RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17041
(202 letters)
>gnl|CDD|221396 pfam12051, DUF3533, Protein of unknown function (DUF3533). This
family of transmembrane proteins is functionally
uncharacterized. This protein is found in bacteria and
eukaryotes. Proteins in this family are typically
between 393 to 772 amino acids in length.
Length = 379
Score = 31.5 bits (72), Expect = 0.26
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 97 YDDYYPDPESAINAVRVGDAWGALYFTDNFTDALVA 132
++ E V WGA+Y N T+ L A
Sbjct: 72 PSEFPEIEEEVRRLVHHEKYWGAIYVKPNATERLYA 107
>gnl|CDD|217710 pfam03747, ADP_ribosyl_GH, ADP-ribosylglycohydrolase. This family
includes enzymes that ADP-ribosylations, for example
ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves
ADP-ribose-L-arginine. The family also includes
dinitrogenase reductase activating glycohydrolase. Most
surprisingly the family also includes jellyfish
crystallins, these proteins appear to have lost the
presumed active site residues.
Length = 284
Score = 30.0 bits (68), Expect = 0.77
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 117 WGALYFTDNFTDALVARMVLGRDAD 141
+ L TD+F +AL+ + LG D D
Sbjct: 237 YALLRATDDFEEALLLAVNLGGDTD 261
>gnl|CDD|233282 TIGR01130, ER_PDI_fam, protein disulfide isomerase, eukaryotic.
This model represents eukaryotic protein disulfide
isomerases retained in the endoplasmic reticulum (ER)
and closely related forms. Some members have been
assigned alternative or additional functions such as
prolyl 4-hydroxylase and
dolichyl-diphosphooligosaccharide-protein
glycotransferase. Members of this family have at least
two protein-disulfide domains, each similar to
thioredoxin but with the redox-active disulfide in the
motif PWCGHCK, and an ER retention signal at the extreme
C-terminus (KDEL, HDEL, and similar motifs).
Length = 462
Score = 29.6 bits (67), Expect = 1.0
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 20/76 (26%)
Query: 10 ESPQVLLQTYG-----CQSLEEVFLKLSRKQGN----------DATANNVPEVNIANNIS 54
E+ VL++ Y C++L ++ +L+ K + DATAN+VP +
Sbjct: 363 ETKDVLVEFYAPWCGHCKNLAPIYEELAEKYKDAESDVVIAKMDATANDVPPFEVE---G 419
Query: 55 LATLQW--GNKKDEPV 68
T+++ KK EPV
Sbjct: 420 FPTIKFVPAGKKSEPV 435
>gnl|CDD|190502 pfam03014, SP2, Structural protein 2. This family represents
structural protein 2 of the hepatitis E virus. The high
basic amino acid content of this protein has lead to the
suggestion of a role in viral genomic RNA encapsidation.
Length = 619
Score = 29.3 bits (65), Expect = 1.7
Identities = 35/172 (20%), Positives = 65/172 (37%), Gaps = 45/172 (26%)
Query: 12 PQVLLQTYGCQSLEEVFLKLSRKQGNDATANNVPEVNIANNISLATLQWGNKKDEPVYVT 71
P L+ + G Q L SR + AN P V + ++ A ++D+ + +
Sbjct: 344 PTELISSAGGQ------LFYSRPVVS---ANGEPTVKLYTSVENA------QQDKGIMIP 388
Query: 72 EESGVVGLMFHQSKEILIQDHSNGHYDDY---YPDPESAINAVRVGDA-W---------- 117
+ + + ++IQD+ N H D P P + +R D W
Sbjct: 389 HDIDL------GTSRVVIQDYDNQHEQDRPTPSPAPSRPFSVLRANDVLWLSLTAAEYDQ 442
Query: 118 -------GALYFTDNFTDALVARMVLGRDADEETLDQSEIRPNGKSVMMIEQ 162
+Y +D T V + G A +LD +++ +G+ + I+Q
Sbjct: 443 GTYGSSTNPMYVSDTVT---VVNVATGAQAVARSLDWTKVTLDGRPLKTIQQ 491
>gnl|CDD|143435 cd07117, ALDH_StaphAldA1, Uncharacterized Staphylococcus aureus
AldA1 (SACOL0154) aldehyde dehydrogenase-like.
Uncharacterized aldehyde dehydrogenase from
Staphylococcus aureus (AldA1, locus SACOL0154) and other
similar sequences are present in this CD.
Length = 475
Score = 28.6 bits (64), Expect = 2.4
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 50 ANNISLATLQWGNKK------DEPVYVTEESGVVGLMFHQSK------EILIQDHSNGHY 97
A + ATL+ G K D E +G++F+Q + I +Q+ G Y
Sbjct: 235 AKKLIPATLELGGKSANIIFDDANWDKALEGAQLGILFNQGQVCCAGSRIFVQE---GIY 291
Query: 98 DDYYPDPESAINAVRVGDAW 117
D++ + V+VG+
Sbjct: 292 DEFVAKLKEKFENVKVGNPL 311
>gnl|CDD|183190 PRK11548, PRK11548, outer membrane biogenesis protein BamE;
Provisional.
Length = 113
Score = 27.0 bits (60), Expect = 3.4
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 14 VLLQTYGCQSLEEVFLKLSRKQGNDATANNVPEV 47
+L+ T GC +LE V + QGN T N+V ++
Sbjct: 13 LLMLTAGCSTLERVVYRPDINQGNYLTPNDVAKI 46
>gnl|CDD|240354 PTZ00310, PTZ00310, AMP deaminase; Provisional.
Length = 1453
Score = 28.2 bits (63), Expect = 4.0
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 18/42 (42%)
Query: 52 NISLATLQWGNKKDEPVYVTEESGVVGLMFHQSKEILIQDHS 93
N+SL+T D+P LMFHQ++E LI+++S
Sbjct: 1186 NVSLST-------DDP-----------LMFHQTQEPLIEEYS 1209
>gnl|CDD|173859 cd08494, PBP2_NikA_DppA_OppA_like_6, 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 = 448
Score = 27.2 bits (61), Expect = 6.5
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 100 YYPDPESAINAVRVGD 115
Y+ DP + NA+ GD
Sbjct: 190 YFSDPTALTNALLAGD 205
>gnl|CDD|218438 pfam05108, DUF690, Protein of unknown function (DUF690). This
family contains several uncharacterized bacterial
membrane proteins.
Length = 481
Score = 27.0 bits (60), Expect = 6.9
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 103 DPESAINAVRVGDAWGALYFTDNFTDALVARMVLGRDADEETLDQSEI 150
D ++ VRVGD + N T A R++ GR A+ T+ SE+
Sbjct: 78 DRDTGALYVRVGDRLHPVL---NLTSA---RLITGRPANPTTVKSSEL 119
>gnl|CDD|220382 pfam09754, PAC2, PAC2 family. This PAC2 (Proteasome assembly
chaperone) family of proteins is found in bacteria,
archaea and eukaryotes. Proteins in this family are
typically between 247 and 307 amino acids in length.
These proteins function as a chaperone for the 26S
proteasome. The 26S proteasome mediates
ubiquitin-dependent proteolysis in eukaryotic cells. A
number of studies including very recent ones have
revealed that assembly of its 20S catalytic core
particle is an ordered process that involves several
conserved proteasome assembly chaperones (PACs). Two
heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4,
promote the assembly of rings composed of seven alpha
subunits.
Length = 220
Score = 26.5 bits (59), Expect = 7.9
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 74 SGVVGLMFHQSKEILIQDHSN-GHYDDYYPDPESAINAVRV 113
G+ GL+ ++++ I S Y PDP++A+ +
Sbjct: 147 VGISGLLLGEAEQRGIPAVSLLAEVPHYLPDPKAALALLEA 187
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 27.0 bits (61), Expect = 8.1
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 2/18 (11%)
Query: 2 RSGRLLAEESPQVLLQTY 19
R+GR AE+ +VL+QTY
Sbjct: 532 RAGR--AEKPGEVLIQTY 547
>gnl|CDD|112770 pfam03971, IDH, Monomeric isocitrate dehydrogenase.
NADP(+)-dependent isocitrate dehydrogenase (ICD) is an
important enzyme of the intermediary metabolism, as it
controls the carbon flux within the citric acid cycle
and supplies the cell with 2-oxoglutarate EC:1.1.1.42
and NADPH for biosynthetic purposes.
Length = 735
Score = 27.1 bits (60), Expect = 8.2
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 77 VGLMFHQSKEILIQDHSNGHYDDYYPDPESAINAVRVGDAWGALYFTDNFTDALVARMVL 136
VGLM +++E G +D + + VRV DA G + + + RM
Sbjct: 406 VGLMAQKAEEY-------GSHDKTFEIQADGV--VRVVDAAGEVLLEHSVEAGDIWRMCQ 456
Query: 137 GRDA 140
+DA
Sbjct: 457 TKDA 460
>gnl|CDD|236864 PRK11154, fadJ, multifunctional fatty acid oxidation complex
subunit alpha; Reviewed.
Length = 708
Score = 26.8 bits (60), Expect = 8.9
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 79 LMFHQSKEILIQDHSNGHYDDYYPDPESAINAVRVG 114
L+F Q+++ + G+Y P PE ++ VR G
Sbjct: 228 LLFKQARK-KTLAKTQGNY----PAPERILDVVRTG 258
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
0.315 0.132 0.391
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,011,117
Number of extensions: 905416
Number of successful extensions: 748
Number of sequences better than 10.0: 1
Number of HSP's gapped: 748
Number of HSP's successfully gapped: 14
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
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 (21.6 bits)
S2: 56 (25.3 bits)