RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 027801
(218 letters)
>gnl|CDD|178026 PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine synthase.
Length = 141
Score = 262 bits (672), Expect = 7e-91
Identities = 120/140 (85%), Positives = 132/140 (94%)
Query: 70 LTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL 129
L EGLRF +VVARFNE++TK LLEGALETFK+YSVKEENIDVVWVPGSFEI VVAQ+L
Sbjct: 2 LLDGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRL 61
Query: 130 GKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALN 189
KSGKY A+LCIGAV+RGDTTHYDAVANSAASGVLSAG+NSGVPCIFGVLTCD+M+QALN
Sbjct: 62 AKSGKYDAILCIGAVIRGDTTHYDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMEQALN 121
Query: 190 RAGGKSGNKGAEAALTAIEM 209
RAGGK+GNKGAEAALTA+EM
Sbjct: 122 RAGGKAGNKGAEAALTAVEM 141
>gnl|CDD|187742 cd09209, Lumazine_synthase-I, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-I. Type-I LS, also known as RibH1,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyse the
formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the
lumazine intermediate dismutates to yield riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase synthase (RS);
RS belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-I LSs form
pentamers. The pathogen Brucella spp. encode both a
Type-I LS and a Type-II LS called RibH1 and RibH2,
respectively. RibH1/type-I LS appears to be the
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS. The pathogen
Brucella spp. have both a type-I LS and a type-II LS
called RibH1 and RibH2, respectively. RibH1/type-I LS
appears to be a functional LS in Brucella spp., whereas
RibH2/type-II LS has much lower catalytic activity as
LS.
Length = 133
Score = 218 bits (559), Expect = 1e-73
Identities = 79/133 (59%), Positives = 103/133 (77%)
Query: 78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
A+VV+RFNE +T LLEGAL+ K++ VKEENIDVV VPG+FEI + A++L +SGKY A
Sbjct: 1 IAIVVSRFNEEITDALLEGALDALKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDA 60
Query: 138 VLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKSGN 197
++ +G V+RG+T H+D V N G++ + +GVP IFGVLT DN +QAL RAGGK+GN
Sbjct: 61 IIALGCVIRGETPHFDYVCNEVTRGLMRLSLETGVPVIFGVLTTDNEEQALERAGGKAGN 120
Query: 198 KGAEAALTAIEMA 210
KGAEAAL A+EMA
Sbjct: 121 KGAEAALAALEMA 133
>gnl|CDD|234606 PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase;
Provisional.
Length = 154
Score = 215 bits (550), Expect = 5e-72
Identities = 81/141 (57%), Positives = 108/141 (76%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
+GLR +VVARFN+ +T LLEGAL+ K++ V EENIDVV VPG+FEI + A++L +SG
Sbjct: 11 KGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESG 70
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
KY AV+ +GAV+RG+T H+D VAN A G+ + +GVP FGVLT D ++QA+ RAG
Sbjct: 71 KYDAVIALGAVIRGETPHFDYVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAIERAGT 130
Query: 194 KSGNKGAEAALTAIEMASLFE 214
K+GNKGAEAAL A+EMA+L +
Sbjct: 131 KAGNKGAEAALAALEMANLLK 151
>gnl|CDD|201491 pfam00885, DMRL_synthase, 6,7-dimethyl-8-ribityllumazine synthase.
This family includes the beta chain of 6,7-dimethyl-8-
ribityllumazine synthase EC:2.5.1.9, an enzyme involved
in riboflavin biosynthesis. The family also includes a
subfamily of distant archaebacterial proteins that may
also have the same function.
Length = 144
Score = 206 bits (528), Expect = 8e-69
Identities = 80/141 (56%), Positives = 106/141 (75%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
GLR A+VVARFN +T LLEGAL+ K++ V EE+IDVV VPG+FE+ + A++L KSG
Sbjct: 2 TGLRIAIVVARFNADITDRLLEGALDALKRHGVSEEDIDVVRVPGAFELPLAAKKLAKSG 61
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
+Y AV+ +GAV+RG T H+D VA + G++ + +GVP FGVLT D +QAL RAGG
Sbjct: 62 RYDAVVALGAVIRGGTYHFDYVAQEVSRGLMQVSLETGVPVGFGVLTTDTFEQALERAGG 121
Query: 194 KSGNKGAEAALTAIEMASLFE 214
K+GNKGAEAAL A+EMA+L +
Sbjct: 122 KAGNKGAEAALAALEMANLLK 142
>gnl|CDD|223132 COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme
metabolism].
Length = 152
Score = 194 bits (495), Expect = 1e-63
Identities = 77/141 (54%), Positives = 108/141 (76%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
+GLR A+VVARFN+ +T LLEGA++ K++ +NIDVV VPG+FEI + A++L ++G
Sbjct: 11 KGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTG 70
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGG 193
KY AV+ +GAV+RG+T H+D VAN A G++ + +GVP FGVLT DN++QA+ RAG
Sbjct: 71 KYDAVVALGAVIRGETYHFDYVANEVARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGT 130
Query: 194 KSGNKGAEAALTAIEMASLFE 214
K+GNKGAEAA A+EMA+L +
Sbjct: 131 KAGNKGAEAAEAALEMANLLK 151
>gnl|CDD|211550 TIGR00114, lumazine-synth, 6,7-dimethyl-8-ribityllumazine synthase.
This enzyme catalyzes the cyclo-ligation of
3,4-dihydroxy-2-butanone-4-P and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to
form 6,7-dimethyl-8-ribityllumazine, the immediate
precursor of riboflavin. Sometimes referred to as
riboflavin synthase, beta subunit, this should not be
confused with the alpha subunit which carries out the
subsequent reaction. Archaeal members of this family are
considered putative, although included in the seed and
scoring above the trusted cutoff [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 138
Score = 168 bits (428), Expect = 8e-54
Identities = 65/138 (47%), Positives = 101/138 (73%)
Query: 76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
+R +V+ARFN +T +LL+GA++ K+ + +NIDV+WVPG+FE+ + ++L +SGKY
Sbjct: 1 VRVGIVIARFNRFITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAESGKY 60
Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMDQALNRAGGKS 195
AV+ +G V+RG T H++ VA+ AA G+ ++ G P IFG+LT + ++QA+ RAG K+
Sbjct: 61 DAVIALGTVIRGGTPHFEYVADEAAKGIADLALDYGKPVIFGILTTETIEQAIERAGTKA 120
Query: 196 GNKGAEAALTAIEMASLF 213
GNKG EAA+ A+EMA+L
Sbjct: 121 GNKGVEAAVKALEMANLL 138
>gnl|CDD|187740 cd08371, Lumazine_synthase-like, lumazine synthase and riboflavin
synthase; involved in the riboflavin (vitamin B2)
biosynthetic pathway. This superfamily contains
lumazine synthase (6,7-dimethyl-8-ribityllumazine
synthase, LS) and riboflavin synthase (RS). Both enzymes
play important roles in the riboflavin biosynthetic
pathway. Riboflavin is the precursor of flavin
mononucleotide (FMN) and flavin adenine dinucleotide
(FAD) which are essential cofactors for the catalysis of
a wide range of redox reactions. These cofactors are
also involved in many other processes involving DNA
repair, circadian time-keeping, light sensing, and
bioluminescence. Riboflavin is biosynthesized in plants,
fungi and certain microorganisms; as animals lack the
necessary enzymes to produce this vitamin, they acquire
it from dietary sources. In the final steps of the
riboflavin biosynthetic pathway, LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and RS catalyzes a dismutation of DMRL which
yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. In bacteria and
eukaryotes, there are two types of LS: type-I LS forms
homo-pentamers or icosahedrally arranged dodecamers of
pentamers, type-II LS forms decamers (dimers of
pentamers). In archaea LSs and RSs appear to have
diverged early in the evolution of archaea from a common
ancestor.
Length = 129
Score = 97.1 bits (242), Expect = 6e-26
Identities = 53/132 (40%), Positives = 80/132 (60%), Gaps = 4/132 (3%)
Query: 78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
+V ARFN + L++GA+ + I VV VPG++EI + A++L + Y A
Sbjct: 1 VGIVDARFNRDIVDALVKGAIAELAELGG-NIKIIVVTVPGAYEIPLAAKKLLEKEDYDA 59
Query: 138 VLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD-QALNRAGGKSG 196
V+ IG V++G+T H++ VA+ + G+++ + + P IFGVLT DN + QA RA K G
Sbjct: 60 VVAIGVVIKGETYHFEIVAHEVSRGLMNLQLETDKPVIFGVLTPDNAEEQADERA--KRG 117
Query: 197 NKGAEAALTAIE 208
NKG EAA A+E
Sbjct: 118 NKGEEAARAAVE 129
>gnl|CDD|187744 cd09211, Lumazine_synthase_archaeal, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2). Archaeal LS is an important enzyme in the
riboflavin biosynthetic pathway. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. In the final steps
of the riboflavin biosynthetic pathway LS catalyzes the
condensation of the
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with
3,4-dihydroxy- 2-butanone-4-phosphate to release water,
inorganic phosphate and 6,7-dimethyl-8-ribityllumazine
(DMRL), and riboflavin synthase (RS) catalyzes a
dismutation of DMRL which yields riboflavin and
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In
the latter reaction, a four-carbon moiety is transferred
between two DMRL molecules serving as donor and
acceptor, respectively. Both the LS and RS catalyzed
reactions are thermodynamically irreversible and can
proceed in the absence of a catalyst. LS from
Methanococcus jannaschii forms capsids with icosahedral
532 symmetry consisting of 60 subunits. Archaeal LSs
share sequence similarity with archaeal RSs, both appear
to have diverged early in the evolution of archaea from
a common ancestor.
Length = 131
Score = 68.1 bits (167), Expect = 7e-15
Identities = 42/134 (31%), Positives = 68/134 (50%), Gaps = 8/134 (5%)
Query: 79 ALVVARFNELVTKLLLEGALET--FKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYT 136
+VVA FN +T ++ E ALE F VK V+ VPG F++ + ++L +
Sbjct: 2 GIVVAEFNYDITYMMEEKALEHAKFLGAEVKY----VLRVPGVFDMPLAVKKLLEKDDID 57
Query: 137 AVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVL-TCDNMDQALNRAGGKS 195
AV+ +GAV++G+T H + +AN AA +L + G P G+ + QAL R
Sbjct: 58 AVVTLGAVIKGETKHDELIANQAARKILDLSLEYGKPVTLGISGPGMSRLQALERI-EYY 116
Query: 196 GNKGAEAALTAIEM 209
+ EAA+ ++
Sbjct: 117 AKRAVEAAVKMVKR 130
>gnl|CDD|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional.
Length = 158
Score = 67.0 bits (164), Expect = 4e-14
Identities = 39/146 (26%), Positives = 63/146 (43%), Gaps = 7/146 (4%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
R A + AR++ + +G + +D+ VPG+FEI + AQ L K+G
Sbjct: 9 TPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTG 68
Query: 134 KYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNMD-----QAL 188
+Y A++ VV G ++ VA + G++ +++ VP VLT +
Sbjct: 69 RYAAIVAAALVVDGGIYRHEFVAQAVIDGLMRVQLDTEVPVFSVVLTPHHFHESEEHHDF 128
Query: 189 NRAGGKSGNKGAEAALTAIEMASLFE 214
RA KGAEAA + E
Sbjct: 129 FRAHFVV--KGAEAAHACADTLLSRE 152
>gnl|CDD|187741 cd09208, Lumazine_synthase-II, lumazine synthase
(6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes
the penultimate step in the biosynthesis of riboflavin
(vitamin B2); type-II. Type-II LS also known as RibH2,
catalyzes the penultimate step in the biosynthesis of
riboflavin in plants and microorganisms. LS catalyses
the formation of 6,7-dimethyl-8-ribityllumazine by the
condensation of 5-amino-6-ribitylamino-
2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-
2-butanone-4-phosphate. Subsequently, the lumazine
intermediate dismutates yielding riboflavin and
5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a
reaction catalyzed by riboflavin synthase (RS); RS
belongs to a different family of the
Lumazine-synthase-like superfamily. Riboflavin is the
precursor of flavin mononucleotide (FMN) and flavin
adenine dinucleotide (FAD) which are essential cofactors
for the catalysis of a wide range of redox reactions.
These cofactors are also involved in many other
processes involving DNA repair, circadian time-keeping,
light sensing, and bioluminescence. Riboflavin is
biosynthesized in plants, fungi and certain
microorganisms; as animals lack the necessary enzymes to
produce this vitamin, they acquire it from dietary
sources. Type II LSs are distinct from type-I LS not
only in protein sequence, but in that they exhibit
different quaternary assemblies; type-II LSs form
decamers (dimers of pentamers). The pathogen Brucella
spp. have both a type-I LS and a type-II LS called RibH1
and RibH2, respectively. RibH1/type-I LS appears to be a
functional LS in Brucella spp., whereas RibH2/type-II LS
has much lower catalytic activity as LS and may be
regulated by a riboswitch that senses FMN, suggesting
that the type-II LSs may have evolved into very poor
catalysts or, that they may harbor a new, as-yet-unknown
function.
Length = 137
Score = 61.7 bits (150), Expect = 2e-12
Identities = 32/137 (23%), Positives = 60/137 (43%), Gaps = 3/137 (2%)
Query: 76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
R A + AR++ + +G + +D+ VPG+FEI + A++L ++G+Y
Sbjct: 1 FRIAFIQARWHADIVDQARKGFEAEMAAKGGASDEVDIFDVPGAFEIPLHAKRLARTGRY 60
Query: 136 TAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSGVPCIFGVLTCDNM---DQALNRAG 192
A++ VV G ++ VA + G++ + + VP VLT + +
Sbjct: 61 AAIVGAALVVDGGIYRHEFVAQAVIDGLMRVQLETEVPVFSVVLTPHHFHEHKEHHEFFF 120
Query: 193 GKSGNKGAEAALTAIEM 209
KG E A + +
Sbjct: 121 AHFKKKGVEVAHACLAI 137
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 29.8 bits (67), Expect = 1.1
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 30 TSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTG 68
++S S+ + AI++ RLS Q EAVRH+TG
Sbjct: 328 EALSQSQGHGVSPPIVDAAIDQHYRLSEEQYEAVRHVTG 366
>gnl|CDD|234176 TIGR03351, PhnX-like, phosphonatase-like hydrolase. This clade of
sequences are the closest homologs to the PhnX enzyme,
phosphonoacetaldehyde (Pald) hydrolase (phosphonatase,
TIGR01422). This phosphonatase-like enzyme and PhnX
itself are members of the haloacid dehalogenase (HAD)
superfamily (pfam00702) having a a number of distinctive
features that set them apart from typical HAD enzymes.
The typical HAD N-terminal motif DxDx(T/V) here is DxAGT
and the usual conserved lysine prior to the C-terminal
motif is instead an arginine. Also distinctive of
phosphonatase, and particular to its bi-catalytic
mechanism is a conserved lysine in the variable "cap"
domain. This lysine forms a Schiff base with the
aldehyde of phosphonoacetaldehyde, providing, through
the resulting positive charge, a polarization of the C-P
bond necesary for cleavage as well as a route to the
initial product of cleavage, an ene-amine. The
conservation of these elements in this
phosphonatase-like enzyme suggests that the substrate is
also, like Pald, a 2-oxo-ethylphosphonate. Despite this,
the genomic context of members of this family are quite
distinct from PhnX, which is almost invariably
associated with the 2-aminoethylphosphonate transaminase
PhnW (TIGR02326), the source of the substrate Pald.
Members of this clade are never associated with PhnW,
but rather associate with families of FAD-dependent
oxidoreductases related to deaminating amino acid
oxidases (pfam01266) as well as zinc-dependent
dehydrogenases (pfam00107). Notably, family members from
Arthrobacter aurescens TC1 and Nocardia farcinica IFM
10152 are adjacent to the PhnCDE ABC cassette
phosphonates transporter (GenProp0236) typically found
in association with the phosphonates C-P lyase system
(GenProp0232). These observations suggest two
possibilities. First, the substrate for this enzyme
family is also Pald, the non-association with PhnW not
withstanding. Alternatively, the substrate is something
very closely related such as
hydroxyphosphonoacetaldehyde (Hpald). Hpald could come
from oxidative deamination of
1-hydroxy-2-aminoethylphosphonate (HAEP) by the
associated oxidase. HAEP would not be a substrate for
PhnW due to its high specificity for AEP. HAEP has been
shown to be a constituent of the sphingophosphonolipid
of Bacteriovorax stolpii, and presumably has other
natural sources. If Hpald is the substrate, the product
would be glycoaldehyde (hydroxyacetaldehyde), and the
associated alcohol dehydrogenase may serve to convert
this to glycol.
Length = 220
Score = 28.6 bits (64), Expect = 2.0
Identities = 39/159 (24%), Positives = 57/159 (35%), Gaps = 31/159 (19%)
Query: 61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKL-------LLEGALETFKKYSVKEENIDV 113
EA+R L +E A F E + + L GA E F+ S++ I V
Sbjct: 50 EAIRALLAADGADEA-EAQAAFADFEERLAEAYDDGPPVALPGAEEAFR--SLRSSGIKV 106
Query: 114 VWVPGSFEIGVVAQQLGKSG-----KYTAVLCIGAVVRGDTTHYDAVANSAASGV----- 163
G F+ + L K G AV+C V G + +GV
Sbjct: 107 ALTTG-FDRDTAERLLEKLGWTVGDDVDAVVCPSDVAAGRPAPDLILRAMELTGVQDVQS 165
Query: 164 ----------LSAGVNSGVPCIFGVLTCDNMDQALNRAG 192
L AG+N+G + GVLT + + L+R
Sbjct: 166 VAVAGDTPNDLEAGINAGAGAVVGVLTGAHDAEELSRHP 204
>gnl|CDD|107262 cd06267, PBP1_LacI_sugar_binding_like, Ligand binding domain of the
LacI tanscriptional regulator family belonging to the
type I periplasmic-binding fold protein superfamily.
Ligand binding domain of the LacI tanscriptional
regulator family belonging to the type I
periplasmic-binding fold protein superfamily. In most
cases, ligands are monosaccharide including lactose,
ribose, fructose, xylose, arabinose, galactose/glucose,
and other sugars. The LacI family of proteins consists
of transcriptional regulators related to the lac
repressor. In this case, the domain sugar binding
changes the DNA binding activity of the repressor
domain.
Length = 264
Score = 28.3 bits (64), Expect = 3.0
Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 12/85 (14%)
Query: 61 EAVRHLTGFLTKNEGL---RFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVP 117
AV HL L R A + + + LEG E ++ + + +V
Sbjct: 106 LAVEHLIE-------LGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGD 158
Query: 118 GSFEIG--VVAQQLGKSGKYTAVLC 140
S E G + L + TA+
Sbjct: 159 FSEESGYEAARELLASGERPTAIFA 183
>gnl|CDD|163623 cd07380, MPP_CWF19_N, Schizosaccharomyces pombe CWF19 and related
proteins, N-terminal metallophosphatase domain. CWF19
cell cycle control protein (also known as CWF19-like 1
(CWF19L1) in Homo sapiens), N-terminal
metallophosphatase domain. CWF19 contains C-terminal
domains similar to that found in the CwfJ cell cycle
control protein. The metallophosphatase domain belongs
to the metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 150
Score = 27.6 bits (62), Expect = 3.2
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 116 VPGSFE--IGVVAQQLGKSGKYTAVLCIG 142
V G + V K G + A+LC+G
Sbjct: 6 VNGRLKALFEKVNTINKKKGPFDALLCVG 34
>gnl|CDD|214591 smart00264, BAG, BAG domains, present in regulator of Hsp70
proteins. BAG domains, present in Bcl-2-associated
athanogene 1 and silencer of death domains.
Length = 79
Score = 26.5 bits (59), Expect = 3.6
Identities = 9/43 (20%), Positives = 21/43 (48%)
Query: 53 ERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLE 95
++++ V E + + + +G + R +E + KLLL+
Sbjct: 3 KKINEVLDEVQKKIEKEVQVADGKKDDKEYLRLSEELMKLLLK 45
>gnl|CDD|238423 cd00827, init_cond_enzymes, "initiating" condensing enzymes are a
subclass of decarboxylating condensing enzymes,
including beta-ketoacyl [ACP] synthase, type III and
polyketide synthases, type III, which include chalcone
synthase and related enzymes. They are characterized by
the utlization of CoA substrate primers, as well as the
nature of their active site residues.
Length = 324
Score = 27.8 bits (62), Expect = 5.3
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 4/43 (9%)
Query: 125 VAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAG 167
+A L +SG + L VV D Y SA L G
Sbjct: 118 LAANLVESGPWRYAL----VVASDIASYLLDEGSALEPTLGDG 156
>gnl|CDD|173682 cd05591, STKc_nPKC_epsilon, Catalytic domain of the Protein
Serine/Threonine Kinase, Novel Protein Kinase C epsilon.
Serine/Threonine Kinases (STKs), Novel Protein Kinase C
(nPKC), epsilon isoform, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The nPKC subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PKCs are classified into three groups
(classical, atypical, and novel) depending on their mode
of activation and the structural characteristics of
their regulatory domain. nPKCs are calcium-independent,
but require DAG (1,2-diacylglycerol) and
phosphatidylserine (PS) for activity. There are four
nPKC isoforms, delta, epsilon, eta, and theta.
PKC-epsilon has been shown to behave as an oncoprotein.
Its overexpression contributes to neoplastic
transformation depending on the cell type. It
contributes to oncogenesis by inducing disordered cell
growth and inhibiting cell death. It also plays a role
in tumor invasion and metastasis. PKC-epsilon has also
been found to confer cardioprotection against ischemia
and reperfusion-mediated damage. Other cellular
functions include the regulation of gene expression,
cell adhesion, and cell motility.
Length = 321
Score = 27.5 bits (61), Expect = 6.5
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 61 EAVRHLTGFLTKNEGLRFALVVARFNE 87
EAV L F+TKN R V ++ E
Sbjct: 222 EAVSILKAFMTKNPNKRLGCVASQGGE 248
>gnl|CDD|182193 PRK10014, PRK10014, DNA-binding transcriptional repressor MalI;
Provisional.
Length = 342
Score = 27.4 bits (61), Expect = 6.7
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 124 VVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASGVLSAGVNSG 171
+ L + +AV+C + + +A A G+L AG SG
Sbjct: 233 AITALLRHNPTISAVVC----------YNETIAMGAWFGLLRAGRQSG 270
>gnl|CDD|226871 COG4465, CodY, Pleiotropic transcriptional repressor
[Transcription].
Length = 261
Score = 27.0 bits (60), Expect = 8.4
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 55 LSFVQTEAVRHLTGFLTKNEGLRFALVVA 83
LS+ + EAV H+ L NEGL A +A
Sbjct: 183 LSYSELEAVEHIFEELDGNEGLLVASKIA 211
>gnl|CDD|216192 pfam00920, ILVD_EDD, Dehydratase family.
Length = 521
Score = 27.0 bits (61), Expect = 8.7
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 151 HYDAVANSAASGVLSAGVNSGVPCIFGVLT-CDNMDQA 187
H +A + GV +AG G P FG + CD +
Sbjct: 19 HLRDLAEAVKEGVRAAG---GTPVEFGTIAVCDGITMG 53
>gnl|CDD|131834 TIGR02787, codY_Gpos, GTP-sensing transcriptional pleiotropic
repressor CodY. This model represents the full length
of CodY, a pleiotropic repressor in Bacillus subtilis
and other Firmicutes (low-GC Gram-positive bacteria)
that responds to intracellular levels of GTP and
branched chain amino acids. The C-terminal
helix-turn-helix DNA-binding region is modeled by
pfam08222 in Pfam [Regulatory functions, DNA
interactions].
Length = 251
Score = 26.6 bits (59), Expect = 9.2
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 46 QIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVA 83
Q+AI LS+ + EAV H+ L NEGL A +A
Sbjct: 171 QMAINT---LSYSELEAVEHIFEELDGNEGLLVASKIA 205
>gnl|CDD|240307 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 26.6 bits (59), Expect = 10.0
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 117 PGSFEIGVVAQQLGKSGKYTAVLCIGAVVRGDTTHYDAVANSAASG 162
PG +IG++ + K G IG V R T Y+AVA + A G
Sbjct: 154 PGECKIGIMPGHIHKKG------KIGIVSRSGTLTYEAVAQTTAVG 193
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
0.317 0.131 0.370
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,666,204
Number of extensions: 994383
Number of successful extensions: 924
Number of sequences better than 10.0: 1
Number of HSP's gapped: 921
Number of HSP's successfully gapped: 39
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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 (21.7 bits)
S2: 57 (25.7 bits)