RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4109
(77 letters)
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 27.6 bits (62), Expect = 0.30
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 10 VARDREVEGDLVLSDLGQGVPFRAGAFDGAISISALQWLCNADK 53
+AR R V+ D + +PF +FD +S L L + ++
Sbjct: 34 LARKRA-PRKFVVGDA-EDLPFPDESFDVVVSSLVLHHLPDPER 75
>gnl|CDD|233446 TIGR01513, NAPRTase_put, putative nicotinate
phosphoribosyltransferase. A deep split separates two
related families of proteins, one of which includes
experimentally characterized examples of nicotinate
phosphoribosyltransferase, an the first enzyme of NAD
salvage biosynthesis. This model represents the other
family. Members have a different (longer) spacing of
several key motifs and have an additional C-terminal
domain of up to 100 residues. One argument suggesting
that this family represents the same enzyme is that no
species has a member of both families. Another is that
the gene encoding this protein is located near other NAD
salvage biosynthesis genes in Nostoc and in at least
four different Gram-positive bacteria. NAD and NADP are
ubiquitous in life. Most members of this family are
Gram-positive bacteria. An additional set of mutually
closely related archaeal sequences score between the
trusted and noise cutoffs [Biosynthesis of cofactors,
prosthetic groups, and carriers, Pyridine nucleotides].
Length = 443
Score = 28.1 bits (63), Expect = 0.37
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 8 TNVARDREVEGDLVLSDLGQGVPFRAGAFDGAISISALQWLCNADKTSHNPAKRLY 63
T AR G L + G RA D A+ + ++ AD TS+ A RLY
Sbjct: 133 TKAARIVLAAGGKPLLEFGLR---RAQGPDAALKAARAAYIGGADGTSNVLAGRLY 185
>gnl|CDD|163639 cd07396, MPP_Nbla03831, Homo sapiens Nbla03831 and related
proteins, metallophosphatase domain. Nbla03831 (also
known as LOC56985) is an uncharacterized Homo sapiens
protein with a domain that belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 267
Score = 27.3 bits (61), Expect = 0.70
Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 14/54 (25%)
Query: 32 RAGAFDGAISISALQWLCN----ADKT-------SHNPAKRLYKFFSSLFACLW 74
R ++G I LQWL N AD SH P L+ +S LW
Sbjct: 152 RFVDWNGGIGEEQLQWLRNELQEADANGEKVIIFSHFP---LHPESTSPHGLLW 202
>gnl|CDD|178473 PLN02885, PLN02885, nicotinate phosphoribosyltransferase.
Length = 545
Score = 27.3 bits (61), Expect = 0.73
Identities = 24/57 (42%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 8 TNVARDREVEGD-LVLSDLGQGVPFRAGAFDGAISISALQWLCNADKTSHNPAKRLY 63
TN AR R V G VL + G RA DG IS S +L D TS+ A RL+
Sbjct: 147 TNAARHRLVAGKSKVLLEFGLR---RAQGPDGGISASKYCYLGGFDATSNVEAGRLF 200
>gnl|CDD|132925 cd07014, S49_SppA, Signal peptide peptidase A. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
an intramembrane enzyme found in all three domains of
life and is involved in the cleavage of signal peptides
after their removal from the precursor proteins by
signal peptidases. Unlike the eukaryotic functional
homologs that are proposed to be aspartic proteases,
site-directed mutagenesis and sequence analysis have
shown these bacterial, archaeal and thylakoid SppAs to
be ClpP-like serine proteases. The predicted active site
serine for members in this family occurs in a
transmembrane domain, cleaving peptide bonds in the
plane of the lipid bilayer. Mutagenesis studies also
suggest that the catalytic center comprises a Ser-Lys
dyad (both residues absolutely conserved within
bacteria, chloroplast and mitochondrial signal peptidase
family members) and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases. In
addition to the carboxyl-terminal protease domain that
is conserved in all the S49 family members, the E. coli
SppA contains an amino-terminal domain (sometimes
referred to as 67K type). Others, including sohB
peptidase, protein C, protein 1510-N and archaeal signal
peptide peptidase, do not contain the amino-terminal
domain (sometimes referred to as 36K type).
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain. This family also contains
homologs that either have been found experimentally to
be without peptidase activity, or lack amino acid
residues that are believed to be essential for the
catalytic activity of peptidases.
Length = 177
Score = 26.8 bits (59), Expect = 0.99
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 6 FYTNVARDREVEGDLVLSDLGQG 28
F T VA +R + + + QG
Sbjct: 127 FITLVADNRHSTPEQQIDKIAQG 149
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 26.4 bits (59), Expect = 1.3
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 27 QGVPFRAGAFDGAISISALQWLCNADK 53
G+PF G+FD S LQ L + +
Sbjct: 79 DGLPFPDGSFDAVRSDRVLQHLEDPAR 105
>gnl|CDD|172906 PRK14430, PRK14430, acylphosphatase; Provisional.
Length = 92
Score = 26.0 bits (57), Expect = 1.4
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 27 QGVPFRAGAFDGAISISALQWLCN-ADKT----SHNPAKRL 62
QGV +RA D A + W+ N AD T + ++L
Sbjct: 15 QGVGYRAACADAADDLGLGGWVRNRADGTVEVMASGTVRQL 55
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 25.8 bits (57), Expect = 2.0
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 1 MKKNAFYTNVARDREVEGDLVLSDLGQG 28
MKK A N+AR ++ D VL+ L G
Sbjct: 252 MKKGALLVNIARGGLLDYDAVLAALESG 279
>gnl|CDD|182340 PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional.
Length = 251
Score = 25.5 bits (56), Expect = 2.8
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 11 ARDREVEGDLVLSDLGQGVPFRAGAFDGAISISALQW 47
AR ++ + D+ + +P FD A S A+QW
Sbjct: 80 ARQKDAADHYLAGDI-ESLPLATATFDLAWSNLAVQW 115
>gnl|CDD|202701 pfam03610, EIIA-man, PTS system fructose IIA component.
Length = 115
Score = 25.3 bits (56), Expect = 2.9
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 10 VARDREVEGDLVLSDLGQGVPFRAGA 35
+A +G LVL DLG G PF A A
Sbjct: 50 IAELDSGDGVLVLVDLGGGTPFNAAA 75
>gnl|CDD|181716 PRK09236, PRK09236, dihydroorotase; Reviewed.
Length = 444
Score = 25.6 bits (57), Expect = 3.1
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 37 DGAISISALQWLCNADKTSHNPAKR 61
+G +S+ + +KTSH PA
Sbjct: 345 EGKLSLEKV-----VEKTSHAPAIL 364
>gnl|CDD|182682 PRK10729, nudF, ADP-ribose pyrophosphatase NudF; Provisional.
Length = 202
Score = 25.5 bits (56), Expect = 3.1
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 34 GAFDGAISISALQWL 48
G D A S+ ALQWL
Sbjct: 175 GKIDNAASVIALQWL 189
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 25.4 bits (57), Expect = 3.4
Identities = 13/39 (33%), Positives = 14/39 (35%), Gaps = 10/39 (25%)
Query: 1 MKKNAFYTNVARDREVEGDLVLSD-----LGQGVPFRAG 34
MK A N AR G +V D L G AG
Sbjct: 224 MKPTAILINTAR-----GGVVDEDALVEALKSGKIAGAG 257
>gnl|CDD|237587 PRK14019, PRK14019, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II-like
protein; Provisional.
Length = 367
Score = 25.3 bits (56), Expect = 3.4
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 13 DREVEGDLVL 22
DRE EGDLV+
Sbjct: 26 DRENEGDLVM 35
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 25.3 bits (56), Expect = 3.5
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 1 MKKNAFYTNVARDREVEGDLVLSDLGQGVPFRAG 34
MK A N AR V+ D +L L G A
Sbjct: 220 MKPGAVLVNTARGGLVDEDALLRALKSGKIAGAA 253
>gnl|CDD|233636 TIGR01916, F420_cofE, F420-0:gamma-glutamyl ligase. This model
represents an enzyme of coenzyme F(420) biosynthesis, as
catalyzed by MJ0768 of Methanococcus jannaschii and by
the N-terminal half of FbiB of Mycobacterium bovis
strain BCG. Note that only two glutamates are ligated in
M. jannaschii, but five to six in the Mycobacterium
lineage. In M. jannaschii, CofE catalyzes the
GTP-dependent addition of two L-glutamates [Biosynthesis
of cofactors, prosthetic groups, and carriers, Other].
Length = 243
Score = 25.1 bits (55), Expect = 3.6
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 21 VLSDLGQGVPFRAGAFDGAISISAL 45
+++D G PFR G AI + L
Sbjct: 146 IITDT-NGRPFREGQVGVAIGAAGL 169
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 24.9 bits (55), Expect = 4.1
Identities = 10/37 (27%), Positives = 13/37 (35%)
Query: 1 MKKNAFYTNVARDREVEGDLVLSDLGQGVPFRAGAFD 37
M K+A N AR V + L L + A
Sbjct: 219 MLKDAVAINNARGGGVIEEAALDALLEEGIAAAALDV 255
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 24.9 bits (55), Expect = 4.3
Identities = 9/21 (42%), Positives = 9/21 (42%), Gaps = 5/21 (23%)
Query: 1 MKKNAFYTNVARDREVEGDLV 21
MK A N AR G LV
Sbjct: 226 MKPGAILVNTAR-----GGLV 241
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 24.8 bits (55), Expect = 5.0
Identities = 8/21 (38%), Positives = 9/21 (42%), Gaps = 5/21 (23%)
Query: 1 MKKNAFYTNVARDREVEGDLV 21
MK A NV R G +V
Sbjct: 215 MKPGAVLINVGR-----GSVV 230
>gnl|CDD|181775 PRK09314, PRK09314, bifunctional 3,4-dihydroxy-2-butanone
4-phosphate synthase/GTP cyclohydrolase II protein;
Provisional.
Length = 339
Score = 24.6 bits (54), Expect = 5.6
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 13 DREVEGDLVLS 23
DRE EGDLV +
Sbjct: 26 DRENEGDLVYA 36
>gnl|CDD|185075 PRK15120, PRK15120, lipopolysaccharide ABC transporter permease
LptF; Provisional.
Length = 366
Score = 24.7 bits (54), Expect = 5.9
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 11 ARDREVEGDLVLSDLGQGVP 30
A D ++ +LVLS LG GVP
Sbjct: 38 AVDGDIPTNLVLSLLGLGVP 57
>gnl|CDD|221197 pfam11739, DctA-YdbH, Dicarboxylate transport. In certain
bacterial families this protein is expressed from the
ydbH gene, and there is a suggestion that this is a
form of DctA or dicarboxylate transport protein.
Dicarboxylate transport proteins are found in aerobic
bacteria which grow on succinate or other
C4-dicarboxylates.
Length = 207
Score = 24.5 bits (54), Expect = 6.3
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 6/35 (17%)
Query: 13 DREVEGDLVLSDLGQGVPFRAGAFDGAISISALQW 47
G L LS+ A G +S+ L+
Sbjct: 24 PGSEPGPLRLSN------ASAPLLGGTLSLPPLRL 52
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 24.2 bits (53), Expect = 7.2
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 29 VPFRAGAFDGAISISALQWLCNADKTSHNPAKRLYKFFSSL 69
+P +FD +S ALQW + ++ L + L
Sbjct: 92 LPLEDSSFDLIVSNLALQWC-------DDLSQALSELARVL 125
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR
family domains have the characteristic active site
tetrad and a well-conserved NAD(P)-binding motif. This
subgroup is not well characterized, its members are
annotated as having a variety of putative functions.
One characterized member is Pseudomonas fluorescens
MupV a protein involved in the biosynthesis of
Mupirocin, a polyketide-derived antibiotic. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
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. 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. 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 = 293
Score = 24.2 bits (53), Expect = 7.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 11 ARDREVEGDLVLSDLG 26
R R +EGDL +LG
Sbjct: 49 DRVRVLEGDLTQPNLG 64
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
0.324 0.136 0.429
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,832,877
Number of extensions: 285136
Number of successful extensions: 378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 26
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)