RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6420
(169 letters)
>gnl|CDD|220715 pfam10358, NT-C2, N-terminal C2 in EEIG1 and EHBP1 proteins. This
version of the C2 domain was initally identified in the
vertebrate estrogen early-induced gene 1 (EEIG1), and
its Drosophila ortholog required for uptake of dsRNA via
the endocytotic machinery to induce RNAi silencing. It
is also in C.elegans ortholog Sym-3 (SYnthetic lethal
with Mec-3) and the mammalian protein EHBP1 (EH domain
Binding Protein-1) that regulates endocytotic recycling
and two plant proteins, RPG that regulates
Rhizobium-directed polar growth and PMI1 (Plastid
Movement Impaired 1) that is essential for intracellular
movement of chloroplasts in response to blue light.
Length = 142
Score = 35.4 bits (82), Expect = 0.004
Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 10/78 (12%)
Query: 28 HFVKRIHLLKIVFSSHPRTPSKLSIVWTRRSRRVVTEPMLWEPTMTDPLRGVVVWAVPEN 87
F IH L+ V P +L + W R ++ + + G VW E
Sbjct: 8 QFDLSIHELQNV----PLVNGELFVKWKRGDKKGNS----GTTSKALVNNGRAVW--NEE 57
Query: 88 KTISVTLFKDPRYQTFFP 105
+I TLF D + F P
Sbjct: 58 FSIPCTLFVDKKGGKFEP 75
>gnl|CDD|234031 TIGR02840, spore_YtaF, putative sporulation protein YtaF. This
protein family was identified, at the time of the
publication of the Carboxydothermus hydrogenoformans
genome, as having a phylogenetic profile that exactly
matches the subset of the Firmicutes capable of forming
endospores. The species include Bacillus anthracis,
Clostridium tetani, Thermoanaerobacter tengcongensis,
Geobacillus kaustophilus, etc. This protein, previously
named YtaF, is therefore a putative sporulation protein
[Cellular processes, Sporulation and germination].
Length = 206
Score = 27.6 bits (62), Expect = 2.6
Identities = 8/41 (19%), Positives = 12/41 (29%)
Query: 100 YQTFFPPKNGHKRSHSVKIKFKFSKQLGNHRICSSKENGSM 140
Y F P K RS + +I + E +
Sbjct: 80 YNAFRPKKEVKDRSSEPDSTKELKSFGFVIQILRNPEVADL 120
>gnl|CDD|176146 cd08457, PBP2_OccR, The C-terminal substrate-domain of LysR-type
transcriptional regulator, OccR, involved in the
catabolism of octopine, contains the type 2 periplasmic
binding fold. This CD includes the C-terminal
substrate-domain of LysR-type transcriptional regulator
OccR, which is involved in the catabolism of octopine.
Opines are low molecular weight compounds found in
plant crown gall tumors produced by the parasitic
bacterium Agrobacterium. There are at least 30
different opines identified so far. Opines are utilized
by tumor-colonizing bacteria as a source of carbon,
nitrogen, and energy. In Agrobacterium tumefaciens,
OccR protein activates the occQ operon of the Ti
plasmid in response to octopine. This operon encodes
proteins required for the uptake and catabolism of
octopine, an arginine derivative. The occ operon also
encodes the TraR protein, which is a quorum-sensing
transcriptional regulator of the Ti plasmid tra
regulon. This substrate-binding domain shows
significant homology to the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake
of a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 196
Score = 26.7 bits (59), Expect = 6.3
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 38 IVFSSHPRTPSKLSIVWTRRSRRVVTEPM 66
+ + P + ++ TR VV PM
Sbjct: 52 LGIADGPLEERQGFLIETRSLPAVVAVPM 80
>gnl|CDD|220827 pfam10627, CsgE, Curli assembly protein CsgE. Curli are a class
highly aggregated surface fibres that are part of a
complex extracellular matrix. They promote biofilm
formation in addition to other activities. CsgE is a
non-structural protein involved in curli biogenesis.
CsgE forms an outer membrane complex with the curli
assembly proteins CsgG and CsgF.
Length = 107
Score = 25.7 bits (57), Expect = 6.6
Identities = 8/34 (23%), Positives = 11/34 (32%), Gaps = 9/34 (26%)
Query: 74 DPLRGVVVWAVPENKTISVTLFKDPRYQTFFPPK 107
G ++ K I YQTF P+
Sbjct: 44 TARAGSLITVEHNRKVI---------YQTFLGPR 68
>gnl|CDD|187684 cd09626, DOMON_glucodextranase_like, DOMON-like domain of various
glycoside hydrolases. This DOMON-like domain is found
at the C-terminus of various bacterial proteins that
play roles in metabolizing carbohydrates, such as
glucodextranase (hydrolyzes alpha-1,6-glucosidic
linkages of dextran from the non-reducing end), glucan
alpha-1,4-glucosidase, pullulanase (degrades pullulan, a
polysaccharide built from maltotriose units),
arabinogalactan endo-1,4-beta-galactosidase, and others.
Consequently, the DOMON-like domains in this family
co-occur with catalytic domains from various glycosyl
hydrolase families. The precise function of the DOMON
domains in these proteins is not clear, they may be
involved in interactions with carbohydrates.
Length = 220
Score = 26.1 bits (58), Expect = 9.5
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 69 EPTMTDPLRGVVVWAVPENKTISVTLFKD 97
E + D L V+A P+ TI+VT+ K
Sbjct: 115 EESAADLLAAPSVYADPDGNTITVTVPKK 143
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
0.323 0.135 0.435
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,568,063
Number of extensions: 736819
Number of successful extensions: 501
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 9
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.0 bits)