RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6788
(61 letters)
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.6 bits (67), Expect = 0.056
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1 MEGAESKVPPVQFPDIKRPEDVVQMIMKDELKFGVLIGLI 40
+E +V VQ D++ PEDV +M+ + + KFG + LI
Sbjct: 45 IEQFPGQVLTVQM-DVRNPEDVQKMVEQIDEKFGRIDALI 83
>gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional.
Length = 765
Score = 25.4 bits (56), Expect = 2.1
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 23 VQMIMKDELKFGVLIGLIEVGEVSNREVVNTILH 56
+ M M DE L GL++ G+V+ E+ + + H
Sbjct: 315 IDMSMSDEYYSKYLPGLVKSGKVTMAELDDAVRH 348
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup
has a fairly well conserved active site tetrad and
domain size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). 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 = 250
Score = 24.6 bits (54), Expect = 3.0
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 15 DIKRPEDVVQMIMKDELKFGVLIGLIEVGEVSNRE 49
DI E + ++I KFG + LI S +
Sbjct: 60 DITSKESIKELIESYLEKFGRIDILINNAYPSPKV 94
>gnl|CDD|184256 PRK13700, PRK13700, conjugal transfer protein TraD; Provisional.
Length = 732
Score = 24.9 bits (54), Expect = 3.4
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 19 PEDVVQMIMKDELKFGVLIGLIEVGEVSNREVVNTILH 56
P+DV +M+ KD + IG + + + + E+ N LH
Sbjct: 156 PKDVARMLKKDGKDSDIRIGDLPI--IRDSEIQNFCLH 191
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 24.5 bits (54), Expect = 3.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 34 GVLIGLIEVGEVSNREVVN 52
GVL+GL +G+V E+ +
Sbjct: 40 GVLVGLTNIGDVHGYEIDD 58
>gnl|CDD|145511 pfam02405, Permease, Permease. This domain functions as a
permease. In a hypothetical protein from Neisseria it is
involved in L-glutamate import into the cell. In
Arabidopsis ABC transporter I family member 14 it is
involved in lipid transfer within the cell.
Length = 215
Score = 23.5 bits (52), Expect = 8.2
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 14/57 (24%)
Query: 12 QFPDIKRPEDVVQMIMKDELKFGVLIGLI-------------EVGEVSNREVVNTIL 55
F P DV+ ++K + FG++I LI VG + R VV +I+
Sbjct: 147 SFQSFVDPTDVLVGLIK-AVVFGLIIALIGCYYGLTAKGGAEGVGRATTRAVVTSIV 202
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
0.319 0.141 0.390
Gapped
Lambda K H
0.267 0.0885 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,119,690
Number of extensions: 227099
Number of successful extensions: 205
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 9
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (23.9 bits)