RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10446
(158 letters)
>gnl|CDD|217545 pfam03416, Peptidase_C54, Peptidase family C54.
Length = 277
Score = 123 bits (312), Expect = 1e-35
Identities = 47/114 (41%), Positives = 67/114 (58%), Gaps = 5/114 (4%)
Query: 27 GRDWQWNVNSKEEA-YLKILKMFEDRRTAPYSIHQIALTGASE-GKAVGEWFGPNTVAQV 84
GRDW+W + + Y KIL F D AP+SIHQ G S GK GEWFGPNTVA++
Sbjct: 58 GRDWRWPAEKEPDEEYKKILAWFGDSPDAPFSIHQFVQMGKSLCGKKPGEWFGPNTVARI 117
Query: 85 LRKLAKYDDWSSIVFHVALDNTLVVNQVKKLCTTNKRKLAKYDDWSSIVFHVAL 138
L+KL K+DDWS + +VA+D T+V + + + C+ + W ++ + L
Sbjct: 118 LKKLVKFDDWSGLAVYVAMDGTVVYDDIVEKCSAPNNGQSA---WKPLLLLIPL 168
>gnl|CDD|216677 pfam01747, ATP-sulfurylase, ATP-sulfurylase. This domain is the
catalytic domain of ATP-sulfurylase or sulfate
adenylyltransferase EC:2.7.7.4 some of which are part of
a bifunctional polypeptide chain associated with
adenosyl phosphosulphate (APS) kinase pfam01583. Both
enzymes are required for PAPS
(phosphoadenosine-phosphosulfate) synthesis from
inorganic sulphate. ATP sulfurylase catalyzes the
synthesis of adenosine-phosphosulfate APS from ATP and
inorganic sulphate.
Length = 214
Score = 31.0 bits (71), Expect = 0.16
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 34 VNSKEEAYLKILKMFEDRRTAPYSIH-QIALTG------ASEGKAVGEWFGPNTVAQVLR 86
V +E Y K +T P+ +I+L+G EG+ EWF VA+VLR
Sbjct: 152 VPFREAVYCKKCGEMVSTKTCPHGKEDRISLSGTKLREMLREGEEPPEWFSRPEVAKVLR 211
Query: 87 K 87
+
Sbjct: 212 E 212
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 29.6 bits (68), Expect = 0.69
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 9/31 (29%)
Query: 80 TVAQVLRKLAKYDDWSSIVFHVALDNTLVVN 110
TVAQV+RKL ++ A++ T+VV
Sbjct: 204 TVAQVVRKLEEHG---------AMEYTIVVA 225
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 27.7 bits (62), Expect = 0.88
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 11/49 (22%)
Query: 28 RDWQWNVNSKEEAYLKILKMFEDRRTAPYSIHQIALTGASEGKAVGEWF 76
R W + K++ D+ T P + S +A EWF
Sbjct: 30 RTWPPMI-----------KIYTDKETEPKGEATVTYDDPSAAQAAIEWF 67
>gnl|CDD|173895 cd00517, ATPS, ATP-sulfurylase. ATP-sulfurylase (ATPS), also known
as sulfate adenylate transferase, catalyzes the transfer
of an adenylyl group from ATP to sulfate, forming
adenosine 5'-phosphosulfate (APS). This reaction is
generally accompanied by a further reaction, catalyzed
by APS kinase, in which APS is phosphorylated to yield
3'-phospho-APS (PAPS). In some organisms the APS kinase
is a separate protein, while in others it is
incorporated with ATP sulfurylase in a bifunctional
enzyme that catalyzes both reactions. In bifunctional
proteins, the domain that performs the kinase activity
can be attached at the N-terminal end of the sulfurylase
unit or at the C-terminal end, depending on the
organism. While the reaction is ubiquitous among
organisms, the physiological role of the reaction
varies. In some organisms it is used to generate APS
from sulfate and ATP, while in others it proceeds in the
opposite direction to generate ATP from APS and
pyrophosphate. ATP sulfurylase can be a monomer, a
homodimer, or a homo-oligomer, depending on the
organism. ATPS belongs to a large superfamily of
nucleotidyltransferases that includes pantothenate
synthetase (PanC), phosphopantetheine
adenylyltransferase (PPAT), and the amino-acyl tRNA
synthetases. The enzymes of this family are structurally
similar and share a dinucleotide-binding domain.
Length = 353
Score = 28.4 bits (64), Expect = 1.5
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 34 VNSKEEAYLKILKMFEDRRTAPYSIHQIALTG------ASEGKAVGEWFGPNTVAQVLRK 87
V +E AY T P+ + ++G EG+ EWF VA+VLR+
Sbjct: 293 VPFREAAYCPKCDGMASEDTCPHGEDFLNISGTKLRKMLREGEKPPEWFMRPEVAKVLRE 352
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 27.0 bits (60), Expect = 4.4
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 6 PKDQDFLID-WKGVTFEPSSFSGRDWQWNVNSKEEAYLKILKMFEDRRTAPY 56
P DQ F W V F P + + V + E LK ++M++ R PY
Sbjct: 88 PDDQVFSSTVWDDVAFGPVNMGLD--KDEVERRVEEALKAVRMWDFRDKPPY 137
>gnl|CDD|234344 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
family. Members of this protein are assigned by
homology to the TraD family of conjugative coupling
factor. This particular clade serves as a marker for an
extended gene region that occurs occasionally on
plasmids, including the toluene catabolism TOL plasmid.
More commonly, the gene region is chromosomal, flanked
by various markers of conjugative transfer and
insertion.
Length = 643
Score = 27.3 bits (61), Expect = 4.6
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 62 ALTGASEGKAVGE--WFGPNTVAQVLRKLAKYDDWSSIVFHV 101
L+G A E W N VA+ L L + D+ I+ +V
Sbjct: 272 QLSGEGNSAAFKEFAWRFVNIVARALVALGQRPDYQLILRYV 313
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 27.0 bits (60), Expect = 5.0
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 9/31 (29%)
Query: 80 TVAQVLRKLAKYDDWSSIVFHVALDNTLVVN 110
TVAQV+RKL ++ A+ T+VV
Sbjct: 203 TVAQVVRKLEEHG---------AMAYTIVVA 224
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 26.8 bits (60), Expect = 6.5
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 9/31 (29%)
Query: 79 NTVAQVLRKLAKYDDWSSIVFHVALDNTLVV 109
+TVA V+R L ++ A+D T+VV
Sbjct: 203 STVANVVRTLEEHG---------AMDYTIVV 224
>gnl|CDD|184028 PRK13398, PRK13398, 3-deoxy-7-phosphoheptulonate synthase;
Provisional.
Length = 266
Score = 26.2 bits (58), Expect = 8.7
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 52 RTAPYSIHQIALTGASEGKAVGEWFGPNTVAQVL-----RKLAKYDD 93
RT+PYS + G K VG+ + V +V+ ++A Y D
Sbjct: 66 RTSPYSFQGLGEEGLKILKEVGDKYNLPVVTEVMDTRDVEEVADYAD 112
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant
RNA polymerase IV, C-terminal domain. Higher plants
have five multi-subunit nuclear RNA polymerases: RNAP I,
RNAP II and RNAP III, which are essential for viability;
plus the two isoforms of the non-essential polymerase
RNAP IV (IVa and IVb), which specialize in small
RNA-mediated gene silencing pathways. RNAP IVa and/or
RNAP IVb might be involved in RNA-directed DNA
methylation of endogenous repetitive elements, silencing
of transgenes, regulation of flowering-time genes,
inducible regulation of adjacent gene pairs, and
spreading of mobile silencing signals. NRPD1a is the
largest subunit of RNAP IVa, whereas NRPD1b is the
largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 26.2 bits (58), Expect = 8.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 18 VTFEPSSFSGRDWQWNVNSKEEAYLKILKMFEDRRTAPYSIHQIA 62
VT E S R WNV +A + ++ + + R+ PYSI QI
Sbjct: 224 VTVEESCKKTRGNAWNV--VMDACIPVMDLIDWERSMPYSIQQIK 266
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 0.133 0.415
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,866,598
Number of extensions: 678481
Number of successful extensions: 538
Number of sequences better than 10.0: 1
Number of HSP's gapped: 536
Number of HSP's successfully gapped: 18
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
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: 55 (25.0 bits)