RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8389
(156 letters)
>gnl|CDD|203841 pfam08030, NAD_binding_6, Ferric reductase NAD binding domain.
Length = 149
Score = 57.0 bits (138), Expect = 4e-11
Identities = 26/109 (23%), Positives = 43/109 (39%), Gaps = 16/109 (14%)
Query: 47 VFKNHHGASGYTNESFCSLPEDFKMGNIGVYCF-------------SLTNSPYPLSSQEK 93
++ + + L E ++GNI ++ + S + S+
Sbjct: 40 AVRDLSSLEWFKD-VLNELEELKELGNIEIHIYLTGEYEAEDASDASDSEQISMFDSKNH 98
Query: 94 RDLITGLKTRTNAGRPNWDRVFKHLLDQK-KGKVTVFYCGPPQLARILR 141
+ I+G + + GRPNW V K + Q + VF CGPP L LR
Sbjct: 99 -EEISGTRVEFHFGRPNWKEVLKDIAKQHPNNSIGVFCCGPPSLVDELR 146
>gnl|CDD|99783 cd06186, NOX_Duox_like_FAD_NADP, NADPH oxidase (NOX) catalyzes the
generation of reactive oxygen species (ROS) such as
superoxide and hydrogen peroxide. ROS were originally
identified as bactericidal agents in phagocytes, but are
now also implicated in cell signaling and metabolism.
NOX has a 6-alpha helix heme-binding transmembrane
domain fused to a flavoprotein with the nucleotide
binding domain located in the cytoplasm. Duox enzymes
link a peroxidase domain to the NOX domain via a single
transmembrane and EF-hand Ca2+ binding sites. The
flavoprotein module has a ferredoxin like FAD/NADPH
binding domain. In classical phagocytic NOX2, electron
transfer occurs from NADPH to FAD to the heme of cytb to
oxygen leading to superoxide formation.
Length = 210
Score = 32.3 bits (74), Expect = 0.062
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 126 VT-VFYCGPPQLARILRLKC---DQFGFSFRKEVF 156
VT V CGPP L +R G F +E F
Sbjct: 176 VTRVVVCGPPGLVDDVRNAVAKKGGTGVEFHEESF 210
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 30.0 bits (68), Expect = 0.38
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 37 VDANIRGKMVVFKNHHGASGYTNESFCSLPEDFKMGNIGVYCFS-----LTNSPYPLSSQ 91
V+A + GK + +K G S Y + K G++ ++ LTN+ L S
Sbjct: 129 VEALLLGKGLNYKRLSGESLYEE----NHKVSDKKGSLSLWIHLTTSDGLTNTDSSLLSN 184
Query: 92 EKRDLI 97
K DLI
Sbjct: 185 YKFDLI 190
>gnl|CDD|215769 pfam00175, NAD_binding_1, Oxidoreductase NAD-binding domain.
Xanthine dehydrogenases, that also bind FAD/NAD, have
essentially no similarity.
Length = 106
Score = 28.4 bits (64), Expect = 0.82
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 112 DRVFKHLLDQKKGKVTVFYCGPPQLARILR 141
D + + L + G V+ CGPP + + +R
Sbjct: 76 DALLEEHLSEDLGDTDVYVCGPPPMMKAVR 105
>gnl|CDD|234766 PRK00447, PRK00447, hypothetical protein; Provisional.
Length = 144
Score = 27.7 bits (62), Expect = 1.6
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 40 NIRGKMVVFKNHHGASGYTNESFCSLPEDFKMGNIGVYCFSLTNSPYPLSSQEKRDLITG 99
I G + F H A+ SF E+ +G I + + +++I
Sbjct: 77 GIEGNEITFMVHKQAAYVGVLSFVDSDEESPLGPITITIRY----------KNPQEVIDW 126
Query: 100 LKTRTNAGRPNWDR 113
L RT G P W+
Sbjct: 127 LAPRTARGVPLWEN 140
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 28.3 bits (64), Expect = 1.7
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 10 RLLATLERKFSGKVLGGGKQNGGTGGSVDANIRGKMVVFKNH 51
RL+A LE+ SG+VL G+ G G VF+
Sbjct: 47 RLIAGLEKPTSGEVLLDGRPVTGPG-------PDIGYVFQED 81
>gnl|CDD|199903 cd10150, CobN_like, CobN subunit of cobaltochelatase, bchH and chlH
subunits of magnesium chelatases, and similar proteins.
Cobaltochelatase is a complex enzyme that catalyzes the
insertion of cobalt into hydrogenobyrinic acid
a,c-diamide, resulting in cobyrinic acid, as
demonstrated for Pseudomonas denitrificans. This is an
essential step in the bacterial synthesis of cobalamine
(B12). The insertion of cobalt requires a complex
composed of three polypeptides, cobN, cobS, and cobT.
Also included in this family are protoporphyrin IX
magnesium chelatases involved in the synthesis of
chlorophyll and bacteriochlorophyll, specifically the
large (chlH or bchH) subunits.They are thought to bind
both the protoporphyrin and the magnesium ion.
Hydrolysis of ATP by the smaller subunits in the complex
may trigger a conformational change that results in the
insertion of the ion into the protoporphyrin scaffold.
Cryo electron microscopy studies have suggested that a
distinct bchH C-terminal domain may bind tightly to the
N-terminal domain upon substrate binding, requiring a
substantial conformational change of the bchH subunit.
It has also been suggested that chlH of higher plants
binds abscisic acid via a C-terminal domain and plays a
role in abscisic acid signaling, and that the protein
spans the chloroplast envelope, with the C-terminus
exposed to the cytosol.
Length = 910
Score = 27.5 bits (62), Expect = 3.5
Identities = 12/87 (13%), Positives = 24/87 (27%)
Query: 35 GSVDANIRGKMVVFKNHHGASGYTNESFCSLPEDFKMGNIGVYCFSLTNSPYPLSSQEKR 94
V+ + V+ G Y L + I + + LS+ +
Sbjct: 14 LYVETTLSKADVIILRLLGGFSYWPYGLELLAALARANGIPLIVLPGDDEEDLLSTVDLE 73
Query: 95 DLITGLKTRTNAGRPNWDRVFKHLLDQ 121
+ L G N + ++L
Sbjct: 74 NWARLLAYLRYGGPENLRNLLRYLAAL 100
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 27.4 bits (61), Expect = 3.7
Identities = 22/79 (27%), Positives = 28/79 (35%), Gaps = 19/79 (24%)
Query: 3 NKVKKRQRLLATLERKFSGKVLGGGKQNGGTGGSVDANIRGKMVVFKNHHGASGYTNESF 62
KV + R LA L+ + +G V A + V G TN SF
Sbjct: 966 GKVLAQGRDLALLKERLAGDV--------------RAALS---AVADVGIEKPGLTNWSF 1008
Query: 63 CSLPEDF--KMGNIGVYCF 79
LPE K GN V +
Sbjct: 1009 GPLPERMEQKTGNYKVTAY 1027
>gnl|CDD|223395 COG0318, CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases
II [Lipid metabolism / Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 534
Score = 27.4 bits (61), Expect = 3.9
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 116 KHLLDQKKGKVTVFYCGPPQLARILR 141
+ L +K KVTV P L +L
Sbjct: 255 EVLWLIEKYKVTVLSGVPTFLRELLD 280
>gnl|CDD|107357 cd06362, PBP1_mGluR, Ligand binding domain of the metabotropic
glutamate receptors (mGluR). Ligand binding domain of
the metabotropic glutamate receptors (mGluR), which are
members of the family C of G-protein-coupled receptors
that transduce extracellular signals into G-protein
activation and ultimately into cellular responses.
mGluRs bind to glutamate and function as an excitatory
neurotransmitter; they are involved in learning, memory,
anxiety, and the perception of pain. Eight subtypes of
mGluRs have been cloned so far, and are classified into
three groups according to their sequence similarities,
transduction mechanisms, and pharmacological profiles.
Group I is composed of mGlu1R and mGlu5R that both
stimulate PLC hydrolysis. Group II includes mGlu2R and
mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R,
mGlu6R, mGlu7R, and mGlu8R, which form group III.
Length = 452
Score = 26.8 bits (60), Expect = 5.3
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 101 KTRTNAGRPNWDRVFKHLLDQKKGKVTVFYCGPPQLARILR 141
K ++A +D + + LL + +V V +C + +L
Sbjct: 208 KIPSSATEEEFDNIIRKLLSKPNARVVVLFCREDDIRGLLA 248
>gnl|CDD|143455 cd07137, ALDH_F3FHI, Plant aldehyde dehydrogenase family 3 members
F1, H1, and I1 and related proteins. Aldehyde
dehydrogenase family members 3F1, 3H1, and 3I1 (ALDH3F1,
ALDH3H1, and ALDH3I1), and similar plant sequences, are
in this CD. In Arabidopsis thaliana, stress-regulated
expression of ALDH3I1 was observed in leaves and
osmotic stress expression of ALDH3H1 was observed in
root tissue, whereas, ALDH3F1 expression was not stress
responsive. Functional analysis of ALDH3I1 suggest it
may be involved in a detoxification pathway in plants
that limits aldehyde accumulation and oxidative stress.
Length = 432
Score = 27.0 bits (60), Expect = 5.4
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 117 HLLDQKKGKVTVFYCGPPQLARIL 140
LL+QK K+ F+ G P++ RI+
Sbjct: 172 ALLEQKWDKI--FFTGSPRVGRII 193
>gnl|CDD|235593 PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated.
Length = 177
Score = 26.3 bits (59), Expect = 5.6
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 84 SPYPLSSQEKRDLITGLKTRTNA 106
S +PLS ++ L L+ R
Sbjct: 113 SAFPLSEEQLDKLKAALEKRLGR 135
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 26.7 bits (59), Expect = 6.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 17 RKFSGKV--LGGGKQNGGTGGSVDANIRGKM 45
RK S K+ LGGGK G GGS R ++
Sbjct: 46 RKLSKKLGGLGGGKGTGSGGGSSSQGPRPQL 76
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 26.2 bits (59), Expect = 7.9
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 8/41 (19%)
Query: 16 ERKFSGKVLGGGKQ-----NGGTGGSVDANIRGKMVVFKNH 51
ER +G V G G+ +G VDA G M++ +N
Sbjct: 423 ERSVAGTVFGDGEPRIVEIDGY---RVDAKPEGHMLIIRNR 460
>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain. The Methyl-CpG binding
domain (MBD) binds to DNA that contains one or more
symmetrically methylated CpGs. DNA methylation in
animals is associated with alterations in chromatin
structure and silencing of gene expression. MBD has
negligible non-specific affinity for DNA. In vitro
foot-printing with MeCP2 showed the MBD can protect a 12
nucleotide region surrounding a methyl CpG pair. MBDs
are found in several Methyl-CpG binding proteins and
also DNA demethylase.
Length = 75
Score = 25.0 bits (55), Expect = 8.6
Identities = 15/58 (25%), Positives = 18/58 (31%), Gaps = 13/58 (22%)
Query: 109 PNWDRVFKHLLDQKK-GKVTVFYCGP--------PQLARILRLKCDQFG----FSFRK 153
P W R + GKV V+Y P +L R L D F F
Sbjct: 12 PGWRREERQRKSGSSAGKVDVYYYSPTGKKFRSKSELIRYLEKNGDTSLKLEDFDFTV 69
>gnl|CDD|233233 TIGR01015, hmgA, homogentisate 1,2-dioxygenase. Missing in human
disease alkaptonuria [Energy metabolism, Amino acids and
amines].
Length = 429
Score = 26.3 bits (58), Expect = 9.1
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 84 SPYPLSSQEKRDLITGLKTRTNAGRP 109
SP+P+ S E D + GL T AG
Sbjct: 96 SPFPIPSDEAVDFVDGLHTLCGAGDA 121
>gnl|CDD|236032 PRK07495, PRK07495, 4-aminobutyrate aminotransferase; Provisional.
Length = 425
Score = 26.2 bits (58), Expect = 9.6
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 129 FYCGPPQLARILRLKCDQFG 148
FY P + LR CDQ G
Sbjct: 213 FYPAPAAFMKALRELCDQHG 232
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
0.321 0.139 0.425
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,974,122
Number of extensions: 703187
Number of successful extensions: 627
Number of sequences better than 10.0: 1
Number of HSP's gapped: 626
Number of HSP's successfully gapped: 21
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.0 bits)