RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14100
(137 letters)
>gnl|CDD|236502 PRK09410, ulaA, PTS system ascorbate-specific transporter subunit
IIC; Reviewed.
Length = 452
Score = 29.8 bits (68), Expect = 0.38
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 41 IEEININKVLLFLRDNVVGTVVVV 64
E+I + K L FLRD+ V T + +
Sbjct: 207 TEDIKLPKSLSFLRDSTVSTAITM 230
>gnl|CDD|227625 COG5309, COG5309, Exo-beta-1,3-glucanase [Carbohydrate transport
and metabolism].
Length = 305
Score = 28.3 bits (63), Expect = 1.4
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 57 VVGTVVVVSAAL---WIPASCLISYIDRAR 83
V TV V + AL + AS LI YID R
Sbjct: 133 DVTTVTVGNEALNRNDLTASQLIEYIDDVR 162
>gnl|CDD|233978 TIGR02701, shell_carb_anhy, carboxysome shell carbonic anhydrase.
This model describes a carboxysome shell protein that
proves to be a novel class, designated epsilon, of
carbonic anhydrase. It tends to be encoded near genes
for RuBisCo and for other carboxysome shell proteins
[Central intermediary metabolism, One-carbon
metabolism].
Length = 450
Score = 28.2 bits (63), Expect = 1.4
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 75 LISYIDRARLRAAYNEHRKRNAHLEPMFNPEALRPRRIIKTRVTR 119
L+ YI LR + R R A+ MF+ EA R IKT + R
Sbjct: 131 LLPYI----LRLPLDAVRYRKAYAGAMFDVEA-DVARWIKTELRR 170
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 315
Score = 27.1 bits (61), Expect = 3.0
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 46 INKVLLFLRDNVVGTVVVVSAAL 68
I+ F+R NV+GT ++ AA
Sbjct: 91 ISDPEPFIRTNVLGTYTLLEAAR 113
>gnl|CDD|237262 PRK12997, PRK12997, PTS system ascorbate-specific transporter
subunit IIC; Reviewed.
Length = 466
Score = 27.2 bits (61), Expect = 3.0
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 41 IEEININKVLLFLRDNVVGTVVVV 64
E + + K L RD VV +V+
Sbjct: 222 TENLKLPKWLSIFRDTVVAIAIVM 245
>gnl|CDD|217638 pfam03611, EIIC-GAT, PTS system sugar-specific permease component.
This family includes bacterial transmembrane proteins
with a putative sugar-specific permease function,
including and analogous to the IIC component of the PTS
system. It has been suggested that this permease may
form part of an L-ascorbate utilisation pathway, with
proposed specificity for 3-keto-L-gulonate (formed by
hydrolysis of L-ascorbate). This family includes the IIC
component of the galactitol specific GAT family PTS
system.
Length = 406
Score = 27.1 bits (61), Expect = 3.2
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 41 IEEININKVLLFLRDNVVGTVVV 63
E+I + K L F D++V ++
Sbjct: 205 TEDIKLPKKLGFFGDSMVAGAIL 227
>gnl|CDD|129836 TIGR00753, undec_PP_bacA, undecaprenyl-diphosphatase UppP. This is
a family of small, highly hydrophobic proteins.
Overexpression of this protein in Escherichia coli is
associated with bacitracin resistance, and the protein
was originally proposed to be an undecaprenol kinase and
called bacA. It is now known to be an undecaprenyl
pyrophosphate phosphatase (EC 3.6.1.27) and is renamed
UppP [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 255
Score = 27.0 bits (60), Expect = 3.5
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 37 FWDIIEEININKVLLFLRDNVVGTVVVVSAALWIPASCLISYIDRARLRAA 87
F D+I+ + N +L + +VG +++ A + L +R LR A
Sbjct: 98 FKDLIKSLLFNFLLTVVIALIVGAGLLI-LAEEVNRQTLKRDFERLTLRDA 147
>gnl|CDD|114659 pfam05950, Orthopox_A36R, Orthopoxvirus A36R protein. This family
consists of several Orthopoxvirus A36R proteins. The
A36R protein is predicted to be a type Ib membrane
protein.
Length = 158
Score = 26.6 bits (58), Expect = 4.0
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 60 TVVVVSAALWIPASCLISYIDRARLRAAYNEHRKRNAHLEPMFNPEA 106
TV VV+ + + C I YI R ++R YN+++ L+ + + +
Sbjct: 8 TVTVVAGTILV---CYILYICRKKIRTVYNDNKIIMTKLKKIKSSNS 51
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 272
Score = 26.4 bits (58), Expect = 5.1
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 12 FYQMEHPVYKASG----TCEKTIQDVV 34
F+Q+ H VY+ +G C+ I+ VV
Sbjct: 232 FFQLSHRVYQRTGEPCLNCKTPIRRVV 258
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 26.5 bits (59), Expect = 5.5
Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 21/97 (21%)
Query: 27 EKTIQDVVERFWDIIEEININKVLLFLRDNVVGTVVVVSAALW-IPASCL------ISYI 79
+ +++ E+ + +++IN N+ +++ + ++ L +P+S IS
Sbjct: 141 QSDYKELYEKLKEELKKINFNEESF---NSL---LSLLEKYLSYVPSSTDTGEVPDISLY 194
Query: 80 DRARLRAA--------YNEHRKRNAHLEPMFNPEALR 108
D +L AA E+ + L+ N + R
Sbjct: 195 DHLKLTAAIALCLYRYLKENNITDYKLKLFKNSDDFR 231
>gnl|CDD|234933 PRK01285, PRK01285, pyruvoyl-dependent arginine decarboxylase;
Reviewed.
Length = 155
Score = 26.0 bits (58), Expect = 5.6
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 9/64 (14%)
Query: 13 YQMEHPVYKASGTCEKTIQDVVE-----RFWDIIEEININKVLLFLRDNVVGTVVVVSAA 67
Y EH + E ++E R I++EI I + T V +AA
Sbjct: 96 YISEHHGFGEKEEAEDLAATMLEEGFKMRGK-ILDEIKITASEH--GVEGIWTTVA-AAA 151
Query: 68 LWIP 71
+W P
Sbjct: 152 VWYP 155
>gnl|CDD|187641 cd08936, CR_SDR_c, Porcine peroxisomal carbonyl reductase like,
classical (c) SDR. This subgroup contains porcine
peroxisomal carbonyl reductase and similar proteins. The
porcine enzyme efficiently reduces retinals. This
subgroup also includes human dehydrogenase/reductase
(SDR family) member 4 (DHRS4), and human DHRS4L1. DHRS4
is a peroxisomal enzyme with 3beta-hydroxysteroid
dehydrogenase activity; it catalyzes the reduction of
3-keto-C19/C21-steroids into 3beta-hydroxysteroids more
efficiently than it does the retinal reduction. The
human DHRS4 gene cluster contains DHRS4, DHRS4L2 and
DHRS4L1. DHRS4L2 and DHRS4L1 are paralogs of DHRS4,
DHRS4L2 being the most recent member. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 256
Score = 26.0 bits (57), Expect = 6.7
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 29 TIQDVVERFWDIIEEININKVLLFLRDNVV--------GTVVVVSA-ALWIPASCLISY 78
I D E WD I ++N+ K + VV G+VV+VS+ A + P L Y
Sbjct: 103 NILDSTEEVWDKILDVNV-KATALMTKAVVPEMEKRGGGSVVIVSSVAAFHPFPGLGPY 160
>gnl|CDD|240092 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class
1A FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are
membrane associated and monomeric. The class 1 enzymes
can be further divided into subtypes 1A and 1B which
are homodimers and heterotetrameric proteins,
respectively.
Length = 294
Score = 26.1 bits (58), Expect = 7.1
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 14 QMEHPVYKASGTCEKTIQDVVE 35
+ P+ A+G T++D++E
Sbjct: 7 TISPPLMNAAGPWCTTLEDLLE 28
>gnl|CDD|236364 PRK09034, PRK09034, aspartate kinase; Reviewed.
Length = 454
Score = 26.3 bits (59), Expect = 7.1
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 9 LLIFYQMEHPVYKASGTCEKTIQDVVERFWDIIEEININKVLL 51
LLI Y A E + ++ R+ +I +E+ ++ +L
Sbjct: 51 LLILY---AEAVLAGEDYEDIFEAIIARYAEIAKELGLDADIL 90
>gnl|CDD|214523 smart00119, HECTc, Domain Homologous to E6-AP Carboxyl Terminus
with. E3 ubiquitin-protein ligases. Can bind to E2
enzymes.
Length = 328
Score = 26.0 bits (58), Expect = 7.8
Identities = 4/24 (16%), Positives = 11/24 (45%)
Query: 31 QDVVERFWDIIEEININKVLLFLR 54
++ FW+++E + L+
Sbjct: 238 SQTIKWFWEVVESFTNEERRKLLQ 261
>gnl|CDD|225579 COG3037, SgaT, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 481
Score = 25.7 bits (57), Expect = 9.2
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 42 EEININKVLLFLRDNVVGTVVVV 64
E++ + K L RD++V +
Sbjct: 219 EDLKLPKWLSIFRDSIVAITATM 241
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
0.326 0.136 0.413
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,209,830
Number of extensions: 657924
Number of successful extensions: 966
Number of sequences better than 10.0: 1
Number of HSP's gapped: 966
Number of HSP's successfully gapped: 30
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.5 bits)