RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032216
(145 letters)
>gnl|CDD|178026 PLN02404, PLN02404, 6,7-dimethyl-8-ribityllumazine synthase.
Length = 141
Score = 138 bits (350), Expect = 4e-43
Identities = 61/76 (80%), Positives = 68/76 (89%)
Query: 70 LTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQL 129
L EGLRF +VVARFNE++TK LLEGALETFK+YSVKEENIDVVWVPGSFEI VVAQ+L
Sbjct: 2 LLDGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRL 61
Query: 130 GKSGKYTAVLCIGAVV 145
KSGKY A+LCIGAV+
Sbjct: 62 AKSGKYDAILCIGAVI 77
>gnl|CDD|234606 PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase;
Provisional.
Length = 154
Score = 112 bits (282), Expect = 2e-32
Identities = 42/72 (58%), Positives = 57/72 (79%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
+GLR +VVARFN+ +T LLEGAL+ K++ V EENIDVV VPG+FEI + A++L +SG
Sbjct: 11 KGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESG 70
Query: 134 KYTAVLCIGAVV 145
KY AV+ +GAV+
Sbjct: 71 KYDAVIALGAVI 82
>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 = 109 bits (275), Expect = 1e-31
Identities = 39/68 (57%), Positives = 54/68 (79%)
Query: 78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
A+VV+RFNE +T LLEGAL+ K++ VKEENIDVV VPG+FEI + A++L +SGKY A
Sbjct: 1 IAIVVSRFNEEITDALLEGALDALKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDA 60
Query: 138 VLCIGAVV 145
++ +G V+
Sbjct: 61 IIALGCVI 68
>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 = 106 bits (267), Expect = 2e-30
Identities = 41/72 (56%), Positives = 56/72 (77%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
GLR A+VVARFN +T LLEGAL+ K++ V EE+IDVV VPG+FE+ + A++L KSG
Sbjct: 2 TGLRIAIVVARFNADITDRLLEGALDALKRHGVSEEDIDVVRVPGAFELPLAAKKLAKSG 61
Query: 134 KYTAVLCIGAVV 145
+Y AV+ +GAV+
Sbjct: 62 RYDAVVALGAVI 73
>gnl|CDD|223132 COG0054, RibH, Riboflavin synthase beta-chain [Coenzyme
metabolism].
Length = 152
Score = 99 bits (250), Expect = 8e-28
Identities = 38/72 (52%), Positives = 56/72 (77%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
+GLR A+VVARFN+ +T LLEGA++ K++ +NIDVV VPG+FEI + A++L ++G
Sbjct: 11 KGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTG 70
Query: 134 KYTAVLCIGAVV 145
KY AV+ +GAV+
Sbjct: 71 KYDAVVALGAVI 82
>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 = 84.7 bits (210), Expect = 6e-22
Identities = 31/70 (44%), Positives = 52/70 (74%)
Query: 76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
+R +V+ARFN +T +LL+GA++ K+ + +NIDV+WVPG+FE+ + ++L +SGKY
Sbjct: 1 VRVGIVIARFNRFITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAESGKY 60
Query: 136 TAVLCIGAVV 145
AV+ +G V+
Sbjct: 61 DAVIALGTVI 70
>gnl|CDD|237096 PRK12419, PRK12419, riboflavin synthase subunit beta; Provisional.
Length = 158
Score = 50.8 bits (122), Expect = 1e-08
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 74 EGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSG 133
R A + AR++ + +G + +D+ VPG+FEI + AQ L K+G
Sbjct: 9 TPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTG 68
Query: 134 KYTAVLCIGAVV 145
+Y A++ VV
Sbjct: 69 RYAAIVAAALVV 80
>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 = 49.3 bits (118), Expect = 2e-08
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 78 FALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYTA 137
+V ARFN + L++GA+ + I VV VPG++EI + A++L + Y A
Sbjct: 1 VGIVDARFNRDIVDALVKGAIAELAELGG-NIKIIVVTVPGAYEIPLAAKKLLEKEDYDA 59
Query: 138 VLCIGAVV 145
V+ IG V+
Sbjct: 60 VVAIGVVI 67
>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 = 46.6 bits (111), Expect = 2e-07
Identities = 19/70 (27%), Positives = 36/70 (51%)
Query: 76 LRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKY 135
R A + AR++ + +G + +D+ VPG+FEI + A++L ++G+Y
Sbjct: 1 FRIAFIQARWHADIVDQARKGFEAEMAAKGGASDEVDIFDVPGAFEIPLHAKRLARTGRY 60
Query: 136 TAVLCIGAVV 145
A++ VV
Sbjct: 61 AAIVGAALVV 70
>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 = 45.8 bits (109), Expect = 4e-07
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 6/69 (8%)
Query: 79 ALVVARFNELVTKLLLEGALET--FKKYSVKEENIDVVWVPGSFEIGVVAQQLGKSGKYT 136
+VVA FN +T ++ E ALE F VK V+ VPG F++ + ++L +
Sbjct: 2 GIVVAEFNYDITYMMEEKALEHAKFLGAEVKY----VLRVPGVFDMPLAVKKLLEKDDID 57
Query: 137 AVLCIGAVV 145
AV+ +GAV+
Sbjct: 58 AVVTLGAVI 66
>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 = 30.5 bits (69), Expect = 0.31
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|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 = 28.7 bits (65), Expect = 0.92
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 = 27.3 bits (61), Expect = 2.5
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|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 = 27.1 bits (60), Expect = 3.7
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|106967 PHA00658, PHA00658, putative lysin.
Length = 720
Score = 27.1 bits (59), Expect = 3.9
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 26 SPKPTSMSFSRSSSLKGF--GTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLR 77
+PK S R +++ F G IA +R+ F E +HL KN +R
Sbjct: 612 TPKDGSSDAERVGAMRKFIDGYFIAAQREAGKKFTDAEVEQHLDALFMKNATVR 665
>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 = 25.7 bits (57), Expect = 4.1
Identities = 9/43 (20%), Positives = 21/43 (48%)
Query: 53 ERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLE 95
++++ V E + + + +G + R +E + KLLL+
Sbjct: 3 KKINEVLDEVQKKIEKEVQVADGKKDDKEYLRLSEELMKLLLK 45
>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1). The
homeobox gene Prox1 is expressed in a subpopulation of
endothelial cells that, after budding from veins, gives
rise to the mammalian lymphatic system. Prox1 has been
found to be an early specific marker for the developing
liver and pancreas in the mammalian foregut endoderm.
This family contains an atypical homeobox domain.
Length = 908
Score = 27.0 bits (59), Expect = 4.2
Identities = 11/27 (40%), Positives = 11/27 (40%)
Query: 10 HHSPLASSSRQFINGFSPKPTSMSFSR 36
HH PL SS GF P P F
Sbjct: 615 HHQPLHPSSLSASMGFHPPPFRHPFPL 641
>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 = 5.6
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|226871 COG4465, CodY, Pleiotropic transcriptional repressor
[Transcription].
Length = 261
Score = 26.2 bits (58), Expect = 6.0
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|181162 PRK07904, PRK07904, short chain dehydrogenase; Provisional.
Length = 253
Score = 26.2 bits (58), Expect = 6.1
Identities = 28/99 (28%), Positives = 42/99 (42%), Gaps = 18/99 (18%)
Query: 41 KGFGTQIAI-----ERKERLSFVQTEAVRHLTGF-LTKNEGLR---FALVVARFNELVTK 91
+GFG IA+ ER R +FV L GF L E LR ++V R ++ T+
Sbjct: 136 QGFGQIIAMSSVAGERVRRSNFVYGSTKAGLDGFYLGLGEALREYGVRVLVVRPGQVRTR 195
Query: 92 L---LLEGALETFKKYSVK------EENIDVVWVPGSFE 121
+ E L K+ K + ++VW P +F
Sbjct: 196 MSAHAKEAPLTVDKEDVAKLAVTAVAKGKELVWAPPAFR 234
>gnl|CDD|178629 PLN03080, PLN03080, Probable beta-xylosidase; Provisional.
Length = 779
Score = 26.7 bits (59), Expect = 6.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 29 PTSMSFSRSSSLKGFGTQIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFN 86
P +S SRSS + ++R++ L +VQ E + E LRF + ++ N
Sbjct: 644 PKKLSLSRSSVQDSISRKPLLQRRDELDYVQIEDI-------ASCESLRFNVHISVSN 694
>gnl|CDD|224525 COG1609, PurR, Transcriptional regulators [Transcription].
Length = 333
Score = 26.1 bits (58), Expect = 7.3
Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 7/83 (8%)
Query: 61 EAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFKKYSVKEENIDVVWVPGSF 120
A HL + R A + + ++ LEG ++ + +V S
Sbjct: 165 LATEHLIELGHR----RIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWIVEGDFSE 220
Query: 121 EIGVVA-QQLGKSGKY--TAVLC 140
E G A ++L G+ TA+ C
Sbjct: 221 ESGYEAAERLLARGEPRPTAIFC 243
>gnl|CDD|107253 cd01540, PBP1_arabinose_binding, Periplasmic L-arabinose-binding
protein (ABP), a member of a family of pentose/hexose
sugar-binding proteins of the type I periplasmic binding
protein superfamily. Periplasmic L-arabinose-binding
protein (ABP), a member of a family of pentose/hexose
sugar-binding proteins of the type I periplasmic binding
protein superfamily. ABP is only involved in transport
contrary to other related sugar-binding proteins such as
the glucose/galactose-binding protein (GGBP) and the
ribose-binding protein (RBP), both of which are involved
in chemotaxis as well as transport. The periplasmic ABP
consists of two alpha/beta globular domains connected by
a three-stranded hinge, a Venus flytrap-like domain,
which undergoes a transition from an open to a closed
conformational state upon ligand binding. Moreover, ABP
is homologous to the ligand-binding domain of eukaryotic
receptors such as metabotropic glutamate receptor
(mGluR) and DNA-binding transcriptional repressors such
as LacI and GalR.
Length = 289
Score = 26.2 bits (58), Expect = 7.4
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 86 NELVT-KLLLEGALETFKKYSVKEENI 111
+EL T K +GALE K E NI
Sbjct: 140 DELDTAKPRTDGALEALKAPGFPEANI 166
>gnl|CDD|218304 pfam04876, Tenui_NCP, Tenuivirus major non-capsid protein. This
protein of unknown function accumulates in large amounts
in tenuivirus infected cells. It is found in all forms
of the inclusion bodies that are formed after infection.
Length = 175
Score = 26.0 bits (57), Expect = 7.4
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 91 KLLLEGALETFKKYSVKEENIDVVW--VPGSFEI 122
K LL +E K S E + VW +P F
Sbjct: 134 KTLLTQIIEMAKAESSDTETYEKVWKKMPAYFSN 167
>gnl|CDD|216121 pfam00790, VHS, VHS domain. Domain present in VPS-27, Hrs and
STAM.
Length = 136
Score = 25.7 bits (57), Expect = 8.1
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 59 QTEAVR--HLTGFLTKNEGLRFALVVARF---NELVTKLLLEGALETFKKYSVKEENIDV 113
A+ L KN G +F L +A NELV + + + K VK++ +++
Sbjct: 52 PHVALLALTLLDACVKNCGSKFHLEIASKEFLNELVKLIPNKPYGKPAK---VKKKILEL 108
Query: 114 V 114
+
Sbjct: 109 I 109
>gnl|CDD|240156 cd05030, calgranulins, Calgranulins: S-100 domain found in proteins
belonging to the Calgranulin subgroup of the S100 family
of EF-hand calcium-modulated proteins, including S100A8,
S100A9, and S100A12 . Note that the S-100 hierarchy, to
which this Calgranulin group belongs, contains only
S-100 EF-hand domains, other EF-hands have been modeled
separately. These proteins are expressed mainly in
granulocytes, and are involved in inflammation, allergy,
and neuritogenesis, as well as in host-parasite
response. Calgranulins are modulated not only by
calcium, but also by other metals such as zinc and
copper. Structural data suggested that calgranulins may
exist in multiple structural forms, homodimers, as well
as hetero-oligomers. For example, the S100A8/S100A9
complex called calprotectin plays important roles in the
regulation of inflammatory processes, wound repair, and
regulating zinc-dependent enzymes as well as microbial
growth.
Length = 88
Score = 25.0 bits (55), Expect = 8.2
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 94 LEGALETFKKYSVKEENIDVV 114
+E + F +YSV++ + D +
Sbjct: 7 IETIINVFHQYSVRKGHPDTL 27
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 26.0 bits (58), Expect = 8.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 125 VAQQLGKSGKYTAVLCIGA 143
VA L +SG Y VL +GA
Sbjct: 122 VADGLIRSGGYKNVLVVGA 140
>gnl|CDD|227826 COG5539, COG5539, Predicted cysteine protease (OTU family)
[Posttranslational modification, protein turnover,
chaperones].
Length = 306
Score = 26.0 bits (57), Expect = 9.0
Identities = 21/99 (21%), Positives = 33/99 (33%), Gaps = 14/99 (14%)
Query: 46 QIAIERKERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETFK--- 102
++ I E+ Q+ V N L A + + V KL +LE
Sbjct: 94 ELGISSFEKSVSQQSINVLEDMPGQDDNSRLFQAERYSLRDASVAKLREVVSLEVLSNPD 153
Query: 103 KYSVKEENIDVV-----------WVPGSFEIGVVAQQLG 130
Y+ IDV+ G EI +++ QL
Sbjct: 154 LYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLP 192
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 25.7 bits (57), Expect = 9.1
Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 8/93 (8%)
Query: 46 QIAIERK----ERLSFVQTEAVRHLTGFLTKNEGLRFALVVARFNELVTKLLLEGALETF 101
++ RK + + L + AL + E+ T+ L+E L+
Sbjct: 7 KLLEARKALSSAERKAASSAIAKRLLALIEWKNAKTIALYLPLRGEVDTRPLIEQLLKEG 66
Query: 102 KKY----SVKEENIDVVWVPGSFEIGVVAQQLG 130
K+ + + + S E + G
Sbjct: 67 KRVALPKVDGDGKEMLFFRIWSPEQPLTKGPFG 99
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
0.319 0.133 0.370
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,137,386
Number of extensions: 635522
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 42
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.8 bits)
S2: 54 (24.4 bits)