RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6185
(79 letters)
>gnl|CDD|197716 smart00422, HTH_MERR, helix_turn_helix, mercury resistance.
Length = 70
Score = 30.6 bits (70), Expect = 0.015
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
GLL + T+ GYRL+S ++ L I
Sbjct: 23 IGLLPPPIRTEGGYRLYSDEDLERLRFI 50
>gnl|CDD|133417 cd04790, HTH_Cfa-like_unk, Helix-Turn-Helix DNA binding domain of
putative Cfa-like transcription regulators. Putative
helix-turn-helix (HTH) MerR-like transcription
regulator; conserved, Cfa-like, unknown proteins (~172
a.a.). The N-terminal domain of these proteins appears
to be related to the HTH domain of Cfa, a cyclopropane
fatty acid synthase. These Cfa-like proteins have a
unique C-terminal domain with conserved histidines
(motif HXXFX7HXXF). Based on sequence similarity of the
N-terminal domains, these proteins are predicted to
function as transcription regulators that mediate
responses to stress in eubacteria. They belong to the
MerR superfamily of transcription regulators that
promote transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 172
Score = 30.5 bits (69), Expect = 0.049
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
GLLS S ++S YRL+ ++ LEQI
Sbjct: 24 IGLLSPSARSESNYRLYGERDLERLEQI 51
>gnl|CDD|133415 cd04788, HTH_NolA-AlbR, Helix-Turn-Helix DNA binding domain of
the transcription regulators NolA and AlbR.
Helix-turn-helix (HTH) transcription regulators NolA
and AlbR, N-terminal domain. In Bradyrhizobium
(Arachis) sp. NC92, NolA is required for efficient
nodulation of host plants. In Xanthomonas albilineans,
AlbR regulates the expression of the pathotoxin,
albicidin. These proteins are putatively comprised of
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their conserved N-terminal domains contain
predicted winged HTH motifs that mediate DNA binding,
while the C-terminal domains are often unrelated and
bind specific coactivator molecules. They 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 = 96
Score = 29.7 bits (67), Expect = 0.055
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 8 GLLSLSVGTKSGYRLFSLNSIDTLEQI 34
GLLS S T+ G+RL+ I L QI
Sbjct: 24 GLLSPSQRTEGGHRLYDRADIRRLHQI 50
>gnl|CDD|133389 cd04761, HTH_MerR-SF, Helix-Turn-Helix DNA binding domain of
transcription regulators from the MerR superfamily.
Helix-turn-helix (HTH) transcription regulator MerR
superfamily, N-terminal domain. The MerR family
transcription regulators have been shown to mediate
responses to stress including exposure to heavy metals,
drugs, or oxygen radicals in eubacterial and some
archaeal species. They regulate transcription of
multidrug/metal ion transporter genes and oxidative
stress regulons by reconfiguring the spacer between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 49
Score = 28.3 bits (64), Expect = 0.087
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
GLLS T+ GYRL+S ++ L I
Sbjct: 23 IGLLS-PARTEGGYRLYSDADLERLRLI 49
>gnl|CDD|133381 cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of
the transcription regulators TipAL, Mta, and SkgA.
Helix-turn-helix (HTH) TipAL, Mta, and SkgA
transcription regulators, and related proteins,
N-terminal domain. TipAL regulates resistance to and
activation by numerous cyclic thiopeptide antibiotics,
such as thiostrepton. Mta is a global transcriptional
regulator; the N-terminal DNA-binding domain of Mta
interacts directly with the promoters of mta, bmr, blt,
and ydfK, and induces transcription of these
multidrug-efflux transport genes. SkgA has been shown
to control stationary-phase expression of
catalase-peroxidase in Caulobacter crescentus. These
proteins are comprised of distinct domains that harbor
an N-terminal active (DNA-binding) site and a
regulatory (effector-binding) site. The conserved
N-terminal domain of these transcription regulators
contains winged HTH motifs that mediate DNA binding.
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.
Unique to this family, is a TipAL-like, lineage
specific Bacilli subgroup, which has five conserved
cysteines in the C-terminus of the protein.
Length = 103
Score = 28.2 bits (64), Expect = 0.22
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
GLL S T++GYRL++ ++ L+QI
Sbjct: 23 IGLLKPSRRTENGYRLYTEEDLERLQQI 50
>gnl|CDD|223860 COG0789, SoxR, Predicted transcriptional regulators
[Transcription].
Length = 124
Score = 27.4 bits (61), Expect = 0.57
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
KGLLS + GYR ++ ++ L+ I
Sbjct: 23 KGLLSPERRDEGGYRYYTPEDLELLQII 50
>gnl|CDD|236907 PRK11410, PRK11410, hypothetical protein; Provisional.
Length = 561
Score = 26.6 bits (59), Expect = 1.2
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 48 LFSSSLVAVVSLSSPRKLTKEEGKNEEEEK 77
LF+S ++ LSSP L ++G++ E
Sbjct: 195 LFASKGDRLLVLSSPGMLFDDDGQDTEATA 224
>gnl|CDD|213351 cd12791, RasGAP_plexin_B3, Ras-GTPase Activating Domain of
plexin-B3. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity. Plexin-B3
is the receptor of semaphorin 5A. It is a highly potent
stimulator of neurite outgrowth of primary murine
cerebellar neurons. Plexin-B3 has been linked to verbal
performance and white matter volume in human brain.
Furthermore, Sema5A and plexin-B3 have been implicated
in the progression of various types of cancer. They
play an important role in the invasion and metastasis
of gastric carcinoma. The protein and mRNA expression
of Sema5A and its receptor plexin-B3 increased
gradually in non-neoplastic mucosa, primary gastric
carcinoma, and lymph node metastasis, and their
expression is correlated. The stimulation of plexin-B3
by Sema5A binding in human glioma cells results in the
inhibition of cell migration and invasion. Plexins
contain a C-terminal RasGAP domain, which functions as
an enhancer of the hydrolysis of GTP that is bound to
Ras-GTPases. Plexins display GAP activity towards the
Ras homolog Rap. Although the Rho (Ras homolog) GTPases
are most closely related to members of the Ras family,
RhoGAP and RasGAP show no sequence homology at their
amino acid level. RasGTPases function as molecular
switches in a large number of of signaling pathways.
When bound to GTP they are in the on state and when
bound to GDP they are in the off state. The RasGAP
domain speeds up the hydrolysis of GTP in Ras-like
proteins acting as a negative regulator.
Length = 397
Score = 26.0 bits (57), Expect = 1.9
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 21 RLFSLNSIDTLEQIYENSQEDVCIVERLFSSSL 53
+LF L I TLE+ SQ D C V L S +L
Sbjct: 54 KLFLLTLIHTLEEQPSFSQRDRCHVASLLSLAL 86
>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 = 25.6 bits (57), Expect = 1.9
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTL 31
GL+ + +GYR+++ I+ L
Sbjct: 23 IGLIPPPSRSDNGYRVYNQRDIEEL 47
>gnl|CDD|221653 pfam12588, PSDC, Phophatidylserine decarboxylase. This domain
family is found in bacteria and eukaryotes, and is
approximately 140 amino acids in length. The family is
found in association with pfam02666. Phosphatidylserine
decarboxylase (PSD) is an important enzyme in the
synthesis of phosphatidylethanolamine in both
prokaryotes and eukaryotes.
Length = 141
Score = 25.7 bits (57), Expect = 2.1
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 4 VPLKGLLSLSVGTKSGYRLF 23
P+ LL +GT SGY F
Sbjct: 74 FPINALLDWPMGTPSGYAAF 93
>gnl|CDD|213347 cd12787, RasGAP_plexin_B, Ras-GTPase Activating Domain of type B
plexins. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity.There are
three members of the Plexin-B subfamily, namely B1, B2
and B3. Plexins-B1, B2 and B3 are receptors for Sema4D,
Sema4C and Sema4G, and Sema5A, respectively. The
activation of plexin-B1 by Sema4D produces an acute
collapse of axonal growth cones in hippocampal and
retinal neurons over the early stages of neurite
outgrowth and promotes branching and complexity. By
signaling the effect of Sema4C and Sema4G, the
plexin-B2 receptor is critically involved in neural
tube closure and cerebellar granule cell development.
Plexin-B3, the receptor of Sema5A, is a highly potent
stimulator of neurite outgrowth of primary murine
cerebellar neurons. Plexin-B3 has been linked to verbal
performance and white matter volume in human brain.
Small GTPases play important roles in plexin-B
signaling. Plexin-B1 activates Rho through Rho-specific
guanine nucleotide exchange factors, leading to neurite
retraction. Plexin-B1 possesses an intrinsic
GTPase-activating protein activity for R-Ras and
induces growth cone collapse through R-Ras
inactivation. Plexins contain a C-terminal RasGAP
domain, which functions as an enhancer of the
hydrolysis of GTP that is bound to Ras-GTPases. Plexins
display GAP activity towards the Ras homolog Rap.
Although the Rho (Ras homolog) GTPases are most closely
related to members of the Ras family, RhoGAP and RasGAP
show no sequence homology at their amino acid level.
RasGTPases function as molecular switches in a large
number of of signaling pathways. When bound to GTP they
are in the on state and when bound to GDP they are in
the off state. The RasGAP domain speeds up the
hydrolysis of GTP in Ras-like proteins acting as a
negative regulator.
Length = 391
Score = 25.7 bits (56), Expect = 2.9
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 2 CSVPLKGLLSLSVGTKSGYRLFSLNSIDTLEQIYENSQEDVCIVERLFSSSL 53
+GL LS S +LF +N I TLE E S D V L + +L
Sbjct: 37 RPTVEQGLYQLSNLLNS--KLFLINFIHTLENQREFSARDRVYVASLLTVAL 86
>gnl|CDD|179503 PRK02929, PRK02929, L-arabinose isomerase; Provisional.
Length = 499
Score = 25.6 bits (57), Expect = 3.0
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 29 DTLEQIYENSQEDVCIVERLFSSSLVAV 56
+TL Q+ E+++E IV+ L +S + V
Sbjct: 22 ETLRQVAEHAEE---IVDGLNASGKLPV 46
>gnl|CDD|133378 cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of
MerR-like transcription regulators. Helix-turn-helix
(HTH) MerR-like transcription regulator, N-terminal
domain. The MerR family transcription regulators have
been shown to mediate responses to stress including
exposure to heavy metals, drugs, or oxygen radicals in
eubacterial and some archaeal species. They regulate
transcription of multidrug/metal ion transporter genes
and oxidative stress regulons by reconfiguring the
spacer between the -35 and -10 promoter elements. A
typical MerR regulator is comprised of two distinct
domains that harbor the regulatory (effector-binding)
site and the active (DNA-binding) site. Their
N-terminal domains are homologous and contain a
DNA-binding winged HTH motif, while the C-terminal
domains are often dissimilar and bind specific
coactivator molecules such as metal ions, drugs, and
organic substrates.
Length = 100
Score = 24.9 bits (55), Expect = 3.9
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTLEQI 34
KGLL +++GYRL+S ++ L I
Sbjct: 23 KGLLPPER-SENGYRLYSEEDLERLRLI 49
>gnl|CDD|221178 pfam11709, Mit_ribos_Mrp51, Mitochondrial ribosomal protein
subunit. This family is the mitochondrial ribosomal
small-subunit protein Mrp51. Its function is not
entirely clear, but deletion of the MRP51 gene
completely blocked mitochondrial gene expression.
Length = 302
Score = 25.0 bits (55), Expect = 4.1
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 17 KSGYRLFSLNSIDTLEQI 34
KS R S+N +DTLE +
Sbjct: 60 KSKSRHISVNDLDTLEHM 77
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 24.5 bits (54), Expect = 7.6
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 9/29 (31%)
Query: 55 AVVSLSSPR---------KLTKEEGKNEE 74
AV ++S PR KL KE+G+ EE
Sbjct: 326 AVYTISDPRAVILKKFAEKLAKEKGREEE 354
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 24.4 bits (53), Expect = 8.4
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 14 VGTKSGYRLFSLNSIDTLEQIYENSQEDVCIVE 46
+ T G + L TL+ + E D I
Sbjct: 247 ITTAHGNGIEDLIKRPTLKDLVEIQAFDRGIEL 279
>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 = 23.9 bits (52), Expect = 8.9
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 7 KGLLSLSVGTKSGYRLFSLNSIDTL 31
KGL+ + ++ GYR ++ +D L
Sbjct: 23 KGLIPPPLRSEGGYRTYTQQHLDEL 47
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
0.310 0.128 0.334
Gapped
Lambda K H
0.267 0.0823 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,718,492
Number of extensions: 277301
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 26
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
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: 53 (24.0 bits)