
cerevisiae (YMR110C) and most closely related to the
plant and animal ALDHs and fatty ALDHs family 3 members,
and similar fungal sequences, are present in this CD.
Length = 436
Score = 29.5 bits (67), Expect = 2.6
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 15/75 (20%)
Query: 108 SAYTTIAADAIARFQRLLGKKV--IFITGTDEHGEKIAAAAAD---------GGSSP--- 153
A+ + + LL +K IF TG+ G IA AAA GG SP
Sbjct: 165 DAFQVVQG-GVPETTALLEQKFDKIFYTGSGRVGRIIAEAAAKHLTPVTLELGGKSPVIV 223
Query: 154 SEHCDVVSQAYKTLW 168
+++ D+ A + LW
Sbjct: 224 TKNADLELAAKRILW 238
>gnl|CDD|143426 cd07108, ALDH_MGR_2402, Magnetospirillum NAD(P)+-dependent aldehyde
dehydrogenase MSR-1-like. NAD(P)+-dependent aldehyde
dehydrogenase of Magnetospirillum gryphiswaldense MSR-1
(MGR_2402) , and other similar sequences, are present in
this CD.
Length = 457
Score = 29.6 bits (67), Expect = 2.6
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 10/37 (27%)
Query: 127 KKVIFITGTDEHGEKIAAAAAD---------GGSSPS 154
KV F TG+ E G+ I AAAD GG SP
Sbjct: 197 DKVTF-TGSTEVGKIIYRAAADRLIPVSLELGGKSPM 232
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 27.2 bits (61), Expect = 3.2
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 106 MGSAYTTIAADAIARFQRLLGKKVIFITGTDEHGEKIAAAAAD 148
G A + + + K+VI T D GE IA +
Sbjct: 29 SGHALDLEHIKELKKALKGA-KEVILATDPDREGEAIALKLLE 70
>gnl|CDD|143580 cd07176, terB, tellurite resistance protein terB. This family
contains uncharacterized bacterial proteins involved in
tellurium resistance. The prototype of this CD is the
Kp-terB protein from Klebsiella pneumoniae, whose 3D
structure was recently determined. The biological
function of terB and the mechanism responsible for
tellurium resistance are unknown.
Length = 111
Score = 28.0 bits (63), Expect = 3.3
Identities = 18/69 (26%), Positives = 22/69 (31%), Gaps = 16/69 (23%)
Query: 114 AADAIARFQRLLG----------KKVIFITGTDEHGEKIAA-----AAADGGSSPSEHCD 158
IA +LL K E E A AAADG P E
Sbjct: 42 RERLIALLDKLLALLRPEGLAALLKAAAKLLPPELRETAFAVAVDIAAADGEVDPEER-A 100
Query: 159 VVSQAYKTL 167
V+ + Y+ L
Sbjct: 101 VLEKLYRAL 109
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 29.0 bits (65), Expect = 3.6
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 117 AIARFQRLLGKKVIFITGTDEHGEKIAAAAADGGSSPSEHCDVVSQA 163
A AR G +V+ D+ G+ +AA D S HCDV +A
Sbjct: 19 ATARLFAKHGARVVIADIDDDAGQAVAAELGDPDIS-FVHCDVTVEA 64
>gnl|CDD|215863 pfam00332, Glyco_hydro_17, Glycosyl hydrolases family 17.
Length = 310
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 301 VPNDNKQTIYVWFDALLGYISALSEDRDQPSLRTAVS-SGWP 341
D FDA++ + A E PS+ VS SGWP
Sbjct: 197 TVVDGGLGYQNLFDAMVDAVYAALEKAGGPSVEVVVSESGWP 238
>gnl|CDD|237720 PRK14463, PRK14463, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 349
Score = 29.0 bits (65), Expect = 4.3
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 104 PHMGSAYTTIAADAIARFQR-LLGKKVIFITGTDEHGEKIAAA 145
H G + + +AI RF + LL K V IT G I+AA
Sbjct: 289 EHEGCDFRSPTQEAIDRFHKYLLDKHVTVIT-RSSRGSDISAA 330
>gnl|CDD|189011 cd09604, M1_APN_5, Peptidase M1 family containing bacterial
Aminopeptidase N. This family contains bacterial
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 435
Score = 28.9 bits (65), Expect = 4.3
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 97 LYYVNAPPHMGSAYTTIAADAIARFQRLLGK 127
YY + Y A A+ + L G
Sbjct: 222 AYYFPEDAELAKRYLDAAKKALEFYSELFGP 252
>gnl|CDD|238807 cd01573, modD_like, ModD; Quinolinate phosphoribosyl transferase
(QAPRTase or QPRTase) present in some modABC operons in
bacteria, which are involved in molybdate transport. In
general, QPRTases are part of the de novo synthesis
pathway of NAD in both prokaryotes and eukaryotes. They
catalyse the reaction of quinolinic acid (QA) with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to produce nicotinic acid mononucleotide (NAMN),
pyrophosphate and carbon dioxide.
Length = 272
Score = 28.8 bits (65), Expect = 4.3
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 105 HMGSAYTTIAADAIARF-QRLLGKKVIFITGTDEHGEKIAAAAAD 148
H A+AR KK++ + E A A AD
Sbjct: 161 HRAFLGGPEPLKALARLRATAPEKKIVVEVDSLEEALAAAEAGAD 205
>gnl|CDD|143450 cd07132, ALDH_F3AB, Aldehyde dehydrogenase family 3 members A1, A2,
and B1 and related proteins. NAD(P)+-dependent,
aldehyde dehydrogenase, family 3 members A1 and B1
(ALDH3A1, ALDH3B1, EC=1.2.1.5) and fatty aldehyde
dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3),
and similar sequences are included in this CD. Human
ALDH3A1 is a homodimer with a critical role in cellular
defense against oxidative stress; it catalyzes the
oxidation of various cellular membrane lipid-derived
aldehydes. Corneal crystalline ALDH3A1 protects the
cornea and underlying lens against UV-induced oxidative
stress. Human ALDH3A2, a microsomal homodimer, catalyzes
the oxidation of long-chain aliphatic aldehydes to fatty
acids. Human ALDH3B1 is highly expressed in the kidney
and liver and catalyzes the oxidation of various medium-
and long-chain saturated and unsaturated aliphatic
aldehydes.
Length = 443
Score = 28.0 bits (63), Expect = 7.4
Identities = 32/130 (24%), Positives = 49/130 (37%), Gaps = 42/130 (32%)
Query: 130 IFITGTDEHGEKIAAAAAD---------GGSSP---SEHCDVVSQAYKTLW-KDLD---- 172
IF TG+ G+ + AAA GG SP + CD+ A + W K ++
Sbjct: 180 IFYTGSTSVGKIVMQAAAKHLTPVTLELGGKSPCYVDKSCDIDVAARRIAWGKFINAGQT 239
Query: 173 -IAYD----------KFIRTTEPKHEAIVKEFYSSVLANGDIYKADYEGLYC--VNCEEY 219
IA D KF+ + +KEFY D ++ Y +N +
Sbjct: 240 CIAPDYVLCTPEVQEKFV----EALKKTLKEFYGE-----DPKESPD---YGRIINDRHF 287
Query: 220 KDEKELLENQ 229
+ K+LL
Sbjct: 288 QRLKKLLSGG 297
>gnl|CDD|235101 PRK03059, PRK03059, PII uridylyl-transferase; Provisional.
Length = 856
Score = 27.9 bits (63), Expect = 8.4
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 162 QAYKTLWKDLDIAYDKFIRTTEPKHEA 188
A++ LW LD+ Y F+R H+A
Sbjct: 628 DAHEALWDQLDVGY--FLR-----HDA 647
>gnl|CDD|213270 cd04433, AFD_class_I, Adenylate forming domain, Class I. This
family includes acyl- and aryl-CoA ligases, as well as
the adenylation domain of nonribosomal peptide
synthetases and firefly luciferases. The
adenylate-forming enzymes catalyze an ATP-dependent
two-step reaction to first activate a carboxylate
substrate as an adenylate and then transfer the
carboxylate to the pantetheine group of either coenzyme
A or an acyl-carrier protein. The active site of the
domain is located at the interface of a large N-terminal
subdomain and a smaller C-terminal subdomain.
Length = 338
Score = 27.6 bits (62), Expect = 9.7
Identities = 12/31 (38%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 313 FDALLGYISALSEDRDQPSLRTAVSSGWPAS 343
+DAL A D SLR +S G P S
Sbjct: 101 YDALAKA--AEDRGYDLSSLRLLISGGEPLS 129
>gnl|CDD|226497 COG4009, COG4009, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 88
Score = 25.9 bits (57), Expect = 10.0
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 21 LQKEFEEMAARINYSIQNSL 40
+++E E+M A IN + SL
Sbjct: 65 VERELEDMGAEINRDSKASL 84
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
0.317 0.132 0.399
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,473,207
Number of extensions: 1673875
Number of successful extensions: 1807
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1780
Number of HSP's successfully gapped: 82
Length of query: 345
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 247
Effective length of database: 6,590,910
Effective search space: 1627954770
Effective search space used: 1627954770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)