RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6621
(133 letters)
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 164 bits (417), Expect = 4e-48
Identities = 52/82 (63%), Positives = 59/82 (71%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V PMGWDAFGLPAENAA + G P EWT NIA MK QL+ G ++W E+ATCDP+Y
Sbjct: 72 VLHPMGWDAFGLPAENAAIKTGTHPAEWTYENIANMKKQLKSLGFSYDWSREIATCDPEY 131
Query: 100 YKWTQALFLDLYHAGLVYRKEV 121
YKWTQ +FL LY GL YRKE
Sbjct: 132 YKWTQWIFLKLYEKGLAYRKES 153
>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 = 141 bits (357), Expect = 4e-40
Identities = 51/83 (61%), Positives = 62/83 (74%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V P+GWDAFGLPAENAA + GI P +WT NIA MK QLQ G ++W+ E+ATCDP+Y
Sbjct: 69 VLHPIGWDAFGLPAENAAIKRGIHPAKWTYENIANMKKQLQALGFSYDWDREIATCDPEY 128
Query: 100 YKWTQALFLDLYHAGLVYRKEVD 122
YKWTQ +FL+L+ GL Y KE D
Sbjct: 129 YKWTQWIFLELFEKGLAYVKEAD 151
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 136 bits (345), Expect = 2e-38
Identities = 53/93 (56%), Positives = 60/93 (64%), Gaps = 2/93 (2%)
Query: 39 RVFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPK 98
V PMGWDAFGLPAENAA + G DP +WT NIA MK QL+ G +W E ATCDP+
Sbjct: 73 NVLHPMGWDAFGLPAENAAIKIGTDPAKWTYYNIAYMKKQLKSLGFSIDWRREFATCDPE 132
Query: 99 YYKWTQALFLDLYHAGLVYRKE--VDYSQNLPT 129
YYKW Q FL LY GL YRKE V++ T
Sbjct: 133 YYKWIQWQFLKLYEKGLAYRKEAPVNWCPVDGT 165
>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 = 130 bits (330), Expect = 3e-38
Identities = 49/87 (56%), Positives = 60/87 (68%), Gaps = 2/87 (2%)
Query: 39 RVFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPK 98
V PMG+DAFGLPAENAA + G DP +WT NI MK QL+ G ++W E TCDP+
Sbjct: 39 NVLFPMGFDAFGLPAENAAIKIGRDPEDWTEYNIKKMKEQLKRMGFSYDWRREFTTCDPE 98
Query: 99 YYKWTQALFLDLYHAGLVYRKE--VDY 123
YYK+TQ LFL LY GL Y+KE V++
Sbjct: 99 YYKFTQWLFLKLYEKGLAYKKEAPVNW 125
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 113 bits (285), Expect = 3e-30
Identities = 42/82 (51%), Positives = 56/82 (68%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V PMGWDAFGLPAE A + G P+ T+ NIA +SQL+ G ++W+ E++T +P+Y
Sbjct: 151 VLHPMGWDAFGLPAEQYAIETGTHPKITTLKNIARFRSQLKSLGFSYDWDREISTTEPEY 210
Query: 100 YKWTQALFLDLYHAGLVYRKEV 121
YKWTQ +FL L GL Y+ EV
Sbjct: 211 YKWTQWIFLQLLKRGLAYQAEV 232
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 77.2 bits (191), Expect = 1e-17
Identities = 33/97 (34%), Positives = 42/97 (43%), Gaps = 19/97 (19%)
Query: 40 VFQPMGWDAFGLP----AENAAHQHGI--DP----------REWTVGNIATMKSQLQGFG 83
VF P GWD GLP E +GI D RE T + + + G
Sbjct: 78 VFFPQGWDDNGLPTERKVEK---YYGIRKDDISREEFIELCRELTDEDEKKFRELWRRLG 134
Query: 84 CKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
+W E T P+Y + +Q FLDLY GL+YR E
Sbjct: 135 LSVDWSLEYQTISPEYRRISQKSFLDLYKKGLIYRAE 171
>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 = 66.5 bits (163), Expect = 7e-14
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 16/95 (16%)
Query: 40 VFQPMGWDAFGLPAEN---------AAHQHGIDPR-------EWTVGNIATMKSQLQGFG 83
V P G D G+ + +H + EW + ++ QL+ G
Sbjct: 41 VLWPPGTDHAGIATQVVVEKKLGIEGKTRHDLGREEFLEKCWEWKEESGGKIREQLKRLG 100
Query: 84 CKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 118
+W E T DP + Q F+ LY GL+YR
Sbjct: 101 ASVDWSREYFTMDPGLSRAVQEAFVRLYEKGLIYR 135
>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 = 64.7 bits (158), Expect = 2e-13
Identities = 28/95 (29%), Positives = 39/95 (41%), Gaps = 13/95 (13%)
Query: 39 RVFQPMGWDAFGLPAENAAHQHGI-------------DPREWTVGNIATMKSQLQGFGCK 85
V GWD GLP E A + G DP+E+ K + G
Sbjct: 39 EVPFLPGWDTHGLPIELKAERKGGRKKKTIWIEEFREDPKEFVEEMSGEHKEDFRRLGIS 98
Query: 86 FNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
++W E T +P+Y K + +F LY GL+YR
Sbjct: 99 YDWSDEYITTEPEYSKAVELIFSRLYEKGLIYRGT 133
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 65.3 bits (160), Expect = 2e-13
Identities = 27/97 (27%), Positives = 38/97 (39%), Gaps = 16/97 (16%)
Query: 40 VFQPMGWDAFGLPAENA-----------AHQHGIDP-----REWTVGNIATMKSQLQGFG 83
V P G D G+ + H G + EW + T++ QL+ G
Sbjct: 73 VLWPPGTDHAGIATQVVVEKQLAAEGITRHDLGREEFLKKCWEWKEESGGTIREQLRRLG 132
Query: 84 CKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
+W E T DP + Q F+ LY GL+YR E
Sbjct: 133 VSVDWSRERFTMDPGLSRAVQEAFVRLYEKGLIYRGE 169
>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 = 58.1 bits (141), Expect = 6e-11
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 17/96 (17%)
Query: 41 FQPMGWDAFGLPAENAAH-QHGID-------PRE--------WTVGNIATMKSQLQGFGC 84
+ P G D G+ + + G + RE W + T+K+Q++ G
Sbjct: 75 WLP-GTDHAGIATQVKVEKKLGAEGKTKHDLGREEFREKIWEWKEESGGTIKNQIKRLGA 133
Query: 85 KFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
+W E T D K + F+ LY GL+YR E
Sbjct: 134 SLDWSRERFTMDEGLSKAVKEAFVRLYEKGLIYRGE 169
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 44.2 bits (105), Expect = 4e-06
Identities = 27/96 (28%), Positives = 38/96 (39%), Gaps = 10/96 (10%)
Query: 25 CRLAGINSIIKGPVRVFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC 84
RL G VF G D G E A + GI P+E N K +
Sbjct: 38 LRLRGYE--------VFFLTGTDEHGTKIELKAEKEGITPQELVDKNHEEFKELFKALNI 89
Query: 85 KFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
F ++ + T P++ + Q FL LY G +Y +E
Sbjct: 90 SF--DNFIRTTSPEHKELVQEFFLKLYENGDIYLRE 123
>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 = 43.3 bits (103), Expect = 7e-06
Identities = 23/97 (23%), Positives = 34/97 (35%), Gaps = 10/97 (10%)
Query: 25 CRLAGINSIIKGPVRVFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC 84
RL G + V G D G E A + G+ P+E K +
Sbjct: 33 QRLRGYD--------VLFVTGTDEHGTKIEQKAEEEGVTPQELCDKYHEIFKDLFKWLNI 84
Query: 85 KFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKEV 121
F++ T P++ + Q F LY G +Y E
Sbjct: 85 SFDYFIR--TTSPRHKEIVQEFFKKLYENGYIYEGEY 119
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 39.9 bits (94), Expect = 1e-04
Identities = 22/82 (26%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 44 MGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWT 103
G D G E AA + G+ P+E K + F F+ T ++ +
Sbjct: 43 TGTDEHGTKIELAAEKEGVTPQELVDRYHEEFKELFKKFNISFDDFIR--TTSERHKELV 100
Query: 104 QALFLDLYHAGLVYRKEVDYSQ 125
Q FL LY G +Y E Y
Sbjct: 101 QEFFLKLYEKGDIYEGE--YEG 120
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 8/93 (8%)
Query: 45 GWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQ 104
G D G E A Q G+ P+E K + F + + T D ++ + Q
Sbjct: 44 GTDEHGTKIELKAEQEGLTPKELVDKYHEEFKDDWKWLNISF--DRFIRTTDEEHKEIVQ 101
Query: 105 ALFLDLYHAGLVYRKE------VDYSQNLPTKF 131
+F L G +Y KE + LP ++
Sbjct: 102 KIFQKLKENGYIYEKEIKQLYCPECEMFLPDRY 134
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 32/108 (29%), Positives = 47/108 (43%), Gaps = 20/108 (18%)
Query: 41 FQPMGWDAFGLPAE------------NAAHQHGIDP-----REWTVGNIATMKSQLQGFG 83
+ P GWD GLP E H+ G + REW + ++SQ + G
Sbjct: 65 WVP-GWDHHGLPTEQKVEKKLGIKGKKDRHKLGREKFREKCREWKMEYADEIRSQFKRLG 123
Query: 84 CKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR--KEVDYSQNLPT 129
+W+ E T DP +F+ L+ GL+YR K V++S L T
Sbjct: 124 VSGDWDREYFTLDPGLEAAVWRVFVRLHDKGLIYRGKKPVNWSPALNT 171
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 37.8 bits (89), Expect = 8e-04
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 47 DAFGLPAENAAHQHGIDPREWTVGNIATM-KSQLQGFGCKF-NWESELATCDPKYYKWTQ 104
DA G P A + GI P E + K GFG F N+ S T + + Q
Sbjct: 49 DAHGTPIMLKAEKEGITPEE-LIARYHAEHKRDFAGFGISFDNYGS---THSEENRELAQ 104
Query: 105 ALFLDLYHAGLVYRKEV 121
++L L G +Y K +
Sbjct: 105 EIYLKLKENGYIYEKTI 121
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 37.5 bits (88), Expect = 0.001
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 45 GWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQ 104
G D G P E AA + G+ P+E K + G ++ + T P +++ Q
Sbjct: 49 GSDEHGTPIELAAKKEGVTPQELADKYHEEHKEDFKKLGISYDLFTR--TTSPNHHEVVQ 106
Query: 105 ALFLDLYHAGLVYRKEV 121
FL LY G +Y+K +
Sbjct: 107 EFFLKLYENGYIYKKTI 123
>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
Length = 511
Score = 37.2 bits (87), Expect = 0.001
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 4/77 (5%)
Query: 45 GWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKF-NWESELATCDPKYYKWT 103
G D G + A + GI P+E N A K + + ++ + T DP++ +
Sbjct: 46 GTDEHGQKIQRKAEEAGISPQELADRNSAAFKRLWEALNISYDDF---IRTTDPRHKEAV 102
Query: 104 QALFLDLYHAGLVYRKE 120
Q +F L G +Y +
Sbjct: 103 QEIFQRLLANGDIYLGK 119
>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 = 37.4 bits (87), Expect = 0.001
Identities = 33/122 (27%), Positives = 49/122 (40%), Gaps = 28/122 (22%)
Query: 31 NSIIKGPVRVFQPM---------GWDAFGLPAENAAHQ----HGIDP------------- 64
N I+K + ++ M GWD GLP E+ + G
Sbjct: 58 NKILKDIILRYKTMQGFNVTRKPGWDTHGLPIEHKVEKKLGISGKKEISSLEIEEFREKC 117
Query: 65 REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR--KEVD 122
RE+ + I + Q Q G +WE+ T DP Y + LF + + GL+YR K V
Sbjct: 118 REFALKQIEEQREQFQRLGVWGDWENPYKTMDPSYEESQWWLFKEAHEKGLLYRGLKPVY 177
Query: 123 YS 124
+S
Sbjct: 178 WS 179
>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 = 34.1 bits (79), Expect = 0.013
Identities = 30/114 (26%), Positives = 46/114 (40%), Gaps = 26/114 (22%)
Query: 31 NSIIKGPVRVFQPM---------GWDAFGLPAENAAHQH------------GIDP----- 64
N I+K + ++ M GWD GLP E + GI
Sbjct: 23 NKILKDIINRYKTMQGYYVPRRPGWDCHGLPIELKVEKELGISGKKDIEKMGIAEFNAKC 82
Query: 65 REWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 118
RE+ + + + Q Q G +WE+ T DP+Y + +F L+ GL+YR
Sbjct: 83 REFALRYVDEQEEQFQRLGVWVDWENPYKTMDPEYMESVWWVFKQLHEKGLLYR 136
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 33.9 bits (79), Expect = 0.016
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 74 TMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T+ +QL+ G +W E T D K + +F+ LY GL+YR +
Sbjct: 126 TITNQLRRLGASCDWSRERFTMDEGLSKAVREVFVRLYEKGLIYRGK 172
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 32.9 bits (75), Expect = 0.039
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 74 TMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR 118
T+ +QL+ G +W E T D + K F+ LY GL+YR
Sbjct: 219 TILNQLRRLGASLDWSRECFTMDEQRSKAVTEAFVRLYKEGLIYR 263
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 32.7 bits (75), Expect = 0.039
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
EW + + +QL+ G +W E+ T D + K + F+ LY GL+YR
Sbjct: 143 EWKDKHGNNICNQLRRLGSSLDWSREVFTMDEQRSKAVKEAFVRLYEDGLIYRDT 197
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 32.3 bits (73), Expect = 0.063
Identities = 13/55 (23%), Positives = 26/55 (47%)
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE 120
W + + Q + G +W+ E T D + + +F+ L+ GL+YR++
Sbjct: 131 AWKEQYGSRIGEQHKALGASLDWQRERFTMDEGLSRAVREVFVRLHEEGLIYREK 185
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 31.8 bits (72), Expect = 0.078
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYRKE--VDY 123
EW T+ +Q++ G +W E T D + + F+ L+ GL+Y+ V++
Sbjct: 170 EWKEKYGGTITNQIKRLGASCDWSRERFTLDEQLSRAVVEAFVRLHEKGLIYQGSYMVNW 229
Query: 124 SQNLPT 129
S NL T
Sbjct: 230 SPNLQT 235
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 30.5 bits (69), Expect = 0.23
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 16/102 (15%)
Query: 39 RVFQPMGWDAFGLPAE-------NAAHQHGIDP-------REWTVGNIATMKSQLQGFGC 84
+V GWD GLP E + + + P ++ + T + + +G
Sbjct: 71 KVHYVPGWDCHGLPIELKVLQSLDQEARKELTPIKLRAKAAKFAKKTVDTQRESFKRYGV 130
Query: 85 KFNWESELATCDPKYYKWTQALFLDLYHAGLVYR--KEVDYS 124
+WE+ T DP+Y +F ++ G +YR K V +S
Sbjct: 131 WGDWENPYLTLDPEYEAAQIEVFGQMFLNGYIYRGRKPVHWS 172
>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 = 27.9 bits (63), Expect = 0.41
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 49 FGLPAENAAHQHGIDPRE 66
F L AE AA ++G+DPR+
Sbjct: 21 FLLHAERAAERYGVDPRD 38
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 29.5 bits (67), Expect = 0.58
Identities = 34/125 (27%), Positives = 49/125 (39%), Gaps = 35/125 (28%)
Query: 31 NSIIKGPVRVFQPM---------GWDAFGLPAENAAHQ-HGIDP---------------R 65
N I+K + ++ M GWD GLP E + GI R
Sbjct: 71 NKILKDIIVRYKTMQGYDVPYVPGWDCHGLPIELKVEKKLGIGKKDIESFGVEEFREKCR 130
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQA----LFLDLYHAGLVYR--K 119
E+ + + K Q + G +WE+ T DP Y + F +LY GL+YR K
Sbjct: 131 EFALEQVDEQKEQFKRLGVWGDWENPYKTMDPSY----EESVWWAFKELYEKGLLYRGYK 186
Query: 120 EVDYS 124
V +S
Sbjct: 187 PVPWS 191
>gnl|CDD|239618 cd03556, L-fucose_isomerase, L-fucose isomerase (FucIase); FucIase
converts L-fucose, an aldohexose, to its ketose form,
which prepares it for aldol cleavage (similar to the
isomerization of glucose during glycolysis). L-fucose
(or 6-deoxy-L-galactose) is found in blood group
determinants as well as in various oligo- and
polysaccharides, and glycosides in mammals, bacteria and
plants.
Length = 584
Score = 27.9 bits (62), Expect = 1.6
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 10/51 (19%)
Query: 14 GVVVKTHSGAECRLAGINSIIKGPV--------RVFQPMGWDAFGLPAENA 56
G + H GA+ L + S+++ PV ++F+P W+AFG+ E A
Sbjct: 523 GAITHGHIGAD--LITLASMLRIPVCMHNVPEEKIFRPNAWNAFGMDLEGA 571
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 27.5 bits (62), Expect = 2.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 49 FGLPAENAAHQHGIDPRE 66
F L AE AA ++G+D R+
Sbjct: 289 FLLHAERAAERYGVDARD 306
>gnl|CDD|111760 pfam02907, Peptidase_S29, Hepatitis C virus NS3 protease.
Hepatitis C virus NS3 protein is a serine protease
which has a trypsin-like fold. The non-structural (NS)
protein NS3 is one of the NS proteins involved in
replication of the HCV genome. NS2-3 proteinase, a
zinc-dependent enzyme, performs a single proteolytic
cut to release the N-terminus of NS3. The action of NS3
proteinase (NS3P), which resides in the N-terminal
one-third of the NS3 protein, then yields all remaining
non-structural proteins. The C-terminal two-thirds of
the NS3 protein contain a helicase. The functional
relationship between the proteinase and helicase
domains is unknown. NS3 has a structural zinc-binding
site and requires cofactor NS4A.
Length = 149
Score = 26.6 bits (59), Expect = 3.7
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 10 TCLGGVVVKTHSGAECR-LAGINSIIKGPVRVFQPMGWDA 48
TC+ GV+ + GA R LAG KGPV M A
Sbjct: 17 TCVNGVLWTVYHGAGSRTLAG----PKGPV---NQMYTSA 49
>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the
first step in fucose metabolism, and has been
characterized in Escherichia coli and Bacteroides
thetaiotaomicron [Energy metabolism, Sugars].
Length = 587
Score = 26.1 bits (57), Expect = 6.8
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 10/51 (19%)
Query: 14 GVVVKTHSGAECRLAGINSIIKGPV--------RVFQPMGWDAFGLPAENA 56
GV+ H GA+ L + S+++ PV ++F+P W+AFG+ E
Sbjct: 526 GVLTIGHVGAD--LITLASMLRIPVCMHNVEETKIFRPSAWNAFGMDKEGQ 574
>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
Length = 588
Score = 26.1 bits (58), Expect = 7.5
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 14 GVVVKTHSGAECRLAGINSIIKGPV--------RVFQPMGWDAFGLPAENA 56
GV+ H GA+ L + S+++ PV ++F+P W AFG+ E
Sbjct: 527 GVLTYGHVGAD--LITLASMLRIPVCMHNVEEEKIFRPSAWAAFGMDKEGQ 575
>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 = 25.9 bits (57), Expect = 7.6
Identities = 20/102 (19%), Positives = 30/102 (29%), Gaps = 24/102 (23%)
Query: 39 RVFQPMGWDAFGLP---------------AENAAHQHGI---------DPREWTVGNIAT 74
V P+G+ G P +N H I DP
Sbjct: 64 NVLFPLGFHVTGTPILGLAELIKRRDELTIKNYTEVHAIPREELLKFTDPEYIVEYFSRE 123
Query: 75 MKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLV 116
+S + G +W T DP Y ++ + L GL+
Sbjct: 124 AESACKSMGYSIDWRRSFKTTDPYYDRFIEWQMNKLKELGLI 165
>gnl|CDD|223373 COG0296, GlgB, 1,4-alpha-glucan branching enzyme [Carbohydrate
transport and metabolism].
Length = 628
Score = 26.1 bits (58), Expect = 8.0
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 9/31 (29%)
Query: 41 FQPMGWDA----FGLPAE-----NAAHQHGI 62
+Q G+ A +G P + +AAHQ GI
Sbjct: 198 YQGTGYYAPTSRYGTPEDFKALVDAAHQAGI 228
>gnl|CDD|132592 TIGR03553, F420_FbiB_CTERM, F420 biosynthesis protein FbiB,
C-terminal domain. Coenzyme F420 differs between the
Archaea and the Actinobacteria, where the numbers of
glutamate residues attached are 2 (Archaea) or 5-6
(Mycobacterium). The enzyme in the Archaea is homologous
to the N-terminal domain of FbiB from Mycobacterium
bovis, and is responsible for glutamate ligation.
Therefore it seems likely that the C-terminal domain of
FbiB, modeled by This model, is involved in additional
glutamate ligation [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 194
Score = 25.5 bits (56), Expect = 8.2
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 41 FQPMGWDAFGLPAENAAHQHGIDP 64
++P+G A G PAE + DP
Sbjct: 164 WEPLGAVAVGHPAEPPGPRPPRDP 187
>gnl|CDD|199897 cd10911, LabA, LabA_like proteins. A well conserved group of
bacterial and archaeal proteins with no defined
function. LabA, a member from Synechococcus elongatus
PCC 7942, has been shown to play a role in
cyanobacterial circadian timing. It is required for
negative feedback regulation of the
autokinase/autophosphatase KaiC, a central component of
the circadian clock system. In particular, LabA seems
necessary for KaiC-dependent repression of gene
expression. LabA_like domains exhibit some similarity to
the NYN domain, a distant relative of the PIN-domain
nucleases.
Length = 155
Score = 25.6 bits (57), Expect = 8.3
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 105 ALFLD---LYHAGLVYRKEVDYSQ 125
A+F+D LY+A ++DY +
Sbjct: 4 AVFVDGANLYYAARNLGWKIDYEK 27
>gnl|CDD|180261 PRK05790, PRK05790, putative acyltransferase; Provisional.
Length = 393
Score = 25.9 bits (58), Expect = 8.4
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
DAF G+ AEN A Q+GI RE
Sbjct: 149 TDAFNGYHMGITAENLAEQYGIT-RE 173
>gnl|CDD|165451 PHA03180, PHA03180, helicase-primase primase subunit; Provisional.
Length = 1071
Score = 26.0 bits (57), Expect = 8.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 22 GAECRLAGINSIIKGPV---RVFQPMGWDAFGL 51
G L GI+S GP+ R+ G AFG+
Sbjct: 534 GPANMLMGISSASNGPLPVYRIGMSKGKQAFGV 566
>gnl|CDD|176504 cd08561, GDPD_cytoplasmic_ScUgpQ2_like, Glycerophosphodiester
phosphodiesterase domain of Streptomyces coelicolor
cytoplasmic phosphodiesterases UgpQ2 and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in a group of uncharacterized cytoplasmic
phosphodiesterases which predominantly exist in
bacteria. The prototype of this family is a putative
cytoplasmic phosphodiesterase encoded by gene ulpQ2
(SCO1419) in the Streptomyces coelicolor genome. It is
distantly related to the Escherichia coli cytoplasmic
phosphodiesterases UgpQ that catalyzes the hydrolysis of
glycerophosphodiesters at the inner side of the
cytoplasmic membrane to produce sn-glycerol-3-phosphate
(G3P) and the corresponding alcohols.
Length = 249
Score = 25.7 bits (57), Expect = 8.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 55 NAAHQHGIDPREWTVGNIATMK 76
AAH G++ WTV + A M+
Sbjct: 206 RAAHAAGLEVHVWTVNDPAEMR 227
>gnl|CDD|226790 COG4340, COG4340, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 226
Score = 25.6 bits (56), Expect = 9.3
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 47 DAFGLPAENAAHQHGID 63
D GLPA AHQ G+D
Sbjct: 130 DEQGLPAPEGAHQDGVD 146
>gnl|CDD|239526 cd03442, BFIT_BACH, Brown fat-inducible thioesterase (BFIT).
Brain acyl-CoA hydrolase (BACH). These enzymes
deacylate long-chain fatty acids by hydrolyzing
acyl-CoA thioesters to free fatty acids and CoA-SH.
Eukaryotic members of this family are expressed in
brain, testis, and brown adipose tissues. The archeal
and eukaryotic members of this family have two tandem
copies of the conserved hot dog fold, while most
bacterial members have only one copy.
Length = 123
Score = 25.2 bits (56), Expect = 9.3
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 12 LGGVVVKTHSGAECRLAGINSI-IKGPVRV 40
L G+ H+G A ++ I PVRV
Sbjct: 37 LAGIAAYRHAGGRVVTASVDRIDFLKPVRV 66
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
0.321 0.137 0.456
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: 6,779,006
Number of extensions: 568905
Number of successful extensions: 462
Number of sequences better than 10.0: 1
Number of HSP's gapped: 448
Number of HSP's successfully gapped: 49
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)