RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2864
(85 letters)
>gnl|CDD|173789 cd04059, Peptidases_S8_Protein_convertases_Kexins_Furin-like,
Peptidase S8 family domain in Protein convertases.
Protein convertases, whose members include furins and
kexins, are members of the peptidase S8 or Subtilase
clan of proteases. They have an Asp/His/Ser catalytic
triad that is not homologous to trypsin. Kexins are
involved in the activation of peptide hormones, growth
factors, and viral proteins. Furin cleaves cell
surface vasoactive peptides and proteins involved in
cardiovascular tissue remodeling in the TGN, at cell
surface, or in endosomes but rarely in the ER. Furin
also plays a key role in blood pressure regulation
though the activation of transforming growth factor
(TGF)-beta. High specificity is seen for cleavage after
dibasic (Lys-Arg or Arg-Arg) or multiple basic residues
in protein convertases. There is also strong sequence
conservation.
Length = 297
Score = 64.5 bits (158), Expect = 5e-14
Identities = 25/35 (71%), Positives = 27/35 (77%)
Query: 48 PSDPYFPFQWYLKNTGQNGGKAKLDLNVEAAWAQG 82
P+DP FP+QWYLKNTGQ GG LDLNV AW QG
Sbjct: 1 PNDPLFPYQWYLKNTGQAGGTPGLDLNVTPAWEQG 35
>gnl|CDD|234834 PRK00777, PRK00777, phosphopantetheine adenylyltransferase;
Provisional.
Length = 153
Score = 29.4 bits (67), Expect = 0.14
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 22 KRVKRGYKPLKVENLVPDIVMKESQDP 48
R +RG KPL++ V D V+ E P
Sbjct: 108 IRRERGLKPLEIV--VIDFVLAEDGKP 132
>gnl|CDD|182923 PRK11041, PRK11041, DNA-binding transcriptional regulator CytR;
Provisional.
Length = 309
Score = 28.8 bits (65), Expect = 0.23
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 17/58 (29%)
Query: 3 KVEQSRRNYVHQAVQQSGF------KRVKRG-YKPLKVENLVPDIVMKESQDPSDPYF 53
KV Q+ R V QAV + G+ + +KR + + V +VPDI DP+F
Sbjct: 3 KVSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILV--IVPDI--------CDPFF 50
>gnl|CDD|173810 cd07484, Peptidases_S8_Thermitase_like, Peptidase S8 family
domain in Thermitase-like proteins. Thermitase is a
non-specific, trypsin-related serine protease with a
very high specific activity. It contains a subtilisin
like domain. The tertiary structure of thermitase is
similar to that of subtilisin BPN'. It contains a
Asp/His/Ser catalytic triad. Members of the peptidases
S8 (subtilisin and kexin) and S53 (sedolisin) clan
include endopeptidases and exopeptidases. The S8
family has an Asp/His/Ser catalytic triad similar to
that found in trypsin-like proteases, but do not share
their three-dimensional structure and are not
homologous to trypsin. Serine acts as a nucleophile,
aspartate as an electrophile, and histidine as a base.
The S53 family contains a catalytic triad Glu/Asp/Ser
with an additional acidic residue Asp in the oxyanion
hole, similar to that of subtilisin. The serine
residue here is the nucleophilic equivalent of the
serine residue in the S8 family, while glutamic acid
has the same role here as the histidine base.
However, the aspartic acid residue that acts as an
electrophile is quite different. In S53 the it
follows glutamic acid, while in S8 it precedes
histidine. The stability of these enzymes may be
enhanced by calcium, some members have been shown to
bind up to 4 ions via binding sites with different
affinity. There is a great diversity in the
characteristics of their members: some contain
disulfide bonds, some are intracellular while others
are extracellular, some function at extreme
temperatures, and others at high or low pH values.
Length = 260
Score = 28.8 bits (65), Expect = 0.25
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 48 PSDPYFPFQWYLKNTGQNGG 67
P+DPY+ +QW L G
Sbjct: 2 PNDPYYSYQWNLDQIGAPKA 21
>gnl|CDD|145910 pfam03012, PP_M1, Phosphoprotein. This family includes the M1
phosphoprotein non-structural RNA polymerase alpha
subunit, which is thought to be a component of the
active polymerase, and may be involved in template
binding.
Length = 298
Score = 28.2 bits (63), Expect = 0.40
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 39 DIVMKESQDPSDPYFPFQWYLKNTG 63
D M E +DP Y PFQ YL G
Sbjct: 80 DFYMTEGEDP---YIPFQSYLDEIG 101
>gnl|CDD|233756 TIGR02166, dmsA_ynfE, anaerobic dimethyl sulfoxide reductase, A
subunit, DmsA/YnfE family. Members of this family
include known and probable dimethyl sulfoxide reductase
(DMSO reductase) A chains. In E. coli, dmsA encodes the
canonical anaerobic DMSO reductase A chain. The paralog
ynfE, as part of ynfFGH expressed from a multicopy
plasmid, could complement a dmsABC deletion, suggesting
a similar function and some overlap in specificity,
although YnfE could not substitute for DmsA in a mixed
complex.
Length = 797
Score = 28.2 bits (63), Expect = 0.44
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 67 GKAKLDLNVEAAWAQGGNC 85
GK KLD N++ W GNC
Sbjct: 450 GKDKLDSNIKFLWNYAGNC 468
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 26.1 bits (58), Expect = 2.1
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 47 DPSDPYFPFQW 57
DPS + P+QW
Sbjct: 1263 DPSLSFHPWQW 1273
>gnl|CDD|131211 TIGR02156, PA_CoA_Oxy1, phenylacetate-CoA oxygenase, PaaG subunit.
Phenylacetate-CoA oxygenase is comprised of a five gene
complex responsible for the hydroxylation of
phenylacetate-CoA (PA-CoA) as the second catabolic step
in phenylacetic acid (PA) degradation. Although the
exact function of this enzyme has not been determined,
it has been shown to be required for phenylacetic acid
degradation and has been proposed to function in a
multicomponent oxygenase acting on phenylacetate-CoA
[Energy metabolism, Other].
Length = 289
Score = 26.0 bits (57), Expect = 2.2
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 3 KVEQSRRNYVHQAVQQSGFKRVKRGYKPLKVENL 36
K + R ++V+ + FK+V +G P E L
Sbjct: 240 KQNEERGHWVYGEIDWDEFKQVIKGNGPCNKERL 273
>gnl|CDD|234301 TIGR03663, TIGR03663, TIGR03663 family protein. Members of this
protein family, uncommon and rather sporadically
distributed, are found almost always in the same genomes
as members of family TIGR03662, and frequently as a
nearby gene. Members show some N-terminal sequence
similarity with Pfam family pfam02366,
dolichyl-phosphate-mannose-protein mannosyltransferase.
The few invariant residues in this family, found toward
the N-terminus, include a dipeptide DE, a tripeptide
HGP, and two different Arg residues. Up to three members
may be found in a genome. The function is unknown.
Length = 439
Score = 26.2 bits (58), Expect = 2.2
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 47 DPSDPYFPFQWYLK 60
P + Y+P WYL+
Sbjct: 419 GPVNLYWPLPWYLR 432
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 89
Score = 25.2 bits (56), Expect = 2.4
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 19/53 (35%)
Query: 11 YVHQAVQQSGFKRVK-----------RGYKPLKVENLVPDIVMKESQDPSDPY 52
YV + + RVK +GY L NLV D ++ +DP DPY
Sbjct: 10 YVDKKI------RVKFQGGREVTGILKGYDQLL--NLVLDDTVEYLRDPEDPY 54
>gnl|CDD|223950 COG1019, COG1019, Predicted nucleotidyltransferase [General
function prediction only].
Length = 158
Score = 25.3 bits (56), Expect = 3.3
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 22 KRVKRGYKPLKVENLVPDIVMKESQDP 48
R KRG PL++ V D V+ E P
Sbjct: 112 IREKRGLPPLEII--VIDYVLAEDGKP 136
>gnl|CDD|233554 TIGR01739, tegu_FGAM_synt, herpesvirus tegument
protein/v-FGAM-synthase. This model describes a family
of large proteins of herpesvirues. The protein is
described variably as tegument protein or
phosphoribosylformylglycinamidine synthase
(FGAM-synthase). Most of the length of the protein shows
homology to eukaryotic FGAM-synthase. Functional
characterizations were not verified during construction
of this model.
Length = 1202
Score = 25.8 bits (57), Expect = 3.4
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 47 DPSDPYFPFQW 57
DPS +FP+QW
Sbjct: 1164 DPSLSFFPWQW 1174
>gnl|CDD|233802 TIGR02258, 2_5_ligase, 2'-5' RNA ligase. This protein family
consists of bacterial and archaeal proteins with two
tandem copies of Pfam domain pfam02834. Members for
which activity has been measured perform a reversible,
ATP-independent 2'-5'-ligation of what is presumably a
non-phyiological substrate: half-tRNA splice
intermediates from an intron-containing yeast tRNA. The
physiological substrate(s) in prokaryotes may include
small 2'-5'-link-containing oligonucleotides, perhaps
with regulatory or biosynthetic roles [Transcription,
RNA processing].
Length = 179
Score = 25.3 bits (56), Expect = 3.4
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 4 VEQSR-----RNYVHQAVQQSGFKRVKRGYKP----LKVENLVPDIVMKESQDPSDPYFP 54
VEQS + + + + GF + +R + P + ++ P + + ++ +
Sbjct: 92 VEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVPEFLQEFANEEFGS 151
Query: 55 FQ 56
F
Sbjct: 152 FH 153
>gnl|CDD|219279 pfam07044, DUF1329, Protein of unknown function (DUF1329). This
family consists of several hypothetical bacterial
proteins of around 475 residues in length. The majority
of family members are from Pseudomonas species but the
family also contains sequences from Shewanella
oneidensis and Thauera aromatica.
Length = 368
Score = 25.2 bits (56), Expect = 4.1
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 38 PDIVMKESQDPSDPYFPFQWYLKNTGQNGGKAKLD 72
PD M +P + T +N GKAKLD
Sbjct: 26 PDYRMPVYPTHRTAAYP-DEVYEATKKNAGKAKLD 59
>gnl|CDD|240303 PTZ00170, PTZ00170, D-ribulose-5-phosphate 3-epimerase;
Provisional.
Length = 228
Score = 25.3 bits (56), Expect = 4.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 1 MPKVEQSRRNYVHQAVQQSG 20
MPKV + R+ Y H +Q G
Sbjct: 161 MPKVRELRKRYPHLNIQVDG 180
>gnl|CDD|234456 TIGR04074, bacter_Hen1, 3' terminal RNA ribose
2'-O-methyltransferase Hen1. Members of this protein
family are bacterial Hen1, a 3' terminal RNA ribose
2'-O-methyltransferase that acts in bacterial RNA
repair. All members of the seed alignment belong to a
cassette with the RNA repair enzyme polynucleotide
kinase-phosphatase (Pnkp). Chemically similar Hen1 in
eukaryotes acts instead on small regulatory RNAs
[Transcription, RNA processing, Protein synthesis, tRNA
and rRNA base modification].
Length = 462
Score = 25.0 bits (55), Expect = 6.0
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 2 PKVEQSRRNYVHQAVQQSGFKRV 24
P + + R V A+++SG + V
Sbjct: 264 PSLNRQRLEAVVAALRESGARSV 286
>gnl|CDD|131458 TIGR02405, trehalos_R_Ecol, trehalose operon repressor,
proteobacterial. This family consists of repressors of
the LacI family typically associated with trehalose
utilization operons. Trehalose is imported as
trehalose-6-phosphate and then hydrolyzed by
alpha,alpha-phosphotrehalase to glucose and
glucose-6-P. This family includes repressors mostly
from Gammaproteobacteria and does not include the GntR
family TreR of Bacillus subtilis [Regulatory functions,
DNA interactions].
Length = 311
Score = 24.8 bits (54), Expect = 6.3
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 2 PKVEQSRRNYVHQAVQQSGF 21
PKV R V Q +QQSGF
Sbjct: 26 PKVSIETRERVEQVIQQSGF 45
>gnl|CDD|241369 cd13215, PH-GRAM1_AGT26, Autophagy-related protein 26/Sterol
3-beta-glucosyltransferase Pleckstrin homology (PH)
domain, repeat 1. ATG26 (also called
UGT51/UDP-glycosyltransferase 51), a member of the
glycosyltransferase 28 family, resulting in the
biosynthesis of sterol glucoside. ATG26 in decane
metabolism and autophagy. There are 32 known
autophagy-related (ATG) proteins, 17 are components of
the core autophagic machinery essential for all
autophagy-related pathways and 15 are the additional
components required only for certain pathways or
species. The core autophagic machinery includes 1) the
ATG9 cycling system (ATG1, ATG2, ATG9, ATG13, ATG18,
and ATG27), 2) the phosphatidylinositol 3-kinase
complex (ATG6/VPS30, ATG14, VPS15, and ATG34), and 3)
the ubiquitin-like protein system (ATG3, ATG4, ATG5,
ATG7, ATG8, ATG10, ATG12, and ATG16). Less is known
about how the core machinery is adapted or modulated
with additional components to accommodate the
nonselective sequestration of bulk cytosol
(autophagosome formation) or selective sequestration of
specific cargos (Cvt vesicle, pexophagosome, or
bacteria-containing autophagosome formation). The
pexophagosome-specific additions include the
ATG30-ATG11-ATG17 receptor-adaptors complex, the
coiled-coil protein ATG25, and the sterol
glucosyltransferase ATG26. ATG26 is necessary for the
degradation of medium peroxisomes. It contains 2 GRAM
domains and a single PH domain. PH domains are only
found in eukaryotes. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. PH domains also have
diverse functions. They are often involved in targeting
proteins to the plasma membrane, but few display strong
specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 130
Score = 24.1 bits (53), Expect = 8.9
Identities = 4/9 (44%), Positives = 6/9 (66%)
Query: 46 QDPSDPYFP 54
+ +D YFP
Sbjct: 61 RSSTDLYFP 69
>gnl|CDD|184952 PRK14990, PRK14990, anaerobic dimethyl sulfoxide reductase subunit
A; Provisional.
Length = 814
Score = 24.6 bits (53), Expect = 9.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 67 GKAKLDLNVEAAWAQGGNC 85
GK KLD+ ++ W GNC
Sbjct: 467 GKDKLDVPIKMIWNYAGNC 485
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
0.315 0.133 0.412
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,226,435
Number of extensions: 316169
Number of successful extensions: 189
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 21
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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: 42 (22.0 bits)
S2: 53 (24.1 bits)