RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11519
(150 letters)
>gnl|CDD|216263 pfam01044, Vinculin, Vinculin family.
Length = 850
Score = 66.3 bits (162), Expect = 2e-13
Identities = 25/85 (29%), Positives = 41/85 (48%)
Query: 66 LCRLENVTNFTEFVKAFSQFGGEMVELAHVTGERGGDLKDERRRAQMSAARQVLERSTML 125
L E + V+ + G M +L + R +L + R ++AAR L++ +
Sbjct: 141 LAVAEVAETMEDLVQFYKDLGPNMTKLNKMVDRRQQELTHQVHRDILAAARDTLKKLAPI 200
Query: 126 LLTSSKTCLRHPDSETARQNRDTVF 150
L+T+ K +RHP E AR+NRD
Sbjct: 201 LITAMKIFVRHPGVEEARENRDYTA 225
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4).
LepA (also known as elongation factor 4, EF4) belongs
to the GTPase family and exhibits significant homology
to the translation factors EF-G and EF-Tu, indicating
its possible involvement in translation and association
with the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G
gene in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 29.8 bits (68), Expect = 0.35
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 42 DNIDSLLHLVDPPS-IDFRSTVSRSLC 67
D + LL+L+D P +DF VSRSL
Sbjct: 63 DGEEYLLNLIDTPGHVDFSYEVSRSLA 89
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 30.2 bits (69), Expect = 0.37
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 47 LLHLVDPPS-IDFRSTVSRSLCRLE 70
+L+L+D P +DF VSRSL E
Sbjct: 77 VLNLIDTPGHVDFSYEVSRSLAACE 101
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 29.4 bits (66), Expect = 0.79
Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 8/71 (11%)
Query: 86 GGEMVELAHVTGERGGDLKDERRRAQMSAARQVLERSTMLL-------LTSSKTCLRHPD 138
GE + L VT G R RA + L+R +L S K L+ P
Sbjct: 571 AGETMTL-TVTVTNPGTEPLYRVRAWTDSDNNYLDRRELLFGAIPPGESKSWKVKLKLPK 629
Query: 139 SETARQNRDTV 149
+R +R TV
Sbjct: 630 DALSRVDRLTV 640
>gnl|CDD|234913 PRK01175, PRK01175, phosphoribosylformylglycinamidine synthase I;
Provisional.
Length = 261
Score = 28.6 bits (64), Expect = 1.0
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 68 RLENVTNFTEFVKAFSQFGGEMVELAHVTGERGGDLKDERRR 109
R+E E VKAF + G E E H+ DL ER+
Sbjct: 10 RMEGTNCEDETVKAFRRLGVE-PEYVHIN-----DLAAERKS 45
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 27.3 bits (61), Expect = 1.2
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 16/71 (22%)
Query: 72 VTNFTEFV------KAFSQFGGEMVELA-HVTGERGGDLKD-----ERRRAQMSAARQVL 119
V N + FV +AFSQFG VE A + +RG + R+ +A ++
Sbjct: 4 VKNLSPFVSNELLEQAFSQFG--EVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61
Query: 120 ERSTMLLLTSS 130
E LLT+S
Sbjct: 62 EGC--FLLTAS 70
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 27.1 bits (60), Expect = 3.6
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 105 DERRRAQMSAARQVLERSTM-LLLTSSKTCLRHPDSETARQNRDTV 149
D R+A SA R V+ + TM +LT +T +R S+T R+ +T+
Sbjct: 182 DSLRQATDSALRGVIGKYTMDRILTEGRTVIR---SDTQRELEETI 224
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated
eEF2 reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation
rates by activating the kinase responsible for
phosphorylating eEF2. In contrast, treatment of cells
with insulin increases elongation rates by promoting
eEF2 dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins,
it is presumed that modification by the endogenous
enzyme also inhibits eEF2 activity.
Length = 218
Score = 26.8 bits (60), Expect = 4.3
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 42 DNIDSLLHLVDPPS-IDFRSTVSRSL 66
D D L++L+D P +DF S V+ +L
Sbjct: 68 DGNDYLINLIDSPGHVDFSSEVTAAL 93
>gnl|CDD|218670 pfam05639, Pup, Pup-like protein. This family consists of
several short bacterial proteins formely known as
(DUF797). It was recently shown that Mycobacterium
tuberculosis contains a small protein, Pup (Rv2111c),
that is covalently conjugated to the e-NH2 groups of
lysines on several target proteins (pupylation) such as
the malonyl CoA acyl carrier protein (FabD). Pupylation
of FabD was shown to result in its recruitment to the
mycobacterial proteasome and subsequent degradation
analogous to eukaryotic ubiquitin-conjugated proteins.
Searches recovered Pup orthologs in all major
actinobacteria lineages including the basal
bifidobacteria and also sporadically in certain other
bacterial lineages. The Pup proteins were all between
50-90 residues in length and a multiple alignment shows
that they all contain a conserved motif with a G [EQ]
signature at the C-terminus. Thus, all of them are
suitable for conjugation via the terminal glutamate or
the deamidated glutamine (as shown in the case of the
Mycobacterium Pup). The conserved globular core of Pup
is predicted to form a bihelical unit with the extreme
C-terminal 6-7 residues forming a tail in the extended
conformation. Thus, Pup is structurally unrelated to
the ubiquitin fold and has convergently evolved the
function of protein modifier.
Length = 66
Score = 25.4 bits (56), Expect = 4.4
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 69 LENVTNFTEFVKAFSQFGGE 88
LE N EFV+++ Q GGE
Sbjct: 49 LEE--NAEEFVRSYVQKGGE 66
>gnl|CDD|217911 pfam04123, DUF373, Domain of unknown function (DUF373). Archaeal
domain of unknown function. Predicted to be an integral
membrane protein with six transmembrane regions.
Length = 344
Score = 26.8 bits (60), Expect = 4.6
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 5/32 (15%)
Query: 87 GEMVELAHVTGERGGDLKDERRRAQMSAARQV 118
GE VE+A V+G ++ A A Q+
Sbjct: 64 GEDVEVAVVSGSPDVGVE-----ADRKIAEQL 90
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast)
originated within the bacterial LepA family. The
function is unknown [Unknown function, General].
Length = 595
Score = 26.9 bits (60), Expect = 4.6
Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 47 LLHLVDPPS-IDFRSTVSRSL 66
+L+L+D P +DF VSRSL
Sbjct: 71 VLNLIDTPGHVDFSYEVSRSL 91
>gnl|CDD|227576 COG5251, TAF40, Transcription initiation factor TFIID, subunit
TAF11 [Transcription].
Length = 199
Score = 26.5 bits (58), Expect = 5.3
Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 74 NFTEFVKAFSQ-FGGEMVELAHVTGERGGDLKDERRRAQM 112
N F++ + F GE++ELA + ++++ +
Sbjct: 136 NIRIFLQGVGKVFVGEIIELAMI-------VQNKWLTSGP 168
>gnl|CDD|239805 cd04278, ZnMc_MMP, Zinc-dependent metalloprotease, matrix
metalloproteinase (MMP) sub-family. MMPs are responsible
for a great deal of pericellular proteolysis of
extracellular matrix and cell surface molecules, playing
crucial roles in morphogenesis, cell fate specification,
cell migration, tissue repair, tumorigenesis, gain or
loss of tissue-specific functions, and apoptosis. In
many instances, they are anchored to cell membranes via
trans-membrane domains, and their activity is controlled
via TIMPs (tissue inhibitors of metalloproteinases).
Length = 157
Score = 26.4 bits (59), Expect = 5.6
Identities = 19/72 (26%), Positives = 25/72 (34%), Gaps = 20/72 (27%)
Query: 52 DPPSIDFRSTVSRSLCRLENVTN--FTE------------FVKAFSQ----FGGEMVELA 93
D P D R ++R+ +VT F E F + F G LA
Sbjct: 17 DLPRDDVRRAIARAFRVWSDVTPLTFREVTSGQEADIRISFARGNHGDGYPFDGPGGTLA 76
Query: 94 H--VTGERGGDL 103
H G GGD+
Sbjct: 77 HAFFPGGIGGDI 88
>gnl|CDD|239214 cd02863, Ubiquinol_oxidase_III, Ubiquinol oxidase subunit III
subfamily. Ubiquinol oxidase, the terminal oxidase in
the respiratory chains of aerobic bacteria, is a
multi-chain transmembrane protein located in the cell
membrane. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane.
Ubiquinol oxidases feature four subunits in contrast to
the 13 subunit bovine cytochrome c oxidase (CcO).
Subunits I, II, and III of bovine CcO are encoded within
the mitochondrial genome and the remaining 10 subunits
are encoded within the nuclear genome. Subunits I, II
and III of ubiquinol oxidase are homologous to the
corresponding subunits in bovine CcO. Although not
required for catalytic activity, subunit III appears to
be involved in assembly of the multimer complex.
Length = 186
Score = 25.7 bits (57), Expect = 8.5
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 122 STMLLLTSSKTC 133
T LLL SS TC
Sbjct: 56 ETFLLLLSSFTC 67
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 26.0 bits (58), Expect = 9.7
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 12/53 (22%)
Query: 60 STVSRSLCRLENVTNFTEFVKAFSQFGGEMVELAHVTGERGGDLKDERRRAQM 112
ST++R L L + G ++ GG+L+ RRR QM
Sbjct: 331 STLARILAGLLPPS------------SGSIIFDGQDLDLTGGELRRLRRRIQM 371
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
0.321 0.131 0.374
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,091,322
Number of extensions: 612474
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 521
Number of HSP's successfully gapped: 22
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
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 (21.9 bits)
S2: 54 (24.7 bits)