RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy281
(162 letters)
>gnl|CDD|227462 COG5133, COG5133, Uncharacterized conserved protein [Function
unknown].
Length = 181
Score = 145 bits (366), Expect = 7e-45
Identities = 77/146 (52%), Positives = 93/146 (63%), Gaps = 7/146 (4%)
Query: 17 SKCEDRPVTAEDQN--DYITDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQV--- 71
S E P+ +E+ + D D +EI+DLI +I DPEHPLTLE+L VV L I V
Sbjct: 32 SLEERHPIESENGVLQNEEPDLIDQQEIYDLIADIRDPEHPLTLEQLSVVSLEDISVPDG 91
Query: 72 --NNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAIN 129
N +KV TPTIPHCSMATLIGL IRVRL R LP RF V V I G+H +E +N
Sbjct: 92 IAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLERHLPPRFHVQVHIKKGTHISERQVN 151
Query: 130 KQLADKERVAAALENSTLIGVINQCI 155
KQL DKERVAAA EN L+ V+ + +
Sbjct: 152 KQLNDKERVAAACENEQLLDVMEKML 177
>gnl|CDD|225062 COG2151, PaaD, Predicted metal-sulfur cluster biosynthetic enzyme
[General function prediction only].
Length = 111
Score = 41.9 bits (99), Expect = 1e-05
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 9/81 (11%)
Query: 41 EIFDLIRNIYDPEHPLTLEELHVVDLSLI---QVNNETNQIKVNFTPTIPHCSMATLIGL 97
+I + ++ + DPE + +VDL L+ +++ +KV T T P C +A +I
Sbjct: 16 DILEALKTVIDPEIGID-----IVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIAD 70
Query: 98 SIRVRLIRALPARFKVVVEIT 118
+ + +P V VE+T
Sbjct: 71 QVE-AALEEIPGVEDVEVELT 90
>gnl|CDD|216762 pfam01883, DUF59, Domain of unknown function DUF59. This family
has an alpha/beta topology, with 13 conserved
hydrophobic residues at its core and a putative active
site containing a highly conserved cysteine. Members of
this family are involved in a range of physiological
functions. The family includes PaaJ (PhaH) from
Pseudomonas putida. PaaJ forms a complex with PaaG
(PhaF), PaaI (PhaG) and PaaK (PhaI), which hydroxylates
phenylacetic acid to 2-hydroxyphenylacetic acid. It also
includes PaaD from Escherichia coli, a member of a
multicomponent oxygenase involved in phenylacetyl-CoA
hydroxylation. It is found near the N-terminus of the
chloroplast scaffold protein HCF101, involved in the
assembly of [4Fe-4S] clusters and their transfer to
apoproteins.
Length = 72
Score = 36.8 bits (86), Expect = 4e-04
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 5/75 (6%)
Query: 41 EIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIR 100
+ ++ + DPE + L L +V I + +++ + T P C I +
Sbjct: 3 AVLAALKTVTDPETGVDLVSLGMV--RNITIEG--GKVRFDIELTYPACPQMEPIRKAAE 58
Query: 101 VRLIRALPARFKVVV 115
+RALP V V
Sbjct: 59 -AALRALPGVVSVSV 72
>gnl|CDD|213809 TIGR03406, FeS_long_SufT, probable FeS assembly SUF system protein
SufT. The function is unknown for this protein family,
but members are found almost always in operons for the
the SUF system of iron-sulfur cluster biosynthesis. The
SUF system is present elsewhere on the chromosome for
those few species where SUF genes are not adjacent. This
family shares this property of association with the SUF
system with a related family, TIGR02945. TIGR02945
consists largely of a DUF59 domain (see pfamam family
pfam01883), while this protein is about double the
length, with a unique N-terminal domain and DUF59
C-terminal domain. A location immediately downstream of
the cysteine desulfurase gene sufS in many contexts
suggests the gene symbol sufT. Note that some other
homologs of this family and of TIGR02945, but no actual
members of this family, are found in operons associated
with phenylacetic acid (or other ring-hydroxylating)
degradation pathways [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 174
Score = 37.7 bits (88), Expect = 0.001
Identities = 21/96 (21%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 23 PVTAEDQNDYITDEFDSREIFDLIRNIYDPEHPLTLEELHVV-DLSLIQVNNETNQIKVN 81
P D + E + ++++ +R +YDPE P+ + +L +V + ++ ++ +
Sbjct: 59 PPPPLDLPENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIE 118
Query: 82 FTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEI 117
T T P C M ++ + + A+P +V VE+
Sbjct: 119 MTLTAPGCGMGPVLVEDVE-DKVLAVPNVDEVEVEL 153
>gnl|CDD|131990 TIGR02945, SUF_assoc, FeS assembly SUF system protein. Members of
this family belong to the broader Pfam family pfam01883,
or Domain of Unknown Function DUF59. Many members of
DUF59 are candidate ring hydroxylating complex subunits.
However, members of the narrower family defined here all
are found in genomes that carry the FeS assembly SUF
system. For 70 % of these species, the member of this
protein family is found as part of the SUF locus,
usually immediately downstream of the sufS gene
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 99
Score = 33.4 bits (77), Expect = 0.013
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 40 REIFDLIRNIYDPEHPLTLEELHVVDLSLI---QVNNETNQIKVNFTPTIPHCSMATLIG 96
+ + ++ +YDPE P +++ +L LI V ++ + + T T P+C +A +
Sbjct: 4 DAVIEALKTVYDPEIP-----VNIYELGLIYDIDV-DDDGHVDIQMTLTAPNCPVAGSMP 57
Query: 97 LSIRVRLIRALPARFKVVVEIT 118
+ +RA+P V VE+
Sbjct: 58 GEVENA-VRAVPGVGSVTVELV 78
>gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine
dehydrogenase I; Provisional.
Length = 819
Score = 33.2 bits (77), Expect = 0.055
Identities = 26/108 (24%), Positives = 47/108 (43%), Gaps = 22/108 (20%)
Query: 45 LIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLS------ 98
LI+N ++P+ P T LI ++ + + V + + +M + G
Sbjct: 281 LIKNTFNPQAPGT----------LIGAESDEDSLPVKGISNLNNMAMFNVSGPGMKGMVG 330
Query: 99 IRVRLIRALPARFKV-VVEITPGS--HSTEFAINKQLADKERVAAALE 143
+ R+ AL +R + VV IT S +S F + + +D + ALE
Sbjct: 331 MASRVFAAL-SRAGISVVLITQSSSEYSISFCVPQ--SDAAKAKRALE 375
>gnl|CDD|187666 cd09806, type1_17beta-HSD-like_SDR_c, human estrogenic
17beta-hydroxysteroid dehydrogenase type 1 (type 1
17beta-HSD)-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. This classical SDR subgroup
includes human type 1 17beta-HSD, human retinol
dehydrogenase 8, zebrafish photoreceptor associated
retinol dehydrogenase type 2, and a chicken
ovary-specific 17beta-hydroxysteroid dehydrogenase. 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 = 258
Score = 27.8 bits (62), Expect = 2.4
Identities = 18/58 (31%), Positives = 22/58 (37%), Gaps = 14/58 (24%)
Query: 86 IPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALE 143
I CS IGL + VRL RFKV +A + L K R+ A
Sbjct: 5 ITGCSSG--IGLHLAVRLASDPSKRFKV------------YATMRDLKKKGRLWEAAG 48
>gnl|CDD|131214 TIGR02159, PA_CoA_Oxy4, phenylacetate-CoA oxygenase, PaaJ subunit.
Phenylacetate-CoA oxygenase is comprised of a five gene
complex responsible for the hydroxylation of
phenylacetate-CoA (PA-CoA) as the second catabolic step
in phenylacetic acid (PA) degradation. Although the
exact function of this enzyme has not been determined,
it has been shown to be required for phenylacetic acid
degradation and has been proposed to function in a
multicomponent oxygenase acting on phenylacetate-CoA
[Energy metabolism, Other].
Length = 146
Score = 27.4 bits (61), Expect = 2.7
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 51 DPEHPLTLEELHVVDLSLIQ-VNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPA 109
DPE P+ + V DL +++ V+ + + V FTPT C +I IR + RAL
Sbjct: 3 DPEIPV----VSVTDLGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAV-RALGV 57
Query: 110 -RFKVVVEITP 119
+V + P
Sbjct: 58 EVVEVSTSLDP 68
>gnl|CDD|213629 TIGR01489, DKMTPPase-SF, 2,3-diketo-5-methylthio-1-phosphopentane
phosphatase. This phosphatase is a member of the IB
subfamily (TIGR01488) of the haloacid dehalogenase
(HAD) superfamily of aspartate-nucleophile hydrolases.
With the exception of OMNI|NTL01BS01361 from B.
subtilis and GP|15024582 from Clostridium
acetabutylicum, the members of this group are all
eukaryotic, spanning metazoa, plants and fungi. The B.
subtilus gene (YkrX, renamed MtnX) is part of an operon
for the conversion of methylthioribose (MTR) to
methionine. It works with the enolase MtnW, a RuBisCO
homolog. The combination of MtnW and MtnX achieves the
same overall reaction as the enolase-phosphatase MtnC.
The function of MtnX was shown by Ashida, et al. (2003)
to be 2,3-diketo-5-methylthio-1-phosphopentane
phosphatase, rather than
2,3-diketo-5-methylthio-1-phosphopentane phosphatase as
proposed earlier. See the Genome Property for
methionine salvage for more details. In eukaryotes,
methionine salvage from methylthioadenosine also
occurs. It seems reasonable that members of this family
in eukaryotes fulfill a similar role as in Bacillus. A
more specific, equivalog-level model is TIGR03333. Note
that a member of this family from S. cerevisiae is
annotated as a "probable membrane protein" due to a
predicted transmembrane helix. The region in question
contains the second of the three conserved HAD
superfamily catalytic motifs and thus, considering the
fold of the HAD catalytic domain, is unlikely to be a
transmembrane region in fact [Central intermediary
metabolism, Other].
Length = 188
Score = 27.4 bits (61), Expect = 3.2
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 21 DRPVTAEDQNDYITDEFDSREIFDLIRNIY 50
D +T D +D+ITD+F E L+ +
Sbjct: 9 DGTITLNDSDDWITDKFGPPEANRLLDGVL 38
>gnl|CDD|182985 PRK11130, moaD, molybdopterin synthase small subunit; Provisional.
Length = 81
Score = 26.1 bits (58), Expect = 3.6
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 119 PGSHSTEFAINKQLADK-ERVAAALENSTLIGVINQCIS 156
T A+ + LA K +R A ALE+ L+ +NQ +
Sbjct: 22 AADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLV 60
>gnl|CDD|240325 PTZ00237, PTZ00237, acetyl-CoA synthetase; Provisional.
Length = 647
Score = 26.2 bits (58), Expect = 9.1
Identities = 12/49 (24%), Positives = 23/49 (46%)
Query: 41 EIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHC 89
EI N+ + T + +V+ L + +E++ K+ PTIP+
Sbjct: 179 EIITFTPNLKEAIELSTFKPSNVITLFRNDITSESDLKKIETIPTIPNT 227
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
0.318 0.135 0.385
Gapped
Lambda K H
0.267 0.0886 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,479,412
Number of extensions: 777429
Number of successful extensions: 789
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 26
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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 (21.7 bits)
S2: 55 (24.7 bits)