RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3529
(97 letters)
>gnl|CDD|216301 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of
this family are implicated in bringing cargo forward
from the ER and binding to coat proteins by their
cytoplasmic domains. This domain corresponds closely to
the beta-strand rich GOLD domain described in. The GOLD
domain is always found combined with lipid- or
membrane-association domains.
Length = 178
Score = 45.3 bits (108), Expect = 3e-07
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 1 MESSTQEIHKSLNTIIDYQTHHRLREAQGRKRAEDLNER 39
+E +++ LN I Q + R REA+ R+ E N R
Sbjct: 112 LEEELKKLEDQLNDIKREQKYLREREARHRETNESTNSR 150
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. 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. 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 a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. 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 = 293
Score = 27.1 bits (61), Expect = 1.2
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 44 ALSLGARIAKIVPSAADAALIR-LYPTGTQITNSRNLTVDANIR 86
A LGA + V S +R L I +SR+L+ I
Sbjct: 129 AQHLGAEVFATVGSEEKREFLRELGGPVDHIFSSRDLSFADGIL 172
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 27.1 bits (60), Expect = 1.2
Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 13 NTIIDYQTHHRLREAQGRKRAEDLNERAGRPALSLGARIAKIVPSAAD-AALIRLYPTGT 71
N I +Q +R + R A DL R P L I ++ ALIR
Sbjct: 96 NLIFPWQIRNRRPD---RAAALDLLARFALPDSILTKNITELSGGEKQRIALIRNLQFMP 152
Query: 72 QI 73
+I
Sbjct: 153 KI 154
>gnl|CDD|143448 cd07130, ALDH_F7_AASADH, NAD+-dependent alpha-aminoadipic
semialdehyde dehydrogenase, ALDH family members 7A1 and
7B. Alpha-aminoadipic semialdehyde dehydrogenase
(AASADH, EC=1.2.1.31), also known as ALDH7A1,
Antiquitin-1, ALDH7B, or
delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH),
is a NAD+-dependent ALDH. Human ALDH7A1 is involved in
the pipecolic acid pathway of lysine catabolism,
catalyzing the oxidation of alpha-aminoadipic
semialdehyde to alpha-aminoadipate. Arabidopsis
thaliana ALDH7B4 appears to be an
osmotic-stress-inducible ALDH gene encoding a
turgor-responsive or stress-inducible ALDH. The
Streptomyces clavuligerus P6CDH appears to be involved
in cephamycin biosynthesis, catalyzing the second stage
of the two-step conversion of lysine to
alpha-aminoadipic acid. The ALDH7A1 enzyme and others
in this group have been observed as tetramers, yet the
bacterial P6CDH enzyme has been reported as a monomer.
Length = 474
Score = 27.2 bits (61), Expect = 1.6
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 29 GRKRAEDLNERAGRPALSLGARIAKIVPSAADAAL 63
GR+ + + R GR L LG A IV AD L
Sbjct: 227 GRQVGQAVAARFGRSLLELGGNNAIIVMEDADLDL 261
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 26.7 bits (59), Expect = 2.0
Identities = 26/78 (33%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 4 STQEIHKSLNTIIDYQTHHRLR---EAQGRKRAEDLNERAGR----PALSLGARIAKIVP 56
+T E K TI+ H R R E + + L E GR AL L AR+A
Sbjct: 152 ATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAM 211
Query: 57 SAADAALIRLYPTGTQIT 74
A++ L RL GT +T
Sbjct: 212 RDAESLLERLLALGTPVT 229
>gnl|CDD|176892 cd08883, RHO_alpha_C_CMO-like, C-terminal catalytic domain of
plant choline monooxygenase (CMO) and related aromatic
ring hydroxylating dioxygenases. C-terminal catalytic
domain of plant choline monooxygenase and related
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs, also known as aromatic ring
hydroxylating dioxygenases). RHOs utilize non-heme
Fe(II) to catalyze the addition of hydroxyl groups to
the aromatic ring, an initial step in the oxidative
degradation of aromatic compounds. RHOs are composed of
either two or three protein components, and are
comprised of an electron transport chain (ETC) and an
oxygenase. The ETC transfers reducing equivalents from
the electron donor to the oxygenase component, which in
turn transfers electrons to the oxygen molecules. The
oxygenase components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and a C-terminal domain
which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues. Plant
choline monooxygenase catalyzes the first step in a
two-step oxidation of choline to the osmoprotectant
glycine betaine. This subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 175
Score = 26.2 bits (58), Expect = 3.0
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 7/45 (15%)
Query: 8 IHKSLNTIIDYQT-------HHRLREAQGRKRAEDLNERAGRPAL 45
H L ++DY T + L+ A R R G AL
Sbjct: 28 AHPGLAAVLDYATYRTELFEYVSLQSAPARAEEGSFFYRLGNAAL 72
>gnl|CDD|185755 cd09216, GH64-LPHase-like, glycoside hydrolase family 64:
laminaripentaose-producing, beta-1,3-glucanase
(LPHase)-like. This subfamily is represented by the
laminaripentaose-producing, beta-1,3-glucanase (LPHase)
of Streptomyces matensis and related bacterial and
ascomycete proteins. LPHase is a member of glycoside
hydrolase family 64 (GH64), it is an inverting enzyme
involved in the cleavage of long-chain polysaccharide
beta-1,3-glucans, into specific pentasaccharide
oligomers. LPHase is a two-domain crescent fold
structure: one domain is composed of 10 beta-strands,
eight coming from the N-terminus of the protein and two
from the C-terminal region, and the protein has a
second inserted domain; this cd includes both domains.
This protein has an electronegative, substrate-binding
cleft, and conserved Glu and Asp residues involved in
the cleavage of the beta-1,3-glucan, laminarin, a plant
and fungal cell wall component. Among bacteria, many
beta-1,3-glucanases are implicated in fungal cell wall
degradation. Also included in this family is GluB , the
beta-1,3-glucanase B from Lysobacter enzymogenes Strain
N4-7. Recombinant GluB demonstrated higher relative
activity toward the branched-chain beta-1,3 glucan
substrate zymosan A than toward linear beta-1,3 glucan
substrates. Sometimes these two domains are found
associated with other domains such as in the
Catenulispora acidiphila DSM 44928 carbohydrate binding
family 6 protein in which they are positioned
N-terminal of a carbohydrate binding module, family 6
(CBM_6) domain. In the Cellulosimicrobium cellulans,
glucan endo-1,3-beta-glucosidase, they are positioned
N-terminal of a RICIN, carbohydrate-binding domain.
Length = 353
Score = 26.3 bits (58), Expect = 3.1
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 54 IVPSAADAALIRLYPTGTQITNSRNLTVDANIRIHAPPS 92
I ++ I LY GT + R VDA+ H P
Sbjct: 5 ITNNSGRNNQIYLYVVGTDLQTGRQGWVDADGAAHPVPP 43
>gnl|CDD|143405 cd07086, ALDH_F7_AASADH-like, NAD+-dependent alpha-aminoadipic
semialdehyde dehydrogenase and related proteins. ALDH
subfamily which includes the NAD+-dependent,
alpha-aminoadipic semialdehyde dehydrogenase (AASADH,
EC=1.2.1.31), also known as Antiquitin-1, ALDH7A1,
ALDH7B or delta-1-piperideine-6-carboxylate
dehydrogenase (P6CDH), and other similar sequences, such
as the uncharacterized aldehyde dehydrogenase of
Candidatus kuenenia AldH (locus CAJ73105).
Length = 478
Score = 26.0 bits (58), Expect = 3.8
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 29 GRKRAEDLNERAGRPALSLGARIAKIVPSAADAAL 63
GR+ E + R GR L LG A IV AD L
Sbjct: 228 GRRVGETVARRFGRVLLELGGNNAIIVMDDADLDL 262
>gnl|CDD|234921 PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase II;
Provisional.
Length = 724
Score = 25.8 bits (58), Expect = 4.7
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 54 IVPSAADAALIRLYPTGTQITNSRNLTVDANIR 86
+V DAA++R+ G + LT D N R
Sbjct: 423 VVKPGGDAAVLRIRGGGKGLA----LTTDCNPR 451
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 25.3 bits (56), Expect = 5.8
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 30 RKRAEDLNERAGRPALSLGARIAKIVPSAADA 61
KR L R R LSLGA +AK V +A +A
Sbjct: 369 EKREALLGGRLDRQTLSLGADLAKAVAAALEA 400
>gnl|CDD|220426 pfam09823, DUF2357, Domain of unknown function (DUF2357). This
entry was previously the N terminal portion of DUF524
(pfam04411) before it was split into two. This domain
has no known function. It is predicted to adopt an all
beta secondary structure pattern followed by mainly
alpha-helical structures.
Length = 246
Score = 25.3 bits (56), Expect = 6.0
Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 10 KSLNTIIDYQTHHRLREAQGRKRAEDLNERAGRPALSLGARIAKI--VPSAADAALIRLY 67
+++ I+ Q HHRL + RA+ + L A++ V L R
Sbjct: 94 QAIKRILR-QPHHRLVTEEEVVRADKVKRLDSAVLRELAKNPARLQWVEDGGRKYLPRRV 152
Query: 68 PTGTQITNSRNLTVD 82
+ LTVD
Sbjct: 153 RQDK-----KELTVD 162
>gnl|CDD|132281 TIGR03237, dnd_assoc_2, DNA phosphorothioation-dependent
restriction protein DptH. A DNA sulfur modification
(phosphorothioation) system, dnd (degradation during
electrophoresis), is sparsely and sporadically
distributed among the bacteria. This protein is one
member of a three-gene restriction enzyme cassette that
depends on DNA phosphorothioation [DNA metabolism,
Restriction/modification].
Length = 1256
Score = 25.2 bits (55), Expect = 6.9
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 7 EIHKSLNTIIDYQTHHRLREAQGRKRAEDLNER 39
++ L+ +D+ T+H RE E+ ++
Sbjct: 208 GENRELSDKLDFITYHFPRELHDGLGTEEFEKK 240
>gnl|CDD|131469 TIGR02416, CO_dehy_Mo_lg, carbon-monoxide dehydrogenase, large
subunit. This model represents the large subunits of
group of carbon-monoxide dehydrogenases that include
molybdenum as part of the enzymatic cofactor. There are
various forms of carbon-monoxide dehydrogenase;
Salicibacter pomeroyi DSS-3, for example, has two forms.
Note that, at least in some species, the active site Cys
is modified with a selenium attached to (rather than
replacing) the sulfur atom. This is termed
selanylcysteine, and created post-translationally, in
contrast to selenocysteine incorporation during
translation as for many other selenoproteins [Energy
metabolism, Other].
Length = 770
Score = 25.3 bits (55), Expect = 7.1
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 9 HKSLNTIIDYQTHHRLREAQGRKRAEDLNERAGRPALSLGARIAKIVPSA---------A 59
++ +D +H+LR Q KR +S I PS
Sbjct: 416 PLAMKKAMDTVDYHQLRAEQAAKRKRGETRELMGIGISFFTEIVGAGPSKNCDILGVGMF 475
Query: 60 DAALIRLYPTGTQI 73
D+ IR++PTG+ I
Sbjct: 476 DSCEIRIHPTGSAI 489
>gnl|CDD|177868 PLN02222, PLN02222, phosphoinositide phospholipase C 2.
Length = 581
Score = 25.0 bits (54), Expect = 7.9
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 63 LIRLYPTGTQITNS 76
L+R+YP GT++T+S
Sbjct: 371 LLRIYPKGTRVTSS 384
>gnl|CDD|176888 cd08879, RHO_alpha_C_AntDO-like, C-terminal catalytic domain of the
oxygenase alpha subunit of Pseudomonas resinovorans
strain CA10 anthranilate 1,2-dioxygenase and related
aromatic ring hydroxylating dioxygenases. C-terminal
catalytic domain of the oxygenase alpha subunit of
anthranilate 1,2-dioxygenase (AntDO) and related
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs, also known as aromatic ring
hydroxylating dioxygenases). RHOs utilize non-heme
Fe(II) to catalyze the addition of hydroxyl groups to
the aromatic ring, an initial step in the oxidative
degradation of aromatic compounds. RHOs are composed of
either two or three protein components, and are
comprised of an electron transport chain (ETC) and an
oxygenase. The ETC transfers reducing equivalents from
the electron donor to the oxygenase component, which in
turn transfers electrons to the oxygen molecules. The
oxygenase components are oligomers, either (alpha)n or
(alpha)n(beta)n. The alpha subunits are the catalytic
components and have an N-terminal domain, which binds a
Rieske-like 2Fe-2S cluster, and the C-terminal catalytic
domain which binds the non-heme Fe(II). The Fe(II) is
co-ordinated by conserved His and Asp residues.
Oxygenases belonging to this subgroup include the alpha
subunits of AntDO, aniline dioxygenase, Acinetobacter
calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate
1,2-dioxygenase from Pseudomonas cepacia 2CBS,
2,4,5-trichlorophenoxyacetic acid oxygenase from
Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic
acid oxygenase from Bradyrhizobium sp. strain HW13,
p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase
form Pseudomonas cepacia 2CBS, and Pseudomonas putida
IacC, which may be involved in the catabolism of the
plant hormone indole 3-acetic acid. This subfamily
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 237
Score = 24.6 bits (54), Expect = 8.5
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 8/56 (14%)
Query: 23 RLREAQGRKRAEDLNERAGR-----PALSL---GARIAKIVPSAADAALIRLYPTG 70
L A G +RA + GR P L + +I I P A D + +
Sbjct: 94 ALVAAHGEERARRILRGRGRNLNIFPNLFIIDISQQIRVIRPIAVDETEVTSWALR 149
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and archaea
also match the model The seed members used to make the
model include Nitrate reductases from Pseudomonas
fluorescens (GP:11344601), E.coli and B.subtilis. All
seed members are experimentally characterized. Some
unpublished nitrate reductases, that are shorter
sequences, and probably fragments fall in between the
noise and trusted cutoffs. Pfam models pfam00384
(Molybdopterin oxidoreductase) and pfam01568(Molydopterin
dinucleotide binding domain) will also match the nitrate
reductase, alpha subunit [Energy metabolism, Anaerobic].
Length = 1235
Score = 24.9 bits (54), Expect = 9.9
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 70 GTQITNSRNLTVDANIRIHAPPSFMV 95
G++IT R ++ RI P+ M+
Sbjct: 1174 GSEITQQRGGIHNSVTRITPKPTHMI 1199
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
0.317 0.129 0.354
Gapped
Lambda K H
0.267 0.0822 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,869,387
Number of extensions: 409411
Number of successful extensions: 441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 441
Number of HSP's successfully gapped: 45
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)