RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy505
(161 letters)
>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 = 26.8 bits (60), Expect = 0.98
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
T+ GYRL+S ++ L I
Sbjct: 31 TEGGYRLYSDADLERLRLI 49
>gnl|CDD|197716 smart00422, HTH_MERR, helix_turn_helix, mercury resistance.
Length = 70
Score = 27.1 bits (61), Expect = 1.3
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
T+ GYRL+S ++ L I
Sbjct: 32 TEGGYRLYSDEDLERLRFI 50
>gnl|CDD|184416 PRK13955, mscL, large-conductance mechanosensitive channel;
Provisional.
Length = 130
Score = 27.1 bits (60), Expect = 2.8
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 144 KLNRKKEEEEDEEEE 158
KL KKEEE++EE
Sbjct: 92 KLTSKKEEEKEEEIP 106
>gnl|CDD|221418 pfam12094, DUF3570, Protein of unknown function (DUF3570). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 396 to 444 amino acids in length.
Length = 407
Score = 27.4 bits (61), Expect = 3.5
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 56 AHDSPLAALASLSVGTKSGYRLFSLNSIDTLEQIYENSQED 96
+ D L+A + ++G K G +L ID + Y+ +
Sbjct: 341 SSDYRLSAFGAYTIGLKFGKKLSGGLEIDLRYEYYQQNPGL 381
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the
BmrR transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic
substances and antibiotics. BmrR is comprised of two
distinct domains that harbor a regulatory
(effector-binding) site and an active (DNA-binding)
site. The conserved N-terminal domain contains a winged
HTH motif that mediates DNA binding, while the
C-terminal domain binds coactivating, toxic compounds.
BmrR shares 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 = 108
Score = 26.3 bits (59), Expect = 4.5
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 24/64 (37%)
Query: 36 SIGEV-QIFDADNLHAKTM---------IPAHDSPLAALASLSVGTKSGYRLFSLNSIDT 85
+IGE ++ NL K + PA+ V +GYR +S ++
Sbjct: 2 TIGEFAKLS---NLSIKALRYYDKIGLLKPAY-----------VDPDTGYRYYSAEQLER 47
Query: 86 LEQI 89
L +I
Sbjct: 48 LNRI 51
>gnl|CDD|239011 cd02056, alpha-1-antitrypsin_like, alpha-1-antitrypsin_like. This
family contains a variety of different members of clade
A of the serpin superfamily. They include the classical
serine proteinase inhibitors, alpha-1-antitrypsin and
alpha-1-antichymotrypsin, protein C inhibitor,
kallistatin, and noninhibitory serpins, like
corticosteroid and thyroxin binding globulins. In
general, SERine Proteinase INhibitors (serpins) exhibit
conformational polymorphism shifting from native to
cleaved, latent, delta, or polymorphic forms. Many
serpins, such as antitrypsin and antichymotrypsin,
function as serine protease inhibitors which regulate
blood coagulation cascades. Non-inhibitory serpins
perform many diverse functions such as chaperoning
proteins or transporting hormones. Serpins are of
medical interest because mutants have been associated
with blood clotting disorders, emphysema, cirrhosis,
and dementia.
Length = 361
Score = 27.2 bits (61), Expect = 4.6
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 13/36 (36%)
Query: 59 SPL---AALASLSVGTKSGYRLFSLNSIDTLEQIYE 91
SP+ ALA LS+G +S TL QI E
Sbjct: 25 SPVSISTALAMLSLGARS----------STLAQILE 50
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 25.7 bits (57), Expect = 4.8
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 148 KKEEEEDEEEE 158
KKEEEE+EEE+
Sbjct: 70 KKEEEEEEEED 80
>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 = 26.2 bits (58), Expect = 6.8
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 64 LASLSVGTKSGYRLFSLNSIDTLEQI 89
L S S ++S YRL+ ++ LEQI
Sbjct: 26 LLSPSARSESNYRLYGERDLERLEQI 51
>gnl|CDD|185334 PRK15437, PRK15437, histidine ABC transporter substrate-binding
protein HisJ; Provisional.
Length = 259
Score = 26.5 bits (58), Expect = 6.8
Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 12/110 (10%)
Query: 22 VNSDNCYLAYPGSNSIGEVQIFDADNLHA-----KTMIPAHDSPLAALASLSVGTKSGYR 76
+ +D Y + NS GE+ FD D T ++PL AL S+ K
Sbjct: 30 IGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIP-SLKAKK--- 85
Query: 77 LFSLNSIDTLEQIYENSQEDVCIVERLFSSSLVAVVSLSSPRKLTVCHFK 126
+++I + I E Q+++ ++L+++ VV+ +S + TV K
Sbjct: 86 ---IDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLK 132
>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 = 26.7 bits (59), Expect = 7.2
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 76 RLFSLNSIDTLEQIYENSQEDVCIVERLFSSSL 108
+LF L I TLE+ SQ D C V L S +L
Sbjct: 54 KLFLLTLIHTLEEQPSFSQRDRCHVASLLSLAL 86
>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 = 25.5 bits (57), Expect = 7.9
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
T++GYRL++ ++ L+QI
Sbjct: 32 TENGYRLYTEEDLERLQQI 50
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 25.5 bits (56), Expect = 8.9
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 147 RKKEEEEDEEEEKK 160
R++EEEE+EE EK+
Sbjct: 95 RQEEEEEEEENEKQ 108
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
0.316 0.131 0.378
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: 7,849,067
Number of extensions: 674918
Number of successful extensions: 1151
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1144
Number of HSP's successfully gapped: 20
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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 (21.6 bits)
S2: 55 (24.8 bits)