RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4746
(314 letters)
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 55.3 bits (133), Expect = 2e-08
Identities = 62/257 (24%), Positives = 106/257 (41%), Gaps = 44/257 (17%)
Query: 90 WYIS--------WLCLVTLSYLYNCFVIPLRVTFPYQT-RSNLITWFVFDYVMDVIYILD 140
W IS W L+ + Y+ +V P V F + + L + D V+D+ + +D
Sbjct: 52 WIISPMDSRYRWWETLMVVLVAYSAWVYPFEVAFLNASPKRGL---EIADNVVDLFFAVD 108
Query: 141 LLL------IKPRLIYLDDGFWIKDSKLTRIQYRRKLQYKNDLLSLMPFDLLYFVFGFEC 194
++L I PR L ++D K ++Y + D+ S +PF L ++
Sbjct: 109 IVLTFFVAYIDPRTQLL-----VRDRKKIAVRYLSTW-FLMDVASTIPFQALAYLITGTV 162
Query: 195 T---------FLRLPRLIKIQTFWEFCNHFDSVLASPYVVRVARTLTYMIYLVHLNACAY 245
LR RL +++ F + S + +R AR L+ ++LVH C Y
Sbjct: 163 KLNLSYSLLGLLRFWRLRRVKQL--FTRLEKDIRFSYFWIRCARLLSVTLFLVHCAGCLY 220
Query: 246 YEISVREGLGINSWVYDGKGN--------AYIRCFYFATKTATSIG-KNPRPTNEMEYVF 296
Y I+ R +W+ N YI Y++ T T++G + N +E +F
Sbjct: 221 YLIADRYPHQGKTWIGAVIPNFRETSLWIRYISAIYWSITTMTTVGYGDLHAVNTIEMIF 280
Query: 297 MTVSWLLGVFVFAVLIG 313
+ L + + A LIG
Sbjct: 281 IIFYMLFNLGLTAYLIG 297
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 43.0 bits (102), Expect = 5e-05
Identities = 39/210 (18%), Positives = 70/210 (33%), Gaps = 42/210 (20%)
Query: 128 VFDYVMDVIYILDLLLIKPRLIYLDDGFWIKDSKLTRIQYRRKLQYKNDLLSLMPFDLLY 187
+ DYV VI+ L++LL + I L Y R D L ++P +
Sbjct: 1 ILDYVFTVIFTLEMLL---KFIALGFKRK----------YFRSPWNILDFLVVLPSLVSL 47
Query: 188 FVFGFE--------CTFLRLPRLIKIQTFWEFCNHFDSVLASPYVVRVARTLTYMIYLVH 239
+F LRL RL+++ + + R ++L ++ L+
Sbjct: 48 ILFLLGEDSGLLRVLRLLRLLRLLRLLRRFPGLRTL-----LQSLGRSLKSLLNLLLLLL 102
Query: 240 LNACAY---------YEISVREGLGINSWVYDGKGNAYIRCFYFATKTATSIGKNP---- 286
L + E+ N + ++Y + +T T+ G
Sbjct: 103 LLLFIFAIIGVQLFGGELDKCCDKNENPINGNSNFDSYGEALLWLFRTLTTEGWGDVMYD 162
Query: 287 --RPTNEMEYVFM-TVSWLLGVFVFAVLIG 313
P + +F L GV + +LIG
Sbjct: 163 TLVPGTVLGKIFFVIFIILGGVLLLNLLIG 192
>gnl|CDD|184210 PRK13651, PRK13651, cobalt transporter ATP-binding subunit;
Provisional.
Length = 305
Score = 30.4 bits (69), Expect = 1.0
Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 147 RLIYLDDGFWIKDSKLTRIQYRRKLQYKNDLLSLMPFDLLYFVFGFECTFLRLPRLIKIQ 206
R I+ DG IKD I K +N++ P LL FV E + +P++ I+
Sbjct: 234 RTIFFKDGKIIKDGDTYDILSDNKFLIENNM---EPPKLLNFVNKLEKKGIDVPKVTSIE 290
Query: 207 TFWEFCN 213
N
Sbjct: 291 ELASEIN 297
>gnl|CDD|212540 cd11598, HDAC_Hos2, Class I histone deacetylases including ScHos2
and SpPhd1. This subfamily includes Class I histone
deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as
well as a histone deacetylase Phd1 from
Schizosaccharomyces pombe. Hos2 binds to the coding
regions of genes during gene activation, specifically it
deacetylates the lysines in H3 and H4 histone tails. It
is preferentially associated with genes of high activity
genome-wide and is shown to be necessary for efficient
transcription. Thus, Hos2 is directly required for gene
activation in contrast to other class I histone
deacetylases. Protein encoded by phd1 is inhibited by
trichostatin A (TSA), a specific inhibitor of histone
deacetylase, and is involved in the meiotic cell cycle
in S. pombe. Class 1 HDACs are Zn-dependent enzymes that
catalyze hydrolysis of N(6)-acetyl-lysine residues in
histone amino termini to yield a deacetylated histone
(EC 3.5.1.98).
Length = 311
Score = 29.7 bits (67), Expect = 2.0
Identities = 13/25 (52%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 129 FDYVMD-VIYILDLLLIKPRLIYLD 152
F YV D V+ IL+LL PR++Y+D
Sbjct: 141 FCYVNDIVLAILNLLRYFPRVLYID 165
>gnl|CDD|238798 cd01557, BCAT_beta_family, BCAT_beta_family: Branched-chain
aminotransferase catalyses the transamination of the
branched-chain amino acids leusine, isoleucine and
valine to their respective alpha-keto acids,
alpha-ketoisocaproate, alpha-keto-beta-methylvalerate
and alpha-ketoisovalerate. The enzyme requires pyridoxal
5'-phosphate (PLP) as a cofactor to catalyze the
reaction. It has been found that mammals have two foms
of the enzyme - mitochondrial and cytosolic forms while
bacteria contain only one form of the enzyme. The
mitochondrial form plays a significant role in skeletal
muscle glutamine and alanine synthesis and in interorgan
nitrogen metabolism.Members of this subgroup are widely
distributed in all three forms of life.
Length = 279
Score = 27.9 bits (63), Expect = 6.3
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 249 SVREGLGINS-WV-YDGKGNAYIRCFYFATKTATSIGKNPRPTNEMEYVFMTVSW 301
+++E + +++ WV Y G + YIR F F T +G +P EY+F +
Sbjct: 61 AIKELVKLDADWVPYGGGASLYIRPFIFG--TDPQLGVSPAL----EYLFAVFAS 109
>gnl|CDD|225103 COG2192, COG2192, Predicted carbamoyl transferase, NodU family
[Posttranslational modification, protein turnover,
chaperones].
Length = 555
Score = 28.1 bits (63), Expect = 6.5
Identities = 8/39 (20%), Positives = 19/39 (48%)
Query: 37 DIIATATKGQTEYRKLMDETLDYLRRLNVPPRIRERVKQ 75
D +A A K ++R+++ L L +++ +K+
Sbjct: 61 DAVAVAGKPSAKFRRILAGYLKRKPELFGKLLLKKLLKR 99
>gnl|CDD|212529 cd10005, HDAC3, Histone deacetylase 3 (HDAC3). HDAC3 is a
Zn-dependent class I histone deacetylase that catalyzes
hydrolysis of N(6)-acetyl-lysine residue of a histone to
yield a deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
In order to target specific chromatin regions, HDAC3 can
interact with DNA-binding proteins (transcriptional
factors) either directly or after forming complexes with
a number of other proteins, as observed for the
SMPT/N-CoR complex which recruits human HDAC3 to
specific chromatin loci and activates deacetylation.
Human HDAC3 is also involved in deacetylation of
non-histone substrates such as RelA, SPY and p53
factors. This protein can also down-regulate p53
function and subsequently modulate cell growth and
apoptosis. This gene is therefore regarded as a
potential tumor suppressor gene. HDAC3 plays a role in
various physiological processes, including subcellular
protein localization, cell cycle progression, cell
differentiation, apoptosis and survival. HDAC3 has been
found to be overexpressed in some tumors including
leukemia, lung carcinoma, colon cancer and maxillary
carcinoma. Thus, inhibitors precisely targeting HDAC3
(in some cases together with retinoic acid or
hyperthermia) could be a therapeutic drug option.
Length = 381
Score = 28.1 bits (63), Expect = 6.7
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 129 FDYVMD-VIYILDLLLIKPRLIYLD 152
F YV D VI IL+LL PR++Y+D
Sbjct: 142 FCYVNDIVIAILELLKYHPRVLYID 166
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 27.9 bits (63), Expect = 9.4
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 32 CSQIRD----IIATATKGQ---TEYRKLMDETLDYLRR--LNVPPRIRERVKQW 76
S D + A K + E R+L++ L RR L++P RERVK
Sbjct: 79 LSMREDVYRALKAVDEKNEELDPETRRLLERLLRDFRRNGLDLPEATRERVKAL 132
>gnl|CDD|224664 COG1750, COG1750, Archaeal serine proteases [General function
prediction only].
Length = 579
Score = 27.8 bits (62), Expect = 9.8
Identities = 14/69 (20%), Positives = 21/69 (30%)
Query: 241 NACAYYEISVREGLGINSWVYDGKGNAYIRCFYFATKTATSIGKNPRPTNEMEYVFMTVS 300
NA AYY+ + L + V I ++ T TS + T
Sbjct: 501 NAAAYYKDASELALLMGEVVSSTGSKETISSPIYSATTQTSTATVTTTIENTVQLGSTAI 560
Query: 301 WLLGVFVFA 309
L + V
Sbjct: 561 LLPLLLVLL 569
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
0.330 0.143 0.477
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,480,007
Number of extensions: 1592321
Number of successful extensions: 2005
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1998
Number of HSP's successfully gapped: 25
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
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 (21.9 bits)
S2: 59 (26.4 bits)