RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4627
(270 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 71.0 bits (175), Expect = 2e-16
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 158 QRILANVRERQRTQSLNEAFTSLRKLIPALPSDKLSKIQTLKLASRYIHFL 208
+R N RER+R +N+AF LR+L+P P+ KLSK + L+LA YI L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHL 51
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 61.1 bits (149), Expect = 1e-12
Identities = 27/52 (51%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 163 NVRERQRTQSLNEAFTSLRKLIPALPSD-KLSKIQTLKLASRYIHFLCEILH 213
N RER+R + +NEAF LR L+P LP + KLSK + L+LA YI L E L
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 58.8 bits (143), Expect = 8e-12
Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 157 SQRILANVRERQRTQSLNEAFTSLRKLIPALPSD-KLSKIQTLKLASRYIHFL 208
S+R N+RER+R + +N+AF LR L+P LP KLSK + L+ A YI L
Sbjct: 3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSL 55
>gnl|CDD|143308 cd05900, Ig_Aggrecan, Immunoglobulin (Ig)-like domain of the
chondroitin sulfate proteoglycan core protein (CSPG),
aggrecan. Ig_Aggrecan: immunoglobulin (Ig)-like domain
of the chondroitin sulfate proteoglycan core protein
(CSPG), aggrecan. These aggregates contribute to the
tissue's load bearing properties. In CSPGs, the Ig-like
domain is followed by hyaluronan (HA)-binding tandem
repeats, and a C-terminal region with epidermal growth
factor-like, lectin-like, and complement regulatory
protein-like domains. Separating these N- and C-terminal
regions is a nonhomologous glycosaminoglycan attachment
region. In cartilage, aggrecan forms cartilage link
protein stabilized aggregates with HA. These aggregates
contribute to the tissue's load bearing properties.
Aggrecan has a wide distribution in connective tissue
and extracellular matrices. Members of the vertebrate
HPLN (hyaluronan/HA and proteoglycan binding link)
protein family are physically linked adjacent to CSPG
genes.
Length = 112
Score = 28.0 bits (62), Expect = 2.4
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 185 PALPSDKLSKIQTLKLASRYIHFLCEILHGSED 217
PA+PSD +I L+ + CE++HG ED
Sbjct: 68 PAIPSDATLEITELRSNDSGT-YRCEVMHGIED 99
>gnl|CDD|221449 pfam12165, DUF3594, Domain of unknown function (DUF3594). This
presumed domain is functionally uncharacterized.This
domain family is found in eukaryotes, and is
approximately 140 amino acids in length. The family is
found in association with pfam00628.
Length = 137
Score = 27.5 bits (61), Expect = 5.1
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 10 TEVDENKSETIYRSENMDMYGVKNENPEISVNVEK---DIPEDNLDHN-----LNSKNLL 61
T+V++ + EN+ +YG+ NE+ E+++ E+ ++PE L N + K+ L
Sbjct: 23 TDVEDFYQQCDPEKENLCLYGLPNESWEVNLPAEEVPPELPEPALGINFARDGMQEKDWL 82
Query: 62 ILEQMKSETAHPYLTDYFYTEVDQNKSE 89
L + S++ + YF N+++
Sbjct: 83 SLVAVHSDSWLLSVAFYFGARFGFNRND 110
>gnl|CDD|109652 pfam00604, Flu_PB2, Influenza RNA-dependent RNA polymerase subunit
PB2. PB2 can bind 5' end cap structure of RNA.
Length = 759
Score = 27.9 bits (62), Expect = 6.1
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 103 LVKTEKPEEENYYMDEGDIMNNKRRKRSISSSSKSSSGDMKIR 145
L K E+ N + +GD++ +RKR + S+ S + +IR
Sbjct: 713 LSNLAKGEKANVLIGQGDVVLVMKRKRDSAISTDSQTATKRIR 755
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
0.309 0.128 0.351
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,241,861
Number of extensions: 1227382
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 780
Number of HSP's successfully gapped: 20
Length of query: 270
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 175
Effective length of database: 6,723,972
Effective search space: 1176695100
Effective search space used: 1176695100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.2 bits)