RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11533
(92 letters)
>gnl|CDD|222390 pfam13802, Gal_mutarotas_2, Galactose mutarotase-like. This
family is found N-terminal to glycosyl-hydrolase
domains, and appears to be similar to the galactose
mutarotase superfamily.
Length = 68
Score = 69.8 bits (172), Expect = 9e-18
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 2 YRLYNLDVFEYELDSPMSLYAAIPFVTAHNSHHSVGVFWLNAAETWVD 49
YRL+N D + Y+ +S LY +IPF + GVF+ N A TW D
Sbjct: 21 YRLWNTDAYGYDAESTDPLYKSIPFYISLRPSRGYGVFFDNTARTWFD 68
>gnl|CDD|224418 COG1501, COG1501, Alpha-glucosidases, family 31 of glycosyl
hydrolases [Carbohydrate transport and metabolism].
Length = 772
Score = 43.2 bits (102), Expect = 3e-06
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 2 YRLYNLDVFEYELDSPMSLYAAIPFVTAHNSHHSVGVFWLNAAETWVDV 50
YRL+N D Y +LYA+IPF + G+F N+A DV
Sbjct: 172 YRLWNADAGTYTGGDYDNLYASIPFYLSSR---GYGLFVDNSAYGSFDV 217
>gnl|CDD|220247 pfam09451, ATG27, Autophagy-related protein 27.
Length = 265
Score = 27.0 bits (60), Expect = 1.1
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 17/54 (31%)
Query: 36 VGVFWLNA-------------AETWVDVTRSKSTLTGDVMSKIVNFVSGSGGDG 76
+G WLN + D+ DV+ K+V V+GSG G
Sbjct: 216 IGGSWLNYNRYGARGFDLVPHGDFLRDL----PYFAKDVIRKVVGTVTGSGSRG 265
>gnl|CDD|182967 PRK11106, PRK11106, queuosine biosynthesis protein QueC;
Provisional.
Length = 231
Score = 26.2 bits (58), Expect = 2.5
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 19/51 (37%)
Query: 26 FVTAHNSHHSVGV----------FWLNAAETW--------VDVTRSKSTLT 58
FV A N S+G+ WLN AETW +D+ R + TLT
Sbjct: 138 FVKALNHAVSLGMAKDIRFETPLMWLNKAETWALADYYGQLDLVRHE-TLT 187
>gnl|CDD|152310 pfam11874, DUF3394, Domain of unknown function (DUF3394). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 190
amino acids in length. This domain is found associated
with pfam06808.
Length = 183
Score = 24.4 bits (54), Expect = 8.1
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 56 TLTGDVMSKIVNFVSGSGGDGGPR 79
L GD + K V G G DG R
Sbjct: 86 DLEGDPVEKTVLLPLGEGADGEER 109
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e)
SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. 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 = 332
Score = 24.6 bits (54), Expect = 8.2
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 15 DSPMSLYAAIPF---VTAHNSHHSVGV 38
D P+SLYAA + AH H G+
Sbjct: 146 DHPISLYAATKKANELMAHTYSHLYGI 172
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 24.5 bits (54), Expect = 8.7
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 8 DVFEYELDSPMSLYAAIPF 26
+ + L P+SLY IPF
Sbjct: 25 EAYMTALPKPLSLYIHIPF 43
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
0.316 0.131 0.389
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,468,210
Number of extensions: 338432
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 9
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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 (21.6 bits)
S2: 53 (24.0 bits)