RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10760
(356 letters)
>gnl|CDD|146960 pfam04572, Gb3_synth, Alpha 1,4-glycosyltransferase conserved
region. The glycosphingolipids (GSL) form part of
eukaryotic cell membranes. They consist of a hydrophilic
carbohydrate moiety linked to a hydrophobic ceramide
tail embedded within the lipid bilayer of the membrane.
Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common
synthetic precursor to the majority of GSL found in
vertebrates. Alpha 1.4-glycosyltransferases utilise UDP
donors and transfer the sugar to a beta-linked acceptor.
This region appears to be confined to higher eukaryotes.
No function has been yet assigned to this region.
Length = 135
Score = 127 bits (321), Expect = 4e-36
Identities = 45/126 (35%), Positives = 71/126 (56%), Gaps = 1/126 (0%)
Query: 232 IHLDKDHWLSGAALRELRDNFKTTEWGANGPGVLTRLLKAECKPQSYAH-NIISCRNFTI 290
++ + H L+ LR+ NF +WG NGPG++TR+L+ C +A + C FT+
Sbjct: 1 MNFEPHHPLAEMCLRDFAANFNGNKWGHNGPGLVTRVLRKWCNTGDFAGMTRLRCGGFTV 60
Query: 291 YPPRFFYPVHWEHWADYLNETNAPATMSLFRDSYALHVWNSFTKRVPVKLGSEQPYAQIA 350
PP FYP+ W W + E TM+ ++SYA+H+WN +K + V+ GS Y +A
Sbjct: 61 LPPDAFYPIPWPQWKKFFEEPRLEETMNWVKESYAVHLWNKASKGLKVEEGSRVAYGTLA 120
Query: 351 RRYCPR 356
++CPR
Sbjct: 121 EQHCPR 126
>gnl|CDD|218109 pfam04488, Gly_transf_sug, Glycosyltransferase sugar-binding region
containing DXD motif. The DXD motif is a short
conserved motif found in many families of
glycosyltransferases, which add a range of different
sugars to other sugars, phosphates and proteins.
DXD-containing glycosyltransferases all use nucleoside
diphosphate sugars as donors and require divalent
cations, usually manganese. The DXD motif is expected to
play a carbohydrate binding role in sugar-nucleoside
diphosphate and manganese dependent
glycosyltransferases.
Length = 93
Score = 55.8 bits (135), Expect = 4e-10
Identities = 32/109 (29%), Positives = 48/109 (44%), Gaps = 25/109 (22%)
Query: 107 RQACSIESAAMMNPGVQVYVVVIASVRNRTRNPLIDRLYEYQNVHIVQVDLGRYFQNTPL 166
R+ +IES ++P VV+ + +D+ +TP
Sbjct: 3 REMKAIESLISLHPDYC-VVVLNDDL-------------------DKILDINFLKSDTP- 41
Query: 167 HGFYTQDAILTSLWPLSHMSDLLRYVTLYKYGGTYLDLDFIVIKSLESL 215
++ + + L + SDLLRY LYKYGG YLD D I +KSL S+
Sbjct: 42 --WFLE--AYSLLPLFAAKSDLLRYAILYKYGGIYLDTDVIPLKSLNSI 86
>gnl|CDD|221853 pfam12919, TcdA_TcdB, TcdA/TcdB catalytic glycosyltransferase
domain. This domain represents the N-terminal
glycosyltransferase from a set of toxins found in some
bacteria. This domain in TcdB glycosylates the host RhoA
protein.
Length = 472
Score = 40.9 bits (96), Expect = 7e-04
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 141 IDRLYEYQNVHIVQVDLGRYFQNTPLHGFYTQDAILTSLWPLSHMSDLLRYVTLYKYGGT 200
++++ + V I +D F++ L Y Q+ +L W + SD+LR L +YGG
Sbjct: 146 LNKILGNERVDIRDIDELTSFKDVELKQNYEQELLLR--WNYAAASDILRMYALKEYGGI 203
Query: 201 YLDLD 205
Y D+D
Sbjct: 204 YTDVD 208
>gnl|CDD|226297 COG3774, OCH1, Mannosyltransferase OCH1 and related enzymes [Cell
envelope biogenesis, outer membrane].
Length = 347
Score = 38.2 bits (89), Expect = 0.004
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 186 SDLLRYVTLYKYGGTYLDLDFIVIKSLESL 215
+D RY LY YGG YLD+D ++K ++ L
Sbjct: 148 ADFWRYFVLYHYGGIYLDIDTGLVKPIDPL 177
>gnl|CDD|200235 TIGR03033, phage_rel_nuc, putative phage-type endonuclease.
Members of this protein family are found often in phage
genomes and in prokaryotic genomes in uncharacterized
regions that resemble integrated prophage regions.
Length = 153
Score = 31.2 bits (71), Expect = 0.45
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 3/67 (4%)
Query: 31 FLSPRFLNHFVFR-VKQPLRYIEYWRSGYRVQNINCVLSGVEKDFAFDDITRLDVPDNSI 89
F+ P +N ++ VK E +R Y + L E + + L D I
Sbjct: 44 FVEPEDMNEAMYHGVKLEPEAREAFRDKYGIMAEPFCLEHDEYPWMAASLDGLVADDKQI 103
Query: 90 FFLETSC 96
LE C
Sbjct: 104 --LEIKC 108
>gnl|CDD|237554 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 30.7 bits (70), Expect = 1.5
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 16/84 (19%)
Query: 86 DNSIFFLETSCTHADGVELTLR-QACSIESAAMMNPGVQV------------YVVVIASV 132
+N + FLE + + D E + + C E A+ + GVQ+ +V+V +
Sbjct: 571 ENLLKFLELASGYEDIEEFLFKLEPCDKEIASEESKGVQIMTVHKSKGLEFEHVIVCDRL 630
Query: 133 -RNRTRNPLIDRLYEYQNVHIVQV 155
+ + + + L+EY + + Q+
Sbjct: 631 GKPNSDSSNL--LFEYDGIELWQI 652
>gnl|CDD|218707 pfam05704, Caps_synth, Capsular polysaccharide synthesis protein.
This family consists of several capsular polysaccharide
proteins. Capsular polysaccharide (CPS) is a major
virulence factor in Streptococcus pneumoniae.
Length = 279
Score = 29.9 bits (68), Expect = 2.0
Identities = 17/50 (34%), Positives = 18/50 (36%), Gaps = 15/50 (30%)
Query: 184 HMSDLLRYVTLYKYGGT---------------YLDLDFIVIKSLESLHNY 218
H SD+LR L KYGG LD DF KS N
Sbjct: 112 HFSDILRLNLLAKYGGLWIDATIYCTGDLPNYLLDSDFFTFKSSPFDSNK 161
>gnl|CDD|227420 COG5088, SOH1, Rad5p-binding protein [General function prediction
only].
Length = 114
Score = 28.3 bits (63), Expect = 2.3
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 8/35 (22%)
Query: 22 LSFLLGVHIFLSPRFLNHFVFRVKQPLRYIEYWRS 56
L+ L IF S F N+ L+Y+EYWR+
Sbjct: 33 LTLLTQQQIFESENFKNY--------LKYLEYWRN 59
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 29.3 bits (67), Expect = 3.4
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 182 LSHM-SDLLRYVTLYKYGGTYLDLDF 206
L H+ D LRY K T DLDF
Sbjct: 344 LDHLDPDYLRYYLAAKLPETIDDLDF 369
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. 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 = 233
Score = 28.8 bits (65), Expect = 3.4
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 123 QVYVVVIASVRNRTRNP-LIDRLYEYQNVHIVQVDL 157
+ VIA+ R+ + L + +HI+++D+
Sbjct: 21 RGNNTVIATCRDPSAATELAALGASHSRLHILELDV 56
>gnl|CDD|226020 COG3489, COG3489, Predicted periplasmic lipoprotein [General
function prediction only].
Length = 359
Score = 29.1 bits (65), Expect = 4.4
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 11/76 (14%)
Query: 45 KQPLRYIEYWRSGYRVQNINCVLSGVEKDFAFDDITRLDVPD-----NSIFFLETSCTHA 99
+P YWRS + +++ LS V+ F + L D SI F A
Sbjct: 246 PRP-YQAIYWRSKNTLSSLSANLSAVQALFLAAGLAMLLPADQRSIAGSIDFQ-----LA 299
Query: 100 DGVELTLRQACSIESA 115
+ + +
Sbjct: 300 GIIATAAQIEGPLFKL 315
>gnl|CDD|227858 COG5571, COG5571, Autotransporter protein or domain, integral
membrane beta-barrel involved in protein secretion [Cell
motility and secretion].
Length = 239
Score = 28.2 bits (63), Expect = 5.9
Identities = 36/163 (22%), Positives = 57/163 (34%), Gaps = 13/163 (7%)
Query: 195 YKYGGTYLDLDFIVIKSLESLH-NYAGA-ESSSVVAAGVIHLDKDHWLSGAALRELRDNF 252
YK G L + + + N + + H + + L
Sbjct: 6 YKSGERVT-LSGLAAGVISADFLNTNYRWQQEYIQLGQFGHSTEGPTWLSSHLPVYNTIL 64
Query: 253 KTTEWGA-NGPGVLTRLLKAECKPQSYAHNIISCRNFTIYPPRFFYPV---HWEHW--AD 306
T A G G R+ E +S+ + + F R PV H++ +
Sbjct: 65 STKRQSAQLGAG--ARVQLGETNAESWTARLSAGYEFPFGELRT-GPVAGLHYDKTTVSG 121
Query: 307 YLNETNAPATMSLFRDSYALHVWNSFTKRVPVKLGSEQPYAQI 349
Y NE NA +T F D + +S R+ ++L QPYAQI
Sbjct: 122 Y-NEQNASSTALGFTDQLWHSLVSSLGWRLRLRLADLQPYAQI 163
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
0.325 0.139 0.441
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,652,869
Number of extensions: 1791870
Number of successful extensions: 1861
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1858
Number of HSP's successfully gapped: 18
Length of query: 356
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 258
Effective length of database: 6,590,910
Effective search space: 1700454780
Effective search space used: 1700454780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (27.0 bits)