RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1396
(66 letters)
>gnl|CDD|219533 pfam07718, Coatamer_beta_C, Coatamer beta C-terminal region. This
family is found at the N-terminus of the coatamer beta
subunit proteins (Beta-coat proteins). This C-terminal
domain probably adapts the function of the N-terminal
pfam01602 domain.
Length = 279
Score = 99.0 bits (247), Expect = 2e-27
Identities = 40/59 (67%), Positives = 48/59 (81%)
Query: 8 VLSVTGDTLQNCTLELATLGDLKLVERPQPVVLAPHDFCNIKANVKVASTENGIIFGNI 66
V++ T DTLQN TLELATLGDLK+VE+P P LAP F + +A VKV+STENG+IFGNI
Sbjct: 81 VVNQTKDTLQNATLELATLGDLKIVEQPTPFTLAPESFKSFQATVKVSSTENGVIFGNI 139
>gnl|CDD|227427 COG5096, COG5096, Vesicle coat complex, various subunits
[Intracellular trafficking and secretion].
Length = 757
Score = 34.7 bits (80), Expect = 0.001
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 11 VTGDTLQNCTLELATLGDLKLVERPQPVVLAPHDFCNIKANVKVASTENGIIFGNI 66
T + L+N L+ TLG L + L + VK + E G I GNI
Sbjct: 593 QTPELLENLRLDF-TLGTLSTIPLKPIFNLRKGAVVLQQVTVKKPNAELGFITGNI 647
>gnl|CDD|176045 cd08400, C2_Ras_p21A1, C2 domain present in RAS p21 protein
activator 1 (RasA1). RasA1 is a GAP1 (GTPase
activating protein 1), a Ras-specific GAP member, which
suppresses Ras function by enhancing the GTPase
activity of Ras proteins resulting in the inactive
GDP-bound form of Ras. In this way it can control
cellular proliferation and differentiation. RasA1
contains a C2 domain, a Ras-GAP domain, a pleckstrin
homology (PH)-like domain, a SH3 domain, and 2 SH2
domains. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of
piccolo/aczonin and intersectin which only have a
single C2 domain. C2 domains with a calcium binding
region have negatively charged residues, primarily
aspartates, that serve as ligands for calcium ions.
Members here have a type-I topology.
Length = 126
Score = 28.1 bits (63), Expect = 0.20
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 37 PVVLAPHDFCNIKAN-VKVAST 57
PV PH +C I N VKVA T
Sbjct: 17 PVKHVPHPYCVISLNEVKVART 38
>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
This group contains proteins identified as alcohol
dehydrogenases and glutathione-dependant formaldehyde
dehydrogenases (FDH) of the zinc-dependent/medium chain
alcohol dehydrogenase family. The MDR family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. FDH converts formaldehyde
and NAD to formate and NADH. 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. 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.
Length = 345
Score = 27.7 bits (62), Expect = 0.35
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 27 GDLKLVERPQPVVLAPHDFCNIKANVKVAST 57
GD+++ E P PV+ P D A ++V +T
Sbjct: 10 GDIRVEEVPDPVIEEPTD-----AVIRVVAT 35
>gnl|CDD|149071 pfam07801, DUF1647, Protein of unknown function (DUF1647). The
sequences making up this family are all derived from
hypothetical proteins expressed by C. elegans. The
region in question is approximately 160 amino acids
long. The GO annotation for this protein indicates the
protein to be involved in nematode larval development
and to have a positive regulation on growth rate.
Length = 142
Score = 26.1 bits (58), Expect = 0.97
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 18 NCTLELATLGDLKLVERPQPVV 39
NC+L L+TL DL L+ P+ V
Sbjct: 30 NCSL-LSTLEDLNLIGEPESFV 50
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the
zinc-dependent alcohol dehydrogenases (ADH) of the
medium chain alcohol dehydrogenase/reductase family
(MDR), tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic
domain. Unlike ADH, where NAD(P)(H) acts as a cofactor,
NADH in FDH is a tightly bound redox cofactor (similar
to nicotinamide proteins). 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.
Length = 345
Score = 26.1 bits (58), Expect = 1.2
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 27 GDLKLVERPQPVVLAPHDFCNIKANVKVAST 57
G + +RP+P + P D A VK+ T
Sbjct: 10 GKISWEDRPKPTIQEPTD-----AIVKMLKT 35
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 25.7 bits (57), Expect = 1.5
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 7 KVLSVTGDTLQNCTLELATLGDLKLVERPQPVVL 40
+V V+G TL L A +G+L L+ R P L
Sbjct: 8 RVTEVSG-TLLKAVLPGARVGELCLIRRRDPSQL 40
>gnl|CDD|197298 cd09204, PLDc_N_DEXD_b2, N-terminal putative catalytic domain of
uncharacterized prokaryotic and archeal HKD family
nucleases fused to a DEAD/DEAH box helicase domain.
N-terminal putative catalytic domain of uncharacterized
prokaryotic and archeal HKD family nucleases fused to a
DEAD/DEAH box helicase domain. All members of this
subfamily are uncharacterized. Other characterized
members of the superfamily that have a related domain
architecture ( containing a DEAD/DEAH box helicase
domain), include the DNA/RNA helicase superfamily II
(SF2) and Res-subunit of type III restriction
endonucleases. In addition to the helicase-like region,
members of this subfamily also contain one copy of the
conserved HKD motif (H-x-K-x(4)-D, where x represents
any amino acid residue) in the N-terminal putative
catalytic domain. The HKD motif characterizes the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 139
Score = 25.6 bits (57), Expect = 1.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 46 CNIKANVKVASTENGIIFGNI 66
N + N+KV+STENG + +
Sbjct: 111 SNYEWNLKVSSTENGDLVEQV 131
>gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional.
Length = 334
Score = 25.2 bits (55), Expect = 2.8
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 22 ELATLGDLKLVERPQPVVLAP 42
E A + ++ERP PVV P
Sbjct: 74 EWAHVSSTTMIERPTPVVDLP 94
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. 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. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have 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.
Length = 347
Score = 24.9 bits (55), Expect = 3.2
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 27 GDLKLVERPQPVVLAPHDFCNIKANVKVAST 57
G + L E P P + PHD A V+V +T
Sbjct: 10 GKIGLEEVPDPKIQGPHD-----AIVRVTAT 35
>gnl|CDD|237843 PRK14869, PRK14869, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 546
Score = 24.8 bits (55), Expect = 3.6
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 1 MDQNNYKVLSVTGDTLQNCTLE-LATLGDL--KLVERPQPVVLAPHDFC--NI----KAN 51
MD+NN K L V + L L +L DL ++ P +L+ NI
Sbjct: 94 MDENNVKTLPVVDE---EGKLLGLVSLSDLARAYMDILDPEILSKSPTSLENIIRTLDGE 150
Query: 52 VKVASTENGIIFGNI 66
V V + E+ + G +
Sbjct: 151 VLVGAEEDKVEEGKV 165
>gnl|CDD|143638 cd07557, trimeric_dUTPase, Trimeric dUTP diphosphatases.
Trimeric dUTP diphosphatases, or dUTPases, are the most
common family of dUTPase, found in bacteria,
eukaryotes, and archaea. They catalyze the hydrolysis
of the dUTP-Mg complex (dUTP-Mg) into dUMP and
pyrophosphate. This reaction is crucial for the
preservation of chromosomal integrity as it removes
dUTP and therefore reduces the cellular dUTP/dTTP
ratio, and prevents dUTP from being incorporated into
DNA. It also provides dUMP as the precursor for dTTP
synthesis via the thymidylate synthase pathway.
dUTPases are homotrimeric, except some monomeric viral
dUTPases, which have been shown to mimic a trimer.
Active sites are located at the subunit interface.
Length = 92
Score = 24.4 bits (54), Expect = 3.9
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 28 DLKLVERPQPVVLAPHDFCNIKANVKVASTEN--GIIFG 64
DL+L E + +VL P + + + E G++F
Sbjct: 4 DLRLGEDFEGIVLPPGETVLVPTGEAIELPEGYVGLVFP 42
>gnl|CDD|129148 TIGR00037, eIF_5A, translation elongation factor IF5A. Recent work
(2009) changed the view of eIF5A in eukaryotes and aIF5A
in archaea, hypusine-containing proteins, from
translation initiation factor to translation elongation
factor [Protein synthesis, Translation factors].
Length = 130
Score = 24.4 bits (53), Expect = 4.0
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 1 MDQNNYKVLSVTGDTLQNCTLELATLGDLKLVE 33
+D+ Y+VL++ G +Q L+ +L + E
Sbjct: 71 VDRREYQVLAIMGGMVQLMDLDTYETDELPIPE 103
>gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 1. Members
identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member 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. MDH family uses NAD(H) as a
cofactor in the interconversion of alcohols and
aldehydes, or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. 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.
Length = 386
Score = 24.0 bits (53), Expect = 6.3
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 27 GDLKLVERPQPVVLAPHDFCNIKANVKVAST 57
GD+++ E P P + P D A V+V +T
Sbjct: 10 GDVRVEEVPDPKIEDPTD-----AIVRVTAT 35
>gnl|CDD|222612 pfam14233, DUF4335, Domain of unknown function (DUF4335). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
eukaryotes. Proteins in this family are typically
between 204 and 480 amino acids in length. There are
two completely conserved residues (G and D) that may be
functionally important.
Length = 186
Score = 23.8 bits (52), Expect = 6.7
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 15 TLQNCTLELATLGDL 29
T CTLEL L DL
Sbjct: 4 TQPTCTLELEGLPDL 18
>gnl|CDD|188595 TIGR04080, rSAM_pep_cyc, KxxxW cyclic peptide radical SAM maturase.
Members of this family are radical SAM enzymes that
appear to perform a cyclization on an adjacent cognate
peptide from family TIGR04079. Genomes with the complete
system include Streptococcus thermophilus LMD-9 and
Lactococcus lactis subsp. cremoris MG1363, among others.
The gene symbol assigned is kwcM, for KxxxW Cyclic
peptide Maturase [Protein fate, Protein modification and
repair].
Length = 440
Score = 23.8 bits (51), Expect = 8.4
Identities = 7/48 (14%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 3 QNNYKVLSVTGD-TLQNCTLELATLGDLKLVERPQPVVLAPHDFCNIK 49
+ + D + +A L ++ P +V+ P +C++
Sbjct: 73 DGEIEEKGINPDEIINKAQKHIAELKKHNIISFPLELVIYPSMYCDLH 120
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
0.318 0.136 0.392
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,071,457
Number of extensions: 209676
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 179
Number of HSP's successfully gapped: 16
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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 (24.2 bits)