RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15304
(96 letters)
>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
Length = 801
Score = 87.9 bits (218), Expect = 7e-22
Identities = 43/98 (43%), Positives = 59/98 (60%), Gaps = 4/98 (4%)
Query: 1 MRGVTSEAMVMCASTPD--KVEILAPPSAAKPGDLIQVEGYTRNPDPVLNPKKKIFETVA 58
MRG+ S+AMV+ AS D KVE++ PP +A G+ + G+ PD VLNPKKK++ET+
Sbjct: 706 MRGIKSQAMVLAASNSDHTKVELVEPPESAAVGERVTFPGFEGEPDDVLNPKKKVWETLQ 765
Query: 59 PDLKTNDSNQATYKGKVWTVENVEGFVTSQSLANVNIK 96
PDL TN A YK +T G S+AN +I+
Sbjct: 766 PDLHTNSELVACYKDVPFTTS--AGVCKVASIANGSIR 801
>gnl|CDD|239198 cd02799, tRNA_bind_EMAP-II_like, tRNA-binding-domain-containing
EMAP2-like proteins. This family contains a diverse
fraction of tRNA binding proteins, including
Caenorhabditis elegans methionyl-tRNA synthetase
(CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS),
Saccharomyces cerevisiae Arc1p, human p43 and EMAP2.
CeMetRS and hTyrRS aminoacylate their cognate tRNAs.
Arc1p is a transactivator of yeast methionyl-tRNA and
glutamyl-tRNA synthetases. This domain has general tRNA
binding properties. In a subset of this family this
domain has the added capability of a cytokine. For
example the p43 component of the Human aminoacyl-tRNA
synthetase complex is cleaved to release EMAP-II
cytokine. EMAP-II has multiple activities during
apoptosis, angiogenesis and inflammation and
participates in malignant transformation. A EMAP-II-like
cytokine also is released from hTyrRS upon cleavage. The
active cytokine heptapeptide locates to this domain.
Length = 105
Score = 56.9 bits (138), Expect = 4e-12
Identities = 21/36 (58%), Positives = 26/36 (72%), Gaps = 2/36 (5%)
Query: 1 MRGVTSEAMVMCASTPD--KVEILAPPSAAKPGDLI 34
MRGV S+ MV+CAS D KVE+L PP AKPG+ +
Sbjct: 69 MRGVKSQGMVLCASNADHEKVELLEPPEGAKPGERV 104
>gnl|CDD|216589 pfam01588, tRNA_bind, Putative tRNA binding domain. This domain
is found in prokaryotic methionyl-tRNA synthetases,
prokaryotic phenylalanyl tRNA synthetases the yeast GU4
nucleic-binding protein (G4p1 or p42, ARC1), human
tyrosyl-tRNA synthetase, and endothelial-monocyte
activating polypeptide II. G4p1 binds specifically to
tRNA form a complex with methionyl-tRNA synthetases. In
human tyrosyl-tRNA synthetase this domain may direct
tRNA to the active site of the enzyme. This domain may
perform a common function in tRNA aminoacylation.
Length = 95
Score = 41.0 bits (97), Expect = 4e-06
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 1 MRGVTSEAMVMCAST--PDKVEILAPPSAAKPGD 32
+RGV SE M++ A V +L PP PG
Sbjct: 61 LRGVESEGMILSAEELDGGSVGLLEPPGDVPPGT 94
>gnl|CDD|239066 cd02153, tRNA_bindingDomain, The tRNA binding domain is also
known as the Myf domain in literature. This domain is
found in a diverse collection of tRNA binding proteins,
including prokaryotic phenylalanyl tRNA synthetases
(PheRS), methionyl-tRNA synthetases (MetRS), human
tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces
cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex
aeolicus Trbp111, human p43 and human EMAP-II. PheRS,
MetRS and hTyrRS aminoacylate their cognate tRNAs.
Arc1p is a transactivator of yeast methionyl-tRNA and
glutamyl-tRNA synthetases. The molecular chaperones
Trbp111 and CsaA also contain this domain. CsaA has
export related activities; Trbp111 is
structure-specific recognizing the L-shape of the tRNA
fold. This domain has general tRNA binding properties.
In a subset of this family this domain has the added
capability of a cytokine. For example the p43 component
of the Human aminoacyl-tRNA synthetase complex is
cleaved to release EMAP-II cytokine. EMAP-II has
multiple activities during apoptosis, angiogenesis and
inflammation and participates in malignant
transformation. An EMAP-II-like cytokine is released
from hTyrRS upon cleavage. The active cytokine
heptapeptide locates to this domain. For homodimeric
members of this group which include CsaA, Trbp111 and
Escherichia coli MetRS this domain acts as a
dimerization domain.
Length = 99
Score = 40.6 bits (96), Expect = 7e-06
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 1 MRGVTSEAMVMCASTP----DKVEILAPPSAAKPGDLI 34
+RGV SE M++ A V IL P A GD I
Sbjct: 62 LRGVESEGMLLSAEELGLEEGSVGILELPEDAPVGDRI 99
>gnl|CDD|239199 cd02800, tRNA_bind_EcMetRS_like, tRNA-binding-domain-containing
Escherichia coli methionyl-tRNA synthetase
(EcMetRS)-like proteins. This family includes EcMetRS
and Aquifex aeolicus Trbp111 (AaTrbp111). This domain
has general tRNA binding properties. MetRS
aminoacylates methionine transfer RNAs (tRNAmet).
AaTrbp111 is structure-specific molecular chaperone
recognizing the L-shape of the tRNA fold. AaTrbp111
plays a role in nuclear trafficking of tRNAs. The
functional unit of EcMetRs and AaTrbp111 is a homodimer,
this domain acts as the dimerization domain.
Length = 105
Score = 38.3 bits (90), Expect = 5e-05
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 1 MRGVTSEAMVMCASTPDKVEILAPPSAAKPGDLI 34
+RGV S+ M++ A K+++L P +PG +
Sbjct: 71 LRGVESQGMILAAEDGGKLKLLTPDEEVEPGSRV 104
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 34.4 bits (80), Expect = 0.004
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 2 RGVTSEAMVMCASTPDK-VEILAPPSAAKPGDLIQ 35
GV SE MV+ A + +L P AKPG ++
Sbjct: 640 FGV-SEGMVLAAGPGGGDLFLLEPDEGAKPGMRVK 673
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 33.6 bits (78), Expect = 0.008
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 1 MRGVTSEAMVMCASTPDKVEILAPPSAAKPGDLI 34
+ G S+ M++ A K+ +L G +
Sbjct: 614 LMGEESQGMILAAEDDGKLTLLTVDKEVPNGSKV 647
>gnl|CDD|223151 COG0073, ARC1, EMAP domain [General function prediction only].
Length = 123
Score = 31.5 bits (72), Expect = 0.020
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 1 MRGVTSEAMVMCASTPD----KVEILAPPSAAKPGDLI 34
+RGV SE M++ A V IL PG +
Sbjct: 86 LRGVESEGMLLSAEELGLSDENVGILTLDEGVPPGTKV 123
>gnl|CDD|239197 cd02798, tRNA_bind_CsaA, tRNA-binding-domain-containing CsaA-like
proteins. CsaA is a molecular chaperone with export
related activities. CsaA has a putative tRNA binding
activity. The functional unit of CsaA is a homodimer and
this domain acts as a dimerization domain.
Length = 107
Score = 30.3 bits (69), Expect = 0.049
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 1 MRGVTSEAMVMCASTP-DKVEILAPPSAAKPGDLI 34
+ GV SE +V+ A +V +L P G +
Sbjct: 73 IAGVLSEVLVLGADDEGGEVVLLVPDREVPNGAKV 107
>gnl|CDD|232958 TIGR00399, metG_C_term, methionyl-tRNA synthetase C-terminal
region/beta chain. The methionyl-tRNA synthetase (metG)
is a class I amino acyl-tRNA ligase. This model
describes a region of the methionyl-tRNA synthetase that
is present at the C-terminus of MetG in some species (E.
coli, B. subtilis, Thermotoga maritima, Methanobacterium
thermoautotrophicum), and as a separate beta chain in
Aquifex aeolicus. It is absent in a number of other
species (e.g. Mycoplasma genitalium, Mycobacterium
tuberculosis), while Pyrococcus horikoshii has both a
full length MetG and a second protein homologous to the
beta chain only. Proteins hit by This model should
called methionyl-tRNA synthetase beta chain if and only
if the model metG hits a separate protein not also hit
by This model [Protein synthesis, tRNA aminoacylation].
Length = 137
Score = 28.2 bits (63), Expect = 0.38
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 1 MRGVTSEAMVMCASTPDKV-EILAPPSAAKPGDLI 34
+ GV SE M++ A KV +L+P A G+ I
Sbjct: 102 LFGVKSEGMILAAEDDGKVLFLLSPDQEAIAGERI 136
>gnl|CDD|211834 TIGR03536, DapD_gpp, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase.
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase (DapD) is involved in the
succinylated branch of the "lysine biosynthesis via
diaminopimelate (DAP)" pathway (GenProp0125). This
model represents a clade of DapD sequences most closely
related to the actinobacterial DapD family represented
by the TIGR03535 model. All of the genes evaluated for
the seed of this model are found in genomes where the
downstream desuccinylase is present, but known DapD
genes are absent. Additionally, many of the genes
identified by this model are found proximal to genes
involved in this lysine biosynthesis pathway.
Length = 341
Score = 28.6 bits (64), Expect = 0.45
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 43 PDPVLNPKKKIFETVAPDLKTNDSNQA 69
P P+LNP ++ VA L NQA
Sbjct: 23 PTPLLNPSAELVAAVAEVLGYAGGNQA 49
>gnl|CDD|201117 pfam00255, GSHPx, Glutathione peroxidase.
Length = 108
Score = 26.9 bits (60), Expect = 1.1
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 53 IFETVAPDLKTNDSNQATYKGKVWTVENV 81
I++ A D+ Y+GKV + NV
Sbjct: 1 IYDFSAKDINGEPVPLDQYRGKVLLIVNV 29
>gnl|CDD|182232 PRK10089, PRK10089, tRNA-binding protein; Provisional.
Length = 112
Score = 26.7 bits (60), Expect = 1.3
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 1 MRGVTSEAMVMCASTPD-KVEILAPPSAAKPGDLI 34
+ G SE +V+ D +V +L P G +
Sbjct: 77 IAGFMSEVLVLGFEDEDGEVVLLTPDRPVPNGVKL 111
>gnl|CDD|234442 TIGR04021, LLM_DMSO2_sfnG, dimethyl sulfone monooxygenase SfnG.
This family of FMNH2-dependent members of the
luciferase-like monooxygenase (LLM) family includes
SfnG, a monooxygenase that converts dimethylsulphone
(DMSO2) to methanesulphonate. This step can be followed
immediately by methanesulfonate sulfonatase (an
alkanesulfonate monooxygenase - see TIGR03565) for the
FMNH2-dependent conversion an inorganic form [Central
intermediary metabolism, Sulfur metabolism].
Length = 350
Score = 26.2 bits (58), Expect = 2.4
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 31 GDLIQVEGYTRNPDPVLNPKKKIFE 55
GD ++ +T P PV +P +IF+
Sbjct: 158 GDFYRINDFTLKPKPVQHPHPEIFQ 182
>gnl|CDD|166053 PLN02412, PLN02412, probable glutathione peroxidase.
Length = 167
Score = 25.7 bits (56), Expect = 3.2
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 51 KKIFETVAPDLKTNDSNQATYKGKVWTVENV 81
K I++ D+ ND + YKGKV + NV
Sbjct: 7 KSIYDFTVKDIGGNDVSLNQYKGKVLLIVNV 37
>gnl|CDD|227632 COG5322, COG5322, Predicted dehydrogenase [General function
prediction only].
Length = 351
Score = 26.0 bits (57), Expect = 3.4
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 9 MVMCASTPDKVEILAPPSAAKPGDLIQVEGYTRNPDP 45
+V AS P VEI P KPG LI GY ++ D
Sbjct: 234 LVWVASMPKGVEIF--PQHLKPGCLIVDGGYPKDVDT 268
>gnl|CDD|226019 COG3488, COG3488, Predicted thiol oxidoreductase [Energy production
and conversion].
Length = 481
Score = 24.8 bits (54), Expect = 7.8
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 6 SEAMVMCASTPDKVEILAPPSAAKPGDLIQVEGYTRN 42
+ A +C P+ V+ P A L V Y++N
Sbjct: 301 TAAQTLCLDLPNGVQPRLGPVEAPDPVLDLVTFYSQN 337
>gnl|CDD|237661 PRK14291, PRK14291, chaperone protein DnaJ; Provisional.
Length = 382
Score = 24.7 bits (54), Expect = 9.0
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 18 KVEILAPPSAAKPGDLIQVEG 38
KV+I P K GD I+V G
Sbjct: 305 KVKI---PPGTKEGDKIRVPG 322
>gnl|CDD|233387 TIGR01379, thiL, thiamine-monophosphate kinase. This model
describes thiamine-monophosphate kinase, an enzyme that
converts thiamine monophosphate into thiamine
pyrophosphate (TPP, coenzyme B1), an enzyme cofactor.
Thiamine monophosphate may be derived from de novo
synthesis or from unphosphorylated thiamine, known as
vitamin B1. Proteins scoring between the trusted and
noise cutoff for this model include short forms from the
Thermoplasmas (which lack the N-terminal region) and a
highly derived form from Campylobacter jejuni.
Eukaryotes lack this enzyme, and add pyrophosphate from
ATP to unphosphorylated thiamine in a single step
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 317
Score = 24.6 bits (54), Expect = 9.5
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 26 SAAKPGDLIQVEG 38
S AKPGDL+ V G
Sbjct: 145 SGAKPGDLVFVTG 157
>gnl|CDD|221030 pfam11213, DUF3006, Protein of unknown function (DUF3006). This
family of proteins has no known function.
Length = 70
Score = 23.7 bits (52), Expect = 9.6
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 25 PSAAKPGDLIQVEG--YTRNPDPVLNPKKKI 53
P AK GD++++EG +P+ KK+I
Sbjct: 31 PPGAKEGDVLEIEGGEVEIDPEETEARKKRI 61
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
0.310 0.127 0.362
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,665,486
Number of extensions: 373271
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 25
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.1 bits)