RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8133
(99 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 = 69.7 bits (171), Expect = 5e-17
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 1 GRVEVSREN-----KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTI 55
G VEV + + + + L PG +FGELA+L N R+AT++A +D +L + R F+ +
Sbjct: 44 GSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPRSDFRRL 103
Query: 56 MMRTGLIRQAEY 67
+ + +
Sbjct: 104 LQEYPELARRLL 115
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 57.3 bits (139), Expect = 2e-12
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 1 GRVEVSRENK-----YLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTI 55
G+V+V + ++ L+ L PG FGELA+L R+AT+ A +D +L I R+ F +
Sbjct: 26 GKVKVYKLDEDGREQILAFLGPGDFFGELALLGGEPRSATVVALTDSELLVIPREDFLEL 85
Query: 56 MMR 58
+ +
Sbjct: 86 LEQ 88
>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 = 49.7 bits (119), Expect = 3e-09
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 1 GRVEVSR-----ENKYLSTLAPGKVFGELAILYNCKR--TATIKAASDCKLWAIERQCFQ 53
G VEV + E + + TL PG FGELA+L N +R +A A L I+ + F
Sbjct: 44 GEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVALELATLLRIDFRDFL 103
Query: 54 TIMMRTGLI 62
++ +
Sbjct: 104 QLLPELPQL 112
>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 = 49.8 bits (119), Expect = 1e-08
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 1 GRVEVSREN-----KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTI 55
G V++ L L PG FGELA+L R+A+ A +D ++ I R+ F +
Sbjct: 50 GIVKLYANTEDGREIILGFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLEL 109
Query: 56 MMRTGLIRQA 65
+ + + A
Sbjct: 110 LAESPKLALA 119
>gnl|CDD|233835 TIGR02361, dak_ATP, dihydroxyacetone kinase, ATP-dependent. This
family consists of examples of the form of
dihydroxyacetone kinase (also called glycerone kinase)
that uses ATP (2.7.1.29) as the phosphate donor, rather
than a phosphoprotein as in E. coli. This form is
composed of a single chain with separable domains
homologous to the K and L subunits of the E. coli
enzyme, and is found in yeasts and other eukaryotes and
in some bacteria, including Citrobacter freundii. The
member from tomato has been shown to phosphorylate
dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some
other aldoses and ketoses (PMID:11985845).
Length = 574
Score = 28.5 bits (64), Expect = 0.48
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 59 TGLIRQAE-YNDFLKSVPIFKDLPEETLIKISDVLEESLG 97
+ L R AE + LKS + + P L +ISDV+E +G
Sbjct: 409 STLARGAEAILELLKSKKLPLNDPATLLAQISDVVEGVMG 448
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 28.5 bits (64), Expect = 0.52
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 69 DFLKSVPIFKDLPEETLIKISDVLE 93
+FL SVP+ + LP +L KI++V+
Sbjct: 8 EFLGSVPLLQRLPSSSLKKIAEVVV 32
>gnl|CDD|235027 PRK02301, PRK02301, putative deoxyhypusine synthase; Provisional.
Length = 316
Score = 28.1 bits (63), Expect = 0.66
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 65 AEYNDFLKSVPIFKDLPEETLIKISDVLEESLGSA 99
A++ +FL+ V F L EE + I D+L E +G
Sbjct: 139 ADFEEFLQDV--FPGLEEEGTVSIRDLLTE-IGRD 170
>gnl|CDD|239872 cd04407, RhoGAP_myosin_IXB, RhoGAP_myosin_IXB: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in myosins IXB. Class IX myosins
contain a characteristic head domain, a neck domain and
a tail domain which contains a C6H2-zinc binding motif
and a Rho-GAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing neurons
Small GTPases cluster into distinct families, and all
act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 26.9 bits (59), Expect = 1.8
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 6/36 (16%)
Query: 61 LIRQAEYNDFLKSVPIFKDLPE--ETLIKISDVLEE 94
L+ A+YNDFL++V +LPE E L I VLE+
Sbjct: 85 LMTFAQYNDFLRAV----ELPEKQEQLQAIYRVLEQ 116
>gnl|CDD|235623 PRK05849, PRK05849, hypothetical protein; Provisional.
Length = 783
Score = 26.5 bits (59), Expect = 3.0
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 27 LYNCKRTATIKAASDCKLWAIERQCF-QTIMMR----TGLIRQAEYNDFLKSV 74
L +CKR T+ A I R F T +++ G + Q E + FL S+
Sbjct: 441 LEDCKRYGTLPFA------GIARAAFVATQLLKSLVEIGALSQEELDAFLNSL 487
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 25.7 bits (57), Expect = 4.2
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 70 FLKSVPIFKDLPEETLIKI 88
F+ S P K PE+ L +I
Sbjct: 9 FITSAPDIKQYPEDDLPEI 27
>gnl|CDD|223628 COG0554, GlpK, Glycerol kinase [Energy production and conversion].
Length = 499
Score = 25.6 bits (57), Expect = 4.3
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 25 AILYNCKRTATIKAASDC-KLWAIERQCFQTIMMRTGLI 62
AI++ +RTA I C +L A + + I +TGL+
Sbjct: 101 AIVWQDRRTADI-----CEELKADGYE--ERIREKTGLV 132
>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 25.9 bits (57), Expect = 4.7
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 13 STLAPGKVFGELAILYNCKRTATIKAA 39
TL P VF LA + KRT +AA
Sbjct: 552 ITLGPAIVFAYLAARHAAKRTLARRAA 578
>gnl|CDD|184232 PRK13675, PRK13675, GTP cyclohydrolase; Provisional.
Length = 308
Score = 25.7 bits (57), Expect = 4.9
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 72 KSVPIFKDLPEETLIKISDVLEES 95
K V F LP++ ++ + + EES
Sbjct: 262 KVVEEFPHLPDDAVVTVRQINEES 285
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 25.1 bits (56), Expect = 6.1
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 61 LIRQAEYNDFLKSVPIFKDLPEETLIKI 88
I AE F+ S P + LP + +I
Sbjct: 3 FIHNAE---FVTSAPKLEQLPPDDGPEI 27
>gnl|CDD|213852 TIGR03707, PPK2_P_aer, polyphosphate kinase 2, PA0141 family.
Members of this protein family are designated
polyphosphate kinase 2 (PPK2) after the characterized
protein in Pseudomonas aeruginosa. This family comprises
one of three well-separated clades in the larger family
described by pfam03976. PA0141 from this family has been
shown capable of operating in reverse, with GDP
preferred (over ADP) as a substrate, producing GTP (or
ATP) by transfer of a phosphate residue from
polyphosphate. Most species with a member of this family
also encode a polyphosphate kinase 1 (PPK1) [Central
intermediary metabolism, Phosphorus compounds].
Length = 230
Score = 25.3 bits (56), Expect = 6.5
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 64 QAEYNDFLKSVPIFKDLPEETLIK 87
+Y +FL+ VP F E L+
Sbjct: 113 DEQYEEFLRQVPEF----ERMLVD 132
>gnl|CDD|131396 TIGR02343, chap_CCT_epsi, T-complex protein 1, epsilon subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
epsilon chain (part of a paralogous family) from
animals, plants, fungi, and other eukaryotes.
Length = 532
Score = 25.1 bits (55), Expect = 6.9
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 74 VPIFKDLPEETLIKISDVLEESLGS 98
VP F++L ++ L K V E S G+
Sbjct: 337 VPRFQELSKDKLGKAGLVREISFGT 361
>gnl|CDD|147852 pfam05925, IpgD, Enterobacterial virulence protein IpgD. This
family consists of several enterobacterial IpgD like
virulence factor proteins. In the Gram-negative pathogen
Shigella flexneri, the virulence factor IpgD is
translocated directly into eukaryotic cells and acts as
a potent inositol 4-phosphatase that specifically
dephosphorylates phosphatidylinositol 4,5-bisphosphate
[PtdIns(4,5)P(2)] into phosphatidylinositol
5-monophosphate [PtdIns(5)P] that then accumulates.
Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by
IpgD is responsible for dramatic morphological changes
of the host cell, leading to a decrease in membrane
tether force associated with membrane blebbing and actin
filament remodelling.
Length = 569
Score = 25.0 bits (54), Expect = 9.6
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 38 AASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETL 85
+A KL + E++ FQ I++ +G + E N + K LP E+L
Sbjct: 498 SALGSKLDSEEKKIFQKILLNSGNMEDQEMNTGGAGNKVMKKLPLESL 545
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
0.320 0.135 0.387
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: 4,870,383
Number of extensions: 387116
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 25
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)