RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9718
(70 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 47.1 bits (113), Expect = 3e-09
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 1 MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQ 51
E+RRR RIN+ EL+ L+ + KL KA+IL + +++++++Q
Sbjct: 8 RERRRRDRINDAFEELRELLP------TPPNKKLSKAEILRLAIEYIKHLQ 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 = 45.3 bits (108), Expect = 2e-08
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 1 MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQQ 54
E+RRR RIN+ +EL++L+ KL KA+IL V +++++Q
Sbjct: 11 RERRRRERINDAFDELRSLLPTL-----PPSKKLSKAEILRKAVDYIKSLQELL 59
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 43.7 bits (104), Expect = 6e-08
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 5/54 (9%)
Query: 1 MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQQ 54
E+RRR +IN +EL++L+ K + KL KA+IL + +++++++Q +
Sbjct: 3 RERRRRRKINEAFDELRSLLPTLPK-----NKKLSKAEILRLAIEYIKSLQEEL 51
>gnl|CDD|178641 PLN03093, PLN03093, Protein SENSITIVITY TO RED LIGHT REDUCED 1;
Provisional.
Length = 273
Score = 29.8 bits (67), Expect = 0.078
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 3 KRRR--ARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQQLALSAA 60
KRRR E + + ++ DP R +KL + +E+ +K +E+ Q Q L
Sbjct: 23 KRRRKPKPKGTPEEEQQPWVPTDLESDPERQAKLIQK--MEICIKKVESSQFYQAFLEQV 80
Query: 61 TDPHVLKSF 69
P VL SF
Sbjct: 81 KSPEVLDSF 89
>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of CueR-like
transcription regulators. Helix-turn-helix (HTH)
transcription regulators CueR and ActP, copper efflux
regulators. In Bacillus subtilis, copper induced CueR
regulates the copZA operon, preventing copper toxicity.
In Rhizobium leguminosarum, ActP controls copper
homeostasis; it detects cytoplasmic copper stress and
activates transcription in response to increasing copper
concentrations. These proteins are comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their conserved N-terminal domains contain winged
HTH motifs that mediate DNA binding, while the
C-terminal domains have two conserved cysteines that
define a monovalent copper ion binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 127
Score = 26.8 bits (60), Expect = 0.61
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 5 RRAR-INNCLNELKTLILDAMKKDPARHSK------LEKADILEMTVKHLENMQRQQLAL 57
RRAR + L E++ L+ A+ +DP+R S LE LE + L+ M+R L
Sbjct: 51 RRARDLGFSLEEIRELL--ALWRDPSRASADVKALALEHIAELERKIAELQAMRRTLQQL 108
Query: 58 SAA 60
+ +
Sbjct: 109 ADS 111
>gnl|CDD|131099 TIGR02044, CueR, Cu(I)-responsive transcriptional regulator. This
model represents the copper-, silver- and gold- (I)
responsive transcriptional activator of the gamma
proteobacterial copper efflux system. This protein is a
member of the MerR family of transcriptional activators
(pfam00376) and contains a distinctive pattern of
cysteine residues in its metal binding loop, Cys-X7-Cys.
This family also lacks a conserved cysteine at the
N-terminal end of the dimerization helix which is
required for the binding of divalent metals such as
zinc; here it is replaced by a serine residue
[Regulatory functions, DNA interactions].
Length = 127
Score = 25.5 bits (56), Expect = 1.7
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 4 RRRARINNCLNELKTLILDAMKKDPARHSK------LEKADILEMTVKHLENMQRQQLAL 57
R ++ L E K L+ + DP R S LEK +E + L++M+ Q AL
Sbjct: 51 SRARQVGFSLEECKELL--NLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEAL 108
Query: 58 SAA 60
+ A
Sbjct: 109 AQA 111
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 25.6 bits (57), Expect = 1.7
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 1 MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADILEMTVKHLENMQRQQLALSAA 60
M+ R AR EL L L + P + KL+ ++L V+ L R+ L +AA
Sbjct: 1 MQPRSIAR------ELALLSLGQIPAKPEKLEKLQLEELLLAAVRTLTQEVRETLDTAAA 54
>gnl|CDD|198367 cd07795, FGGY_ScGut1p_like, Saccharomyces cerevisiae Gut1p and
related proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
small group of fungal glycerol kinases (GK), including
Saccharomyces cerevisiae Gut1p/YHL032Cp, which
phosphorylates glycerol to glycerol-3-phosphate in the
cytosol. Glycerol utilization has been considered as the
sole source of carbon and energy in S. cerevisiae, and
is mediated by glycerol kinase and glycerol 3-phosphate
dehydrogenase, which is encoded by the GUT2 gene.
Members in this family show high similarity to their
prokaryotic and eukaryotic homologs. GKs belong to the
FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 496
Score = 25.9 bits (57), Expect = 1.8
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 17/56 (30%)
Query: 20 ILDAMKKDP-ARHSKLE--------------KADILEMTVKHLENMQRQQLALSAA 60
ILDAM KD + L +ADIL + V+ E R+ AL AA
Sbjct: 398 ILDAMSKDSGSPLKALAVDGGMSNSDVAMQIQADILGIPVERPEM--RESTALGAA 451
>gnl|CDD|182320 PRK10227, PRK10227, DNA-binding transcriptional regulator CueR;
Provisional.
Length = 135
Score = 25.8 bits (56), Expect = 1.9
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 6/40 (15%)
Query: 27 DPARHS------KLEKADILEMTVKHLENMQRQQLALSAA 60
DP RHS LEK +E ++ L++M+ Q LAL+ A
Sbjct: 72 DPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANA 111
>gnl|CDD|182644 PRK10681, PRK10681, DNA-binding transcriptional repressor DeoR;
Provisional.
Length = 252
Score = 25.8 bits (57), Expect = 1.9
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 12/48 (25%)
Query: 1 MEKRRRARINNCLNELKTLILDAMKKDPARHSKLEKADIL---EMTVK 45
ME RR RI +L A+K+ H K + A +L EMT++
Sbjct: 1 METRRDERIGQ--------LLQALKRSDKLHLK-DAAALLGVSEMTIR 39
>gnl|CDD|143453 cd07135, ALDH_F14-YMR110C, Saccharomyces cerevisiae aldehyde
dehydrogenase family 14 and related proteins. Aldehyde
dehydrogenase family 14 (ALDH14), isolated mainly from
the mitochondrial outer membrane of Saccharomyces
cerevisiae (YMR110C) and most closely related to the
plant and animal ALDHs and fatty ALDHs family 3
members, and similar fungal sequences, are present in
this CD.
Length = 436
Score = 24.9 bits (55), Expect = 3.3
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 11/41 (26%)
Query: 17 KTLILDAMKKDPARHSKLE---------KADILEMTVKHLE 48
+ I++A+KKD R E K DIL M +K+L+
Sbjct: 44 EEAIVEALKKDLGRP-PFETLLTEVSGVKNDILHM-LKNLK 82
>gnl|CDD|240102 cd04754, Commd6, COMM_Domain containing protein 6. The COMM
Domain is found at the C-terminus of a variety of
proteins; presumably all COMM_Domain containing
proteins are located in the nucleus and the COMM domain
plays a role in protein-protein interactions. Several
family members have been shown to bind and inhibit
NF-kappaB.
Length = 86
Score = 24.1 bits (52), Expect = 4.9
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 23 AMKKDPARHSKLEKADILEMTVKHLENMQRQQLALSA 59
A+ A S EMT+ +N RQ ++A
Sbjct: 47 AVTLKVADPSGQVVTKSFEMTIPEFQNFSRQFKEMAA 83
>gnl|CDD|216179 pfam00898, Orbi_VP2, Orbivirus outer capsid protein VP2. VP2
acts as an anchor for VP1 and VP3. VP2 contains a
non-specific DNA and RNA binding domain in the
N-terminus.
Length = 946
Score = 24.2 bits (53), Expect = 7.8
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 20 ILDAMKKDPARHSKLEKADILEMTVKHLENMQRQ 53
I DA+ P R+ + +L++T++ ++ + Q
Sbjct: 41 IRDALNYRPLRNDGIVLPRLLDITLRAYDDRKSQ 74
>gnl|CDD|237364 PRK13361, PRK13361, molybdenum cofactor biosynthesis protein A;
Provisional.
Length = 329
Score = 23.8 bits (52), Expect = 8.1
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 16 LKTLILDAMKKDPARH 31
LK IL A+ P H
Sbjct: 295 LKAAILAAINLKPKGH 310
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 0.129 0.348
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,431,764
Number of extensions: 249023
Number of successful extensions: 369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 28
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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 (21.8 bits)
S2: 53 (24.1 bits)