RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4105
(107 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 60.6 bits (148), Expect = 4e-12
Identities = 31/60 (51%), Positives = 39/60 (65%), Gaps = 4/60 (6%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEAG-PDENE--VTDVPS-LAAWLQLSKFDWQYKTEP 102
G GSAG V+A+RLSE SVLLLEAG PD +P+ LA LQ +++W Y+TEP
Sbjct: 12 GAGSAGCVLANRLSEDPDVSVLLLEAGGPDYRWDFFIQMPAALAFPLQGKRYNWAYETEP 71
>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 = 53.3 bits (128), Expect = 1e-09
Identities = 27/63 (42%), Positives = 41/63 (65%), Gaps = 4/63 (6%)
Query: 44 VSLGGGSAGAVVASRLSEVAHWSVLLLEAG-PD--ENEVTDVPSLAAW-LQLSKFDWQYK 99
+ +GGGSAG+V+A RLSE SVL+LEAG D + + +P+ A+ +++W Y+
Sbjct: 3 IIIGGGSAGSVLAGRLSEDVSNSVLVLEAGGSDYPWDLLIQMPAALAYPAGNKRYNWIYE 62
Query: 100 TEP 102
TEP
Sbjct: 63 TEP 65
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 50.9 bits (122), Expect = 8e-09
Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEAGP-DENEVTDVPSLAAWLQLSKF-DWQYKTEPT 103
G GSAG+V+A+RLS+ SVL+LEAG D + +P+ A+L DW ++TEP
Sbjct: 14 GSGSAGSVLAARLSDAGL-SVLVLEAGGPDRRPLIQMPAAYAFLMNGPRYDWGFRTEPE 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 = 48.3 bits (115), Expect = 7e-08
Identities = 28/63 (44%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEAGPDENEVTDVPS-LAAWLQL-----SKFDWQYKT 100
GGGSAG VVA+RLSE +V +LEAGP + + +P+ L L+L S W+Y
Sbjct: 7 GGGSAGCVVAARLSEDPSCTVTVLEAGPGYRDPSRLPAQLTDGLRLPIGPASPVVWRYGV 66
Query: 101 EPT 103
E T
Sbjct: 67 ELT 69
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 32.4 bits (75), Expect = 0.007
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGPD 75
+G G +G V A L++ VL+LE
Sbjct: 2 VGAGLSGLVAAYLLAK-RGKDVLVLEKRDR 30
>gnl|CDD|233671 TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase,
UbiH/UbiF/VisC/COQ6 family. This model represents a
family of FAD-dependent hydroxylases (monooxygenases)
which are all believed to act in the aerobic ubiquinone
biosynthesis pathway. A separate set of hydroxylases,
as yet undiscovered, are believed to be active under
anaerobic conditions. In E. coli three enzyme
activities have been described, UbiB (which acts first
at position 6, see TIGR01982), UbiH (which acts at
position 4,) and UbiF (which acts at position 5,). UbiH
and UbiF are similar to one another and form the basis
of this subfamily. Interestingly, E. coli contains
another hydroxylase gene, called visC, that is highly
similar to UbiF, adjacent to UbiH and, when mutated,
results in a phenotype similar to that of UbiH (which
has also been named visB). Several other species appear
to have three homologs in this family, although they
assort themselves differently on phylogenetic trees
(e.g. Xylella and Mesorhizobium) making it difficult to
ascribe a specific activity to each one. Eukaryotes
appear to have only a single homolog in this subfamily
(COQ6,) which complements UbiH, but also possess a
non-orthologous gene, COQ7 which complements UbiF
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 387
Score = 32.6 bits (75), Expect = 0.022
Identities = 11/38 (28%), Positives = 14/38 (36%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEAGPDENEVTDVPS 84
GGG G +A L+ V L+EA P
Sbjct: 6 GGGPVGLALALALARSGGLKVALIEATPLPAPADPGFD 43
>gnl|CDD|132263 TIGR03219, salicylate_mono, salicylate 1-monooxygenase. Members
of this protein family are salicylate 1-monooxygenase,
also called salicylate hydroxylase. This enzyme
converts salicylate to catechol, which is a common
intermediate in the degradation of a number of aromatic
compounds (phenol, toluene, benzoate, etc.). The gene
for this protein may occur in catechol degradation
genes, such as those of the meta-cleavage pathway.
Length = 414
Score = 30.2 bits (68), Expect = 0.16
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGPDENEV 79
+GGG AG +A L + +H +V L EA P EV
Sbjct: 6 IGGGIAGVALALNLCKHSHLNVQLFEAAPAFGEV 39
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 29.8 bits (67), Expect = 0.21
Identities = 15/28 (53%), Positives = 22/28 (78%), Gaps = 2/28 (7%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAG 73
+GGG+AG +A+ LS+ ++SVLLLE G
Sbjct: 61 VGGGTAGCPLAATLSQ--NFSVLLLERG 86
>gnl|CDD|233669 TIGR01984, UbiH, 2-polyprenyl-6-methoxyphenol 4-hydroxylase.
This model represents the FAD-dependent monoxygenase
responsible for the second hydroxylation step in the
aerobic ubiquinone bioynthetic pathway. The scope of
this model is limited to the proteobacteria. This
family is closely related to the UbiF hydroxylase which
catalyzes the final hydroxylation step. The enzyme has
also been named VisB due to a mutant VISible light
sensitive phenotype [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 382
Score = 28.8 bits (65), Expect = 0.51
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGPDEN--EVTDVPSLA 86
+GGG G +A LS + + L+EA D SLA
Sbjct: 5 VGGGLVGLSLALALSRLGKIKIALIEANSPSAAQPGFDARSLA 47
>gnl|CDD|235584 PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 395
Score = 27.5 bits (62), Expect = 1.5
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 47 GGGSAGAVVASRLSEVAH--WSVLLLEA 72
GGG AGA +A LS ++H V L+EA
Sbjct: 10 GGGMAGATLALALSRLSHGGLPVALIEA 37
>gnl|CDD|176995 CHL00054, psaB, photosystem I P700 chlorophyll a apoprotein A2.
Length = 734
Score = 27.4 bits (61), Expect = 1.6
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 6/32 (18%)
Query: 36 LVNWGDFPVSLGGGSAGAVVASRLSEVAHWSV 67
L+ W D PV+L ++V +RL +AH+SV
Sbjct: 690 LIRWRDKPVAL------SIVQARLVGLAHFSV 715
>gnl|CDD|153232 cd03138, GATase1_AraC_2, AraC transcriptional regulators having a
Type 1 glutamine amidotransferase (GATase1)-like
domain. A subgroup of AraC transcriptional regulators
having a Type 1 glutamine amidotransferase
(GATase1)-like domain. AraC regulators are defined by
a AraC-type helix-turn-helix DNA binding domain at
their C-terminal. AraC family transcriptional
regulators are widespread among bacteria and are
involved in regulating diverse and important biological
functions, including carbon metabolism, stress
responses and virulence in different microorganisms.
The catalytic triad typical of GATase1 domains is not
conserved in this GATase1-like domain. However, in
common with typical GATase1domains a reactive cys
residue is found in the sharp turn between a beta
strand and an alpha helix termed the nucleophile elbow.
Length = 195
Score = 26.8 bits (60), Expect = 2.2
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 31 PIHSLLVNWGDFPVSLGGGSAGAVVASRLSEVAHWSVLLLEA---GPDENEVTDVPSLAA 87
P LV+ PV L GG A+ L++V ++++ PDE + D P+L A
Sbjct: 37 PFEVRLVSLDGGPVLLAGGILILPDAT-LADVPAPDLVIVPGLGGDPDELLLADNPALIA 95
Query: 88 WLQ 90
WL+
Sbjct: 96 WLR 98
>gnl|CDD|130850 TIGR01790, carotene-cycl, lycopene cyclase family protein. This
family includes lycopene beta and epsilion cyclases
(which form beta and delta carotene, respectively) from
bacteria and plants as well as the plant
capsanthin/capsorubin and neoxanthin cyclases which
appear to have evolved from the plant lycopene
cyclases. The plant lycopene epsilon cyclases also
transform neurosporene to alpha zeacarotene.
Length = 388
Score = 26.6 bits (59), Expect = 2.7
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGPD 75
+GGG AG +A L+ V L+E P
Sbjct: 5 IGGGPAGLAIALELAR-PGLRVQLIEPHPP 33
>gnl|CDD|203096 pfam04820, Trp_halogenase, Tryptophan halogenase. Tryptophan
halogenase catalyzes the chlorination of tryptophan to
form 7-chlorotryptophan. This is the first step in the
biosynthesis of pyrrolnitrin, an antibiotic with
broad-spectrum anti-fungal activity. Tryptophan
halogenase is NADH-dependent.
Length = 457
Score = 26.5 bits (59), Expect = 3.1
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 44 VSLGGGSAGAVVASRLSEVAH--WSVLLLEA------GPDENEVTDVPSLAAWLQLSKFD 95
V +GGG+AG + A+ L+ V L+E+ G E + + + L + + +
Sbjct: 3 VIVGGGTAGWMAAAALARALKGGLDVTLVESEEIGTVGVGEATIPSIRTFNRMLGIDEAE 62
Query: 96 WQYKTEPTGKQ 106
+ T+ T K
Sbjct: 63 FMRATQATFKL 73
>gnl|CDD|236214 PRK08274, PRK08274, tricarballylate dehydrogenase; Validated.
Length = 466
Score = 26.4 bits (59), Expect = 3.2
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 47 GGGSAG--AVVASRLSEVAHWSVLLLEAGPDE 76
GGG+A A +A+R + SVLLLEA P E
Sbjct: 11 GGGNAALCAALAAREAGA---SVLLLEAAPRE 39
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 26.3 bits (58), Expect = 3.6
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEAGP 74
G G AG+ A RL++ VL+LE G
Sbjct: 10 GAGPAGSSAARRLAKAG-LDVLVLEKGS 36
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 26.3 bits (59), Expect = 3.7
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 47 GGGSAGAVVASRLSEVAHWSVLLLEA 72
GGG AGA +A L+ W V L EA
Sbjct: 267 GGGIAGAALALALAR-RGWQVTLYEA 291
>gnl|CDD|218022 pfam04315, DUF462, Protein of unknown function, DUF462. This
family consists of bacterial proteins of
uncharacterized function.
Length = 165
Score = 26.0 bits (58), Expect = 4.0
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 4/19 (21%)
Query: 56 ASRLSEVAHWSVLLLEAGP 74
AS L E+AHW + AG
Sbjct: 43 ASALHEIAHWCI----AGE 57
>gnl|CDD|216122 pfam00792, PI3K_C2, Phosphoinositide 3-kinase C2. Phosphoinositide
3-kinase region postulated to contain a C2 domain.
Outlier of pfam00168 family.
Length = 140
Score = 25.8 bits (57), Expect = 4.2
Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 17/94 (18%)
Query: 18 KPLTNGVCLKAYVPIHSLLVNWG---DFPVSLGGGSAGAVVASRLSEVAHWSVLLLE-AG 73
K L+ V +Y P + + W FP+ + S L A + L E +G
Sbjct: 16 KLLSLPVQSTSYKPFSNPSIKWNEWLTFPIKI----------SDLPRDARLVITLWEISG 65
Query: 74 PDENEVTDVPSLAAWLQLSKFDWQYKTEPTGKQC 107
++E P W+ LS FD G Q
Sbjct: 66 KSKSERKVEP--LGWVNLSLFDK-KGILRQGPQL 96
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 26.0 bits (58), Expect = 4.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGPD 75
+GGG AG A RL++ H V + EA
Sbjct: 5 VGGGIAGLAAAYRLAKRGH-EVTVFEADDQ 33
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 26.0 bits (58), Expect = 4.9
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 46 LGGGSAGAVVASRLSEVAHWSVLLLEAGP 74
+G G AG V A R ++ V L+E G
Sbjct: 10 IGAGPAGYVAAIRAAQ-LGLKVALVEKGE 37
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed.
Length = 508
Score = 25.7 bits (57), Expect = 5.4
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 8/42 (19%)
Query: 51 AGAVVA---SRLSEVAHWSVLLLEAGPDENEVTDVPSLAAWL 89
A VA SRL++VA + LL A P E V + AWL
Sbjct: 9 TSAAVAATSSRLAKVARLAELLRRADPAE-----VAIVVAWL 45
>gnl|CDD|227156 COG4819, EutA, Ethanolamine utilization protein, possible
chaperonin protecting lyase from inhibition [Amino acid
transport and metabolism].
Length = 473
Score = 25.6 bits (56), Expect = 5.5
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 7/53 (13%)
Query: 6 ADEIDPKGKEILKPLTNGVCLKAYVPIHSLLVNWGDFP-------VSLGGGSA 51
++ +E+ + L V A P++ L+ P +S GG A
Sbjct: 215 GAQLVQVTREMAELLVEVVDFGALSPLYEALITTKLLPADVTPEIISFSGGVA 267
>gnl|CDD|178578 PLN03000, PLN03000, amine oxidase.
Length = 881
Score = 25.8 bits (56), Expect = 6.3
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 31 PIHSLLVNWGDFPVSLGGGSAGAVVAS 57
P+ ++ WG P SLG S AV AS
Sbjct: 548 PLQTVCTRWGGDPFSLGSYSNVAVGAS 574
>gnl|CDD|132846 cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins;
homologus to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa
enzyme, is a potent virulence factor of Pseudomonas
aeruginosa. One of the pathogenic mechanisms of P.
aeruginosa is to induce cytotoxicity by the injection
of effector proteins (e.g. ExoU) using the type III
secretion (T3S) system. ExoU is homologus to patatin
and also has the conserved catalytic residues of
mammalian calcium-independent (iPLA2) and cytosolic
(cPLA2) PLA2. In vitro, ExoU cytotoxity is blocked by
the inhibitor of cytosolic and Ca2-independent
phospholipase A2 (cPLA2 and iPLA2) enzymes, suggesting
that phospholipase A2 inhibitors may represent a novel
mode of treatment for acute P. aeruginosa infections.
ExoU requires eukaryotic superoxide dismutase as a
cofactor and cleaves phosphatidylcholine and
phosphatidylethanolamine in vitro. VipD, a 69-kDa
cytosolic protein, belongs to the members of Legionella
pneumophila family and is homologus to ExoU from
Pseudomonas. Even though VipD shows high sequence
similarity with several functional regions of ExoU
(e.g. oxyanion hole, active site serine, active site
aspartate), it has been shown to have no phospholipase
activity. This family includes ExoU from Pseudomonas
aeruginosa and VipD of Legionella pneumophila.
Length = 194
Score = 24.9 bits (55), Expect = 8.0
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 23 GVCLKAYVPIHSLLVNWGDFPVSLGGGSAGAVVAS 57
G AY+ L G + G SAGA+ A+
Sbjct: 8 GAKGIAYIGALKALEEAGILKKRVAGTSAGAITAA 42
>gnl|CDD|240384 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
Length = 567
Score = 25.2 bits (55), Expect = 8.7
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 44 VSLGGGSAGAVVASRLSEVAHWSVLLLE 71
+ +GG AG V+A LS+ VL+LE
Sbjct: 37 IIVGGSIAGPVLAKALSK-QGRKVLMLE 63
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 25.2 bits (56), Expect = 9.2
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 44 VSLGGGSAGAVVASRLSEVAHWSVLLLE 71
+ +G G AG +A+R + V L+E
Sbjct: 9 IVIGAGQAGPPLAARAAG-LGMKVALIE 35
>gnl|CDD|223338 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
metabolism].
Length = 485
Score = 24.9 bits (55), Expect = 9.5
Identities = 14/54 (25%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 50 SAGAVVASRLSEVAHWSVLLLEAGPDENEVTDVPSLAAWLQLSKFDWQYKTEPT 103
A A L + W V LL E+ L +FD +YK+E
Sbjct: 86 RAAGAAARALKKGKAWEVTLLLPELPAAEIAAAAVEGFLLGSYRFD-RYKSEKK 138
>gnl|CDD|225763 COG3222, COG3222, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 211
Score = 24.8 bits (54), Expect = 9.7
Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 2/52 (3%)
Query: 44 VSLGGGSAGAVVASRLSEVAHWSVLLLEAGPDENEVTDVPSLAA-WLQLSKF 94
+ G + L + V LL D + D+P L SKF
Sbjct: 160 IPWGTPDVLELTLKALRQNG-IDVYLLPRLGDVDRPDDLPLLRDCCAPGSKF 210
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
0.315 0.134 0.421
Gapped
Lambda K H
0.267 0.0851 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,506,833
Number of extensions: 459256
Number of successful extensions: 324
Number of sequences better than 10.0: 1
Number of HSP's gapped: 320
Number of HSP's successfully gapped: 40
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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: 42 (22.0 bits)
S2: 53 (24.0 bits)