RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9708
(99 letters)
>gnl|CDD|216992 pfam02358, Trehalose_PPase, Trehalose-phosphatase. This family
consist of trehalose-phosphatases EC:3.1.3.12 these
enzyme catalyze the de-phosphorylation of
trehalose-6-phosphate to trehalose and orthophosphate.
The aligned region is present in trehalose-phosphatases
and comprises the entire length of the protein it is
also found in the C-terminus of trehalose-6-phosphate
synthase EC:2.4.1.15 adjacent to the
trehalose-6-phosphate synthase domain - pfam00982. It
would appear that the two equivalent genes in the E.
coli otsBA operon otsA the trehalose-6-phosphate
synthase and otsB trehalose-phosphatase (this family)
have undergone gene fusion in most eukaryotes. Trehalose
is a common disaccharide of bacteria, fungi and
invertebrates that appears to play a major role in
desiccation tolerance.
Length = 235
Score = 38.1 bits (89), Expect = 2e-04
Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 13/94 (13%)
Query: 5 IERHYCK--QGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGP 62
I Y + G+++E+K L +HY N + + +ES +G
Sbjct: 95 ILEEYTERTPGSYIEDKKSALAWHYRNADDDFGVFQAKELAEHLESVLKDYPDVRVTQG- 153
Query: 63 LLTFHYTNTPVELRPEMVS---LATQLIESAGFK 93
VE+RP VS A +L+E G
Sbjct: 154 -------KKVVEVRPVGVSKGKAAERLLEELGSA 180
Score = 33.5 bits (77), Expect = 0.008
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 26 HYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELR-PEMVSLAT 84
VE +A L E G+++E+K L +HY N + + LA
Sbjct: 77 WTNLAEVEDLDWKKEVAAILEEYTERTPGSYIEDKKSALAWHYRNADDDFGVFQAKELAE 136
Query: 85 QLIE 88
L
Sbjct: 137 HLES 140
>gnl|CDD|224789 COG1877, OtsB, Trehalose-6-phosphatase [Carbohydrate transport and
metabolism].
Length = 266
Score = 29.6 bits (67), Expect = 0.21
Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 14/75 (18%)
Query: 13 GAWVENKGPLLTFHYTNTPVELRPEMVS-LATQLIESAGFKAGAWVENKGPLLTFHYTNT 71
G+++E KG + HY N + + A LI +
Sbjct: 126 GSYIERKGFAVALHYRNAEDDEGAALALAEAATLINELKLRVTPGKMV------------ 173
Query: 72 PVELRPEMVSLATQL 86
VELRP VS +
Sbjct: 174 -VELRPPGVSKGAAI 187
>gnl|CDD|233092 TIGR00685, T6PP, trehalose-phosphatase. Trehalose, a neutral
disaccharide of two glucose residues, is an important
osmolyte for dessication and/or salt tolerance in a
number of prokaryotic and eukaryotic species, including
E. coli, Saccharomyces cerevisiae, and Arabidopsis
thaliana. Many bacteria also utilize trehalose in the
synthesis of trehalolipids, specialized cell wall
constituents believed to be involved in the uptake of
hydrophobic substances. Trehalose dimycolate (TDM, cord
factor) and related substances are important
constituents of the mycobacterial waxy coat and
responsible for various clinically important
immunological interactions with host organism. This
enzyme, trehalose-phosphatase, removes a phosphate group
in the final step of trehalose biosynthesis. The
trehalose-phosphatase from Saccharomyces cerevisiae is
fused to the synthase. At least 18 distinct sequences
from Arabidopsis have been identified, roughly half of
these are of the fungal type, with a fused synthase and
half are like the bacterial members having only the
phosphatase domain. It has been suggested that trehalose
is being used in Arabidopsis as a regulatory molecule in
development and possibly other processes [Cellular
processes, Adaptations to atypical conditions].
Length = 244
Score = 29.4 bits (66), Expect = 0.25
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 2/72 (2%)
Query: 24 TFHYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEM--VS 81
+ E P A +L E + G ++E KG L +HY PV
Sbjct: 80 SCQDWVNLTEKIPSWKVRANELREEITTRPGVFIERKGVALAWHYRQAPVPELARFRAKE 139
Query: 82 LATQLIESAGFK 93
L +++ +
Sbjct: 140 LKEKILSFTDLE 151
Score = 26.3 bits (58), Expect = 2.8
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 13 GAWVENKGPLLTFHYTNTPVELRPEM--VSLATQLIESAGFK 52
G ++E KG L +HY PV L +++ +
Sbjct: 110 GVFIERKGVALAWHYRQAPVPELARFRAKELKEKILSFTDLE 151
>gnl|CDD|223818 COG0747, DdpA, ABC-type dipeptide transport system, periplasmic
component [Amino acid transport and metabolism].
Length = 556
Score = 28.0 bits (62), Expect = 0.71
Identities = 12/53 (22%), Positives = 16/53 (30%), Gaps = 1/53 (1%)
Query: 42 ATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKA 94
A L++ AG+K LT R + QL G K
Sbjct: 369 AKALLDEAGYKDNDGFGGGPLTLTLESAGYNPGARAIAELIQAQL-AKIGIKV 420
>gnl|CDD|173870 cd08505, PBP2_NikA_DppA_OppA_like_18, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant
sequence similarity to NikA, the initial nickel
receptor. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which
precludes any involvement in chemotaxis. Most of other
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the dipeptide/oligopeptide binding proteins. The
structural topology of these domains is most similar to
that of 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.
Besides transport proteins, the PBP2 superfamily
includes the ligand-binding domains from ionotropic
glutamate receptors, LysR-type transcriptional
regulators, and unorthodox sensor proteins involved in
signal transduction.
Length = 528
Score = 28.0 bits (63), Expect = 0.75
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 21 PLLTFHYTNTPVELRPEMVSLATQLIE 47
PLL +HY P EL P + A + E
Sbjct: 33 PLLQYHYLKRPYELVP---NTAAAMPE 56
Score = 28.0 bits (63), Expect = 0.75
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 62 PLLTFHYTNTPVELRPEMVSLATQLIE 88
PLL +HY P EL P + A + E
Sbjct: 33 PLLQYHYLKRPYELVP---NTAAAMPE 56
>gnl|CDD|234004 TIGR02772, Ku_bact, Ku protein, prokaryotic. Members of this
protein family are Ku proteins of non-homologous end
joining (NHEJ) DNA repair in bacteria and in at least
one member of the archaea (Archaeoglobus fulgidus). Most
members are encoded by a gene adjacent to the gene for
the DNA ligase that completes the repair. The NHEJ
system is broadly but rather sparsely distributed, being
present in about one fifth of the first 250 completed
prokarytotic genomes. A few species (e.g. Archaeoglobus
fulgidus and Bradyrhizobium japonicum) have multiple
copies that appear to represent recent paralogous family
expansion [DNA metabolism, DNA replication,
recombination, and repair].
Length = 258
Score = 27.6 bits (62), Expect = 1.0
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 31 PVELRPEMVSLATQLIESAGFKAGAW 56
VE+ PE + LA QLI+ G +
Sbjct: 181 DVEVDPEELELAGQLIDK---MTGKF 203
Score = 26.9 bits (60), Expect = 1.7
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 72 PVELRPEMVSLATQLIES 89
VE+ PE + LA QLI+
Sbjct: 181 DVEVDPEELELAGQLIDK 198
>gnl|CDD|238408 cd00789, KU_like, Ku-core domain, Ku-like subfamily; composed of
prokaryotic homologs of the eukaryotic DNA binding
protein Ku. The alignment includes the core domain
shared by the prokaryotic YkoV-like proteins and the
eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs
are predicted to form homodimers. It is proposed that
the Ku homologs are functionally associated with
ATP-dependent DNA ligase and the eukaryotic-type
primase, probably as components of a double-strand break
repair system.
Length = 256
Score = 27.1 bits (61), Expect = 1.3
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 32 VELRPEMVSLATQLIESAGFKAGAW 56
V++ P+ + +A QLIE G +
Sbjct: 181 VKVDPKELEMAKQLIEQ---LTGDF 202
Score = 26.7 bits (60), Expect = 1.7
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 73 VELRPEMVSLATQLIES 89
V++ P+ + +A QLIE
Sbjct: 181 VKVDPKELEMAKQLIEQ 197
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 27.1 bits (60), Expect = 1.4
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 27 YTNTPVELRPEMVSLATQLIES 48
YT TP+ RPEMV T+L E
Sbjct: 192 YTATPMNTRPEMVHQ-TKLFEE 212
Score = 27.1 bits (60), Expect = 1.4
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 68 YTNTPVELRPEMVSLATQLIES 89
YT TP+ RPEMV T+L E
Sbjct: 192 YTATPMNTRPEMVHQ-TKLFEE 212
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 27.1 bits (60), Expect = 1.8
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 11 KQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG--AWVENKGPLLTFHY 68
KQG V K PL T+++T + E + E A F WV PL F
Sbjct: 404 KQGP-VTVKHPLTTYYFTFKGKDGSEEKFA---YDPEKADFLMAHNGWVMGSDPLRDFAS 459
Query: 69 TNTPVELRPEMVS 81
+ V LR E++
Sbjct: 460 PGSRVYLRRELIC 472
>gnl|CDD|216220 pfam00970, FAD_binding_6, Oxidoreductase FAD-binding domain.
Length = 99
Score = 26.0 bits (58), Expect = 2.1
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 41 LATQLIESAGFKAGAWVENKGPLLTFHY 68
+Q ++S K G VE KGPL F Y
Sbjct: 74 KMSQYLDSL--KIGDTVEVKGPLGHFEY 99
Score = 24.8 bits (55), Expect = 6.6
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 1 MLKWIERHYCKQGAWVENKGPLLTFHY 27
M ++++ K G VE KGPL F Y
Sbjct: 75 MSQYLDS--LKIGDTVEVKGPLGHFEY 99
>gnl|CDD|173882 cd08517, PBP2_NikA_DppA_OppA_like_13, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of 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. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 480
Score = 26.0 bits (58), Expect = 3.3
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 21 PLLTFHYTNTPVELRPEM-VSLATQLIESAGFKAGA 55
P L F Y + V+ A L++ AG+ GA
Sbjct: 296 PSLPFFYDDDVP--TYPFDVAKAEALLDEAGYPRGA 329
>gnl|CDD|227858 COG5571, COG5571, Autotransporter protein or domain, integral
membrane beta-barrel involved in protein secretion [Cell
motility and secretion].
Length = 239
Score = 25.5 bits (56), Expect = 4.9
Identities = 18/90 (20%), Positives = 28/90 (31%), Gaps = 13/90 (14%)
Query: 8 HYCKQGAWVENKGPLLTFHYTN----------TPVEL-RPEMVSLATQLIESAGFKAGAW 56
H + W+ + P+ + V+L S +L F G
Sbjct: 45 HSTEGPTWLSSHLPVYNTILSTKRQSAQLGAGARVQLGETNAESWTARLSAGYEFPFGEL 104
Query: 57 VENKGPLLTFHYTNTPVELRPEMVSLATQL 86
GP+ HY T V E + +T L
Sbjct: 105 R--TGPVAGLHYDKTTVSGYNEQNASSTAL 132
>gnl|CDD|217851 pfam04029, 2-ph_phosp, 2-phosphosulpholactate phosphatase.
Thought to catalyze 2-phosphosulpholactate =
sulpholactate + phosphate. Probable magnesium cofactor.
Involved in the second step of coenzyme M biosynthesis.
Inhibited by vanadate in Methanococcus jannaschii. Also
known as the ComB family.
Length = 231
Score = 24.9 bits (55), Expect = 7.3
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 25 FHYTNTPVELRPEMVS 40
F N+P+E PE V
Sbjct: 74 FDLGNSPLEYTPEDVE 89
Score = 24.9 bits (55), Expect = 7.3
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 66 FHYTNTPVELRPEMVS 81
F N+P+E PE V
Sbjct: 74 FDLGNSPLEYTPEDVE 89
>gnl|CDD|173874 cd08509, PBP2_TmCBP_oligosaccharides_like, The substrate binding
domain of a cellulose-binding protein from Thermotoga
maritima contains the type 2 periplasmic binding fold.
This family represents the substrate-binding domain of a
cellulose-binding protein from the hyperthermophilic
bacterium Thermotoga maritima (TmCBP) and its closest
related proteins. TmCBP binds a variety of lengths of
beta-1,4-linked glucose oligomers, ranging from two
sugar rings (cellobiose) to five (cellopentose). TmCBP
is structurally homologous to domains I and III of the
ATP-binding cassette (ABC)-type oligopeptide-binding
proteins and thus belongs to the type 2 periplasmic
binding fold protein (PBP2) superfamily. The type 2
periplasmic binding proteins are soluble ligand-binding
components of ABC or tripartite ATP-independent
transporters and chemotaxis systems. Members of the PBP2
superfamily function in uptake of a variety of
metabolites in bacteria such as amino acids,
carbohydrate, ions, and polyamines. Ligands are then
transported across the cytoplasmic membrane energized by
ATP hydrolysis or electrochemical ion gradient. Besides
transport proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 509
Score = 25.0 bits (55), Expect = 8.4
Identities = 12/31 (38%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 39 VSLATQLIESAGFKAGA---WVENKGPLLTF 66
A +L+ESAGFK W G L F
Sbjct: 324 PDKAKKLLESAGFKKDKDGKWYTPDGTPLKF 354
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
0.318 0.133 0.418
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,867,827
Number of extensions: 375890
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 390
Number of HSP's successfully gapped: 27
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)