RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2327
(97 letters)
>gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate
(PLP)-binding TIM barrel domain of Type III
PLP-Dependent Enzymes, Eukaryotic YBL036c-like
proteins. This subfamily contains mostly
uncharacterized eukaryotic proteins with similarity to
the yeast hypothetical protein YBL036c, which is
homologous to a Pseudomonas aeruginosa gene that is
co-transcribed with a known proline biosynthetic gene.
YBL036c is a single domain monomeric protein with a
typical TIM barrel fold. It binds the PLP cofactor and
has been shown to exhibit amino acid racemase activity.
The YBL036c structure is similar to the N-terminal
domain of the fold type III PLP-dependent enzymes,
bacterial alanine racemase and eukaryotic ornithine
decarboxylase, which are two-domain dimeric proteins.
The lack of a second domain in YBL036c may explain
limited D- to L-alanine racemase or non-specific
racemase activity. Some members of this subfamily are
also referred to as PROSC (Proline synthetase
co-transcribed bacterial homolog).
Length = 227
Score = 113 bits (284), Expect = 9e-33
Identities = 41/69 (59%), Positives = 51/69 (73%)
Query: 5 IKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEK 64
+ L+++ QA R ++L S+PRLVAVSKTKP ELI EAY+ GQRHFGENYVQEL+EK
Sbjct: 1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEK 60
Query: 65 GHDPEISIQ 73
D I I+
Sbjct: 61 APDLPIDIK 69
>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Yggs-like proteins. This subfamily contains mainly
uncharacterized proteobacterial proteins with
similarity to the hypothetical Escherichia coli protein
YggS, a homolog of yeast YBL036c, which is homologous
to a Pseudomonas aeruginosa gene that is co-transcribed
with a known proline biosynthetic gene. Like yeast
YBL036c, Yggs is a single domain monomeric protein with
a typical TIM-barrel fold. Its structure, which shows a
covalently-bound PLP cofactor, is similar to the
N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. YggS has not been characterized extensively
and its biological function is still unkonwn.
Length = 224
Score = 75.7 bits (187), Expect = 2e-18
Identities = 32/59 (54%), Positives = 38/59 (64%), Gaps = 8/59 (13%)
Query: 9 LEKVEQACA---RRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELLEK 64
+++ QA R P +Q L+AVSKTKP + I EAY GQRHFGENYVQE LEK
Sbjct: 10 KQRIAQAAKQAGRDPSSVQ-----LLAVSKTKPADAIREAYAAGQRHFGENYVQEALEK 63
>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, YBL036c-like proteins. This
family contains mostly uncharacterized proteins, widely
distributed among eukaryotes, bacteria and archaea,
that bear similarity to the yeast hypothetical protein
YBL036c, which is homologous to a Pseudomonas
aeruginosa gene that is co-transcribed with a known
proline biosynthetic gene. YBL036c is a single domain
monomeric protein with a typical TIM barrel fold. It
binds the PLP cofactor and has been shown to exhibit
amino acid racemase activity. The YBL036c structure is
similar to the N-terminal domain of the fold type III
PLP-dependent enzymes, bacterial alanine racemase and
eukaryotic ornithine decarboxylase, which are
two-domain dimeric proteins. The lack of a second
domain in YBL036c may explain limited D- to L-alanine
racemase or non-specific racemase activity.
Length = 222
Score = 72.5 bits (179), Expect = 3e-17
Identities = 27/62 (43%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELL 62
++ + + R P E LVAVSKT P E I EA GQR FGEN VQE L
Sbjct: 6 EEVRERIAAAAERAGRDPDE-----VTLVAVSKTVPAEAIREAIEAGQRDFGENRVQEAL 60
Query: 63 EK 64
+K
Sbjct: 61 DK 62
>gnl|CDD|223402 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold
[General function prediction only].
Length = 228
Score = 69.2 bits (170), Expect = 7e-16
Identities = 30/62 (48%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELL 62
AA++ + + R P LVAVSKT P E I EAY GQRHFGEN VQE L
Sbjct: 8 AAVRERIAAAAERAGRNPGS-----VTLVAVSKTVPAEDIREAYEAGQRHFGENRVQEAL 62
Query: 63 EK 64
+K
Sbjct: 63 DK 64
>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family.
Members of this protein family include YggS from
Escherichia coli and YBL036C, an uncharacterized
pyridoxal protein of Saccharomyces cerevisiae [Unknown
function, Enzymes of unknown specificity].
Length = 229
Score = 64.5 bits (157), Expect = 4e-14
Identities = 30/64 (46%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 3 AAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQELL 62
IK +E R P ++ +L+AVSKTKP I AY+ GQR FGENYVQEL+
Sbjct: 9 EDIKTKIEAANTHVNRNPSKV-----KLLAVSKTKPASAIQIAYDAGQRAFGENYVQELV 63
Query: 63 EKGH 66
EK
Sbjct: 64 EKIK 67
>gnl|CDD|216340 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 217
Score = 37.2 bits (87), Expect = 4e-04
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 4/39 (10%)
Query: 29 RLVAVSKT--KPKELIIEAY--NGGQRHFGENYVQELLE 63
+L+AV K + A G FG +QE LE
Sbjct: 22 KLMAVVKANAYGHGAVRVARALAAGADGFGVATLQEALE 60
>gnl|CDD|215029 PLN00016, PLN00016, RNA-binding protein; Provisional.
Length = 378
Score = 37.0 bits (86), Expect = 5e-04
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 9/75 (12%)
Query: 15 ACARRPQELQWSRPRLVAVSKTKPKE-LIIEAYNGGQRHFGENYVQELLEKGHDPEISIQ 73
+RR A + + K+ LI+ +GG G +EL++ GH+ +
Sbjct: 33 QGSRRA----SQVAGAAAAAAVEKKKVLIVNTNSGGHAFIGFYLAKELVKAGHE----VT 84
Query: 74 LKSRGKTAVKEVVDE 88
L +RGK +++ E
Sbjct: 85 LFTRGKEPSQKMKKE 99
>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction
only].
Length = 235
Score = 28.6 bits (63), Expect = 0.37
Identities = 12/50 (24%), Positives = 17/50 (34%)
Query: 32 AVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTA 81
A L + A NG + LLE G D +++ G T
Sbjct: 101 AKDADGDTPLHLAALNGNPPEGNIEVAKLLLEAGADLDVNNLRDEDGNTP 150
>gnl|CDD|132310 TIGR03266, methan_mark_1, putative methanogenesis marker protein 1.
Members of this protein family represent a distinct
clade among the larger set of proteins that belong to
families TIGR00702 and pfam02624. Proteins from this
clade are found in genome sequence if and only if the
species sequenced is one of the methanogens. All
methanogens belong to the archaea; some but not all of
those sequenced are hyperthermophiles. This protein
family was detected by the method of partial
phylogenetic profiling (see Haft, et al., 2006).
Length = 376
Score = 28.6 bits (64), Expect = 0.43
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 19/74 (25%)
Query: 2 EAAIKGTLEKVEQACARRPQELQWSRPRLVAVSKTKPKELIIEAYNGGQRHFGENYVQEL 61
EA G LE +E+ WS L S+ E+ + A NG Y+ EL
Sbjct: 164 EAIFHGLLEVIERDA--------WS---LAEASRNLGPEINVTAENG--------YLYEL 204
Query: 62 LEKGHDPEISIQLK 75
LEK D + ++L+
Sbjct: 205 LEKFKDAGVDVKLR 218
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs
are distinct from classical SDRs. Members of this
subgroup retain the canonical active site triad (though
not the upstream Asn found in most SDRs) but have an
unusual putative glycine-rich NAD(P)-binding motif,
GGXXXXG, in the usual location. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they 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 numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
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. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, 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.
Length = 250
Score = 28.4 bits (64), Expect = 0.46
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 8/42 (19%)
Query: 41 LIIEAYNGGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAV 82
LII GG R G+ V+ELL GHD + + +RG+T
Sbjct: 4 LII----GGTRFIGKALVEELLAAGHD----VTVFNRGRTKP 37
>gnl|CDD|237026 PRK11930, PRK11930, putative bifunctional
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase/alanine racemase; Provisional.
Length = 822
Score = 27.2 bits (61), Expect = 1.2
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 49 GQRHFGENYVQELLEKG 65
G+R+ G Y+QEL EKG
Sbjct: 47 GERNDGHRYIQELYEKG 63
>gnl|CDD|215903 pfam00405, Transferrin, Transferrin.
Length = 328
Score = 26.7 bits (59), Expect = 1.8
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 31 VAVSKTKPKELIIEAYNGGQRHFGENYVQE 60
VA S ++LI E N Q FG++ +
Sbjct: 251 VARSVDGKEDLIWELLNQAQEKFGKDKSSD 280
>gnl|CDD|213871 TIGR03840, TMPT_Se_Te, thiopurine S-methyltransferase, Se/Te
detoxification family. Members of this family are
thiopurine S-methyltransferase from a branch in which at
least some member proteins can perform selenium
methylation as a means to detoxify selenium, or perform
a related detoxification of tellurium. Note that the EC
number definition does not specify a particular
thiopurine, but rather represents a class of activity.
Length = 213
Score = 25.6 bits (57), Expect = 4.4
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 50 QRHFGENYVQELLEKGHDPEISIQLKSRGKTAVKEVV 86
+ +G +Y ELLE E + + +G + + E V
Sbjct: 173 EALYGGHYEIELLESRDVLEDNPRFGKKGLSRLTESV 209
>gnl|CDD|119424 cd05164, PIKKc, Phosphoinositide 3-kinase-related protein kinase
(PIKK) subfamily, catalytic domain; The PIKK catalytic
domain subfamily is part of a larger superfamily that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), aminoglycoside phosphotransferase, choline
kinase, and RIO kinases. Members include ATM (Ataxia
telangiectasia mutated), ATR (Ataxia telangiectasia and
Rad3-related), TOR (Target of rapamycin), SMG-1
(Suppressor of morphogenetic effect on genitalia-1),
and DNA-PK (DNA-dependent protein kinase). PIKKs have
intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). They show strong
preference for phosphorylating serine/threonine
residues followed by a glutamine and are also referred
to as (S/T)-Q-directed kinases. They all contain a FATC
(FRAP, ATM and TRRAP, C-terminal) domain. PIKKs have
diverse functions including cell-cycle checkpoints,
genome surveillance, mRNA surveillance, and translation
control.
Length = 222
Score = 25.4 bits (56), Expect = 4.7
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 8/37 (21%)
Query: 31 VAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGHD 67
+ SK KPK++ + +G + F L KG +
Sbjct: 10 ILGSKQKPKKITLTGSDGKKYLF--------LVKGGE 38
>gnl|CDD|119429 cd05169, PIKKc_TOR, TOR (Target of rapamycin), catalytic domain;
The TOR catalytic domain subfamily is part of a larger
superfamily that includes the catalytic domains of
other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
RIO kinases. TOR is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). TOR contains a
rapamycin binding domain, a catalytic domain, and a
FATC (FRAP, ATM and TRRAP, C-terminal) domain at the
C-terminus. It is also called FRAP (FK506 binding
protein 12-rapamycin associated protein). TOR is a
central component of the eukaryotic growth regulatory
network. It controls the expression of many genes
transcribed by all three RNA polymerases. It associates
with other proteins to form two distinct complexes,
TORC1 and TORC2. TORC1 is involved in diverse
growth-related functions including protein synthesis,
nutrient use and transport, autophagy and stress
responses. TORC2 is involved in organizing cytoskeletal
structures.
Length = 280
Score = 25.2 bits (56), Expect = 6.4
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 28 PRL-VAVSKTKPKELIIEAYNGGQRHFGENYVQELLEKGH 66
P L V SK +P+ L I +G + F LL KGH
Sbjct: 6 PVLKVIPSKQRPRRLTIVGSDGKEYKF-------LL-KGH 37
>gnl|CDD|233441 TIGR01500, sepiapter_red, sepiapterin reductase. This model
describes sepiapterin reductase, a member of the short
chain dehydrogenase/reductase family. The enzyme
catalyzes the last step in the biosynthesis of
tetrahydrobiopterin. A similar enzyme in Bacillus
cereus was isolated for its ability to convert benzil
to (S)-benzoin, a property sepiapterin reductase also
shares. Cutoff scores for this model are set such that
benzil reductase scores between trusted and noise
cutoffs.
Length = 256
Score = 24.9 bits (54), Expect = 8.0
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 48 GGQRHFGENYVQELLEKGHDPEISIQLKSRGKTAVKEVVDE 88
G R FG QEL + P + L +R A++++ E
Sbjct: 7 GASRGFGRTIAQELAKCLKSPGSVLVLSARNDEALRQLKAE 47
>gnl|CDD|227738 COG5451, COG5451, Predicted secreted protein [Function unknown].
Length = 128
Score = 24.5 bits (53), Expect = 9.1
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 3 AAIKGTLEKVEQACARR-PQELQWSRPRLVAVSKTKPK--ELIIEAYNGGQRHFGENYVQ 59
A G++ + C + Q + L+A + P + A+N G R F Y +
Sbjct: 40 AEALGSVHYLRNLCGEKGDQYWRSRMVALIAAEQADPARRARMTAAFNRGYRSFASEYTR 99
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
0.312 0.130 0.372
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,927,141
Number of extensions: 415575
Number of successful extensions: 344
Number of sequences better than 10.0: 1
Number of HSP's gapped: 344
Number of HSP's successfully gapped: 30
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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 (21.9 bits)
S2: 53 (24.1 bits)