RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7914
(365 letters)
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 334 bits (860), Expect = e-108
Identities = 104/166 (62%), Positives = 120/166 (72%), Gaps = 1/166 (0%)
Query: 185 EDNFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAH 244
+YVL MFPYPSG LHMGHVR YTI D +ARY M G NV PMGWDAFGLPAENAA
Sbjct: 31 SKKYYVLDMFPYPSGGLHMGHVRNYTIGDVIARYKRMQGYNVLHPMGWDAFGLPAENAAI 90
Query: 245 QHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 304
+ G P EWT NIA MK QL+ G ++W E+ATCDP+YYKWTQ +FL LY GL YR
Sbjct: 91 KTGTHPAEWTYENIANMKKQLKSLGFSYDWSREIATCDPEYYKWTQWIFLKLYEKGLAYR 150
Query: 305 KEATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTT 350
KE+ VNW P+D TVLA+EQV + G WR GA VEK+ L QWF++ T
Sbjct: 151 KESPVNWCPVDGTVLANEQVID-GRCWRCGAPVEKKELRQWFLKIT 195
Score = 32.4 bits (75), Expect = 0.46
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 21 AMDLYEGLSDPILQDWKDIV-NLQKHWIGEPNGVRFEFQI 59
A +L + L L+DW + V +Q++WIG G F++
Sbjct: 198 ADELLDDLDK--LEDWPEKVKTMQRNWIGRSEGAEVTFKV 235
>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 = 292 bits (749), Expect = 7e-92
Identities = 105/166 (63%), Positives = 125/166 (75%)
Query: 188 FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHG 247
+Y+LSMFPYPSG+LHMGHVR YTI+D L+RYY M G NV P+GWDAFGLPAENAA + G
Sbjct: 31 YYILSMFPYPSGALHMGHVRNYTITDVLSRYYRMKGYNVLHPIGWDAFGLPAENAAIKRG 90
Query: 248 IDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKEA 307
I P +WT NIA MK QLQ G ++W+ E+ATCDP+YYKWTQ +FL+L+ GL Y KEA
Sbjct: 91 IHPAKWTYENIANMKKQLQALGFSYDWDREIATCDPEYYKWTQWIFLELFEKGLAYVKEA 150
Query: 308 TVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTTRLA 353
VNW P D TVLA+EQVD G SWR VEK+ L QWF++ T A
Sbjct: 151 DVNWCPNDGTVLANEQVDSDGRSWRGDTPVEKKELKQWFLKITAYA 196
Score = 38.6 bits (90), Expect = 0.005
Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 22/104 (21%)
Query: 21 AMDLYEGLSDPILQDWKDIV-NLQKHWIGEPNGVRFEFQILPQPEGTSNSAPTADTLSIW 79
A +L L + L W + V +Q++WIG+ GV F+I A + ++++
Sbjct: 196 AEELLNDLEE--LDHWPESVKEMQRNWIGKSEGVEITFKI----------ADHDEKITVF 243
Query: 80 LPE-DTIEDVAKSQGQYITVKSSHILASK---TKEKLTENVKHQ 119
DTI V Y+ + H L K K+ +K
Sbjct: 244 TTRPDTIFGV-----TYLALAPEHPLVEKAAENNPKVAAFIKKI 282
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 282 bits (724), Expect = 3e-88
Identities = 103/171 (60%), Positives = 119/171 (69%), Gaps = 1/171 (0%)
Query: 180 EGKRREDNFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPA 239
E + + FYVL MFPYPSG+LH+GHVR YTI D +ARY M G NV PMGWDAFGLPA
Sbjct: 28 EDSDKPEKFYVLVMFPYPSGALHVGHVRNYTIGDVIARYKRMQGYNVLHPMGWDAFGLPA 87
Query: 240 ENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHA 299
ENAA + G DP +WT NIA MK QL+ G +W E ATCDP+YYKW Q FL LY
Sbjct: 88 ENAAIKIGTDPAKWTYYNIAYMKKQLKSLGFSIDWRREFATCDPEYYKWIQWQFLKLYEK 147
Query: 300 GLVYRKEATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTT 350
GL YRKEA VNW P+D TVLA+EQV + G WR G VE + L+QWF + T
Sbjct: 148 GLAYRKEAPVNWCPVDGTVLANEQVID-GGCWRCGEPVEIKELTQWFFKIT 197
Score = 30.7 bits (70), Expect = 1.3
Identities = 28/119 (23%), Positives = 43/119 (36%), Gaps = 16/119 (13%)
Query: 17 GRAGAMDLYEGLSDPILQDWKD-IVNLQKHWIGEPNGVRFEFQILPQPEGTSNSAPTADT 75
A +L + L D + W + + +Q++WIG G F + + E S T
Sbjct: 196 ITDYADELLDDL-DKLATLWPETVKGMQRNWIGPSEGYEVAFVVDGEEEIVSIEV--FTT 252
Query: 76 LSIWLPEDTIEDVAKSQGQYITVKSSHILASK-TKEKLTENVKHQI-ENKYKSIVSSDP 132
DT+ V Y+ + H L K T V + E K +V S P
Sbjct: 253 RP-----DTLFGV-----TYVVLAPEHPLVGKLVTNPQTPLVAEFVDECKGTGVVESVP 301
>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 = 222 bits (568), Expect = 2e-70
Identities = 78/125 (62%), Positives = 91/125 (72%)
Query: 188 FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHG 247
FY+L MFPYPSG+LH+GHVR YTI D +ARY M G NV PMG+DAFGLPAENAA + G
Sbjct: 2 FYILVMFPYPSGALHVGHVRTYTIGDIIARYKRMQGYNVLFPMGFDAFGLPAENAAIKIG 61
Query: 248 IDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKEA 307
DP +WT NI MK QL+ G ++W E TCDP+YYK+TQ LFL LY GL Y+KEA
Sbjct: 62 RDPEDWTEYNIKKMKEQLKRMGFSYDWRREFTTCDPEYYKFTQWLFLKLYEKGLAYKKEA 121
Query: 308 TVNWD 312
VNW
Sbjct: 122 PVNWC 126
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 199 bits (508), Expect = 4e-57
Identities = 85/168 (50%), Positives = 112/168 (66%), Gaps = 2/168 (1%)
Query: 188 FYVLSMFPYPSGS-LHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH 246
FYVL MFPYPSG+ LH+GH YT +D LARY M G NV PMGWDAFGLPAE A +
Sbjct: 112 FYVLDMFPYPSGAGLHVGHPEGYTATDILARYKRMQGYNVLHPMGWDAFGLPAEQYAIET 171
Query: 247 GIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 306
G P+ T+ NIA +SQL+ G ++W+ E++T +P+YYKWTQ +FL L GL Y+ E
Sbjct: 172 GTHPKITTLKNIARFRSQLKSLGFSYDWDREISTTEPEYYKWTQWIFLQLLKRGLAYQAE 231
Query: 307 ATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTTRLAN 354
VNW P TVLA+E+V + G+S R G V ++ + QW ++ T A+
Sbjct: 232 VPVNWCPALGTVLANEEVVD-GLSERGGHPVIRKPMRQWMLKITAYAD 278
Score = 29.4 bits (66), Expect = 3.2
Identities = 27/108 (25%), Positives = 39/108 (36%), Gaps = 17/108 (15%)
Query: 24 LYEGLSDPILQDWKD-IVNLQKHWIGEPNGVRFEFQILPQPEGTSNSAPTADTLSIWLPE 82
L E L D DW + I +Q++WIG G +F +L + T T
Sbjct: 280 LLEDLDD---LDWPESIKEMQRNWIGRSEGAELDFSVLDGEGKERDEKITVYTTR----P 332
Query: 83 DTIEDVAKSQGQYITVKSSHILASKTKEKLTENVKHQIENKYKSIVSS 130
DT+ Y+ V H L S LT + + +Y S
Sbjct: 333 DTLFGAT-----YLVVAPEHPLLS----SLTTAEQKEAVEEYVDAASR 371
>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 = 156 bits (396), Expect = 3e-44
Identities = 57/175 (32%), Positives = 77/175 (44%), Gaps = 21/175 (12%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAEN---------AAHQ 245
P +GSLHMGH TI D +ARY M G NV P G D G+ + +
Sbjct: 10 PNVTGSLHMGHALNNTIQDIIARYKRMKGYNVLWPPGTDHAGIATQVVVEKKLGIEGKTR 69
Query: 246 HGIDPR-------EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYH 298
H + EW + ++ QL+ G +W E T DP + Q F+ LY
Sbjct: 70 HDLGREEFLEKCWEWKEESGGKIREQLKRLGASVDWSREYFTMDPGLSRAVQEAFVRLYE 129
Query: 299 AGLVYRKEATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTTRLA 353
GL+YR VNW P T ++D +V RSG +E QWF++ LA
Sbjct: 130 KGLIYRDNRLVNWCPKLRTAISDIEV-----CSRSGDVIEPLLKPQWFVKVKDLA 179
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 149 bits (380), Expect = 7e-40
Identities = 57/143 (39%), Positives = 70/143 (48%), Gaps = 19/143 (13%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLP----AENAAHQHGI-- 248
P SGSLH+GHV YT +D +ARY M G NVF P GWD GLP E +GI
Sbjct: 47 PTVSGSLHIGHVFSYTHTDFIARYQRMRGYNVFFPQGWDDNGLPTERKVEK---YYGIRK 103
Query: 249 DP----------REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYH 298
D RE T + + + G +W E T P+Y + +Q FLDLY
Sbjct: 104 DDISREEFIELCRELTDEDEKKFRELWRRLGLSVDWSLEYQTISPEYRRISQKSFLDLYK 163
Query: 299 AGLVYRKEATVNWDPIDNTVLAD 321
GL+YR EA V W P T +A
Sbjct: 164 KGLIYRAEAPVLWCPRCETAIAQ 186
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 141 bits (357), Expect = 8e-37
Identities = 53/156 (33%), Positives = 71/156 (45%), Gaps = 19/156 (12%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENA-----------A 243
P +GSLHMGH YT+ D LARY M G NV P G D G+ +
Sbjct: 42 PNVTGSLHMGHALNYTLQDILARYKRMRGYNVLWPPGTDHAGIATQVVVEKQLAAEGITR 101
Query: 244 HQHGIDP-----REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYH 298
H G + EW + T++ QL+ G +W E T DP + Q F+ LY
Sbjct: 102 HDLGREEFLKKCWEWKEESGGTIREQLRRLGVSVDWSRERFTMDPGLSRAVQEAFVRLYE 161
Query: 299 AGLVYRKEATVNWDPIDNTVLAD---EQVDEQGISW 331
GL+YR E VNW P T ++D E + +G +
Sbjct: 162 KGLIYRGERLVNWCPKCRTAISDIEVEYKEVEGKLY 197
Score = 29.9 bits (68), Expect = 2.8
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 15/59 (25%)
Query: 295 DLYHAGLVYRKEATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTTRLA 353
DL GL+ + E P ++V G R G +E QWF++ LA
Sbjct: 323 DLEEQGLLVKIE------PHKHSV---------GHCERCGTPIEPLLSKQWFVKVLELA 366
>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 = 123 bits (310), Expect = 1e-30
Identities = 49/147 (33%), Positives = 71/147 (48%), Gaps = 16/147 (10%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAH-QHGID---- 249
P +GSLH+GH ++I D +ARY M G NV G D G+ + + G +
Sbjct: 42 PNVTGSLHIGHALNWSIQDIIARYKRMKGYNVLWLPGTDHAGIATQVKVEKKLGAEGKTK 101
Query: 250 ---PRE--------WTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYH 298
RE W + T+K+Q++ G +W E T D K + F+ LY
Sbjct: 102 HDLGREEFREKIWEWKEESGGTIKNQIKRLGASLDWSRERFTMDEGLSKAVKEAFVRLYE 161
Query: 299 AGLVYRKEATVNWDPIDNTVLADEQVD 325
GL+YR E VNWDP NT ++D +V+
Sbjct: 162 KGLIYRGEYLVNWDPKLNTAISDIEVE 188
>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 = 110 bits (278), Expect = 6e-28
Identities = 47/135 (34%), Positives = 64/135 (47%), Gaps = 13/135 (9%)
Query: 188 FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHG 247
FYV + PY +GSLH+GH + I+D +ARY M G V GWD GLP E A + G
Sbjct: 2 FYVTTPPPYANGSLHLGHALTHIIADFIARYKRMRGYEVPFLPGWDTHGLPIELKAERKG 61
Query: 248 I-------------DPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFL 294
DP+E+ K + G ++W E T +P+Y K + +F
Sbjct: 62 GRKKKTIWIEEFREDPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPEYSKAVELIFS 121
Query: 295 DLYHAGLVYRKEATV 309
LY GL+YR V
Sbjct: 122 RLYEKGLIYRGTHPV 136
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 93.1 bits (232), Expect = 5e-21
Identities = 38/138 (27%), Positives = 57/138 (41%), Gaps = 2/138 (1%)
Query: 188 FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHG 247
F + + PY +G H+GH+ +D ARY + G +V G D G E AA + G
Sbjct: 1 FLITTALPYVNGPPHIGHLYTTIPADVYARYLRLRGYDVLFVTGTDEHGTKIELAAEKEG 60
Query: 248 IDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKEA 307
+ P+E K + F F+ T ++ + Q FL LY G +Y E
Sbjct: 61 VTPQELVDRYHEEFKELFKKFNISFDDFIR--TTSERHKELVQEFFLKLYEKGDIYEGEY 118
Query: 308 TVNWDPIDNTVLADEQVD 325
+ D L D V+
Sbjct: 119 EGWYCVSDERFLPDRYVE 136
>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 = 93.6 bits (233), Expect = 8e-21
Identities = 51/158 (32%), Positives = 74/158 (46%), Gaps = 22/158 (13%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV-FQPMGWDAFGLPAE------------N 241
P +G LH+GH T+ D + RY M G +V + P GWD GLP E
Sbjct: 32 PNATGLLHIGHALNKTLKDIVIRYKRMQGFDVLWVP-GWDHHGLPTEQKVEKKLGIKGKK 90
Query: 242 AAHQHGIDP-----REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDL 296
H+ G + REW + ++SQ + G +W+ E T DP +F+ L
Sbjct: 91 DRHKLGREKFREKCREWKMEYADEIRSQFKRLGVSGDWDREYFTLDPGLEAAVWRVFVRL 150
Query: 297 YHAGLVYRKEATVNWDPIDNTVLADEQV---DEQGISW 331
+ GL+YR + VNW P NT L++ +V D +G S
Sbjct: 151 HDKGLIYRGKKPVNWSPALNTALSEAEVEYKDVKGPSI 188
Score = 32.0 bits (73), Expect = 0.56
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 330 SWRSGARVEKRRLSQWFIRTTRLAN 354
WRSG + R QWF+R LA
Sbjct: 369 CWRSGTPIIYRATPQWFVRMKNLAE 393
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 93.1 bits (232), Expect = 1e-20
Identities = 41/138 (29%), Positives = 59/138 (42%), Gaps = 2/138 (1%)
Query: 187 NFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH 246
V + PYP+G H+GH+ Y +D ARY + G VF G D G E A +
Sbjct: 6 KILVTTALPYPNGPPHLGHLYTYLAADVYARYLRLRGYEVFFLTGTDEHGTKIELKAEKE 65
Query: 247 GIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 306
GI P+E N K + F ++ + T P++ + Q FL LY G +Y +E
Sbjct: 66 GITPQELVDKNHEEFKELFKALNISF--DNFIRTTSPEHKELVQEFFLKLYENGDIYLRE 123
Query: 307 ATVNWDPIDNTVLADEQV 324
+ L D V
Sbjct: 124 YEGLYCVSCERFLPDRYV 141
>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 = 84.9 bits (211), Expect = 1e-18
Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 2/120 (1%)
Query: 187 NFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH 246
+ + PY +G H+GH+ ++D ARY + G +V G D G E A +
Sbjct: 1 KVLITTALPYVNGVPHLGHLYGTVLADVFARYQRLRGYDVLFVTGTDEHGTKIEQKAEEE 60
Query: 247 GIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 306
G+ P+E K + F++ T P++ + Q F LY G +Y E
Sbjct: 61 GVTPQELCDKYHEIFKDLFKWLNISFDYFIR--TTSPRHKEIVQEFFKKLYENGYIYEGE 118
>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 = 84.7 bits (210), Expect = 6e-18
Identities = 36/139 (25%), Positives = 55/139 (39%), Gaps = 2/139 (1%)
Query: 188 FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHG 247
+ + PY +G H+GH ++D ARY + G V G D G E A Q G
Sbjct: 1 ILITTALPYANGKPHLGHAYTTILADVYARYKRLRGYEVLFVCGTDEHGTKIELKAEQEG 60
Query: 248 IDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKEA 307
+ P+E K + F + + T D ++ + Q +F L G +Y KE
Sbjct: 61 LTPKELVDKYHEEFKDDWKWLNISF--DRFIRTTDEEHKEIVQKIFQKLKENGYIYEKEI 118
Query: 308 TVNWDPIDNTVLADEQVDE 326
+ P L D V+
Sbjct: 119 KQLYCPECEMFLPDRYVEG 137
>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 = 80.5 bits (199), Expect = 2e-16
Identities = 49/166 (29%), Positives = 71/166 (42%), Gaps = 19/166 (11%)
Query: 182 KRREDN--FYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPA 239
K + F PY +GS+H+GH + D + RY M G NV + GWD GLP
Sbjct: 30 KLNKGKPEFIFHDGPPYANGSIHLGHALNKILKDIILRYKTMQGFNVTRKPGWDTHGLPI 89
Query: 240 ENAAHQ----HGIDP-------------REWTVGNIATMKSQLQGFGCKFNWESELATCD 282
E+ + G RE+ + I + Q Q G +WE+ T D
Sbjct: 90 EHKVEKKLGISGKKEISSLEIEEFREKCREFALKQIEEQREQFQRLGVWGDWENPYKTMD 149
Query: 283 PKYYKWTQALFLDLYHAGLVYRKEATVNWDPIDNTVLADEQVDEQG 328
P Y + LF + + GL+YR V W P T LA+ +V+ +
Sbjct: 150 PSYEESQWWLFKEAHEKGLLYRGLKPVYWSPRCRTALAEAEVEYKE 195
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 77.8 bits (193), Expect = 1e-15
Identities = 52/159 (32%), Positives = 66/159 (41%), Gaps = 39/159 (24%)
Query: 199 GSLHMGHVRVYTISDTLARYYAMNGKNV-FQPMGWDAFG----------LPAENAAHQHG 247
GSLHMGH T+ D L RY M G N + P G D G L AE G
Sbjct: 49 GSLHMGHALNNTLQDILIRYKRMQGYNTLWLP-GTDHAGIATQMVVERQLAAE------G 101
Query: 248 IDPR------------EWTV---GNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQAL 292
EW G I +QL+ G +W E T D K + +
Sbjct: 102 KSRHDLGREKFLEKVWEWKEESGGTI---TNQLRRLGASCDWSRERFTMDEGLSKAVREV 158
Query: 293 FLDLYHAGLVYRKEATVNWDPIDNTVLADEQV---DEQG 328
F+ LY GL+YR + VNWDP T L+D +V + +G
Sbjct: 159 FVRLYEKGLIYRGKRLVNWDPKLQTALSDLEVEYKEVKG 197
>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 = 75.2 bits (185), Expect = 1e-14
Identities = 41/161 (25%), Positives = 63/161 (39%), Gaps = 24/161 (14%)
Query: 185 EDNFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLP------ 238
+ F++ +PY +G +H GH R +TI + AR+ M GKNV P+G+ G P
Sbjct: 24 REKFFLTMAYPYLNGVMHAGHCRTFTIPEVSARFERMKGKNVLFPLGFHVTGTPILGLAE 83
Query: 239 ---------AENAAHQHGI---------DPREWTVGNIATMKSQLQGFGCKFNWESELAT 280
+N H I DP +S + G +W T
Sbjct: 84 LIKRRDELTIKNYTEVHAIPREELLKFTDPEYIVEYFSREAESACKSMGYSIDWRRSFKT 143
Query: 281 CDPKYYKWTQALFLDLYHAGLVYRKEATVNWDPIDNTVLAD 321
DP Y ++ + L GL+ + E V + P D + D
Sbjct: 144 TDPYYDRFIEWQMNKLKELGLIVKGEHPVRYCPKDGNPVED 184
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 74.9 bits (185), Expect = 1e-14
Identities = 41/139 (29%), Positives = 62/139 (44%), Gaps = 3/139 (2%)
Query: 187 NFYVLSMFPYPSGSLHMGHVRVYTI-SDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQ 245
+ S +PY +G LH+GH+ + +D ARY + G V G D G P E AA +
Sbjct: 4 RILITSAWPYANGPLHLGHLAGSGLPADVFARYQRLKGNEVLFVSGSDEHGTPIELAAKK 63
Query: 246 HGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRK 305
G+ P+E K + G ++ + T P +++ Q FL LY G +Y+K
Sbjct: 64 EGVTPQELADKYHEEHKEDFKKLGISYDLFTR--TTSPNHHEVVQEFFLKLYENGYIYKK 121
Query: 306 EATVNWDPIDNTVLADEQV 324
+ P D L D V
Sbjct: 122 TIEQAYCPSDGRFLPDRYV 140
>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
Length = 511
Score = 73.0 bits (180), Expect = 3e-14
Identities = 34/121 (28%), Positives = 56/121 (46%), Gaps = 4/121 (3%)
Query: 187 NFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH 246
FY+ + YP+G H+GH +D LAR+ + G +VF G D G + A +
Sbjct: 2 KFYITTPIYYPNGKPHIGHAYTTLAADVLARFKRLRGYDVFFLTGTDEHGQKIQRKAEEA 61
Query: 247 GIDPREWTVGNIATMKSQLQGFGCKF-NWESELATCDPKYYKWTQALFLDLYHAGLVYRK 305
GI P+E N A K + + ++ + T DP++ + Q +F L G +Y
Sbjct: 62 GISPQELADRNSAAFKRLWEALNISYDDF---IRTTDPRHKEAVQEIFQRLLANGDIYLG 118
Query: 306 E 306
+
Sbjct: 119 K 119
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 71.3 bits (176), Expect = 2e-13
Identities = 40/129 (31%), Positives = 54/129 (41%), Gaps = 6/129 (4%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHGIDPREWT 254
PY +G +H+GH+ Y +D RY M G V DA G P A + GI P E
Sbjct: 11 PYANGPIHLGHLVEYIQADIWVRYQRMRGHEVLFVCADDAHGTPIMLKAEKEGITPEE-L 69
Query: 255 VGNIATM-KSQLQGFGCKF-NWESELATCDPKYYKWTQALFLDLYHAGLVYRKEATVNWD 312
+ K GFG F N+ S T + + Q ++L L G +Y K +D
Sbjct: 70 IARYHAEHKRDFAGFGISFDNYGS---THSEENRELAQEIYLKLKENGYIYEKTIEQLYD 126
Query: 313 PIDNTVLAD 321
P L D
Sbjct: 127 PEKGMFLPD 135
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 71.1 bits (175), Expect = 3e-13
Identities = 45/145 (31%), Positives = 59/145 (40%), Gaps = 24/145 (16%)
Query: 201 LHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLP----AENAAHQ----------- 245
LH+GH R YTI D +ARY M G NV PM + G P AE A
Sbjct: 1 LHVGHGRTYTIGDVIARYKRMRGYNVLFPMAFHVTGTPILGIAERIARGDPETIELYKSL 60
Query: 246 HGI---------DPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDL 296
+GI DP K ++ G +W E T DP+Y K+ + F L
Sbjct: 61 YGIPEEELEKFKDPEYIVEYFSEEAKEDMKRIGYSIDWRREFTTTDPEYSKFIEWQFRKL 120
Query: 297 YHAGLVYRKEATVNWDPIDNTVLAD 321
GL+ + V + P DN + D
Sbjct: 121 KEKGLIVKGSHPVRYCPNDNNPVGD 145
>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 = 68.0 bits (167), Expect = 9e-13
Identities = 48/175 (27%), Positives = 66/175 (37%), Gaps = 41/175 (23%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH-------- 246
PY +G H GH + D + RY M G V + GWD GLP E +
Sbjct: 10 PYANGLPHYGHALNKILKDIINRYKTMQGYYVPRRPGWDCHGLPIELKVEKELGISGKKD 69
Query: 247 ----GIDP-----REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLY 297
GI RE+ + + + Q Q G +WE+ T DP+Y + +F L+
Sbjct: 70 IEKMGIAEFNAKCREFALRYVDEQEEQFQRLGVWVDWENPYKTMDPEYMESVWWVFKQLH 129
Query: 298 HAGLVYRKEATVNWDPIDNTVLADEQVDEQGISWRSGARVEKRRLSQWFIRTTRL 352
GL+YR V W I R QWFIR T++
Sbjct: 130 EKGLLYRGYKVVPWPLI------------------------YRATPQWFIRVTKI 160
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 67.2 bits (165), Expect = 4e-12
Identities = 49/160 (30%), Positives = 69/160 (43%), Gaps = 29/160 (18%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV-FQPMGWDAFGLPAENAAHQ-HGIDP-- 250
PY +G++H+GH + D + RY M G +V + P GWD GLP E + GI
Sbjct: 58 PYANGNIHIGHALNKILKDIIVRYKTMQGYDVPYVP-GWDCHGLPIELKVEKKLGIGKKD 116
Query: 251 -------------REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQA----LF 293
RE+ + + K Q + G +WE+ T DP Y + F
Sbjct: 117 IESFGVEEFREKCREFALEQVDEQKEQFKRLGVWGDWENPYKTMDPSY----EESVWWAF 172
Query: 294 LDLYHAGLVYRKEATVNWDPIDNTVLAD---EQVDEQGIS 330
+LY GL+YR V W P T LA+ E D + S
Sbjct: 173 KELYEKGLLYRGYKPVPWSPRCETALAEAEVEYGDVKDPS 212
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 66.3 bits (162), Expect = 8e-12
Identities = 39/141 (27%), Positives = 62/141 (43%), Gaps = 14/141 (9%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAE-------NAAHQHG 247
PY +G LH+GH + D + RY + GK V GWD GLP E + +
Sbjct: 41 PYANGDLHIGHALNKILKDFINRYQLLQGKKVHYVPGWDCHGLPIELKVLQSLDQEARKE 100
Query: 248 IDP-------REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAG 300
+ P ++ + T + + +G +WE+ T DP+Y +F ++ G
Sbjct: 101 LTPIKLRAKAAKFAKKTVDTQRESFKRYGVWGDWENPYLTLDPEYEAAQIEVFGQMFLNG 160
Query: 301 LVYRKEATVNWDPIDNTVLAD 321
+YR V+W P T LA+
Sbjct: 161 YIYRGRKPVHWSPSSRTALAE 181
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 65.4 bits (160), Expect = 2e-11
Identities = 44/162 (27%), Positives = 66/162 (40%), Gaps = 19/162 (11%)
Query: 182 KRREDNFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFG----- 236
F ++ P +G LH+GH I D+L RY+ M G G D G
Sbjct: 56 LNSGKKFVIVLPPPNVTGYLHIGHALTGAIQDSLIRYHRMKGDETLWVPGTDHAGIATQV 115
Query: 237 -----LPAENAAHQHGIDPRE--------WTVGNIATMKSQLQGFGCKFNWESELATCDP 283
L E +H + RE W + + +QL+ G +W E+ T D
Sbjct: 116 VVEKKLMKEENKTRHDLG-REEFLKKVWEWKDKHGNNICNQLRRLGSSLDWSREVFTMDE 174
Query: 284 KYYKWTQALFLDLYHAGLVYRKEATVNWDPIDNTVLADEQVD 325
+ K + F+ LY GL+YR VNW T ++D +V+
Sbjct: 175 QRSKAVKEAFVRLYEDGLIYRDTRLVNWCCYLKTAISDIEVE 216
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 63.6 bits (156), Expect = 6e-11
Identities = 38/146 (26%), Positives = 57/146 (39%), Gaps = 21/146 (14%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH-------- 246
P +G H GH+ TI D + RY M G V + GWD GLP E +
Sbjct: 50 PTANGLPHYGHLLTRTIKDVVPRYKTMKGYKVERRAGWDTHGLPVELEVEKELGISGKKD 109
Query: 247 ----GIDP-----REWTVGNIATMKSQLQGFGCKFNWESELATCDPKY--YKWTQALFLD 295
GI+ RE + + + G ++++ T D +Y W
Sbjct: 110 IEEYGIEKFNEKCRESVLRYTDEWEEYTERLGRWVDFDNPYKTLDNEYMESVW--WALKQ 167
Query: 296 LYHAGLVYRKEATVNWDPIDNTVLAD 321
LY GL+Y+ V + P T L++
Sbjct: 168 LYDKGLLYKGYRVVPYCPRCETPLSN 193
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 63.5 bits (154), Expect = 6e-11
Identities = 39/150 (26%), Positives = 66/150 (44%), Gaps = 17/150 (11%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAE------------NA 242
P +GSLH+GH T+ D L R+ M+G N G D G+ + +
Sbjct: 57 PNVTGSLHLGHALTATLQDVLIRWKRMSGFNTLWLPGTDHAGIATQMIVEKELKKTEKKS 116
Query: 243 AHQHGIDP-----REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLY 297
H G + W + + Q + G +W+ E T D + + +F+ L+
Sbjct: 117 RHDLGREAFLERVWAWKEQYGSRIGEQHKALGASLDWQRERFTMDEGLSRAVREVFVRLH 176
Query: 298 HAGLVYRKEATVNWDPIDNTVLADEQVDEQ 327
GL+YR++ +NW P T L+D +V+ +
Sbjct: 177 EEGLIYREKKLINWCPDCRTALSDLEVEHE 206
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 63.4 bits (154), Expect = 6e-11
Identities = 45/155 (29%), Positives = 66/155 (42%), Gaps = 19/155 (12%)
Query: 189 YVLSMFPYP--SGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFG----LPAENA 242
+V+ M P P +GSLHMGH T+ D + RY M G+ G D G L E
Sbjct: 90 FVIPM-PPPNVTGSLHMGHAMFVTLEDIMVRYNRMKGRPTLWIPGTDHAGIATQLVVEKM 148
Query: 243 AHQHGIDPR------------EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQ 290
GI EW T+ +Q++ G +W E T D + +
Sbjct: 149 LASEGIKRTDLGRDEFTKRVWEWKEKYGGTITNQIKRLGASCDWSRERFTLDEQLSRAVV 208
Query: 291 ALFLDLYHAGLVYRKEATVNWDPIDNTVLADEQVD 325
F+ L+ GL+Y+ VNW P T ++D +V+
Sbjct: 209 EAFVRLHEKGLIYQGSYMVNWSPNLQTAVSDLEVE 243
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 63.0 bits (153), Expect = 9e-11
Identities = 48/153 (31%), Positives = 67/153 (43%), Gaps = 21/153 (13%)
Query: 193 MFPYP--SGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFG----------LPAE 240
+ P P +G+LH+GH I DT+ R+ M+G N G D G L E
Sbjct: 133 VLPPPNVTGALHIGHALTAAIEDTIIRWKRMSGYNALWVPGVDHAGIATQVVVEKKLMRE 192
Query: 241 NAAHQHGIDPREWTVGNI--------ATMKSQLQGFGCKFNWESELATCDPKYYKWTQAL 292
+H I RE V + T+ +QL+ G +W E T D + K
Sbjct: 193 RHLTRHDIG-REEFVSEVWKWKDEYGGTILNQLRRLGASLDWSRECFTMDEQRSKAVTEA 251
Query: 293 FLDLYHAGLVYRKEATVNWDPIDNTVLADEQVD 325
F+ LY GL+YR VNWD T ++D +VD
Sbjct: 252 FVRLYKEGLIYRDIRLVNWDCTLRTAISDVEVD 284
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 60.6 bits (148), Expect = 5e-10
Identities = 40/127 (31%), Positives = 59/127 (46%), Gaps = 12/127 (9%)
Query: 185 EDNFYVLSMFPYPSGSLHMGHVRVYT--ISDTLARYYAMNGKNVFQPMGWDAFGLPAENA 242
+ FY+ + YP+G H+GH YT +D LARY + G +VF G D G + A
Sbjct: 3 KKTFYITTPIYYPNGKPHIGHA--YTTIAADALARYKRLQGYDVFFLTGTDEHGQKIQQA 60
Query: 243 AHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESELATCDPKYYKWTQALFLDLYHA 299
A + G P+E+ A K + KF + T D ++ K Q +F LY
Sbjct: 61 AEKAGKTPQEYVDEISAGFKELWKKLDISYDKF-----IRTTDERHKKVVQKIFEKLYEQ 115
Query: 300 GLVYRKE 306
G +Y+ E
Sbjct: 116 GDIYKGE 122
>gnl|CDD|215477 PLN02882, PLN02882, aminoacyl-tRNA ligase.
Length = 1159
Score = 51.3 bits (123), Expect = 6e-07
Identities = 38/127 (29%), Positives = 58/127 (45%), Gaps = 17/127 (13%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH-------- 246
P+ +G H GH+ TI D + RY +M G +V + GWD GLP E +
Sbjct: 47 PFATGLPHYGHILAGTIKDIVTRYQSMTGHHVTRRFGWDCHGLPVEYEIDKKLGIKRRDD 106
Query: 247 ----GIDPREWTVGNIATMKSQ-----LQGFGCKFNWESELATCDPKYYKWTQALFLDLY 297
GID +I T S+ + G ++E++ T DPK+ + +F L+
Sbjct: 107 VLKMGIDKYNEECRSIVTRYSKEWEKTVTRTGRWIDFENDYKTMDPKFMESVWWVFKQLF 166
Query: 298 HAGLVYR 304
GLVY+
Sbjct: 167 EKGLVYK 173
>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
Length = 961
Score = 48.0 bits (115), Expect = 5e-06
Identities = 40/168 (23%), Positives = 64/168 (38%), Gaps = 23/168 (13%)
Query: 179 LEGKRREDN----FYVL-SMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNV-FQPMGW 232
L K RE +VL PY +G++H+GH + D + R M G + + P GW
Sbjct: 42 LYKKLREQAKGRPKFVLHDGPPYANGNIHIGHALNKILKDVIVRSKQMLGFDANYVP-GW 100
Query: 233 DAFGLPAENAAHQHGIDP----------------REWTVGNIATMKSQLQGFGCKFNWES 276
D GLP E + RE+ + I + + + G +W++
Sbjct: 101 DCHGLPIEWKIEEKYRAKGKNKDEVPVAEFRKECREYALSWIDVQREEFKRLGVLGDWDN 160
Query: 277 ELATCDPKYYKWTQALFLDLYHAGLVYRKEATVNWDPIDNTVLADEQV 324
T D F G +YR V W ++ T LA+ ++
Sbjct: 161 PYTTMDFHAEARIAREFGKFAAKGQLYRGSKPVMWSVVERTALAEAEI 208
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 45.5 bits (109), Expect = 3e-05
Identities = 34/146 (23%), Positives = 59/146 (40%), Gaps = 25/146 (17%)
Query: 195 PYPSGSLHMGHVRVYTIS-DTLARYYAMNGKNV-FQPMGWDAFGLPAENAAHQ------H 246
PY +G +H+GH + I D + + M+G + + P GWD GLP E +
Sbjct: 58 PYANGDIHIGHA-LNKILKDIIVKSKTMSGFDAPYVP-GWDCHGLPIELKVEKKLGKKGK 115
Query: 247 GIDP-------REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQA----LFLD 295
+ RE+ + + + + G +W++ T D KY +A
Sbjct: 116 KLSAAEFRKKCREYALEQVDIQREDFKRLGVLGDWDNPYLTMDFKY----EANIIRALGK 171
Query: 296 LYHAGLVYRKEATVNWDPIDNTVLAD 321
+ G +Y+ V W P + LA+
Sbjct: 172 MAKKGYLYKGLKPVYWCPDCGSALAE 197
>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
Length = 1205
Score = 41.9 bits (98), Expect = 4e-04
Identities = 31/127 (24%), Positives = 51/127 (40%), Gaps = 17/127 (13%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQH-------- 246
P+ +G H GH+ I D + RY+ G +V + GWD GLP E +
Sbjct: 111 PFATGLPHYGHLLAGIIKDCVTRYFYQCGFSVERKFGWDCHGLPIEYEIEKENNINKKED 170
Query: 247 ----GIDPREWTVGNIATMKSQ-----LQGFGCKFNWESELATCDPKYYKWTQALFLDLY 297
GID I S ++ G +++++ T D + + +F +LY
Sbjct: 171 ILKMGIDVYNEKCRGIVLKYSNEWVKTVERIGRWIDFKNDYKTMDKTFMESVWWVFSELY 230
Query: 298 HAGLVYR 304
VY+
Sbjct: 231 KNNYVYK 237
>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 = 37.8 bits (88), Expect = 0.002
Identities = 19/71 (26%), Positives = 31/71 (43%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQHGIDPREWT 254
P+G LH+GH+R D LA+ Y G V D G + A++ G + + +
Sbjct: 6 ITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANKKGENAKAFV 65
Query: 255 VGNIATMKSQL 265
I +K +
Sbjct: 66 ERWIERIKEDV 76
>gnl|CDD|239832 cd04366, IlGF_insulin_bombyxin_like, IlGF_like family,
insulin_bombyxin_like subgroup. Members include a number
of peptides including insulin, insulin-like growth
factors I and II, insect prothoracicotropic hormone
(bombyxin), locust insulin-related peptide (LIRP),
molluscan insulin-related peptides 1 to 5 (MIP), and C.
elegans insulin-like peptides. With the exception of
insulin-like growth factors, the active forms of these
peptide hormones are composed of two chains (A and B)
linked by two disulfide bonds; the arrangement of four
cysteines is conserved in the "A" chain: Cys1 is linked
by a disulfide bond to Cys3, Cys2 and Cys4 are linked by
interchain disulfide bonds to cysteines in the "B"
chain. This alignment contains both chains, plus the
intervening linker region, arranged as found in the
propeptide form. Propeptides are cleaved to yield two
separate chains linked covalently by the two disulfide
bonds.
Length = 42
Score = 33.8 bits (78), Expect = 0.008
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 142 CGESLNQVLKLVCDGVYRRRRSI 164
CG L L L+C RR I
Sbjct: 2 CGRHLADTLALLCSEYNSPRRGI 24
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 37.4 bits (87), Expect = 0.012
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 194 FPYP--SGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAA 243
FPYP +G LH+GH + + A Y+ + G NV P + G+P + +A
Sbjct: 51 FPYPYMNGLLHLGHAFSLSKLEFAAAYHRLRGANVLLPFAFHCTGMPIKASA 102
>gnl|CDD|185675 cd00671, ArgRS_core, catalytic core domain of arginyl-tRNA
synthetases. Arginyl tRNA synthetase (ArgRS) 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. There
are at least three subgroups of ArgRS. One type contains
both characteristic class I HIGH and KMSKS motifs, which
are involved in ATP binding. The second subtype lacks
the KMSKS motif; however, it has a lysine N-terminal to
the HIGH motif, which serves as the functional
counterpart to the second lysine of the KMSKS motif. A
third group, which is found primarily in archaea and a
few bacteria, lacks both the KMSKS motif and the HIGH
loop lysine.
Length = 212
Score = 34.5 bits (80), Expect = 0.059
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV 226
P+G LH+GH+R I D+LAR G +V
Sbjct: 9 ANPTGPLHVGHLRNAIIGDSLARILEFLGYDV 40
>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori [Protein synthesis, tRNA
aminoacylation].
Length = 566
Score = 35.0 bits (81), Expect = 0.066
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV 226
P+G LH+GH+R I D+LAR G +V
Sbjct: 121 ANPAGPLHIGHLRNAIIGDSLARILEFLGYDV 152
>gnl|CDD|185682 cd09287, GluRS_non_core, catalytic core domain of
non-discriminating glutamyl-tRNA synthetase.
Non-discriminating Glutamyl-tRNA synthetase (GluRS)
cataytic core domain. These enzymes attach Glu to the
appropriate tRNA. Like other class I tRNA synthetases,
they aminoacylate the 2'-OH of the nucleotide at the 3'
end of the 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. These enzymes function as
monomers. Archaea and most bacteria lack GlnRS. In these
organisms, the "non-discriminating" form of GluRS
aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu,
which is converted to Gln when appropriate by a
transamidation enzyme.
Length = 240
Score = 33.9 bits (78), Expect = 0.11
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 190 VLSMFPYPSGSLHMGHVRVYTISDTLARYY 219
V+ P P+G LH+GH R ++ A+ Y
Sbjct: 3 VMRFAPNPNGPLHLGHARAAILNGEYAKMY 32
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 34.3 bits (78), Expect = 0.11
Identities = 27/121 (22%), Positives = 51/121 (42%), Gaps = 2/121 (1%)
Query: 186 DNFYVLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQ 245
D F + + Y + HMG +D++AR+ + GK V G D G +A
Sbjct: 69 DTFVLTTPLYYVNAPPHMGSAYTTIAADSIARFQRLLGKKVIFITGTDEHGEKIATSAAA 128
Query: 246 HGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRK 305
+G +P E +I + + ++ + T DPK+ + + ++ G +YR
Sbjct: 129 NGRNPPEHC--DIISQSYRTLWKDLDIAYDKFIRTTDPKHEAIVKEFYARVFANGDIYRA 186
Query: 306 E 306
+
Sbjct: 187 D 187
>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
Length = 801
Score = 34.4 bits (79), Expect = 0.12
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 179 LEGKRREDNFYVLSMFPYPSGSLHMGHVRVYTIS-DTLARYYAMNGKNVFQPMGWDAFGL 237
+ GKR N + S PY + H+G++ +S D ARY + G N G D +G
Sbjct: 13 IPGKR---NILITSALPYVNNVPHLGNIIGCVLSADVFARYCRLRGYNAIYICGTDEYGT 69
Query: 238 PAENAAHQHGIDPRE 252
E A + P+E
Sbjct: 70 ATETKALEENCTPKE 84
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 33.0 bits (76), Expect = 0.23
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV 226
P+G LH+GH+R I D+LAR G +V
Sbjct: 126 ANPTGPLHIGHLRNAIIGDSLARILEFLGYDV 157
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 33.0 bits (75), Expect = 0.24
Identities = 19/80 (23%), Positives = 27/80 (33%), Gaps = 22/80 (27%)
Query: 159 RRRRSISSPSDFGVSSVGGTLEG----------KRREDNF----------YVLSMFPYPS 198
R+ S ++S G R+++ F YV + Y
Sbjct: 34 ERQYRSCFFSASALASNGAPASRGRELHLYNTMSRKKELFKPKVEGKVGMYVCGVTAYDL 93
Query: 199 GSLHMGHVRVYTISDTLARY 218
H+GH RVY D L RY
Sbjct: 94 S--HIGHARVYVTFDVLYRY 111
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 31.7 bits (73), Expect = 0.62
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 190 VLSMFPYPSGSLHMGHVRVYTISDTLARYYAMNGK 224
V+ P PSG LH+GH R ++D A+ Y GK
Sbjct: 103 VMRFAPNPSGPLHLGHARAAILNDEYAKMY--GGK 135
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 31.3 bits (72), Expect = 0.78
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 197 PSGSLHMGHVRVYTISDTLARYYAMNGKNV 226
P+G LH+GH+R I D LAR G +V
Sbjct: 122 PTGPLHVGHLRSAVIGDALARILEFAGYDV 151
>gnl|CDD|216097 pfam00750, tRNA-synt_1d, tRNA synthetases class I (R). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only arginyl tRNA
synthetase.
Length = 345
Score = 30.5 bits (69), Expect = 1.3
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGKNV 226
P P+ +H+GH+R I D L+R G +V
Sbjct: 28 PNPAKPIHVGHLRSTIIGDALSRLLEFLGYDV 59
>gnl|CDD|232985 TIGR00463, gltX_arch, glutamyl-tRNA synthetase, archaeal and
eukaryotic family. The glutamyl-tRNA synthetases of the
eukaryotic cytosol and of the Archaea are more similar
to glutaminyl-tRNA synthetases than to bacterial
glutamyl-tRNA synthetases. This model models just the
eukaryotic cytosolic and archaeal forms of the enzyme.
In some eukaryotes, the glutamyl-tRNA synthetase is part
of a longer, multifunctional aminoacyl-tRNA ligase. In
many species, the charging of tRNA(gln) proceeds first
through misacylation with Glu and then transamidation.
For this reason, glutamyl-tRNA synthetases, including
all known archaeal enzymes (as of 2010) may act on both
tRNA(gln) and tRNA(glu) [Protein synthesis, tRNA
aminoacylation].
Length = 556
Score = 30.6 bits (69), Expect = 1.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 190 VLSMFPYPSGSLHMGHVRVYTISDTLARYY 219
V+ P PSG LH+GH R ++ A+ Y
Sbjct: 95 VMRFAPNPSGPLHIGHARAAILNHEYAKKY 124
>gnl|CDD|185672 cd00418, GlxRS_core, catalytic core domain of glutamyl-tRNA and
glutaminyl-tRNA synthetase. Glutamyl-tRNA
synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS)
cataytic core domain. These enzymes attach Glu or Gln,
respectively, to the appropriate tRNA. Like other class
I tRNA synthetases, they aminoacylate the 2'-OH of the
nucleotide at the 3' end of the 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. These enzymes function as monomers. Archaea,
cellular organelles, and some bacteria lack GlnRS. In
these cases, the "non-discriminating" form of GluRS
aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu,
which is converted to Gln when appropriate by a
transamidation enzyme. The discriminating form of GluRS
differs from GlnRS and the non-discriminating form of
GluRS in their C-terminal anti-codon binding domains.
Length = 230
Score = 29.7 bits (67), Expect = 2.0
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYY 219
P P+G LH+GH R + AR Y
Sbjct: 8 PSPTGYLHIGHARTALFNFAFARKY 32
>gnl|CDD|219864 pfam08491, SE, Squalene epoxidase. This domain is found in
squalene epoxidase (SE) and related proteins which are
found in taxonomically diverse groups of eukaryotes and
also in bacteria. SE was first cloned from Saccharomyces
cerevisiae where it was named ERG1. It contains a
putative FAD binding site and is a key enzyme in the
sterol biosynthetic pathway. Putative transmembrane
regions are found to the protein's C-terminus.
Length = 276
Score = 30.0 bits (68), Expect = 2.0
Identities = 22/87 (25%), Positives = 32/87 (36%), Gaps = 23/87 (26%)
Query: 150 LKLVCDGVYRR-RRSISSPSDFGVSSVGGTLEGKRREDNFYVLSMFPYPSGSLHMGHV-- 206
L +VCDG + + R+S+S VG G +L P+ + GHV
Sbjct: 4 LTIVCDGCFSKFRKSLSDN----KVEVGSYFVG-------LILKNADLPAP--NHGHVIL 50
Query: 207 ------RVYTISDTLAR-YYAMNGKNV 226
+Y IS T R G +
Sbjct: 51 GKPSPILLYQISSTETRILCDYPGPKL 77
>gnl|CDD|178772 PLN03233, PLN03233, putative glutamate-tRNA ligase; Provisional.
Length = 523
Score = 30.0 bits (67), Expect = 2.1
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYY 219
P PSG LH+GH + ++D AR Y
Sbjct: 18 PEPSGYLHIGHAKAALLNDYYARRY 42
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 29.9 bits (68), Expect = 2.2
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 9/30 (30%)
Query: 202 HMGHVRVYTISDTLARY---------YAMN 222
H+GH R Y + D L RY Y N
Sbjct: 37 HIGHARTYVVFDVLRRYLRYLGYKVTYVRN 66
>gnl|CDD|233707 TIGR02071, PBP_1b, penicillin-binding protein 1B. Bacterial that
synthesize a cell wall of peptidoglycan (murein)
generally have several transglycosylases and
transpeptidases for the task. This family consists of a
particular bifunctional transglycosylase/transpeptidase
in E. coli and other Proteobacteria, designated
penicillin-binding protein 1B [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 730
Score = 30.1 bits (68), Expect = 2.4
Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 10/89 (11%)
Query: 139 KPVCGESLNQVLKLVCDGVYRRRRSISSPSDFGVSSVGGTLEGKRREDNFYVLSMFPYPS 198
+P S ++L + YR+ ++ P ++ V + ++E RR F +P
Sbjct: 48 EPGMSLSKKELLIELDATQYRQVSHVTLPGEYSVQN--NSIEVIRRP--------FDFPD 97
Query: 199 GSLHMGHVRVYTISDTLARYYAMNGKNVF 227
G+ R+ + L++ ++ F
Sbjct: 98 GAEPQRRARLTFNGNQLSKIENLDNNKEF 126
>gnl|CDD|149094 pfam07836, DmpG_comm, DmpG-like communication domain. This domain
is found towards the C-terminal region of various
aldolase enzymes. It consists of five alpha-helices,
four of which form an antiparallel helical bundle that
plugs the C-terminus of the N-terminal TIM barrel
domain. The communication domain is thought to play an
important role in the heterodimerisation of the enzyme.
Length = 66
Score = 27.1 bits (61), Expect = 2.5
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 235 FGLPAENAAHQHGIDPRE 252
F L AE AA ++G+DPR+
Sbjct: 21 FLLHAERAAERYGVDPRD 38
>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 = 29.1 bits (66), Expect = 2.9
Identities = 12/37 (32%), Positives = 14/37 (37%), Gaps = 9/37 (24%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARY---------YAMN 222
P H+GH R Y + D L RY Y N
Sbjct: 28 PTVYDYAHIGHARTYVVFDVLRRYLEDLGYKVRYVQN 64
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 29.2 bits (66), Expect = 4.1
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 4/32 (12%)
Query: 77 SIW----LPEDTIEDVAKSQGQYITVKSSHIL 104
S+W LP D+++ +A+++G Y+ V S L
Sbjct: 718 SLWSRGILPIDSLKLLAEARGGYLEVDRSSTL 749
>gnl|CDD|99810 cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding
domain of ferredoxin reductase like phenylacetic acid
(PA) degradation oxidoreductase. PA oxidoreductases of
E. coli hydroxylate PA-CoA in the second step of PA
degradation. Members of this group typically fuse a
ferredoxin reductase-like domain with an iron-sulfur
binding cluster domain. Ferredoxins catalyze electron
transfer between an NAD(P)-binding domain of the
alpha/beta class and a discrete (usually N-terminal)
domain which vary in orientation with respect to the
NAD(P) binding domain. The N-terminal portion may
contain a flavin prosthetic group, as in flavoenzymes,
or use flavin as a substrate. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD
as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria and participate in a wide
variety of redox metabolic pathways. The C-terminal
domain contains most of the NADP(H) binding residues
and the N-terminal domain interacts non-covalently with
the isoalloxazine rings of the flavin molecule which
lies largely in a large gap betweed the two domains.
Ferredoxin-NADP+ reductase first accepts one electron
from reduced ferredoxin to form a flavin semiquinone
intermediate. The enzyme then accepts a second electron
to form FADH2 which then transfers two electrons and a
proton to NADP+ to form NADPH.
Length = 241
Score = 28.3 bits (64), Expect = 5.9
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 72 TADTLSIWL--PEDTIEDVAKSQGQYITVK 99
TAD +SI PE+ + GQ++T++
Sbjct: 13 TADAVSITFDVPEELRDAFRYRPGQFLTLR 42
>gnl|CDD|131944 TIGR02898, spore_YhcN_YlaJ, sporulation lipoprotein, YhcN/YlaJ
family. YhcN and YlaJ are predicted lipoproteins that
have been detected as spore proteins but not vegetative
proteins in Bacillus subtilis. Both appear to be
expressed under control of the RNA polymerase sigma-G
factor. The YlaJ-like members of this family have a
low-complexity, strongly acidic 40-residue C-terminal
domain that is not included in the seed alignment for
this model. A portion of the low-complexity region
between the lipoprotein signal sequence and the main
conserved region of the protein family was also excised
from the seed alignment [Cellular processes, Sporulation
and germination].
Length = 158
Score = 27.7 bits (62), Expect = 6.2
Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 24/109 (22%)
Query: 49 EPNGVRFEFQILPQPEGTSNSAPTADTLSIWLPEDTIEDVAKSQGQYITVKSSHILAS-- 106
N V + G + + T D + ++ + AK +G VK + ++ +
Sbjct: 24 PNNNVGETNVMSKNNNGMNTTNDTNDGDLYDVADEIASEAAKVKG----VKDATVVITGN 79
Query: 107 ----------KTKEKLTENVKHQIENKYKSI--------VSSDPMLRDR 137
+ +T+ +K ++ KS VS+DP +R
Sbjct: 80 YAYVGVDLTNGLEGSVTDELKEKVAETVKSTDNRIANVYVSADPDTVER 128
>gnl|CDD|187583 cd05322, SDH_SDR_c_like, Sorbitol 6-phosphate dehydrogenase (SDH),
classical (c) SDRs. Sorbitol 6-phosphate dehydrogenase
(SDH, aka glucitol 6-phosphate dehydrogenase) catalyzes
the NAD-dependent interconversion of D-fructose
6-phosphate to D-sorbitol 6-phosphate. SDH is a member
of the classical SDRs, with the characteristic catalytic
tetrad, but without a complete match to the typical
NAD-binding motif. 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, 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 = 257
Score = 28.2 bits (63), Expect = 6.2
Identities = 8/48 (16%), Positives = 17/48 (35%)
Query: 80 LPEDTIEDVAKSQGQYITVKSSHILASKTKEKLTENVKHQIENKYKSI 127
+ + E VA K+ A T E+ + ++ +K +
Sbjct: 34 INSENAEKVADEINAEYGEKAYGFGADATNEQSVIALSKGVDEIFKRV 81
>gnl|CDD|216482 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
domain. This family includes only cysteinyl tRNA
synthetases.
Length = 301
Score = 28.1 bits (63), Expect = 7.3
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 201 LHMGHVRVYTISDTLARYYAMNGKNV 226
H+GH R D L RY G +V
Sbjct: 23 SHIGHARSAVAFDVLRRYLQALGYDV 48
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 28.1 bits (63), Expect = 8.8
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGK 224
P P+G LH+GH R ++ AR Y GK
Sbjct: 16 PSPTGYLHIGHARTALLNYLYARKY--GGK 43
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 27.9 bits (63), Expect = 9.5
Identities = 31/121 (25%), Positives = 46/121 (38%), Gaps = 23/121 (19%)
Query: 144 ESLNQVLKLVCDG-VYRRRRSISSPSDFGVSSVGGTLEGKRREDNFYVLSMFPYPSGSLH 202
E +VL + + RR I D+ LE R F V + F PSG +H
Sbjct: 27 EPFTEVLPELPEPHPLMRRGIIFGHRDYDK-----ILEAYRNGKPFAVYTGF-MPSGPMH 80
Query: 203 MGHVRVYTISDTLARYYAMNGKNVFQPMGWDAFGLPAENAAHQ-HGIDP---REWTVGNI 258
+GH V+ D L + Q G + + A++ A+ G+ REW I
Sbjct: 81 IGHKMVF---DELKWH---------QEFGANVYIPIADDEAYAARGLSWEETREWAYEYI 128
Query: 259 A 259
Sbjct: 129 L 129
>gnl|CDD|216096 pfam00749, tRNA-synt_1c, tRNA synthetases class I (E and Q),
catalytic domain. Other tRNA synthetase sub-families
are too dissimilar to be included. This family includes
only glutamyl and glutaminyl tRNA synthetases. In some
organisms, a single glutamyl-tRNA synthetase
aminoacylates both tRNA(Glu) and tRNA(Gln).
Length = 314
Score = 27.7 bits (62), Expect = 10.0
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 195 PYPSGSLHMGHVRVYTISDTLARYYAMNGK 224
P P+G LH+GH R + A+ Y NGK
Sbjct: 8 PSPTGYLHIGHARTALFNYLFAKNY--NGK 35
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
0.316 0.132 0.403
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: 18,453,602
Number of extensions: 1744486
Number of successful extensions: 1483
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1444
Number of HSP's successfully gapped: 85
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
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 (21.6 bits)
S2: 60 (26.8 bits)