RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13517
(209 letters)
>gnl|CDD|214773 smart00672, CAP10, Putative lipopolysaccharide-modifying enzyme.
Length = 256
Score = 170 bits (432), Expect = 5e-53
Identities = 65/194 (33%), Positives = 96/194 (49%), Gaps = 24/194 (12%)
Query: 12 LGFFRGSRTS-SERDPLIKLSRENSKLIDAAYTKNQAWKSDADTLHAPPAEEVSFEEHCK 70
++RG+ T SER LIK ++ + +L++A T AP ++ EE CK
Sbjct: 86 YAYWRGNPTVASERLDLIKCNQSSPELVNARITIQDWPGKCDGEEDAPGFKKSPLEEQCK 145
Query: 71 YKYLFNFRGVAASFRFKHLFLCKSLVFHVGDEWIEFFYPAMKPWVSHLKNIARDEWIEFF 130
+KY N GVA S R K++ C S+V V E+ EFF
Sbjct: 146 HKYKINIEGVAWSVRLKYILACDSVVLKVKPEYYEFFS----------------RG---- 185
Query: 131 YPAMKPWVHYVPVNKHASKQEIRDMLHFFMHHDDVAEKIATRGYEFVMKNLKMKHVTQYW 190
++PWVHY P+ S +E+++ + + HD A++I RG EF+ +NL M+ V Y
Sbjct: 186 ---LQPWVHYWPIKSDLSCRELKEAVDWGNEHDKKAQEIGKRGSEFIQQNLSMEDVYDYM 242
Query: 191 EVLLSKYAALLKYK 204
LL +YA LLKYK
Sbjct: 243 FHLLQEYAKLLKYK 256
>gnl|CDD|218692 pfam05686, Glyco_transf_90, Glycosyl transferase family 90. This
family of glycosyl transferases are specifically
(mannosyl) glucuronoxylomannan/galactoxylomannan -beta
1,2-xylosyltransferases, EC:2.4.2.-.
Length = 281
Score = 57.5 bits (139), Expect = 4e-10
Identities = 24/42 (57%), Positives = 29/42 (69%)
Query: 165 VAEKIATRGYEFVMKNLKMKHVTQYWEVLLSKYAALLKYKPR 206
A+KIA RG EF+ +NLKM V Y LL++YA LLKYKP
Sbjct: 172 EAQKIAERGSEFIRENLKMDDVYDYMFHLLTEYAKLLKYKPT 213
>gnl|CDD|222197 pfam13524, Glyco_trans_1_2, Glycosyl transferases group 1.
Length = 92
Score = 36.4 bits (85), Expect = 0.001
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 147 ASKQEIRDMLHFFMHHDDVAEKIATRGYEFVMKNLKMKHVTQYWE 191
+E+ + L + + + IA G E V+ +H +
Sbjct: 47 RDPEELAEKLRYLLADPEERRAIAAAGRERVLAEHTYEHRAEQLL 91
>gnl|CDD|182324 PRK10238, PRK10238, aromatic amino acid transporter; Provisional.
Length = 456
Score = 31.5 bits (71), Expect = 0.32
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 68 HCKYKYLFNFRGVAASFRFKHLFLCKSL--VFHVGDEWIEFFYPAMKPWVS 116
H YKY +F G A+ + + L++ ++ + VG ++I+F+YP + WVS
Sbjct: 80 HFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVG-KYIQFWYPEIPTWVS 129
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 27.9 bits (62), Expect = 1.1
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 143 VNKHASKQEIRDMLHFFMHHDDV----AEKIATRGYEFV 177
+NK A+++E+ ++ + +D+ E +RG FV
Sbjct: 7 LNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFV 45
>gnl|CDD|165570 PHA03324, PHA03324, nuclear egress membrane protein UL34;
Provisional.
Length = 274
Score = 29.3 bits (65), Expect = 1.3
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 12 LGFFRGSRTS---------SERDP-LIKLSRENSKLIDAAYTKNQAWKSDADT 54
+ F+RG + S+ +P LIK+S+ + IDAA +N D+
Sbjct: 141 ICFYRGGKNDITIRFAFYKSDSEPNLIKISKCVQEAIDAAAQENLPKPRGFDS 193
>gnl|CDD|173872 cd08507, PBP2_SgrR_like, The C-terminal solute-binding domain of
DNA-binding transcriptional regulator SgrR is related to
the ABC-type oligopeptide-binding proteins and contains
the type 2 periplasmic-binding fold. A novel family of
SgrR transcriptional regulator contains a two-domain
structure with an N terminal DNA-binding domain of the
winged helix family and a C-terminal solute-binding
domain. The C-terminal domain shows strong homology with
the ABC-type oligopeptide-binding protein family, a
member of the type 2 periplasmic-binding fold protein
(PBP2) superfamily that also includes the C-terminal
substrate-binding domain of LysR-type transcriptional
regulators. SgrR (SugaR transport-related Regulator) is
negatively autoregulated and activates transcription of
divergent operon SgrS, which encodes a small RNA
required for recovery from glucose-phosphate stress.
Hence, the small RNA SgrS and SgrR, the transcription
factor that controls sgrS expression, are both required
for recovery from glucose-phosphate stress. Most of
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.
Length = 448
Score = 28.0 bits (63), Expect = 4.2
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 8/66 (12%)
Query: 61 EEVSFEEHCKYKYLFNFR-GVAASFRF----KHLFLCKSLVFHVGDEWIEFFYPA--MKP 113
+E EE C + LFN R A F L ++L+ H+G E ++PA + P
Sbjct: 221 QESRLEEGCYF-LLFNQRKPGAQDPAFRRALSELLDPEALIQHLGGERQRGWFPAYGLLP 279
Query: 114 WVSHLK 119
K
Sbjct: 280 EWPREK 285
>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 27.9 bits (62), Expect = 4.3
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 105 EFFYPAMKPWVSHLKNIARD 124
E + A K W++HL+ ++R+
Sbjct: 641 ELAHSAHKHWINHLRQLSRN 660
>gnl|CDD|218648 pfam05592, Bac_rhamnosid, Bacterial alpha-L-rhamnosidase. This
family consists of bacterial rhamnosidase A and B
enzymes. L-Rhamnose is abundant in biomass as a common
constituent of glycolipids and glycosides, such as plant
pigments, pectic polysaccharides, gums or
biosurfactants. Some rhamnosides are important bioactive
compounds. For example, terpenyl glycosides, the
glycosidic precursor of aromatic terpenoids, act as
important flavouring substances in grapes. Other
rhamnosides act as cytotoxic rhamnosylated terpenoids,
as signal substances in plants or play a role in the
antigenicity of pathogenic bacteria.
Length = 509
Score = 27.6 bits (62), Expect = 6.0
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 98 HVGD-EWIEFFYPAMKPWVSHLKNIARDE 125
+ GD ++ YP+MK W+ ++ + D
Sbjct: 219 NYGDERILKDQYPSMKRWLDYILQRSDDG 247
>gnl|CDD|239565 cd03483, MutL_Trans_MLH1, MutL_Trans_MLH1: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH1 (MutL homologue
1). This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. MLH1 forms
heterodimers with PMS2, PMS1 and MLH3. These three
complexes have distinct functions in meiosis.
hMLH1-hPMS2 also participates in the repair of all DNA
mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1
or hMLH1-hMLH3 in MMR have not been established. Cells
lacking hMLH1 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hMLH1 causes predisposition to HNPCC, Muir-Torre
syndrome and Turcot syndrome (HNPCC variant). Mutation
in hMLH1 accounts for a large fraction of HNPCC
families.
Length = 127
Score = 26.4 bits (59), Expect = 6.5
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 13/44 (29%)
Query: 135 KPWV--------HYVPVNKHASKQEIRDMLHFFMHHDDVAEKIA 170
P+V V VN H +K+E+ F++ +++ E+I
Sbjct: 81 HPFVYLSLEIPPENVDVNVHPTKREVH-----FLNEEEIIERIQ 119
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 336
Score = 27.1 bits (61), Expect = 7.2
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 161 HHDDVAEKIATRGYEFVMKNLKMKHVTQYWE 191
HH D+AE++ G E V + Q+W+
Sbjct: 202 HHQDLAEQLEALGIEPVDYIFCLTDTDQHWD 232
>gnl|CDD|221156 pfam11649, T4_neck-protein, Virus neck protein. This family of
protein represents gene product 14, a major component of
the neck in T4-like viruses along with gene product 13.
Gene product 14 is rich is beta-sheets. The formation of
the neck to the head of the bacteriophage is crucial for
the tail attachment.
Length = 247
Score = 26.6 bits (59), Expect = 8.1
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 140 YVPVNKHASKQEIRDMLHFFMHHDDVAEKIATRGYEFV 177
YV NK++++Q + D L VAE I RG E
Sbjct: 28 YVNFNKYSNEQTLADDL--------VAESIQMRGVEVY 57
>gnl|CDD|236395 PRK09177, PRK09177, xanthine-guanine phosphoribosyltransferase;
Validated.
Length = 156
Score = 26.4 bits (59), Expect = 8.6
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 10/38 (26%)
Query: 109 PAMKPWV-SHLKNIARDEWIEFFYPAMKPW---VHYVP 142
PA +P V +++ ++ +D WIEF PW + +VP
Sbjct: 119 PAGRPLVDTYVTDVPQDTWIEF------PWDMGLTFVP 150
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
0.324 0.136 0.436
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,807,635
Number of extensions: 989620
Number of successful extensions: 1128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1126
Number of HSP's successfully gapped: 19
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.8 bits)