RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16599
(73 letters)
>gnl|CDD|189907 pfam01249, Ribosomal_S21e, Ribosomal protein S21e.
Length = 81
Score = 98.8 bits (247), Expect = 2e-29
Identities = 41/65 (63%), Positives = 48/65 (73%), Gaps = 1/65 (1%)
Query: 8 SASNRIIAAKDHASIQIAIADVDPATGRTTDNLKMYAICGQIRRMGESDDCIGRLAKDDG 67
SA+NRII AKDHAS+QI IADVD GR T YA+CG IRRMGESDD + RLA+ DG
Sbjct: 18 SATNRIIGAKDHASVQINIADVDE-NGRYTGEFTTYALCGYIRRMGESDDALNRLAQKDG 76
Query: 68 IIAKN 72
++ N
Sbjct: 77 LLPGN 81
>gnl|CDD|192370 pfam09765, WD-3, WD-repeat region. This entry is of a region of
approximately 100 residues containing three WD repeats
and six cysteine residues possibly as three
cystine-bridges. These regions are contained within the
Fancl protein in humans which is the putative E3
ubiquitin ligase subunit of the FA complex (Fanconi
anaemia). Eight subunits of the Fanconi anaemia gene
products form a multisubunit nuclear complex which is
required for mono-ubiquitination of a downstream FA
protein, FANCD2. The WD repeats are required for
interaction with other subunits of the FA complex.
Length = 292
Score = 26.2 bits (58), Expect = 1.3
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 7 SSASNRIIAAKDHASIQIAIADVDP 31
+ A+ R IA ++ S+++ + P
Sbjct: 214 TKATTRRIALGNNVSLKVEVDPRHP 238
>gnl|CDD|182832 PRK10911, PRK10911, oligopeptidase A; Provisional.
Length = 680
Score = 26.3 bits (58), Expect = 1.5
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 56 DDCIGRLAKDDGIIAK 71
DDC+G++ K DG + K
Sbjct: 424 DDCVGQMRKADGSLQK 439
>gnl|CDD|217210 pfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde
dehydrogenase.
Length = 543
Score = 25.7 bits (57), Expect = 2.4
Identities = 5/24 (20%), Positives = 8/24 (33%), Gaps = 1/24 (4%)
Query: 23 QIAIADVDPATGRTTDNLKMYAIC 46
+VD TG L+ +
Sbjct: 465 AAVEVEVDCLTGDVK-VLRTDIVM 487
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 25.0 bits (55), Expect = 4.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 45 ICGQIRRMGESDD 57
IC Q+RR+G S D
Sbjct: 152 ICNQLRRLGSSLD 164
>gnl|CDD|234267 TIGR03573, WbuX, N-acetyl sugar amidotransferase. This enzyme
has been implicated in the formation of the acetamido
moiety (sugar-NC(=NH)CH3) which is found on some
exopolysaccharides and is positively charged at neutral
pH. The reaction involves ligation of ammonia with a
sugar N-acetyl group, displacing water. In E. coli
(O145 strain) and Pseudomonas aeruginosa (O12 strain)
this gene is known as wbuX and ifnA respectively and
likely acts on sialic acid. In Campylobacter jejuni,
the gene is known as pseA and acts on pseudaminic acid
in the process of flagellin glycosylation. In other
Pseudomonas strains and various organisms it is unclear
what the identity of the sugar substrate is, and in
fact, the phylogenetic tree of this family sports a
considerably deep branching suggestive of possible
major differences in substrate structure. Nevertheless,
the family is characterized by a conserved
tetracysteine motif (CxxC.....[GN]xCxxC) possibly
indicative of a metal binding site, as well as an
invariable contextual association with homologs of the
HisH and HisF proteins known as WbuY and WbuZ,
respectively. These two proteins are believed to supply
the enzyme with ammonium by hydrolysis of glutamine and
delivery through an ammonium conduit.
Length = 343
Score = 24.6 bits (54), Expect = 5.4
Identities = 5/22 (22%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 39 NLKMYAICGQIRRMGESD-DCI 59
++ + +I++ G DCI
Sbjct: 42 EKELEELVDKIKKKGGGRYDCI 63
>gnl|CDD|187641 cd08936, CR_SDR_c, Porcine peroxisomal carbonyl reductase like,
classical (c) SDR. This subgroup contains porcine
peroxisomal carbonyl reductase and similar proteins. The
porcine enzyme efficiently reduces retinals. This
subgroup also includes human dehydrogenase/reductase
(SDR family) member 4 (DHRS4), and human DHRS4L1. DHRS4
is a peroxisomal enzyme with 3beta-hydroxysteroid
dehydrogenase activity; it catalyzes the reduction of
3-keto-C19/C21-steroids into 3beta-hydroxysteroids more
efficiently than it does the retinal reduction. The
human DHRS4 gene cluster contains DHRS4, DHRS4L2 and
DHRS4L1. DHRS4L2 and DHRS4L1 are paralogs of DHRS4,
DHRS4L2 being the most recent member. 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 = 256
Score = 24.0 bits (52), Expect = 7.7
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 48 QIRRMGESDDCIG 60
+IRR+G+ +DC G
Sbjct: 216 RIRRLGQPEDCAG 228
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 0.132 0.370
Gapped
Lambda K H
0.267 0.0849 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,527,350
Number of extensions: 264411
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 15
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
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 (21.8 bits)
S2: 53 (24.0 bits)