RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9766
(97 letters)
>gnl|CDD|215799 pfam00219, IGFBP, Insulin-like growth factor binding protein.
Length = 53
Score = 34.3 bits (79), Expect = 8e-04
Identities = 19/43 (44%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 36 DCPDRAGTVWDPCGCCKVCARAENQPCGGPYGFFGSCAHDLEC 78
CP V D CGCCKVCAR E + CG + C L C
Sbjct: 14 GCPPGVRLVLDGCGCCKVCARQEGESCG---VYTPRCHKGLRC 53
>gnl|CDD|197525 smart00121, IB, Insulin growth factor-binding protein homologues.
High affinity binding partners of insulin-like growth
factors.
Length = 75
Score = 30.9 bits (70), Expect = 0.019
Identities = 17/38 (44%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 42 GTVWDPCGCCKVCARAENQPCGGPYGFFGSCAHDLECV 79
D CGCC VCAR E +PCG CA L C
Sbjct: 21 LVRLDGCGCCPVCARQEGEPCGVY---TPRCAPGLRCQ 55
>gnl|CDD|132840 cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF
cytosolic phospholipase A2; catalytic domain;
Ca-dependent. Group IVB, IVD, IVE, and IVF cPLA2
consists of two domains: the regulatory C2 domain and
alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE,
and IVF cPLA2 are also referred to as cPLA2-beta,
-delta, -epsilon, and -zeta respectively. cPLA2-beta is
approximately 30% identical to cPLA2-alpha and it shows
low enzymatic activity compared to cPLA2alpha.
cPLA2-beta hydrolyzes palmitic acid from
1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid
from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from
1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon,
and -zeta are approximately 45-50% identical to
cPLA2-beta and 31-37% identical to cPLA2-alpha. It's
possible that cPLA2-beta, -delta, -epsilon, and -zeta
may have arisen by gene duplication from an ancestral
gene. The catalytic domain of cytosolic phospholipase A2
(PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond
of phospholipids to release arachidonic acid. At the
active site, cPLA2 contains a serine nucleophile through
which the catalytic mechanism is initiated. The active
site is partially covered by a solvent-accessible
flexible lid. cPLA2 displays interfacial activation as
it exists in both "closed lid" and "open lid" forms.
Movement of the cPLA2 lid possibly exposes a greater
hydrophobic surface and the active site. cPLA2 belongs
to the alpha-beta hydrolase family which is identified
by a characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Calcium is required for
cPLA2 to bind with membranes or phospholipids. The
calcium-dependent phospholipid binding domain resides in
the N-terminal region of cPLA2; it is homologous to the
C2 domain superfamily which is not included in this
hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and
PLA2G4F from humans.
Length = 541
Score = 29.6 bits (67), Expect = 0.18
Identities = 10/36 (27%), Positives = 13/36 (36%), Gaps = 7/36 (19%)
Query: 11 SYCLGRSIAFSCVC-------NPAECETLTDDDCPD 39
YC + I F + N EC D D P+
Sbjct: 418 EYCSEQGIPFPKIELSPEDQENLKECYVFEDADNPE 453
>gnl|CDD|223992 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
function prediction only].
Length = 339
Score = 27.9 bits (63), Expect = 0.69
Identities = 9/26 (34%), Positives = 10/26 (38%), Gaps = 2/26 (7%)
Query: 39 DRAGTVW--DPCGCCKVCARAENQPC 62
DR G W CG C+ C C
Sbjct: 83 DRVGVGWLVISCGECEYCRSGNENLC 108
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 27.5 bits (61), Expect = 1.00
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 14 LGRSIAFSCVCNPAECETLTDDDCPDRAGTVWDPCGCCKVC 54
+G++ A C+ + DD D V +PCG C+ C
Sbjct: 49 VGKTTAARVFAKAVNCQRMIDD--ADYLQEVTEPCGECESC 87
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 27.2 bits (60), Expect = 1.6
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 14 LGRSIAFSCVCNPAECETLTDDDCPDRAGTVWDPCGCCKVC 54
+G++ A C+ + DD P V +PCG C+ C
Sbjct: 49 VGKTTAARVFAKAVNCQRMIDD--PVYLQEVTEPCGECESC 87
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 26.7 bits (60), Expect = 2.1
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 39 DRAGTVW--DPCGCCKVCARAENQPC 62
DR G W D CG C+ C + C
Sbjct: 82 DRVGVKWLYDACGKCEYCRTGDETLC 107
>gnl|CDD|132300 TIGR03256, met_CoM_red_alp, methyl-coenzyme M reductase, alpha
subunit. Members of this protein family are the alpha
subunit of methyl coenzyme M reductase, also called
coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This
enzyme, with alpha, beta, and gamma subunits, catalyzes
the last step in methanogenesis. Several methanogens
have encode two such enzymes, designated I and II; this
model does not separate the isozymes [Energy metabolism,
Methanogenesis].
Length = 548
Score = 26.8 bits (59), Expect = 2.2
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 55 ARAENQPCGGPYGFFGSCAHDLECVVTD 82
AR EN+P G P+G D
Sbjct: 270 ARGENEPGGVPFGHLADIVQTSRVNYED 297
>gnl|CDD|203409 pfam06205, GT36_AF, Glycosyltransferase 36 associated family.
Length = 90
Score = 24.8 bits (55), Expect = 5.3
Identities = 11/36 (30%), Positives = 13/36 (36%), Gaps = 8/36 (22%)
Query: 14 LGRSIAFSCVCNPAECETLTDDDCPDRAGTVWDPCG 49
G S+A NPA L + G DPC
Sbjct: 35 RGGSLA-----NPA---ALARGALSNSVGAGLDPCA 62
>gnl|CDD|176207 cd08245, CAD, Cinnamyl alcohol dehydrogenases (CAD) and related
proteins. Cinnamyl alcohol dehydrogenases (CAD),
members of the medium chain dehydrogenase/reductase
family, reduce cinnamaldehydes to cinnamyl alcohols in
the last step of monolignal metabolism in plant cells
walls. CAD binds 2 zinc ions and is NADPH- dependent.
CAD family members are also found in non-plant species,
e.g. in yeast where they have an aldehyde reductase
activity. The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class
I mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P) binding-Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES. The MDR group
contains a host of activities, including the founding
alcohol dehydrogenase (ADH), quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase,
and numerous others. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes, or ketones.
Active site zinc has a catalytic role, while structural
zinc aids in stability. ADH-like proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit. The active site
zinc is coordinated by a histidine, two cysteines, and
a water molecule. The second zinc seems to play a
structural role, affects subunit interactions, and is
typically coordinated by 4 cysteines.
Length = 330
Score = 25.4 bits (56), Expect = 5.3
Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%)
Query: 39 DRAGTVW--DPCGCCKVCAR 56
DR G W CG C+ C R
Sbjct: 79 DRVGVGWLVGSCGRCEYCRR 98
>gnl|CDD|226544 COG4058, McrA, Methyl coenzyme M reductase, alpha subunit [Coenzyme
metabolism].
Length = 553
Score = 25.6 bits (56), Expect = 5.5
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 55 ARAENQPCGGPYGFFGSCAHDLECVVTD 82
AR N+P G P+G V D
Sbjct: 275 ARGPNEPGGVPFGHLADIVQTSRVVSDD 302
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 25.3 bits (56), Expect = 5.6
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 47 PCGCCKVCARAENQPCGGPYGFFGS 71
PCG C+ C + E C Y + GS
Sbjct: 87 PCGKCEYCKKGEYSLCSN-YDYIGS 110
>gnl|CDD|176194 cd08232, idonate-5-DH, L-idonate 5-dehydrogenase. L-idonate
5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion
of L-lodonate to 5-ketogluconate in the metabolism of
L-Idonate to 6-P-gluconate. In E. coli, this GntII
pathway is a subsidiary pathway to the canonical GntI
system, which also phosphorylates and transports
gluconate. L-ido 5-DH is found in an operon with a
regulator indR, transporter idnT, 5-keto-D-gluconate
5-reductase, and Gnt kinase. L-ido 5-DH is a
zinc-dependent alcohol dehydrogenase-like protein. The
alcohol dehydrogenase ADH-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) which displays a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases(~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. ADH-like proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and generally have 2 tightly bound
zinc atoms per subunit. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines.
Length = 339
Score = 25.3 bits (56), Expect = 6.3
Identities = 9/29 (31%), Positives = 9/29 (31%), Gaps = 1/29 (3%)
Query: 47 PCGCCKVCARAENQPCGGPYGFFGSCAHD 75
PCG C C C F GS
Sbjct: 88 PCGTCDYCRAGRPNLCLNMR-FLGSAMRF 115
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 24.8 bits (55), Expect = 9.3
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 47 PCGCCKVCARAENQPCGGPYGFFGSCAHD 75
CG C+ C+R + C G G D
Sbjct: 88 ACGTCRYCSRGQPNLCDLGAGILGGQLPD 116
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes
proposed to be involved with the catabolism of
phosphonate compounds.
Length = 280
Score = 24.8 bits (54), Expect = 9.5
Identities = 16/38 (42%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 30 ETLTDDDCPDRAG--TVWD---PCGCCKVCARAENQPC 62
T DD P R G VW PCG C C R Q C
Sbjct: 17 FTPADDGVPLRLGQRVVWSVTVPCGRCFRCRRGLPQKC 54
>gnl|CDD|131869 TIGR02822, adh_fam_2, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). The gene neighborhood of members
of this family is not conserved and it appears that no
members are characterized. The sequence of the family
includes 6 invariant cysteine residues and one invariant
histidine. It appears that no member is characterized
[Energy metabolism, Fermentation].
Length = 329
Score = 24.9 bits (54), Expect = 9.6
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 39 DRAGTVW--DPCGCCKVCAR-AEN 59
DR G W CG C+ C R AEN
Sbjct: 82 DRVGIAWLRRTCGVCRYCRRGAEN 105
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
0.326 0.141 0.513
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,583,009
Number of extensions: 336672
Number of successful extensions: 383
Number of sequences better than 10.0: 1
Number of HSP's gapped: 382
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)