RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8827
(82 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 50.0 bits (120), Expect = 2e-09
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 9 SFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMY 56
FGELALL N PR+AT++A + L + R F++++ + R++
Sbjct: 68 LFGELALLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 45.8 bits (109), Expect = 4e-08
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 10 FGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKS 48
FGELALL PR+AT+ A + L + R+ F +++ +
Sbjct: 51 FGELALLGGEPRSATVVALTDSELLVIPREDFLELLEQD 89
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 39.7 bits (93), Expect = 1e-05
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 9 SFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEKLI 60
FGELALL N RAA+ A + L + R F+ + + + E L+
Sbjct: 68 FFGELALLTNSRRAASAAAVAL-ELATLLRIDFRDFLQLLPELPQLLLELLL 118
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 37.9 bits (88), Expect = 1e-04
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 10 FGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKS 48
FGELALL PR+A+ A + + + RK F +++ +S
Sbjct: 75 FGELALLGGDPRSASAVALTDVEVLEIPRKDFLELLAES 113
>gnl|CDD|132962 cd06631, STKc_YSK4, Catalytic domain of the Protein
Serine/Threonine Kinase, Yeast Sps1/Ste20-related
kinase 4. Serine/threonine kinases (STKs), yeast
Sps1/Ste20-related kinase 4 (YSK4) subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The YSK4 subfamily is
part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. YSK4 is a putative MAPKKK,
whose mammalian gene has been isolated. MAPKKKs (MKKKs
or MAP3Ks) phosphorylate and activate MAPK kinases
(MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate
and activate MAPKs during signaling cascades that are
important in mediating cellular responses to
extracellular signals.
Length = 265
Score = 26.4 bits (58), Expect = 1.6
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 28 TSTGSLWAMDRKTFKQIVLKSAFK--KRKMYEKLIDAVPMLKSLQVMVFFLYL 78
T+ G L A+ KQ+ L ++ K YEKL + V +LKSL+ + YL
Sbjct: 21 TNQGQLIAV-----KQVELDTSNVLAAEKEYEKLQEEVDLLKSLKHVNIVQYL 68
>gnl|CDD|173732 cd06628, STKc_MAPKKK_Byr2_like, Catalytic domain of fungal
Byr2-like MAP Kinase Kinase Kinases. Serine/threonine
kinases (STKs), mitogen-activated protein kinase (MAPK)
kinase kinase (MAPKKK) subfamily, fungal Byr2-like
proteins, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
MAPKKK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. Members of this group
include the MAPKKKs Schizosaccharomyces pombe Byr2,
Saccharomyces cerevisiae and Cryptococcus neoformans
Ste11, and related proteins. They contain an N-terminal
SAM (sterile alpha-motif) domain, which mediates
protein-protein interaction, and a C-terminal catalytic
domain. MAPKKKs phosphorylate and activate MAPK kinases
(MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate
and activate MAPKs during signaling cascades that are
important in mediating cellular responses to
extracellular signals. Fission yeast Byr2 is regulated
by Ras1. It responds to pheromone signaling and
controls mating through the MAPK pathway. Budding yeast
Ste11 functions in MAPK cascades that regulate mating,
high osmolarity glycerol, and filamentous growth
responses.
Length = 267
Score = 26.3 bits (58), Expect = 1.7
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 8 GSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLK 67
GSFG + L N S+G L A+ + + S +KR M + L + +LK
Sbjct: 11 GSFGSVYLGMN---------ASSGELMAVKQVELPSVSASSKDRKRSMLDALAREIALLK 61
Query: 68 SLQVMVFFLYLVCAL 82
LQ YL +L
Sbjct: 62 ELQHENIVQYLGSSL 76
>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription].
Length = 286
Score = 26.2 bits (57), Expect = 1.9
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 38 RKTFKQIVLKSAFKKRKMYEKLIDAVP 64
R+T ++ + +A KK +M++ LID VP
Sbjct: 160 RRTLQKSDIAAAVKKSEMFDFLIDIVP 186
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 26.1 bits (58), Expect = 2.0
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 36 MDRKTFKQIVLK-SAFKKRKMYEKLIDAVPMLKSLQ 70
+D+ F I LK F Y DAV ML+ L
Sbjct: 258 LDKMGFDYIGLKEEHFDHDLQYT---DAVEMLERLM 290
>gnl|CDD|113081 pfam04297, UPF0122, Putative helix-turn-helix protein, YlxM / p13
like. Members of this family are predicted to contain
a helix-turn-helix motif, for example residues 37-55 in
Mycoplasma mycoides p13. Genes encoding family members
are often part of operons that encode components of the
SRP pathway, and this protein may regulate the
expression of an operon related to the SRP pathway.
Length = 101
Score = 25.4 bits (56), Expect = 2.5
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 4 YEDKGSFGELALLYNMPRAA---TIKATSTGSLWAMDRKTFKQIVLKSAFKKR-KMYEKL 59
Y D S E+A +N+ R A IK T M +++ L +K R ++YEK+
Sbjct: 30 YLDDLSLSEIAEEFNVSRQAVYDNIKRTE-----KMLESYEEKLHLYEKYKLRNELYEKI 84
Query: 60 IDAVPMLKSLQ 70
D K L+
Sbjct: 85 KDKQLKDKDLE 95
>gnl|CDD|131921 TIGR02874, spore_ytfJ, sporulation protein YtfJ. Members of this
protein family, exemplified by YtfJ of Bacillus
subtilis, are encoded by bacterial genomes if and only
if the species is capable of endospore formation. YtfJ
was confirmed in spores of Bacillus subtilis; it appears
to be expressed in the forespore under control of SigF
(see PMID:12480901) [Cellular processes, Sporulation and
germination].
Length = 125
Score = 24.7 bits (54), Expect = 5.6
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 55 MYEKLIDAVPML 66
+YEKLID P L
Sbjct: 102 LYEKLIDLAPQL 113
>gnl|CDD|216127 pfam00800, PDT, Prephenate dehydratase. This protein is involved
in Phenylalanine biosynthesis. This protein catalyzes
the decarboxylation of prephenate to phenylpyruvate.
Length = 181
Score = 24.8 bits (55), Expect = 6.1
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 7 KGSFGELALLYNMPRAATIKATST 30
+G+F E A L ++ + +
Sbjct: 7 EGTFSEQAALKLFGQSVELVPCPS 30
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
0.327 0.135 0.391
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,015,323
Number of extensions: 297546
Number of successful extensions: 324
Number of sequences better than 10.0: 1
Number of HSP's gapped: 323
Number of HSP's successfully gapped: 17
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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 (21.7 bits)
S2: 53 (24.3 bits)