RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15890
(126 letters)
>gnl|CDD|146451 pfam03826, OAR, OAR domain.
Length = 21
Score = 39.3 bits (93), Expect = 1e-05
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 73 MSSSIASLRLKAKQHS 88
SSSIASLRLKAK+HS
Sbjct: 4 RSSSIASLRLKAKEHS 19
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 28.0 bits (62), Expect = 1.5
Identities = 10/53 (18%), Positives = 20/53 (37%)
Query: 40 TCPYVPPTTPYSMYTHRPASSDPSLSRVAECNVMSSSIASLRLKAKQHSNFNY 92
+ P V + + H +S P+L ++ + S + K +FN
Sbjct: 219 SSPPVQSSYYVAPCNHDQRTSHPTLPSDSQPEPSAPSHMPSDARGKHQVDFNQ 271
>gnl|CDD|215170 PLN02301, PLN02301, pectinesterase/pectinesterase inhibitor.
Length = 548
Score = 27.9 bits (62), Expect = 1.7
Identities = 17/79 (21%), Positives = 27/79 (34%), Gaps = 8/79 (10%)
Query: 3 PTGMTAPLTGSASPAGRRSALLMCLWVAELDGSVAAATCPYV------PPTTPYSM--YT 54
+ PL S + L + L + S A T P + PP+ ++
Sbjct: 1 MSTSNQPLLSSPKSSSHHKTLCLVLSFVAILSSAALFTAPLISTNSSSPPSLLQTLCDRA 60
Query: 55 HRPASSDPSLSRVAECNVM 73
H S +S +A VM
Sbjct: 61 HDQDSCQAMVSEIATNTVM 79
>gnl|CDD|106978 PHA00670, PHA00670, hypothetical protein.
Length = 540
Score = 26.7 bits (59), Expect = 4.2
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 45 PPTTPYSMYTHRPASSDPSLSRVAECNVMSSSIASLRLKAKQHSNFN 91
P P+ R A+ DP L+ AE ++ A Q SNF
Sbjct: 75 SPARPW----FRLATRDPELNEDAEVKAWLENVTRDMYSAFQKSNFY 117
>gnl|CDD|224817 COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD subunit
[Energy production and conversion].
Length = 160
Score = 26.1 bits (58), Expect = 4.2
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 13/53 (24%)
Query: 18 GRRSALLMCLWVA-ELDGSVAAATCPYV------PPT------TPYSMYTHRP 57
+RSAL+ L +A E G + + P T Y+ + +P
Sbjct: 22 DKRSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVYGVATFYTQFFLKP 74
>gnl|CDD|107331 cd06336, PBP1_ABC_ligand_binding_like_3, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that
are predicted to be involved in transport of amino
acids, peptides, or inorganic ions. This group
includes the type I periplasmic ligand-binding domain
of uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters (HAAT), such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been
determined experimentally.
Length = 347
Score = 26.5 bits (59), Expect = 4.5
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 5 GMTAPLTGSASPAGRRSALLMCLWVAEL 32
G + PL+G A+ G + L E+
Sbjct: 3 GFSGPLSGPAAAWGLPGLRGVQLAAEEI 30
>gnl|CDD|115952 pfam07328, VirD1, T-DNA border endonuclease VirD1. This family
consists of several T-DNA border endonuclease VirD1
proteins which appear to be found exclusively in
Agrobacterium species. Agrobacterium, a plant pathogen,
is capable to stably transform the plant cell with a
segment of its own DNA called T-DNA (transferred DNA).
This process depends, among others, on the specialised
bacterial virulence proteins VirD1 and VirD2 that
excise the T-DNA from its adjacent sequences. VirD1 is
thought to interact with VirD2 in this process.
Length = 147
Score = 25.8 bits (56), Expect = 5.4
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 56 RPASSDPSLSRVAECNVMSSSIASLRLKAKQHSNFNYTS 94
RP SSD ++++ V + S RL++ ++ +F++ +
Sbjct: 6 RPTSSDIAINQHECLKVEGFKVVSARLRSAEYESFSHQA 44
>gnl|CDD|131013 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit.
This model describes the E chain of complexes that
resemble NADH-quinone oxidoreductases. The electron
acceptor is a quinone, ubiquinone, in mitochondria and
most bacteria, including Escherichia coli, where the
recommended gene symbol is nuoB. This model does not
identify proteins from chloroplast and cyanobacteria
[Energy metabolism, Electron transport].
Length = 148
Score = 25.8 bits (57), Expect = 6.4
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 13/55 (23%)
Query: 16 PAGRRSALLMCLWVA-ELDGSVAAATCPYV------PPT------TPYSMYTHRP 57
+RSA++ L +A E G V V PP T YSM+ P
Sbjct: 11 DDQKRSAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDTEP 65
>gnl|CDD|176109 cd08417, PBP2_Nitroaromatics_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators that
involved in the catabolism of nitroaromatic/naphthalene
compounds and that of related regulators; contains the
type 2 periplasmic binding fold. This CD includes the
C-terminal substrate binding domain of LysR-type
transcriptional regulators involved in the catabolism of
dinitrotoluene and similar compounds, such as DntR,
NahR, and LinR. The transcription of the genes encoding
enzymes involved in such degradation is regulated and
expression of these enzymes is enhanced by inducers,
which are either an intermediate in the metabolic
pathway or compounds to be degraded. Also included are
related LysR-type regulators clustered together in
phylogenetic trees, including NodD, ToxR, LeuO, SyrM,
TdcA, and PnbR. 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 = 200
Score = 25.6 bits (57), Expect = 7.2
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 5/62 (8%)
Query: 6 MTAPLTGSASPAGRRSALLMCL--WVAEL---DGSVAAATCPYVPPTTPYSMYTHRPASS 60
+T P +A + L+ + +AE + P+ P S+Y H
Sbjct: 127 LTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLPLPFELPPFTVSLYWHPRRDR 186
Query: 61 DP 62
DP
Sbjct: 187 DP 188
>gnl|CDD|218673 pfam05642, Sporozoite_P67, Sporozoite P67 surface antigen. This
family consists of several Theileria P67 surface
antigens. A stage specific surface antigen of Theileria
parva, p67, is the basis for the development of an
anti-sporozoite vaccine for the control of East Coast
fever (ECF) in cattle. The antigen has been shown to
contain five distinct linear peptide sequences
recognised by sporozoite-neutralising murine monoclonal
antibodies.
Length = 727
Score = 25.8 bits (56), Expect = 7.8
Identities = 10/28 (35%), Positives = 11/28 (39%)
Query: 36 VAAATCPYVPPTTPYSMYTHRPASSDPS 63
V +T S T PASS PS
Sbjct: 270 VGDSTSSPSTTRPSGSTTTTTPASSGPS 297
>gnl|CDD|233988 TIGR02734, crtI_fam, phytoene desaturase. Phytoene is converted to
lycopene by desaturation at four (two symmetrical pairs
of) sites. This is achieved by two enzymes (crtP and
crtQ) in cyanobacteria (Gloeobacter being an exception)
and plants, but by a single enzyme in most other
bacteria and in fungi. This single enzyme is called the
bacterial-type phytoene desaturase, or CrtI. Most
members of this family, part of the larger Pfam family
pfam01593, which also contains amino oxidases, are CrtI
itself; it is likely that all members act on either
phytoene or on related compounds such as
dehydrosqualene, for carotenoid biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 502
Score = 25.7 bits (57), Expect = 8.1
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 51 SMYTHRPASSDPSL 64
S+Y HRP +DPSL
Sbjct: 350 SLYLHRPTVTDPSL 363
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
0.314 0.123 0.369
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,864,258
Number of extensions: 456783
Number of successful extensions: 381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 380
Number of HSP's successfully gapped: 20
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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: 41 (21.6 bits)
S2: 53 (24.5 bits)