RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 036777
(66 letters)
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 99.4 bits (249), Expect = 1e-26
Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 14 MDLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYILY 65
M L IYN++T+QKE F P+ PGKV MYVCG T YD +H+GHAR+ + F +L
Sbjct: 1 MMLKIYNTLTRQKEEFKPLEPGKVKMYVCGPTVYDYAHIGHARSFVVFDVLR 52
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 92.7 bits (230), Expect = 3e-24
Identities = 35/58 (60%), Positives = 46/58 (79%)
Query: 8 TAAAPKMDLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYILY 65
A+ +L +YN+M+++KELF P V GKVGMYVCGVTAYDLSH+GHAR ++F +LY
Sbjct: 52 APASRGRELHLYNTMSRKKELFKPKVEGKVGMYVCGVTAYDLSHIGHARVYVTFDVLY 109
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 86.5 bits (215), Expect = 5e-22
Identities = 28/48 (58%), Positives = 36/48 (75%)
Query: 18 IYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYILY 65
+YN++T+QKE F PI PGKV MYVCG T YD +H+GHAR + F +L
Sbjct: 4 LYNTLTRQKEEFVPIDPGKVKMYVCGPTVYDYAHIGHARTYVVFDVLR 51
>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 = 81.1 bits (201), Expect = 4e-21
Identities = 26/48 (54%), Positives = 35/48 (72%)
Query: 18 IYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYILY 65
+YN++T+QKE F P+ PG V MYVCG T YD +H+GHAR + F +L
Sbjct: 2 LYNTLTRQKEEFVPLNPGLVTMYVCGPTVYDYAHIGHARTYVVFDVLR 49
>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 = 83.6 bits (207), Expect = 6e-21
Identities = 30/49 (61%), Positives = 37/49 (75%)
Query: 16 LIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYIL 64
L +YN++T+QKE F P+V GKV MYVCG T YD H+GHAR AI F +L
Sbjct: 1 LKLYNTLTRQKEEFEPLVQGKVKMYVCGPTVYDYCHIGHARTAIVFDVL 49
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 68.1 bits (167), Expect = 2e-15
Identities = 23/51 (45%), Positives = 29/51 (56%)
Query: 14 MDLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYIL 64
L + NS+T K F P +V Y CG T YD SHLGHAR ++F I+
Sbjct: 38 TGLKVNNSLTGGKVEFVPQNGRQVRWYTCGPTVYDSSHLGHARTYVTFDII 88
>gnl|CDD|216482 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
domain. This family includes only cysteinyl tRNA
synthetases.
Length = 301
Score = 66.2 bits (162), Expect = 6e-15
Identities = 22/36 (61%), Positives = 28/36 (77%)
Query: 29 FTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYIL 64
F P+ GKV MYVCG T YD SH+GHAR+A++F +L
Sbjct: 2 FVPLHQGKVNMYVCGPTVYDDSHIGHARSAVAFDVL 37
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 65.9 bits (160), Expect = 1e-14
Identities = 27/44 (61%), Positives = 32/44 (72%)
Query: 18 IYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISF 61
IYN++T+QKE F PI P V MYVCG+T YD HLGHAR + F
Sbjct: 230 IYNTLTRQKEPFAPIDPENVRMYVCGMTVYDYCHLGHARVMVVF 273
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 58.8 bits (142), Expect = 4e-12
Identities = 19/44 (43%), Positives = 29/44 (65%)
Query: 14 MDLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARA 57
M L +YN++ +Q+E F PI G V +Y CG T Y+ +H+G+ R
Sbjct: 1 MALRLYNTLGRQQEEFQPIEHGHVRLYGCGPTVYNYAHIGNLRT 44
>gnl|CDD|132488 TIGR03447, mycothiol_MshC, cysteine--1-D-myo-inosityl
2-amino-2-deoxy-alpha-D-glucopyranoside ligase.
Members of this protein family are MshC,
l-cysteine:1-D-myo-inosityl
2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an
enzyme that uses ATP to ligate a Cys residue to a
mycothiol precursor molecule, in the second to last
step in mycothiol biosynthesis. This enzyme shows
considerable homology to Cys--tRNA ligases, and many
instances are misannotated as such. Mycothiol is found
in Mycobacterium tuberculosis, Corynebacterium
glutamicum, Streptomyces coelicolor, and various other
members of the Actinobacteria. Mycothiol is an analog
to glutathione [Biosynthesis of cofactors, prosthetic
groups, and carriers, Glutathione and analogs].
Length = 411
Score = 51.6 bits (124), Expect = 1e-09
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 15 DLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAISFYILY 65
L ++++ Q P + GMYVCG+T YD +HLGHA ++F ++
Sbjct: 17 PLRLFDTADGQVRPVEP--GPEAGMYVCGITPYDATHLGHAATYLTFDLVN 65
>gnl|CDD|183518 PRK12418, PRK12418, cysteinyl-tRNA synthetase; Provisional.
Length = 384
Score = 47.6 bits (114), Expect = 3e-08
Identities = 17/32 (53%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 31 PIVPG-KVGMYVCGVTAYDLSHLGHARAAISF 61
P+ PG MYVCG+T YD +HLGHA ++F
Sbjct: 3 PVAPGGTATMYVCGITPYDATHLGHAATYLAF 34
>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 = 29.8 bits (67), Expect = 0.045
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 39 MYVCGVTAYDLSHLGHARAAISFYIL 64
G+T H+GH R ++F L
Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFL 26
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 29.8 bits (67), Expect = 0.069
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 14 MDLIIYNSMTQQKELFTPIVPGKVGMYVCGVTAYDLSHLGHARAAI 59
M L +YN+ T+ KV Y CG T Y+ +H+G+ R I
Sbjct: 1 MLLKLYNTKTKDLSELKNFSDVKV--YACGPTVYNYAHIGNFRTYI 44
>gnl|CDD|173925 cd02174, CCT, CTP:phosphocholine cytidylyltransferase.
CTP:phosphocholine cytidylyltransferase (CCT) catalyzes
the condensation of CTP and phosphocholine to form
CDP-choline as the rate-limiting and regulatory step in
the CDP-choline pathway. CCT is unique in that its
enzymatic activity is regulated by the extent of its
association with membrane structures. A current model
posts that the elastic stress of the bilayer curvature
is sensed by CCT and this governs the degree of
membrane association, thus providing a mechanism for
both positive and negative regulation of activity.
Length = 150
Score = 28.7 bits (65), Expect = 0.11
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 2/18 (11%)
Query: 40 YVCGVTAYDLSHLGHARA 57
YV G +DL H GHA A
Sbjct: 6 YVDGC--FDLFHYGHANA 21
>gnl|CDD|140329 PTZ00308, PTZ00308, ethanolamine-phosphate cytidylyltransferase;
Provisional.
Length = 353
Score = 28.2 bits (63), Expect = 0.19
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 30 TPIVPGKVGMYVCGVTAYDLSHLGHARA 57
P PG + ++V G +D+ H GHA A
Sbjct: 5 PPKKPGTIRVWVDG--CFDMLHFGHANA 30
Score = 25.1 bits (55), Expect = 2.9
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 34 PGKVGMYVCGVTAYDLSHLGHARA 57
PG +YV G ++DL H+GH R
Sbjct: 190 PGDRIVYVDG--SFDLFHIGHIRV 211
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 27.5 bits (62), Expect = 0.36
Identities = 9/9 (100%), Positives = 9/9 (100%)
Query: 51 HLGHARAAI 59
HLGHARAAI
Sbjct: 115 HLGHARAAI 123
>gnl|CDD|215229 PLN02413, PLN02413, choline-phosphate cytidylyltransferase.
Length = 294
Score = 26.1 bits (57), Expect = 1.3
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 37 VGMYVCGVTAYDLSHLGHARA 57
V +Y G+ YDL H GHAR+
Sbjct: 28 VRVYADGI--YDLFHFGHARS 46
>gnl|CDD|234286 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam
family pfam00297. Eukaryotic proteins are excluded from
this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 330
Score = 25.8 bits (57), Expect = 1.6
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 20 NSMTQQKELFTPI----VPGKVGMYVCGVTAYD 48
NS T+ KE+ P+ P + V + AY
Sbjct: 56 NSPTEGKEISVPVTVLEAP---PLRVAAIRAYG 85
>gnl|CDD|221281 pfam11871, DUF3391, Domain of unknown function (DUF3391). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is typically
between 122 to 139 amino acids in length. This domain
is found associated with pfam01966.
Length = 127
Score = 25.3 bits (56), Expect = 2.1
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 36 KVGMYVCGVTAYDLSHLGHARAAISFYI 63
+VGMYV + D S L H F I
Sbjct: 11 QVGMYVSLL---DRSWLEHPFLRNRFLI 35
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 25.4 bits (56), Expect = 2.1
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 51 HLGHARAAI 59
H+GHAR A+
Sbjct: 23 HIGHARTAL 31
>gnl|CDD|185104 PRK15182, PRK15182, Vi polysaccharide biosynthesis protein TviB;
Provisional.
Length = 425
Score = 25.0 bits (54), Expect = 3.0
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 29 FTPIVPGKVGMYVCGVTAYDLSH 51
F P PG VG + GV Y L+H
Sbjct: 249 FLPFRPGLVGGHCIGVDPYYLTH 271
>gnl|CDD|185054 PRK15099, PRK15099, O-antigen translocase; Provisional.
Length = 416
Score = 24.6 bits (54), Expect = 4.5
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 7/29 (24%)
Query: 36 KVGMYVCGVTAYDLSHLGHARAAISFYIL 64
KVG YV G +L A+A++ FYIL
Sbjct: 344 KVGAYVFG-------YLVIAKASLRFYIL 365
>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 = 24.2 bits (53), Expect = 5.8
Identities = 9/9 (100%), Positives = 9/9 (100%)
Query: 51 HLGHARAAI 59
HLGHARAAI
Sbjct: 15 HLGHARAAI 23
>gnl|CDD|223124 COG0046, PurL, Phosphoribosylformylglycinamidine (FGAM) synthase,
synthetase domain [Nucleotide transport and metabolism].
Length = 743
Score = 24.1 bits (53), Expect = 5.9
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 25 QKELFTPIVPGKVGMY 40
+ L P+V G V +Y
Sbjct: 534 CRALGIPVVGGNVSLY 549
>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 = 24.1 bits (53), Expect = 6.8
Identities = 6/9 (66%), Positives = 7/9 (77%)
Query: 51 HLGHARAAI 59
H+GH R AI
Sbjct: 16 HVGHLRNAI 24
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
0.320 0.132 0.381
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,174,427
Number of extensions: 217657
Number of successful extensions: 208
Number of sequences better than 10.0: 1
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 27
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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 (24.2 bits)