RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9925
(180 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 89.1 bits (222), Expect = 4e-21
Identities = 47/124 (37%), Positives = 70/124 (56%), Gaps = 8/124 (6%)
Query: 53 KVMGGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSEHNLQYNSSQNHAR 111
KV+GG++ +NG++Y RG++ DYD + +L G GW Y + LPYF K+E ++ R
Sbjct: 86 KVLGGSSSINGMVYIRGNAMDYDNWAELPGLEGWSYADCLPYFKKAETRD---GGEDDYR 142
Query: 112 G--GLLTVSHYNDLPD-LGHTLLAAGRELGYPTDVDIGHGRLREGFYRAQMTTRNGARLS 168
G G L+V+ + L + AG + GYP D+ +G +EGF T NG R S
Sbjct: 143 GGDGPLSVTRGKPGTNPLFQAFVEAGVQAGYPRTDDL-NGYQQEGFGPMDRTVTNGRRWS 201
Query: 169 AAKA 172
AA+A
Sbjct: 202 AARA 205
Score = 60.6 bits (148), Expect = 3e-11
Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 2 GGTTVLNGLMYCRGDSSDYDEYEKL-GATGWGYKNVLPYFLKSEHNL 47
GG++ +NG++Y RG++ DYD + +L G GW Y + LPYF K+E
Sbjct: 89 GGSSSINGMVYIRGNAMDYDNWAELPGLEGWSYADCLPYFKKAETRD 135
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 86.7 bits (215), Expect = 3e-20
Identities = 47/124 (37%), Positives = 69/124 (55%), Gaps = 5/124 (4%)
Query: 53 KVMGGTTVLNGLMYCRGDSSDYDEY-EKLGATGWGYKNVLPYFLKSEHNL---QYNSSQN 108
KV+GG++ +NG++Y RG D+D + ++ GA GW Y +VLPYF ++E L +
Sbjct: 85 KVLGGSSSINGMVYVRGHPEDFDAWAQESGAPGWPYDDVLPYFKRAEDLLGVGGQDLRTW 144
Query: 109 HARGGLLTVSHYNDLPDLGHTLLAAGRELGYPTDVDIGHGRLREGFYRAQMTTRNGARLS 168
H GG L VS + + AG +LG+PT +G +EGF +T NG R S
Sbjct: 145 HGGGGPLPVSPPRSPNPIARAFIEAGEQLGFPT-TPDPNGADQEGFGPYCVTICNGRRWS 203
Query: 169 AAKA 172
AA+A
Sbjct: 204 AARA 207
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 81.1 bits (200), Expect = 2e-18
Identities = 41/123 (33%), Positives = 62/123 (50%), Gaps = 7/123 (5%)
Query: 53 KVMGGTTVLNGLMYCRGDSSDYDEYEK-LGATGWGYKNVLPYFLKSEHNLQYNSSQNHAR 111
KV+GG++ +NG++Y RG+ DY+++ K G W Y + LPY+ + E + R
Sbjct: 80 KVLGGSSSINGMIYQRGNPMDYEKWAKPEGMESWDYADCLPYYKRLETT---FGGEKPYR 136
Query: 112 GGLLTVSHYNDLPD--LGHTLLAAGRELGYPTDVDIGHGRLREGFYRAQMTTRNGARLSA 169
G + D L + AG E GY D+ +G +EGF T NG R+SA
Sbjct: 137 GHDGPIKVRRGPADNPLFQAFIEAGVEAGYNKTPDV-NGFRQEGFGPMDSTVHNGRRVSA 195
Query: 170 AKA 172
A+A
Sbjct: 196 ARA 198
Score = 54.5 bits (131), Expect = 4e-09
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 1 MGGTTVLNGLMYCRGDSSDYDEYEK-LGATGWGYKNVLPYFLKSEH 45
+GG++ +NG++Y RG+ DY+++ K G W Y + LPY+ + E
Sbjct: 82 LGGSSSINGMIYQRGNPMDYEKWAKPEGMESWDYADCLPYYKRLET 127
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 60.0 bits (146), Expect = 2e-11
Identities = 35/127 (27%), Positives = 48/127 (37%), Gaps = 26/127 (20%)
Query: 53 KVMGGTTVLNGLMYCRGDSSDYDE-YEKLGATGWGYKNVLPYFLKSEHNLQYNSSQNHAR 111
+GG + +N R ++ DE + G GWGY + LPY K E
Sbjct: 25 STVGGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE------------- 71
Query: 112 GGLLTVSHYNDLPD-LGHTLLAAGRELGYPT-----DVDIGHGRLREGFYRAQMTTRNGA 165
G L V+ L LL A ELGYP + + H GF + GA
Sbjct: 72 -GPLGVTTKGIEESPLNQALLKAAEELGYPVEAVPRNSNGCHY---CGFCG--LGCPTGA 125
Query: 166 RLSAAKA 172
+ S A+
Sbjct: 126 KQSTART 132
Score = 50.0 bits (120), Expect = 7e-08
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 2 GGTTVLNGLMYCRGDSSDYDE-YEKLGATGWGYKNVLPYFLKSE 44
GG + +N R ++ DE + G GWGY + LPY K E
Sbjct: 28 GGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE 71
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 56.4 bits (136), Expect = 9e-10
Identities = 31/121 (25%), Positives = 52/121 (42%), Gaps = 6/121 (4%)
Query: 54 VMGGTTVLNGLMYCRGDSSDYDEYEKLGATGWGYKNVLPYFLKSEHNLQYNSSQNHARGG 113
V+GG+ +NG +CR +D+D + GW + +VLP+F E +L ++ H G
Sbjct: 83 VLGGSGAVNGGYFCRALPADFDAW---PIPGWSWDDVLPHFRAIETDLDFDGPL-HGTAG 138
Query: 114 LLTVSHYNDLPDLGHTLLAAGRELGYPTDVDIG--HGRLREGFYRAQMTTRNGARLSAAK 171
+ V +L + +AA G+ D+ G + G R+S A
Sbjct: 139 PIPVRRTAELDGISAAFVAAALGAGFGWIADLNGSGPDAPTGVGAVPLNVDGGRRVSTAV 198
Query: 172 A 172
A
Sbjct: 199 A 199
Score = 43.3 bits (102), Expect = 3e-05
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 1 MGGTTVLNGLMYCRGDSSDYDEYEKLGATGWGYKNVLPYFLKSEHNLQY 49
+GG+ +NG +CR +D+D + GW + +VLP+F E +L +
Sbjct: 84 LGGSGAVNGGYFCRALPADFDAW---PIPGWSWDDVLPHFRAIETDLDF 129
>gnl|CDD|222548 pfam14109, GldH_lipo, GldH lipoprotein. Members of this protein
family are predicted lipoproteins, exclusive to the
Bacteroidetes phylum. Proteins in this family are
typically between 155 and 167 amino acids in length.
Members include GldH, a protein linked to a type of
rapid surface gliding motility found in certain
Bacteroidetes, such as Flavobacterium johnsoniae and
Cytophaga hutchinsonii. Gliding motility appears
closely linked to chitin utilization in the model
species Flavobacterium johnsoniae. Not all
Bacteroidetes with members of this protein family may
have gliding motility.
Length = 131
Score = 28.3 bits (64), Expect = 1.4
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 16 DSSDYDEYEKLGATGWGYKNVLPYFLK-----SEHNLQYNVR 52
+++ YDEY+ + +GW + L + +NL N+R
Sbjct: 1 ENTVYDEYQSVPDSGWEKNDTLSFEFPITDTSGPYNLFLNLR 42
>gnl|CDD|143493 cd06819, PLPDE_III_LS_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Low Specificity D-Threonine
Aldolase. Low specificity D-threonine aldolase (Low
specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene
from Arthrobacter sp. strain DK-38, is the prototype of
this subfamily. Low specificity D-TAs are fold type III
PLP-dependent enzymes that catalyze the interconversion
between D-threonine/D-allo-threonine and glycine plus
acetaldehyde. Both PLP and divalent cations (eg. Mn2+)
are required for catalytic activity. Members of this
subfamily show similarity to bacterial alanine racemase
(AR), which contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
AR exists as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Based on its similarity to AR, it is possible
that low specificity D-TAs also form dimers in solution.
Experimental data show that the monomeric form of low
specificity D-TAs exhibit full catalytic activity.
Length = 358
Score = 28.3 bits (64), Expect = 2.5
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 117 VSHYNDLPDLGHTLLAAGRELGYPTDVDIGHGR 149
V H +++ L + AG L ++D+G GR
Sbjct: 106 VDHPDNVRALAAAAVEAGVRLDVLVEIDVGQGR 138
>gnl|CDD|147262 pfam04993, TfoX_N, TfoX N-terminal domain. TfoX may play a key
role in the development of genetic competence by
regulating the expression of late competence-specific
genes. This family corresponds to the N-terminal
presumed domain of TfoX. The domain is found as an
isolated domain in some proteins suggesting this is an
autonomous domain.
Length = 94
Score = 26.7 bits (60), Expect = 2.9
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 15/70 (21%)
Query: 48 QYNVRKVMGGTTV-LNGLM---------YCRGDSSDYDEYEKLGATGWGYK-----NVLP 92
R + GG + +G+M Y + D +E G + Y L
Sbjct: 8 PITSRSMFGGYGLYYDGVMFALVSDGELYLKADDETRAYFEAAGCEPYVYVKRGRPVTLN 67
Query: 93 YFLKSEHNLQ 102
Y+L E L+
Sbjct: 68 YYLVPEELLE 77
>gnl|CDD|238859 cd01821, Rhamnogalacturan_acetylesterase_like,
Rhamnogalacturan_acetylesterase_like subgroup of
SGNH-hydrolases. Rhamnogalacturan acetylesterase removes
acetyl esters from rhamnogalacturonan substrates, and
renders them susceptible to degradation by
rhamnogalacturonases. Rhamnogalacturonans are highly
branched regions in pectic polysaccharides, consisting
of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide
units, with many rhamnose residues substituted by
neutral oligosaccharides such as arabinans, galactans
and arabinogalactans. Extracellular enzymes
participating in the degradation of plant cell wall
polymers, such as Rhamnogalacturonan acetylesterase,
would typically be found in saprophytic and plant
pathogenic fungi and bacteria.
Length = 198
Score = 26.0 bits (58), Expect = 9.6
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 69 GDSSDYDEYEKLGATGWGYKNVLPYFLKSEHNLQYNSSQNHARGGLLTVSHYND 122
GDS+ D GWG LP +L + + NHA+GG + S ++
Sbjct: 7 GDSTVADYDPGAPQAGWGQ--ALPQYLDTGITV-----VNHAKGGRSSRSFRDE 53
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 0.138 0.424
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,138,800
Number of extensions: 823686
Number of successful extensions: 649
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 20
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
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: 56 (25.2 bits)