RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14585
(66 letters)
>gnl|CDD|220464 pfam09903, DUF2130, Uncharacterized protein conserved in bacteria
(DUF2130). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 267
Score = 27.6 bits (62), Expect = 0.38
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 40 AVIMSLLEADAGLGGPVDFSGL 61
AV++S LE + G VD SG
Sbjct: 125 AVLVSELEPENYNSGIVDVSGE 146
>gnl|CDD|227171 COG4834, COG4834, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 334
Score = 27.2 bits (60), Expect = 0.53
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 9 GDQDDVISGMISPPSPQSGGAPTTGNDEA 37
G++ D ++G+ PQ G P GN A
Sbjct: 157 GEKKDELTGLYEATHPQIDGVPVLGNGTA 185
>gnl|CDD|182323 PRK10236, PRK10236, hypothetical protein; Provisional.
Length = 237
Score = 26.1 bits (57), Expect = 1.3
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 37 AAMAVIMSLLEADAGLGGPV 56
AAM+V+ L AGLGGPV
Sbjct: 181 AAMSVLGHGLLRGAGLGGPV 200
>gnl|CDD|219193 pfam06824, DUF1237, Protein of unknown function (DUF1237). This
family contains a number of hypothetical proteins of
about 450 residues in length. Their function is unknown,
and most are bacterial. However, structurally this
family is part of the 6 hairpin glycosidase superfamily,
suggesting a glycosyl hydrolase function.
Length = 403
Score = 24.4 bits (54), Expect = 5.3
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 31 TTGNDEAAMAVIMSLLEADAGLG 53
T+ +DE + L DAG G
Sbjct: 349 TSDDDEEIRECLKMLKNTDAGTG 371
>gnl|CDD|107266 cd06271, PBP1_AglR_RafR_like, Ligand-binding domain of DNA
transcription repressors specific for raffinose (RafR)
and alpha-glucosides (AglR) which are members of the
LacI-GalR family of bacterial transcription regulators.
Ligand-binding domain of DNA transcription repressors
specific for raffinose (RafR) and alpha-glucosides
(AglR) which are members of the LacI-GalR family of
bacterial transcription regulators. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 268
Score = 24.1 bits (53), Expect = 6.2
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 26 SGGAPT---TGNDEAAMAVIMSLLEADAGLGGPVDFS 59
PT ++ A+ V+ +L A+AGL D S
Sbjct: 178 LPDRPTAIVCSSELMALGVLAAL--AEAGLRPGRDVS 212
>gnl|CDD|99861 cd06108, Ec2MCS_like, Escherichia coli (Ec) 2-methylcitrate
synthase (2MCS)_like. 2MCS catalyzes the condensation of
propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to
form 2-methylcitrate and coenzyme A (CoA) during
propionate metabolism. Citrate synthase (CS) catalyzes
the condensation of acetyl coenzyme A (AcCoA) and OAA to
form citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). This group
contains proteins similar to the E. coli 2MCS, EcPrpC.
EcPrpC is one of two CS isozymes in the gram-negative E.
coli. EcPrpC is a dimeric (type I ) CS; it is induced
during growth on propionate and prefers PrCoA as a
substrate though it has partial CS activity with AcCoA.
This group also includes Salmonella typhimurium PrpC and
Ralstonia eutropha (Re) 2-MCS1 which are also induced
during growth on propionate and prefer PrCoA as
substrate, but can also use AcCoA. Re 2-MCS1 can use
butyryl-CoA and valeryl-CoA at a lower rate. A second
Ralstonia eutropha 2MCS, Re 2-MCS2, which is induced on
propionate is also found in this group. This group may
include proteins which may function exclusively as a CS,
those which may function exclusively as a 2MCS, or those
with dual specificity which functions as both a CS and a
2MCS.
Length = 363
Score = 23.8 bits (52), Expect = 7.8
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 24 PQSGGAPTTGNDEAAMAVIM---SLLEADAGL 52
P GGA +EAAM +I S EA+ GL
Sbjct: 211 PLHGGA-----NEAAMELIERFKSPEEAEQGL 237
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 23.8 bits (52), Expect = 8.3
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 33 GNDEAAMAVIMSLLEADAGLGGPVDFSGLP 62
G+D A AV+ L E D G P+D L
Sbjct: 155 GDDAEAKAVVAELAE-DIGF-RPLDAGPLE 182
>gnl|CDD|233305 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This
model describes the cyt c biogenesis protein encoded by
ccmA in bacteria. An exception is, an arabidopsis
protein. Quite likely this is encoded by an organelle.
Bacterial c-type cytocromes are located on the
periplasmic side of the cytoplasmic membrane. Several
gene products encoded in a locus designated as 'ccm' are
implicated in the transport and assembly of the
functional cytochrome C. This cluster includes genes:
ccmA;B;C;D;E;F;G and H. The posttranslational pathway
includes the transport of heme moiety, the secretion of
the apoprotein and the covalent attachment of the heme
with the apoprotein. The proteins ccmA and B represent
an ABC transporter; ccmC and D participate in heme
transfer to ccmE, which function as a periplasmic heme
chaperone. The presence of ccmF, G and H is suggested to
be obligatory for the final functional assembly of
cytochrome c [Protein fate, Protein and peptide
secretion and trafficking, Transport and binding
proteins, Other].
Length = 198
Score = 23.5 bits (51), Expect = 9.0
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 30 PTTGNDEAAMAVIMSLLEADAGLGGPV 56
PTT D+A +A++ LL A GG V
Sbjct: 154 PTTALDKAGVALLAGLLRAHLARGGIV 180
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
0.310 0.134 0.408
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,540,001
Number of extensions: 269444
Number of successful extensions: 188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 13
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.1 bits)