RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4106
(209 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 168 bits (427), Expect = 2e-49
Identities = 76/188 (40%), Positives = 105/188 (55%), Gaps = 27/188 (14%)
Query: 18 GWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITE-IPYKTPIAHAFVQSGYQSGY 76
GWSY + P+F K+E D+ Y G L++T P P+ AFV++G Q+GY
Sbjct: 118 GWSYADCLPYFKKAETRDGGEDD----YRGGDGPLSVTRGKPGTNPLFQAFVEAGVQAGY 173
Query: 77 PIV-DVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPIRRRR 135
P D+NG Q GF M R ++ NG RWS +RA+L P +R
Sbjct: 174 PRTDDLNGYQQEGFG-----------PMDR--------TVTNGRRWSAARAYLDPALKRP 214
Query: 136 NLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAINSPQILMVSGI 195
NL + +L +++ + K RAVGVE +G + AR+EV+LSAGAINSPQ+L +SGI
Sbjct: 215 NLTIVTHALTDRILFEGK--RAVGVEYERGGGRETARARREVILSAGAINSPQLLQLSGI 272
Query: 196 GPREHLRE 203
GP EHL+E
Sbjct: 273 GPAEHLKE 280
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 146 bits (370), Expect = 3e-41
Identities = 70/197 (35%), Positives = 102/197 (51%), Gaps = 21/197 (10%)
Query: 12 AYVEG-PGWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQS 70
A G PGW YD+V P+F ++ED +H GG L ++ PIA AF+++
Sbjct: 110 AQESGAPGWPYDDVLPYFKRAEDLLGVGGQDLRTWHGGGGPLPVSPPRSPNPIARAFIEA 169
Query: 71 GYQSGYPIVDV-NGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLH 129
G Q G+P NGA Q GF V++ NG RWS +RA+L
Sbjct: 170 GEQLGFPTTPDPNGADQEGFGPY-------------------CVTICNGRRWSAARAYLK 210
Query: 130 PIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAINSPQI 189
P +R NL + + V +++++ V VE+ G + A +EVVL+AGAINSP++
Sbjct: 211 PALKRPNLTLLTGARVRRILLEGDRAVGVEVEIGDGGTIETAVAAREVVLAAGAINSPKL 270
Query: 190 LMVSGIGPREHLREKSK 206
L++SGIGP +HL E
Sbjct: 271 LLLSGIGPADHLLEHGI 287
>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 = 141 bits (358), Expect = 1e-39
Identities = 69/188 (36%), Positives = 94/188 (50%), Gaps = 28/188 (14%)
Query: 18 GWSYDEVRPFFIKSEDNQI-ENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGY 76
W Y + P++ + E E Y G + + P P+ AF+++G ++GY
Sbjct: 112 SWDYADCLPYYKRLETTFGGEKP-----YRGHDGPIKVRRGPADNPLFQAFIEAGVEAGY 166
Query: 77 PIV-DVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPIRRRR 135
DVNG Q GF + + ++ NG R S +RA+LHP +R
Sbjct: 167 NKTPDVNGFRQEGFGPM-------------------DSTVHNGRRVSAARAYLHPAMKRP 207
Query: 136 NLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAINSPQILMVSGI 195
NL V + VTK+ + RA GVE KG K A KEV+LSAGAINSPQ+L +SGI
Sbjct: 208 NLEVQTRAFVTKINFE--GNRATGVEFKKGGRKEHTEANKEVILSAGAINSPQLLQLSGI 265
Query: 196 GPREHLRE 203
G EHLRE
Sbjct: 266 GDAEHLRE 273
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 106 bits (268), Expect = 6e-29
Identities = 55/191 (28%), Positives = 83/191 (43%), Gaps = 46/191 (24%)
Query: 17 PGWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTIT-EIPYKTPIAHAFVQSGYQSG 75
GW YD+ P+ K E G L +T + ++P+ A +++ + G
Sbjct: 56 EGWGYDDYLPYMDKVE-----------------GPLGVTTKGIEESPLNQALLKAAEELG 98
Query: 76 YPIV----DVNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPI 131
YP+ + NG GF L G + ST+R +L P
Sbjct: 99 YPVEAVPRNSNGCHYCGFCGLGC---------------------PTGAKQSTARTWLRPA 137
Query: 132 RRRRNLHVTKFSLVTKLIIDEKSKRAVGVE--LMKGNSKIRVFARKEVVLSAGAINSPQI 189
R NL + + K+II + RAVGVE G K + A KEVV++AGA+N+P +
Sbjct: 138 LER-NLRILTGAKAEKIIILGRGGRAVGVEARDGGGGIKRLITAAKEVVVAAGALNTPPL 196
Query: 190 LMVSGIGPREH 200
L+ SG+G H
Sbjct: 197 LLRSGLGKNPH 207
>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 = 98.4 bits (245), Expect = 4e-24
Identities = 58/189 (30%), Positives = 85/189 (44%), Gaps = 26/189 (13%)
Query: 17 PGWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGY 76
PGWS+D+V P F E + + D H G + + I+ AFV + +G+
Sbjct: 109 PGWSWDDVLPHFRAIETDL----DFDGPLHGTAGPIPVRRTAELDGISAAFVAAALGAGF 164
Query: 77 P-IVDVNGA-AQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPIRRR 134
I D+NG+ V N G R ST+ A+L P +R
Sbjct: 165 GWIADLNGSGPDAPTGVGAVPLNVD-----------------GGRRVSTAVAYLLPALKR 207
Query: 135 RNLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAINSPQILMVSG 194
NL V + V +++ RAVGVE++ + A + VVL AGA+ S +L++SG
Sbjct: 208 PNLTVEADTRVVRILF--SGTRAVGVEVLGDGGPRTLRADR-VVLCAGAVESAHLLLLSG 264
Query: 195 IGPREHLRE 203
IGP E LR
Sbjct: 265 IGPAEQLRA 273
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 57.9 bits (140), Expect = 6e-10
Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 135 RNLHVTKFSLVTKLIIDEKSK--RAVGVELM--KGNSKIRVFARK---EVVLSAGAINSP 187
L V + V K++ D K RA GV GN + E++LSAGAI SP
Sbjct: 233 NKLRVLLHATVQKIVFDTSGKRPRATGVIFKDENGNQHQAFLSNNKGSEIILSAGAIGSP 292
Query: 188 QILMVSGIGPREHLREK 204
Q+L++SGIGP++ L++
Sbjct: 293 QMLLLSGIGPKKELKKH 309
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 38.7 bits (91), Expect = 0.001
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 121 WSTSRAFLHPIRRRR----NLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKE 176
S A L +R + + + T+LI+D+ R VGVE + + + ARK
Sbjct: 172 DSGGGAMLMDPLAKRAAALGVQIRYDTRATRLIVDD-DGRVVGVEARRYGETVAIRARKG 230
Query: 177 VVLSAG 182
VVL+AG
Sbjct: 231 VVLAAG 236
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 37.5 bits (87), Expect = 0.004
Identities = 41/184 (22%), Positives = 69/184 (37%), Gaps = 31/184 (16%)
Query: 21 YDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPIAHAFVQSGYQSGYPIVD 80
+ E RP S+D ++ D LY + + + + I H V Q Y
Sbjct: 132 HREERPKL--SDDAAEDDAEWDRLYTKAESLIGTSTDQFDESIRHNLVLRKLQDEY---- 185
Query: 81 VNGAAQTGFSFLPVSFNSARLVMGRAWVQSVEVSMRNGTRWSTSRAFLH-----PIRRRR 135
Q F LP++ R VE W ++ R
Sbjct: 186 ---KGQRDFQPLPLA------CHRRTDPTYVE--------WHSADTVFDLQPNDDAPSER 228
Query: 136 NLHVTKFSLVTKLIIDEKSKRAVGVELMKG-NSKIRVFARKEV-VLSAGAINSPQILMVS 193
+T T+L+ +E ++ + L++ S R + +V VL+ GA+++PQIL+ S
Sbjct: 229 FTLLTNHR-CTRLVRNETNESEIEAALVRDLLSGDRFEIKADVYVLACGAVHNPQILVNS 287
Query: 194 GIGP 197
G G
Sbjct: 288 GFGQ 291
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 31.5 bits (72), Expect = 0.25
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 4/85 (4%)
Query: 116 RNGTRWSTSRAFLHPIRRRRNLHVTKF---SLVTKLIIDEKSKRAVGVELMKGNSKIRVF 172
R T A L + F LI+++ V VE + ++R+
Sbjct: 131 RRRGTLGTGHALLARLLEGALKRGIDFQPRHPADDLIVEDGRVTGVVVENRRNGREVRIR 190
Query: 173 ARKEVVLSAGAI-NSPQILMVSGIG 196
A V+L+ G + ++L+ +
Sbjct: 191 AIAGVLLATGGFGRNAELLLPAAGY 215
>gnl|CDD|223108 COG0029, NadB, Aspartate oxidase [Coenzyme metabolism].
Length = 518
Score = 31.5 bits (72), Expect = 0.30
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 125 RAFLHPIRRRRNLHVTKFSLVTKLIIDEKSKRAVGVELMKGNSKIRVFARKEVVLSAGAI 184
A L +R R N+ V + + LII++ GV ++ N ++ F K VVL+ G +
Sbjct: 137 TALLKKVRNRPNITVLEGAEALDLIIEDG-IGVAGVLVLNRNGELGTFRAKAVVLATGGL 195
>gnl|CDD|220812 pfam10566, Glyco_hydro_97, Glycoside hydrolase 97. This is the
97th family of glycosidases, in this case bacterial. The
central part of the GH97 family protein sequences
represents a typical and complete (beta/alpha)8-barrel
or catalytic TIM-barrel type domain. The N- and
C-terminal parts of the sequences, mainly consisting of
beta-strands, most probably form two additional
non-catalytic domains with as yet unknown functions. The
non-catalytic domains of glycosidases from the
alpha-galactosidase and alpha-glucosidase superfamilies
are also predominantly composed of beta-strands, and at
least some of these domains are involved in
oligomerisation and carbohydrate binding. In all known
glycosidases with the (beta-alpha)8-barrel fold, the
amino acid residues at the active site are located on
the C-termini of the beta-strands.
Length = 621
Score = 29.0 bits (65), Expect = 1.7
Identities = 21/93 (22%), Positives = 29/93 (31%), Gaps = 17/93 (18%)
Query: 4 NLVFRQTVAYVEGPGWSYDEVRPFFIKSEDNQIENDNIDSLYHRKGGYLTITEIPYKTPI 63
NLV R AY EG + Y+ I D E Y+ Y Y
Sbjct: 101 NLVVR---AYNEGIAFRYEFPEQKTIVIYDENTE-------YNFPEDYKAYG--MYLPSF 148
Query: 64 AHAFVQSGYQSGYPIVDVNGAAQTGFSFLPVSF 96
Q+ Q+ Y + + Q LP+
Sbjct: 149 -----QTSAQAPYEHLPLEEIKQPNLMDLPLLV 176
>gnl|CDD|223617 COG0543, UbiB, 2-polyprenylphenol hydroxylase and related
flavodoxin oxidoreductases [Coenzyme metabolism / Energy
production and conversion].
Length = 252
Score = 28.5 bits (64), Expect = 2.0
Identities = 22/76 (28%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 109 QSVEVSMRNGTRWSTSRAFLHPIRRRRNLHVTKF--SLVTKLIIDEKSKRAVGVELMKGN 166
Q V + + G R S A + LH+ + VTK I K + V GN
Sbjct: 40 QFVMLRVPGGVRRPYSLASAPDDKGELELHIRVYEVGKVTKYIFGLKEGDKIRVRGPLGN 99
Query: 167 SKIRVFARKEVVLSAG 182
+R K V+L AG
Sbjct: 100 GFLREKIGKPVLLIAG 115
>gnl|CDD|233421 TIGR01453, grpIintron_endo, group I intron endonuclease. This
model represents one subfamily of endonucleases
containing the endo/excinuclease amino terminal domain,
pfam01541 at its amino end. A distinct subfamily
includes excinuclease abc subunit c (uvrC). Members of
pfam01541 are often termed GIY-YIG endonucleases after
conserved motifs near the amino end. This subfamily in
This model is found in open reading frames of group I
introns in both phage and mitochondria. The closely
related endonucleases of phage T4: segA, segB, segC,
segD and segE, score below the trusted cutoff for the
family.
Length = 214
Score = 28.5 bits (64), Expect = 2.3
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 2/74 (2%)
Query: 98 SARLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPIRRRRNLHVT--KFSLVTKLIIDEKSK 155
+ M + + T ++A + + N K S TK I EK K
Sbjct: 102 ETKAKMSKLFSGKKNNPWYGKTHSEETKAKISKNKLGENNPFFGKKHSEETKKKISEKEK 161
Query: 156 RAVGVELMKGNSKI 169
A V + N+ +
Sbjct: 162 GAKKVNVYDKNNGL 175
>gnl|CDD|179387 PRK02228, PRK02228, V-type ATP synthase subunit F; Provisional.
Length = 100
Score = 26.8 bits (60), Expect = 3.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 152 EKSKRAVGVELMK 164
EK KRA+GV+L K
Sbjct: 88 EKIKRAIGVDLWK 100
>gnl|CDD|234809 PRK00654, glgA, glycogen synthase; Provisional.
Length = 466
Score = 28.2 bits (64), Expect = 3.4
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 2/32 (6%)
Query: 78 IVDVNGAAQ--TGFSFLPVSFNSARLVMGRAW 107
++D N TGF F + + RA
Sbjct: 395 VIDYNPEDGEATGFVFDDFNAEDLLRALRRAL 426
>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 27.4 bits (61), Expect = 6.9
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 19/86 (22%)
Query: 100 RLVMGRAWVQSVEVSMRNGTRWSTSRAFLHPIRRRRNLHVTKFSLVTKLIIDEKSKRAVG 159
RLVMG A + + S+R R + + + V L D R +G
Sbjct: 216 RLVMGNALIGRLLYSLR-----------------ARGVRILTQTDVESLETD--HGRVIG 256
Query: 160 VELMKGNSKIRVFARKEVVLSAGAIN 185
+++G + R+ AR VVL+ G N
Sbjct: 257 ATVVQGGVRRRIRARGGVVLATGGFN 282
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 26.9 bits (60), Expect = 8.5
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 162 LMKGNSKIRVFARKEVVLSAGAINSP 187
LM +R + K V+LSAG + SP
Sbjct: 176 LMSS---VRDASGKRVILSAGRVQSP 198
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 85
Score = 25.3 bits (56), Expect = 9.4
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 47 RKGGYLTITEIPYKTPIAHAFVQSGYQSGYPIVDVNG 83
G L IT + +P A A +++G IV ++G
Sbjct: 10 YDDGGLVITSVLPGSPAAKAGIKAGDI----IVAIDG 42
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
0.321 0.136 0.399
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,774,820
Number of extensions: 994624
Number of successful extensions: 800
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 27
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (21.9 bits)
S2: 57 (25.6 bits)