RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13111
(127 letters)
>gnl|CDD|185521 PTZ00235, PTZ00235, DNA polymerase epsilon subunit B; Provisional.
Length = 291
Score = 28.8 bits (64), Expect = 0.76
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 20 QKNLSKPGLVATAIGQNHSAAGPMPIPKVNNYHQTYSPWAFSVP 63
++N + LV+T +GQ+H PIP N + YSP+ F P
Sbjct: 194 ERNNLQNILVSTIVGQSHI----YPIPHDNRILKRYSPFLFLYP 233
>gnl|CDD|240086 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 4. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 353
Score = 27.6 bits (62), Expect = 2.0
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 26 PGL--VATAIGQNHSA--------AGPMPIPKVNNYHQTYSPWAFSVPGSSPHSP 70
PGL +A AI ++ A AG M P + SP A + H+P
Sbjct: 78 PGLRKLAQAI-KSKGAKAILQIFHAGRMANPALVPGGDVVSPSAIAAFRPGAHTP 131
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 27.4 bits (62), Expect = 2.1
Identities = 9/29 (31%), Positives = 11/29 (37%), Gaps = 4/29 (13%)
Query: 39 AAGPMPIPK----VNNYHQTYSPWAFSVP 63
A P P VNN+ P A +P
Sbjct: 54 RAKKEPTPDDWCYVNNFDDPDRPRALRLP 82
>gnl|CDD|173595 PTZ00404, PTZ00404, cytochrome P450; Provisional.
Length = 482
Score = 27.4 bits (61), Expect = 2.1
Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 9/38 (23%)
Query: 41 GPMPIPKVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSY 78
GP+PIP + N HQ G+ PH L M Y
Sbjct: 33 GPIPIPILGNLHQL---------GNLPHRDLTKMSKKY 61
>gnl|CDD|233123 TIGR00770, Dcu, anaerobic c4-dicarboxylate membrane transporter
family protein. These proteins are members of th
C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most
proteins in this family have 12 GES predicted
transmembrane regions; however one member has 10
experimentally determined transmembrane regions with
both the N- and C-termini localized to the periplasm.
The two Escherichia coli proteins, DcuA and DcuB,
transport aspartate, malate, fumarate and succinate, and
function as antiporters with any two of these
substrates. Since DcuA is encoded in an operon with the
gene for aspartase, and DcuB is encoded in an operon
with the gene for fumarase, their physiological
functions may be to catalyze aspartate:fumarate and
fumarate:malate exchange during the anaerobic
utilization of aspartate and fumarate, respectively
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 430
Score = 27.4 bits (61), Expect = 2.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 16 DPEYQKNLSKPGLVATA 32
DPEYQ+ L +V T
Sbjct: 193 DPEYQERLKAGKIVPTR 209
>gnl|CDD|235266 PRK04262, PRK04262, hypothetical protein; Provisional.
Length = 347
Score = 26.8 bits (60), Expect = 3.4
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 25 KPGLVATAIGQNHSAAGPMPIPKV 48
KPGL+ IG +S + + + V
Sbjct: 257 KPGLLTPYIGNTYSGSALLGLAAV 280
>gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, 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 = 473
Score = 26.6 bits (59), Expect = 3.8
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 22 NLS--KPGLVATAIGQNHSAAGPMPIPKVNNYHQTYSPWAF 60
NL+ + G+V G A + +P +N ++ PW +
Sbjct: 254 NLAIDRDGIVGALFGGQGRPATQLVVPGINGHNPDLKPWPY 294
>gnl|CDD|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA
polymerase delta, subunit B [DNA replication,
recombination, and repair].
Length = 481
Score = 26.2 bits (58), Expect = 5.2
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 61 SVPGSSPHSPLKYMKLSYA------SAPGKLPSSPTRK 92
VPG+ SPLK M+ + G LP +P K
Sbjct: 373 LVPGADYDSPLKAMEELLKRRHLAPTYGGTLPIAPETK 410
>gnl|CDD|237366 PRK13370, mhpB, 3-(2,3-dihydroxyphenyl)propionate dioxygenase;
Provisional.
Length = 313
Score = 26.1 bits (58), Expect = 5.8
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 27 GLVATAIGQNHSAAGPMPIP 46
G+ ATA+G +AAGP+P+P
Sbjct: 68 GVSATAVGDYGTAAGPLPVP 87
>gnl|CDD|216371 pfam01222, ERG4_ERG24, Ergosterol biosynthesis ERG4/ERG24 family.
Length = 429
Score = 26.2 bits (58), Expect = 6.1
Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 96 DSKKCRKVYGMEHRDLWCTQCKWK 119
D KC+K YG + +C + +
Sbjct: 401 DEHKCKKKYG-LDWEEYCKRVPYH 423
>gnl|CDD|180937 PRK07337, PRK07337, aminotransferase; Validated.
Length = 388
Score = 26.2 bits (58), Expect = 6.4
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 62 VPGSS--PHSPLKYMKLSYASAPGKL 85
VPG PH+P Y++LSYA++ +L
Sbjct: 351 VPGRDFGPHAPRDYIRLSYATSMSRL 376
>gnl|CDD|221839 pfam12898, Stc1, Stc1 domain. The domain contains 8 conserved
cysteines that may bind to zinc. In S. pombe this
protein acts as a protein linker which links the
chromatin modifying CLRC complex to RNAi by tethering it
to the RITS complex. The region is reported as a LIM
domain here, but has a slightly different arrangement of
its CxxC pairs from the Pfam LIM domain pfam00412, hence
why it is not part of that family. The tandem
zinc-finger structure could mediate protein-protein
interactions.
Length = 84
Score = 25.0 bits (55), Expect = 6.8
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 99 KCRKVYGMEHRDLWCTQCKWKKACSRF 125
KCR+ G + +L C+ C K F
Sbjct: 40 KCRECTGGQVVELECSPCDKTKPLDEF 66
>gnl|CDD|215536 PLN02991, PLN02991, oxidoreductase.
Length = 543
Score = 25.7 bits (56), Expect = 8.5
Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 24/84 (28%)
Query: 30 ATAIGQNHSAAGPMPIPKVNNYH----------------------QTYSPWAFSV-PGSS 66
A AI N +A+GP P P+ +YH Q Y+ + S P +
Sbjct: 319 ARAIKTNLTASGPRPNPQ-GSYHYGKINITRTIRLANSAGNIEGKQRYAVNSASFYPADT 377
Query: 67 PHSPLKYMKLSYASAPGKLPSSPT 90
P Y K++ PG +P PT
Sbjct: 378 PLKLADYFKIAGVYNPGSIPDQPT 401
>gnl|CDD|236020 PRK07449, PRK07449,
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate synthase; Validated.
Length = 568
Score = 25.5 bits (57), Expect = 9.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 27 GLVATAIGQNHSAAGPM 43
GL++TA G ++A P
Sbjct: 429 GLLSTAAGVARASAKPT 445
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 0.129 0.422
Gapped
Lambda K H
0.267 0.0854 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,098,608
Number of extensions: 478456
Number of successful extensions: 355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 24
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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: 53 (24.0 bits)