RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17720
(80 letters)
>gnl|CDD|218010 pfam04293, SpoVR, SpoVR like protein. Bacillus subtilis stage V
sporulation protein R is involved in spore cortex
formation. Little is known about cortex biosynthesis,
except that it depends on several sigma E controlled
genes, including spoVR.
Length = 427
Score = 30.2 bits (69), Expect = 0.059
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 14 FYPENSAQIELVTS-QAMRAGFYGGLVVDYPHSTKAKKF 51
FYP QIE++T+ Q A G+ YPH + K F
Sbjct: 27 FYPN---QIEVITAEQMYDAYASVGMPTRYPHWSFGKHF 62
>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 = 29.8 bits (67), Expect = 0.094
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 7 TARAVFQFYPE--NSAQIELVTSQAMRAGF------YGGLVVDYPHSTKAKKFFL 53
R V ++Y + +I + + +G GG +VD HS+K K FL
Sbjct: 107 VGRLVSEYYGMKFTAREIAHIVGRGGTSGIGVASFEDGGFIVDGGHSSKEKSDFL 161
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. Moreover, CPEB-2 impedes target RNA
translation at elongation; it directly interacts with
the elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a Zn-finger
motif. In addition, they do have conserved nuclear
export signals that are not present in CPEB-1. .
Length = 92
Score = 27.4 bits (61), Expect = 0.42
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 35 YGGLVVDYPHSTKAKKFF 52
+G LVVD+PH ++K +F
Sbjct: 24 FGPLVVDWPHKAESKSYF 41
>gnl|CDD|237348 PRK13320, PRK13320, pantothenate kinase; Reviewed.
Length = 244
Score = 27.5 bits (62), Expect = 0.51
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 14/47 (29%)
Query: 26 TSQAMRAGFY-------GGLVVDYPHSTKAKKF--FLVLMTGGDLPL 63
T + +R+G GL+ Y K LV++TGGD P
Sbjct: 175 TEECIRSGVVWGCVAEIEGLIEAYKS-----KLPELLVILTGGDAPF 216
>gnl|CDD|216427 pfam01308, Chlam_OMP, Chlamydia major outer membrane protein.
The major outer membrane protein of Chlamydia contains
four symmetrically spaced variable domains (VDs I to
IV). This protein is believed to be an integral part to
the pathogenesis, possibly adhesion. Along with the
lipopolysaccharide, the major out membrane protein
(MOMP) makes up the surface of the elementary body
cell. The MOMP is the protein used to determine the
different serotypes.
Length = 389
Score = 25.3 bits (55), Expect = 3.9
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 29 AMRAGFYGGLVVDYPHSTKAKKFFLV 54
++RAG+YG V D T K F +
Sbjct: 59 SLRAGYYGDYVFDRVLKTDVNKTFQM 84
>gnl|CDD|212728 cd11794, SH3_DNMBP_N1, First N-terminal Src homology 3 domain of
Dynamin Binding Protein, also called Tuba. DNMBP or
Tuba is a cdc42-specific guanine nucleotide exchange
factor (GEF) that contains four N-terminal SH3 domains,
a central RhoGEF [or Dbl homology (DH)] domain followed
by a Bin/Amphiphysin/Rvs (BAR) domain, and two
C-terminal SH3 domains. It provides a functional link
between dynamin and key regulatory proteins of the
actin cytoskeleton. It plays an important role in
regulating cell junction configuration. The four
N-terminal SH3 domains of DNMBP binds the GTPase
dynamin, which plays an important role in the fission
of endocytic vesicles. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles
in the cell including the regulation of enzymes,
changing the subcellular localization of signaling
pathway components, and mediating the formation of
multiprotein complex assemblies.
Length = 51
Score = 24.0 bits (52), Expect = 5.0
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 7 TARAVFQFYPENSAQIELVT 26
RA+F F P S ++ L
Sbjct: 1 VVRAIFDFCPSVSEELPLFA 20
>gnl|CDD|233182 TIGR00915, 2A0602, The (Largely Gram-negative Bacterial)
Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. Proteins
scoring above the trusted cutoff (1000) form a tight
clade within the RND (Resistance-Nodulation-Cell
Division) superfamily. Proteins scoring greater than the
noise cutoff (100) appear to form a larger clade, cleanly
separated from more distant homologs that include
cadmium/zinc/cobalt resistance transporters. This family
is one of several subfamilies within the scope of Pfam
model pfam00873 [Cellular processes, Toxin production and
resistance, Transport and binding proteins, Unknown
substrate].
Length = 1044
Score = 24.7 bits (54), Expect = 7.6
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 54 VLMTG-----GDLPLPPALGEGEGSQVAVG 78
+LMT G +PL + G G GSQ A+G
Sbjct: 973 ILMTSLAFILGVVPLAISTGAGSGSQHAIG 1002
>gnl|CDD|182544 PRK10555, PRK10555, aminoglycoside/multidrug efflux system;
Provisional.
Length = 1037
Score = 24.4 bits (53), Expect = 8.6
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 54 VLMTG-----GDLPLPPALGEGEGSQVAVG 78
+LMT G LP+ + G G GSQ AVG
Sbjct: 972 ILMTSLAFIFGVLPMATSTGAGSGSQHAVG 1001
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 24.4 bits (54), Expect = 8.6
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 7 TARAVFQFYPENSAQ--IELVT 26
TAR V +P NS IE+ T
Sbjct: 1000 TARGVIGLFPANSVGDDIEVYT 1021
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 0.137 0.406
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,011,279
Number of extensions: 308071
Number of successful extensions: 228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 227
Number of HSP's successfully gapped: 13
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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: 53 (24.1 bits)