RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13000
(65 letters)
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells.
Vacuoles/lysosomes play an important role in the
degradation of both lipids and cellular proteins. In
order to perform this degradative function,
vacuoles/lysosomes contain numerous hydrolases which
have been transported in the form of inactive
precursors via the biosynthetic pathway and are
proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or
Golgi complex, or remain in the limiting membrane of
the MVB and are thereby transported to the limiting
membrane of the vacuole/lysosome as a consequence of
fusion. Therefore, the MVB sorting pathway plays a
critical role in the decision between recycling and
degradation of membrane proteins. A few archaeal
sequences are also present within this family.
Length = 169
Score = 37.6 bits (88), Expect = 6e-05
Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 20 EAIQKLRETEDMLIKKQEFLEKKIGEEIN-IARTNGTKNKR 59
EAI LR+ L KKQE LEKKI + I + NK
Sbjct: 1 EAILSLRKAIRELDKKQESLEKKIKKLEAEIKKLAKKGNKD 41
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 26.5 bits (59), Expect = 1.0
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 26 RETEDMLIKKQEFLEKKIGEEIN 48
R+ D KK E++ +KIGEE
Sbjct: 612 RDVNDW--KKAEYMSEKIGEEFE 632
>gnl|CDD|163535 TIGR03823, FliZ, flagellar regulatory protein FliZ. FliZ is
involved in the regulation of flagellar assembly and
possibly also the down-regulation of the motile
phenotype. FliZ interacts with the flagellar
translational activator FlhCD complex.
Length = 168
Score = 25.9 bits (57), Expect = 1.4
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 1 MSFFKNIFGKTEEKGPTTGEAIQKLRETEDMLIKKQ--------EFLEKKIGEEI-NIAR 51
M+F + +F +TE T E + +LR +++L+ + FL++++ + + + A
Sbjct: 90 MAFKQYLFEQTEMSHSTVREYVVRLRRLDELLVAQNYPAEQFQDGFLQERLADWLPSTAT 149
Query: 52 TNGTKNKREFDH 63
N R++D
Sbjct: 150 NNYRIALRKYDQ 161
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 25.6 bits (57), Expect = 1.6
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 18 TGEAIQKLRETEDMLIKKQEFLEKKIGEEINIAR 51
T E I+KL + + L K+ LEK + E +
Sbjct: 390 TKEEIEKLEKEIEELEKEIAELEKILASEKKLWI 423
>gnl|CDD|237257 PRK12902, secA, preprotein translocase subunit SecA; Reviewed.
Length = 939
Score = 25.0 bits (55), Expect = 2.8
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 13 EKGPTTGEAIQKLRE 27
EK PT IQKLRE
Sbjct: 611 EKAPTDDPVIQKLRE 625
>gnl|CDD|199210 cd02258, Peptidase_C25_N, Peptidase C25 family N-terminal domain,
found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and
related proteins. Peptidase family C25 is a unique
class of cysteine proteases, exemplified by gingipain,
which is produced by Porphyromonas gingivalis. P.
gingivalis is one of the primary gram-negative pathogens
that causes periodontitis, a disease that is also
associated with other diseases such as diabetes and
cardiovascular disease. Gingipains are a group of
extracellular Arg- and Lys-specific proteinases called
Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and
RgpB are homologous Arg-specific gingipains encoded by
two closely related genes, rgpA and rgpB, while
Lys-specific gingipain is encoded by the single kgp
gene. Mutant studies have shown that, among the large
quantities of proteolytic enzymes produced by P.
gingivalis, these three proteases are major virulence
factors of this bacterium. All three genes encode an
N-terminal pre-pro fragment, followed by the protease
domain; however, rgpA and kgp also encode additional
C-terminal HA (hemaglutinin/adhesion) subunits which
consist of several sequence-related adhesion domains.
Although unique, their cysteine protease active site
residues (His and Cys) forming the catalytic dyad are
well-conserved, cleaving the C-terminal peptide bond
with Arg or Lys residues. Gingipains are evolutionarily
related to other highly specific proteases including
caspases, clostripain, legumains, and separase.
Gingipains function by dysregulating host defense and
inflammatory responses, and degrading host proteins,
e.g. tissue, cells, matrix, plasma and immunological
proteins. They are proposed to enhance gingival
crevicular fluid (GCF) production through activation of
the kallikrein/kinin pathways, thus increasing vascular
permeability and causing gingival inflammation, a
distinctive feature of periodontitis. RgpA and RgpB are
also able to cleave and activate coagulation factors IX
and X in order to activate prothrombin to produce
thrombin, which in turn increases production of GCF. The
gingipains also play a pivotal role in the survival of
P. gingivalis in the host by attacking the host defense
system through cleavage of several immunological
molecules, while at the same time evading the
host-immune response by dysregulating the cytokine
network.
Length = 382
Score = 25.0 bits (55), Expect = 3.3
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 3 FFKNIFGKTEEKGPTTGEAIQK 24
++N+F K + + PT GE ++
Sbjct: 332 LYENLFSKEDGRNPTLGEILRL 353
>gnl|CDD|220580 pfam10115, HlyU, Transcriptional activator HlyU. This domain,
found in various hypothetical prokaryotic proteins, has
no known function. One of the sequences in this family
corresponds to the transcriptional activator HlyU,
indicating a possible similar role in other members.
Length = 91
Score = 24.1 bits (53), Expect = 4.1
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 1 MSFFKNIFGKTEEKGPTTGEAI 22
MSFF +FG ++ P E
Sbjct: 1 MSFFSKLFGGGKKAEPKEAEPE 22
>gnl|CDD|129249 TIGR00144, beta_RFAP_syn, beta-RFAP synthase. This protein
family contains several archaeal examples of
beta-ribofuranosylaminobenzene 5-prime-phosphate
synthase (beta-RFAP synthase), an enzyme involved in
methanopterin biosynthesis. In some species, two
members of this family are found. It is unclear whether
both act as beta-RFAP synthase. This family is related
to the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase). Members
are found so far only in the Archaea and in
Methylobacterium extorquens [Unknown function, Enzymes
of unknown specificity].
Length = 324
Score = 24.4 bits (53), Expect = 4.2
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 24 KLRETEDMLIKKQEFLEKKIGEEINIAR 51
L+E++DM ++ E K+GEE +R
Sbjct: 39 GLKESDDMGVEFTSHAEGKLGEEYRRSR 66
>gnl|CDD|232832 TIGR00116, tsf, translation elongation factor Ts. Translational
elongation factor Ts (EF-Ts) catalyzes the exchange of
GTP for the GDP of the EF-Tu.GDP complex as part of the
cycle of translation elongation. This protein is found
in Bacteria, mitochondria, and chloroplasts [Protein
synthesis, Translation factors].
Length = 291
Score = 24.4 bits (53), Expect = 4.3
Identities = 12/49 (24%), Positives = 18/49 (36%)
Query: 13 EKGPTTGEAIQKLRETEDMLIKKQEFLEKKIGEEINIARTNGTKNKREF 61
TT E +QK ++ L KIGE I + R + +
Sbjct: 102 ANPITTLEELQKQELENKEKVEYLASLAAKIGENIVLRRVAVLEGQSNV 150
>gnl|CDD|236074 PRK07666, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 239
Score = 23.9 bits (52), Expect = 8.0
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 37 EFLEKKIGEEINIARTNGTK 56
+E++ G+ INI+ T G K
Sbjct: 129 SMIERQSGDIINISSTAGQK 148
>gnl|CDD|213028 cd10973, CE4_DAC_u4_5s, Putative catalytic NodB homology domain of
uncharacterized bacterial polysaccharide deacetylases
which consist of a 5-stranded beta/alpha barrel. This
family contains many uncharacterized bacterial
polysaccharide deacetylases. Although their biological
functions remain unknown, all members of the family are
predicted to contain a conserved domain with a
5-stranded beta/alpha barrel, which is similar to the
catalytic NodB homology domain of rhizobial NodB-like
proteins, belonging to the larger carbohydrate esterase
4 (CE4) superfamily.
Length = 157
Score = 23.4 bits (51), Expect = 9.2
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 16 PTTGEAIQKLRETEDMLIKKQEFLEKKIGEEINI 49
Q L + K Q+ EK++G++ +
Sbjct: 74 LGEKMQEQWLEWIRQDIEKSQQRFEKELGKKPKL 107
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 23.7 bits (52), Expect = 9.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 18 TGEAIQKLRETEDMLIKKQEFLEKKIGEE 46
T ++KL + L K+ E LEK + E
Sbjct: 412 TKLEVEKLEKELKELEKEIEDLEKILASE 440
>gnl|CDD|107168 PHA02290, PHA02290, hypothetical protein.
Length = 234
Score = 23.6 bits (50), Expect = 9.7
Identities = 6/26 (23%), Positives = 9/26 (34%)
Query: 6 NIFGKTEEKGPTTGEAIQKLRETEDM 31
+ G G + L E+ED
Sbjct: 86 GYQSTEVQPGQYIGISTGLLSESEDF 111
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
0.311 0.131 0.354
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,311,588
Number of extensions: 249219
Number of successful extensions: 316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 38
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.1 bits)