RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1582
(129 letters)
>gnl|CDD|212664 cd07792, FGGY_GK1-3_metazoa, Metazoan glycerol kinase 1 and 3-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan glycerol kinases (GKs), coded by X
chromosome-linked GK genes, and glycerol kinase
(GK)-like proteins, coded by autosomal testis-specific
GK-like genes (GK-like genes, GK1 and GK3). Sequence
comparison shows that metazoan GKs and GK-like proteins
in this family are closely related to the bacterial GKs,
which catalyze the Mg-ATP dependent phosphorylation of
glycerol to yield glycerol 3-phosphate (G3P). The
metazoan GKs do have GK enzymatic activity. However, the
GK-like metazoan proteins do not exhibit GK activity and
their biological functions are not yet clear. Some of
them lack important functional residues involved in the
binding of ADP and Mg2+, which may result in the loss of
GK catalytic function. Others that have conserved
catalytic residues have lost their GK activity as well;
the reason remains unclear. It has been suggested the
conserved catalytic residues might facilitate them
performing a distinct function. GKs belong to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 504
Score = 142 bits (359), Expect = 4e-41
Identities = 47/91 (51%), Positives = 62/91 (68%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
++R L+ +A T E + SH ++I I P+EGW EQDP EIL +V +++ +KL +
Sbjct: 12 STRFLVFNAKTAELLSSHQVEIKQIFPKEGWVEQDPKEILNSVYECIEKTCKKLKELNID 71
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
DI +GITNQRETTVVWD TGEPLYNAI
Sbjct: 72 VSDIKAIGITNQRETTVVWDKYTGEPLYNAI 102
>gnl|CDD|198347 cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family
of carbohydrate kinases. This subfamily includes
glycerol kinases (GK; EC 2.7.1.30) and glycerol
kinase-like proteins from all three kingdoms of living
organisms. Glycerol is an important intermediate of
energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Human GK deficiency, called
hyperglycerolemia, is an X-linked recessive trait
associated with psychomotor retardation, osteoporosis,
spasticity, esotropia, and bone fractures. Under
different conditions, GKs from different species may
exist in different oligomeric states. The monomer of GKs
is composed of two large domains separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain. The high affinity ATP binding site of GKs is
created only by a substrate-induced conformational
change. Based on sequence similarity, some GK-like
proteins from metazoa, which have lost their GK
enzymatic activity, are also included in this CD.
Members in this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 484
Score = 113 bits (284), Expect = 2e-30
Identities = 42/90 (46%), Positives = 54/90 (60%), Gaps = 4/90 (4%)
Query: 25 SRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSR 84
+R +I E V SH ++ I PQ GW E DP EI V ++ A++KL +S
Sbjct: 12 TRFIIFDR-DGEVVSSHQVEHEQIYPQPGWVEHDPEEIWANVVQCIEEALKKL---RISP 67
Query: 85 DDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+ I +GITNQRETTV WD TG+PLYNAI
Sbjct: 68 EQIKAIGITNQRETTVAWDKETGKPLYNAI 97
>gnl|CDD|233353 TIGR01311, glycerol_kin, glycerol kinase. This model describes
glycerol kinase, a member of the FGGY family of
carbohydrate kinases [Energy metabolism, Other].
Length = 493
Score = 112 bits (282), Expect = 3e-30
Identities = 42/91 (46%), Positives = 56/91 (61%), Gaps = 4/91 (4%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
+SR ++ V H + + I P+ GW E DPMEI ++V + + A+ K G+
Sbjct: 12 SSRAIVFDK-DGNIVAIHQKEFTQIFPKPGWVEHDPMEIWESVLSCIAEALAKA---GIK 67
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
DDI +GITNQRETTVVWD TG+PLYNAI
Sbjct: 68 PDDIAAIGITNQRETTVVWDKATGKPLYNAI 98
>gnl|CDD|198367 cd07795, FGGY_ScGut1p_like, Saccharomyces cerevisiae Gut1p and
related proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
small group of fungal glycerol kinases (GK), including
Saccharomyces cerevisiae Gut1p/YHL032Cp, which
phosphorylates glycerol to glycerol-3-phosphate in the
cytosol. Glycerol utilization has been considered as the
sole source of carbon and energy in S. cerevisiae, and
is mediated by glycerol kinase and glycerol 3-phosphate
dehydrogenase, which is encoded by the GUT2 gene.
Members in this family show high similarity to their
prokaryotic and eukaryotic homologs. GKs belong to the
FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 496
Score = 105 bits (265), Expect = 7e-28
Identities = 43/91 (47%), Positives = 56/91 (61%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
TS I+ + V SH ++ S I P GW E DP EI+ +V + A++ L G S
Sbjct: 12 TSTRFILFNRDGQPVASHQIEFSQIYPHPGWHEHDPEEIVSSVVQCIASALKSLETSGFS 71
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+ D+ +GITNQRETTVVWD TG+PLYNAI
Sbjct: 72 KYDVKVIGITNQRETTVVWDRETGKPLYNAI 102
>gnl|CDD|240348 PTZ00294, PTZ00294, glycerol kinase-like protein; Provisional.
Length = 504
Score = 105 bits (263), Expect = 2e-27
Identities = 45/92 (48%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 23 HTSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGL 82
TS II V SH + I+P GW E DP EIL+ V M+ AI+KL G
Sbjct: 11 TTSTRFIIFDEKGNVVSSHQIPHEQITPHPGWLEHDPEEILRNVYKCMNEAIKKLREKGP 70
Query: 83 SRDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
S I +GITNQRET V WD TG+PLYNAI
Sbjct: 71 SFK-IKAIGITNQRETVVAWDKVTGKPLYNAI 101
>gnl|CDD|234594 PRK00047, glpK, glycerol kinase; Provisional.
Length = 498
Score = 102 bits (256), Expect = 1e-26
Identities = 37/79 (46%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 36 EEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQ 95
V + + I PQ GW E DP EI + + + A L+ G+S D I +GITNQ
Sbjct: 27 NIVSVAQKEFTQIFPQPGWVEHDPNEIWASQLSVIAEA---LAKAGISPDQIAAIGITNQ 83
Query: 96 RETTVVWDLNTGEPLYNAI 114
RETTVVWD TG P+YNAI
Sbjct: 84 RETTVVWDKETGRPIYNAI 102
>gnl|CDD|198361 cd07786, FGGY_EcGK_like, Escherichia coli glycerol kinase-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup is composed of mostly bacterial
and archaeal glycerol kinases (GK), including the well
characterized proteins from Escherichia coli (EcGK),
Thermococcus kodakaraensis (TkGK), and Enterococcus
casseliflavus (EnGK). GKs contain two large domains
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The high affinity ATP binding
site of EcGK is created only by a substrate-induced
conformational change, which is initiated by
protein-protein interactions through complex formation
with enzyme IIAGlc (also known as IIIGlc), the
glucose-specific phosphocarrier protein of the
phosphotransferase system (PTS). EcGK exists in a
dimer-tetramer equilibrium. IIAGlc binds to both EcGK
dimer and tetramer, and inhibits the uptake and
subsequent metabolism of glycerol and maltose. Another
well-known allosteric regulator of EcGK is fructose
1,6-bisphosphate (FBP), which binds to the EcGK tetramer
and plays an essential role in the stabilization of the
inactive tetrameric form. EcGK requires Mg2+ for its
enzymatic activity. Members in this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 486
Score = 101 bits (255), Expect = 2e-26
Identities = 37/90 (41%), Positives = 49/90 (54%), Gaps = 4/90 (4%)
Query: 25 SRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSR 84
SR ++ V + + I P+ GW E DP EI ++ A+ K G+
Sbjct: 12 SRAILFDH-DGNIVAVAQREFTQIYPKPGWVEHDPEEIWESQLAVAREALAK---AGIRA 67
Query: 85 DDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
DI +GITNQRETTVVWD TG+P+YNAI
Sbjct: 68 SDIAAIGITNQRETTVVWDRETGKPVYNAI 97
>gnl|CDD|223628 COG0554, GlpK, Glycerol kinase [Energy production and conversion].
Length = 499
Score = 100 bits (251), Expect = 6e-26
Identities = 38/91 (41%), Positives = 54/91 (59%), Gaps = 4/91 (4%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
+SR ++ V + + I PQ GW E DP+EI +V++ + A+ K G+
Sbjct: 16 SSRAIVFDE-DGNIVAIAQREFTQIYPQPGWVEHDPLEIWASVRSVLKEALAKA---GIK 71
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+I +GITNQRETTVVWD TG+P+YNAI
Sbjct: 72 PGEIAAIGITNQRETTVVWDKETGKPIYNAI 102
>gnl|CDD|215166 PLN02295, PLN02295, glycerol kinase.
Length = 512
Score = 98.6 bits (246), Expect = 3e-25
Identities = 42/78 (53%), Positives = 55/78 (70%), Gaps = 1/78 (1%)
Query: 38 VVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDD-IVTLGITNQR 96
V SH ++ + I PQ GW E DPMEIL++V T + +A+EK +A G + D + +GITNQR
Sbjct: 24 VASHQVEFTQIYPQAGWVEHDPMEILESVLTCIAKALEKAAAKGHNVDSGLKAIGITNQR 83
Query: 97 ETTVVWDLNTGEPLYNAI 114
ETTV W +TG PLYNAI
Sbjct: 84 ETTVAWSKSTGRPLYNAI 101
>gnl|CDD|198368 cd07796, FGGY_NHO1_plant, Arabidopsis NHO1 and related proteins;
belongs to the FGGY family of carbohydrate kinases.
This subgroup includes Arabidopsis NHO1 (also known as
NONHOST1, or noh-host resistant 1) and other putative
plant glycerol kinases, which share strong homology with
glycerol kinases from bacteria, fungi, and animals.
Nonhost resistance of plants refers to the phenomenon
observed when all members of a plant species are
typically resistant to a specific parasite. NHO1 is
required for nonspecific resistance to nonhost
Pseudomonas bacteria, it is also required for resistance
to the fungal pathogen Botrytis cinerea. This subgroup
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 503
Score = 95.4 bits (237), Expect = 4e-24
Identities = 47/92 (51%), Positives = 58/92 (63%), Gaps = 1/92 (1%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
TS II + V SH ++ + I PQ GW E DPMEIL+ V+ M+ A+ K A GL
Sbjct: 10 TSTRFIIYDTAAKVVASHQVEFTQIYPQAGWVEHDPMEILETVKKCMEGALAKAKAKGLD 69
Query: 84 RDD-IVTLGITNQRETTVVWDLNTGEPLYNAI 114
D + +GITNQRETTVVW +TG PLYNAI
Sbjct: 70 VLDGLKAIGITNQRETTVVWSRSTGLPLYNAI 101
>gnl|CDD|198378 cd10427, FGGY_GK_1, Uncharacterized subgroup; belongs to the
glycerol kinases subfamily of the FGGY family of
carbohydrate kinases. This subgroup contains
uncharacterized bacterial proteins belonging to the
glycerol kinase subfamily of the FGGY family of
carbohydrate kinases. The glycerol kinase subfamily
includes glycerol kinases (GK; EC 2.7.1.30), and
glycerol kinase-like proteins from all three kingdoms of
living organisms. Glycerol is an important intermediate
of energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Under different conditions, GKs from
different species may exist in different oligomeric
states. The monomer of GKs is composed of two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain.
Length = 487
Score = 87.4 bits (217), Expect = 3e-21
Identities = 33/67 (49%), Positives = 41/67 (61%), Gaps = 3/67 (4%)
Query: 48 ISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNTG 107
I P+ GW E DP EI + + +E+ G+ +I LGITNQRETTV WD TG
Sbjct: 34 IYPENGWVEHDPEEIYENTLQAVKDLLEE---FGIDPAEIEGLGITNQRETTVAWDKRTG 90
Query: 108 EPLYNAI 114
+PLYNAI
Sbjct: 91 KPLYNAI 97
>gnl|CDD|198362 cd07789, FGGY_CsGK_like, Cellulomonas sp. glycerol kinase-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a small group of
bacterial glycerol kinases (GK) with similarity to
Cellulomonas sp. glycerol kinase (CsGK). CsGK might
exist as a dimer. Its monomer is composed of two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. The regulation
of the catalytic activity of this group has not yet been
examined. Members in this subgroup belong to the FGGY
family of carbohydrate kinases.
Length = 495
Score = 86.7 bits (215), Expect = 5e-21
Identities = 39/91 (42%), Positives = 50/91 (54%), Gaps = 3/91 (3%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
TS I+ V + I P+ GW E DP EI + + + A L+ GL+
Sbjct: 10 TSTRCIVFDHHGRIVSVAQKEHRQIFPRPGWVEHDPEEIWENTRRVISGA---LAKAGLT 66
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+DI +GITNQRETTVVWD TG P+YNAI
Sbjct: 67 PEDIAAVGITNQRETTVVWDRATGRPVYNAI 97
>gnl|CDD|215880 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal
domain. This domain adopts a ribonuclease H-like fold
and is structurally related to the C-terminal domain.
Length = 245
Score = 80.8 bits (200), Expect = 1e-19
Identities = 35/91 (38%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 25 SRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEK-LSAHGLS 83
++ ++ + + V S S + ISP+ GWAEQDP EI QA+ +AI K L G+S
Sbjct: 12 TKAIVFNK-QGKVVASASAPYALISPKPGWAEQDPEEIWQALA----QAIRKILQQSGIS 66
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
I +GI+ Q V+ D N +PLY AI
Sbjct: 67 PKQIKGIGISGQGHGLVLLDKN-DKPLYPAI 96
>gnl|CDD|212658 cd00366, FGGY, FGGY family of carbohydrate kinases. This family is
predominantly composed of glycerol kinase (GK) and
similar carbohydrate kinases including rhamnulokinase
(RhuK), xylulokinase (XK), gluconokinase (GntK),
ribulokinase (RBK), and fuculokinase (FK). These enzymes
catalyze the transfer of a phosphate group, usually from
ATP, to their carbohydrate substrates. The monomer of
FGGY proteins contains two large domains, which are
separated by a deep cleft that forms the active site.
One domain is primarily involved in sugar substrate
binding, and the other is mainly responsible for ATP
binding. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain.
Substrate-induced conformational changes and a divalent
cation may be required for the catalytic activity.
Length = 435
Score = 66.2 bits (162), Expect = 8e-14
Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 40 SHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETT 99
S + P+ GW EQDP EI QA+ + A + S I +G+++Q E
Sbjct: 26 EASREYEVSYPKPGWVEQDPEEIWQALCEVLREAAAQASGG-----QIAAIGVSSQGEGV 80
Query: 100 VVWDLNTGEPLYNAI 114
++ D N G PL AI
Sbjct: 81 ILVDAN-GRPLTPAI 94
>gnl|CDD|198363 cd07791, FGGY_GK2_bacteria, bacterial glycerol kinase 2-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
putative bacterial glycerol kinases (GK), which may be
coded by the GK-like gene, GK2. Sequence comparison
shows members in this CD are homologs of Escherichia
coli GK. They retain all functionally important
residues, and may catalyze the Mg-ATP dependent
phosphorylation of glycerol to yield glycerol
3-phosphate (G3P). GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 484
Score = 65.5 bits (160), Expect = 1e-13
Identities = 30/73 (41%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 38 VVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRE 97
V S S + PQ GW EQD I AVQ +AI A G+ ++ + I+NQRE
Sbjct: 24 VASGSAPVGIQYPQPGWVEQDAEAIWAAVQ----QAIADCLA-GVLAAEVAAIAISNQRE 78
Query: 98 TTVVWDLNTGEPL 110
+ V+WD TG PL
Sbjct: 79 SVVIWDRQTGAPL 91
>gnl|CDD|212665 cd07793, FGGY_GK5_metazoa, metazoan glycerol kinase 5-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan putative glycerol kinases (GK), which may be
coded by the GK-like gene, GK5. Sequence comparison
shows members of this group are homologs of bacterial
GKs, and they retain all functionally important
residues. However, GK-like proteins in this family do
not have detectable GK activity. The reason remains
unclear. It has been suggested tha the conserved
catalytic residues might facilitate them performing a
distinct function. GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 504
Score = 61.6 bits (150), Expect = 4e-12
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 35 QEEVVSHSMD-ISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGIT 93
Q EVV S D I + P+ G+ E DP ++ + + A++ L+ I LGI+
Sbjct: 20 QAEVVGSSYDKIELLYPEPGYVEIDPDKLWTQIVGVIKEAVKD---ANLTAKQIAGLGIS 76
Query: 94 NQRETTVVWDLNTGEPLYNAI 114
QR + + W+ +TG+P +N I
Sbjct: 77 TQRGSFLTWNKSTGKPYHNFI 97
>gnl|CDD|223996 COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate
transport and metabolism].
Length = 502
Score = 60.5 bits (147), Expect = 8e-12
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 26 RVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRD 85
+ ++ E V + + +PQ GWAEQDP E+ QA+ + + +E+ + D
Sbjct: 17 KAVLFDEDGGEVVATARFENPVSTPQPGWAEQDPDELWQAILEALRQLLEE---SKIDPD 73
Query: 86 DIVTLGITNQRETTVVWDLNTGEPLYNAI 114
I +GI+ Q V+ D N GEPL AI
Sbjct: 74 AIAAIGISGQGHGLVLLDAN-GEPLRPAI 101
>gnl|CDD|198366 cd07794, FGGY_GK_like_proteobact, Proteobacterial glycerol
kinase-like proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
small group of proteobacterial glycerol kinase (GK)-like
proteins, including the glycerol kinase from Pseudomonas
aeruginosa. Most bacteria, such as Escherichia coli,
take up glycerol passively by facilitated diffusion. In
contrast, P. aeruginosa may also utilize a binding
protein-dependent active transport system to mediate
glycerol transportation. The glycerol kinase
subsequently phosphorylates the intracellular glycerol
to glycerol 3-phosphate (G3P). GKs belong to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 470
Score = 57.9 bits (140), Expect = 6e-11
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 12/91 (13%)
Query: 24 TSRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLS 83
++RVL+ + ++ ++ P GW E DP+E+L ++ L A G
Sbjct: 12 STRVLVAGEDGKAFIL-LALRHKQHYPNPGWVEHDPLELLANLRAC-------LEAAG-- 61
Query: 84 RDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+ +G+ NQ E+ + WD +GEPL I
Sbjct: 62 --VVDAIGLANQGESCLAWDARSGEPLSPVI 90
>gnl|CDD|212662 cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins. This
subfamily consists of uncharacterized hypothetical
bacterial proteins with similarity to Escherichia coli
sugar kinase ygcE , whose functional roles are not yet
clear. Escherichia coli ygcE is recognized by this
model, but is not present in the alignment as it
contains a deletion relative to other members of the
group. These proteins belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 488
Score = 56.9 bits (138), Expect = 2e-10
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 49 SPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNTGE 108
SP+ GWAEQDP QA+ E+ + I + +T QRET V+ D + G+
Sbjct: 36 SPKPGWAEQDPDYYWQALCEACRELWEQ---IPVDPGRIAGVALTTQRETFVLLDKD-GK 91
Query: 109 PLYNAI 114
PL AI
Sbjct: 92 PLRPAI 97
>gnl|CDD|198374 cd07808, FGGY_D-XK_EcXK-like, Escherichia coli xylulokinase-like
D-xylulose kinases; a subgroup of the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial D-xylulose kinases (XK, also known
as xylulokinase; EC 2.7.1.17), which catalyze the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. D-xylulose has been used as a source of carbon
and energy by a variety of microorganisms. Some
uncharacterized sequences are also included in this
subgroup. The prototypical member of this CD is
Escherichia coli xylulokinase (EcXK), which exists as a
dimer. Each monomer consists of two large domains
separated by an open cleft that forms an active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The presence of Mg2+ or Mn2+
is required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 482
Score = 54.8 bits (133), Expect = 7e-10
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 9/94 (9%)
Query: 24 TS--RVLIISALTQEEVV-SHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAH 80
TS + L++ EVV S S + P+ GW+EQDP + +A + + + K
Sbjct: 9 TSGVKALLVDE--DGEVVASASAEYPLSQPKPGWSEQDPEDWWEATKAAIRELLAK---S 63
Query: 81 GLSRDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
G++ ++ +G++ Q V+ D G+ L AI
Sbjct: 64 GIAGGEVRGIGLSGQMHGLVLLD-KDGKVLRPAI 96
>gnl|CDD|233354 TIGR01312, XylB, D-xylulose kinase. This model describes
D-xylulose kinases, a subfamily of the FGGY family of
carbohydrate kinases. The member from Klebsiella
pneumoniae, designated DalK (see PMID:9324246), was
annotated erroneously in GenBank as D-arabinitol kinase
but is authentic D-xylulose kinase. D-xylulose kinase
(XylB) generally is found with xylose isomerase (XylA)
and acts in xylose utilization [Energy metabolism,
Sugars].
Length = 481
Score = 52.7 bits (127), Expect = 5e-09
Identities = 30/90 (33%), Positives = 43/90 (47%), Gaps = 7/90 (7%)
Query: 26 RVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSA-HGLSR 84
+ L++ E + S S + ISP GW+EQDP + A + AI++L
Sbjct: 11 KALLVDE-QGEVIASGSAPHTVISPHPGWSEQDPEDWWDAT----EEAIKELLEQASEMG 65
Query: 85 DDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
DI +GI+ Q V+ D N GE L AI
Sbjct: 66 QDIKGIGISGQMHGLVLLDAN-GEVLRPAI 94
>gnl|CDD|198376 cd07810, FGGY_D-XK_2, D-xylulose kinases, subgroup 2; members of
the FGGY family of carbohydrate kinases. This subgroup
is predominantly composed of bacterial D-xylulose
kinases (XK, also known as xylulokinase; EC 2.7.1.17).
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. EcXK exists as a dimer. Each monomer consists
of two large domains separated by an open cleft that
forms an active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 490
Score = 47.4 bits (113), Expect = 3e-07
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 26 RVLIISALTQEEVVSHS-----MDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAH 80
+ ++ A T + + S S M+I +SPQ GWAEQDP + I +
Sbjct: 13 KAALVDAETGKSLASVSYPEQEMEI--LSPQPGWAEQDPEIWWDYTCAATKQLINQGKED 70
Query: 81 GLSRDDIVTLGITNQRETTVVWDLNTGEPLYNAI 114
+I +GI+ Q V+ D G L AI
Sbjct: 71 L---SNIQAIGISYQMHGLVLVDKQ-GNVLRPAI 100
>gnl|CDD|212666 cd07802, FGGY_L-XK, L-xylulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial L-xylulose kinases (L-XK, also
known as L-xylulokinase; EC 2.7.1.53), which catalyze
the ATP-dependent phosphorylation of L-xylulose to
produce L-xylulose 5-phosphate and ADP. The presence of
Mg2+ might be required for catalytic activity. Some
uncharacterized sequences are also included in this
subfamily. L-XKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 447
Score = 47.2 bits (113), Expect = 3e-07
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 36 EEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQ 95
E+ S T++PQ G+ EQD E+ +AV + +EK G+ +DI +G+T Q
Sbjct: 22 REIAVASRRNPTLTPQPGYVEQDMDELWEAVAAVIRELLEKA---GVDAEDIAGIGVTGQ 78
Query: 96 RETTVVWDLNTGEPLYNAI 114
+ + D G+P+ I
Sbjct: 79 GDGLWLVD-KEGKPVGPGI 96
>gnl|CDD|198373 cd07805, FGGY_XK_like_2, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
proteins with similarity to bacterial D-Xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 514
Score = 47.2 bits (113), Expect = 4e-07
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 50 PQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNTGEP 109
G AEQDP + AV R +E G++ + + + Q + V D G P
Sbjct: 36 LPGGGAEQDPEDWWDAVVRATRRLLED---SGVNPRRVAGISFSGQMQGVVPVD-EDGRP 91
Query: 110 LYNAI 114
L AI
Sbjct: 92 LRPAI 96
>gnl|CDD|198372 cd07804, FGGY_XK_like_1, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
bacterial and archaeal xylulose kinases-like proteins
with similarity to bacterial D-xylulose kinases (XK,
also known as xylulokinase; EC 2.7.1.17), which catalyze
the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 492
Score = 46.4 bits (111), Expect = 5e-07
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 38 VVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRE 97
+ S + +PQ GWAEQDP AV + + K +I +G++ Q
Sbjct: 24 LAQASREYELSTPQPGWAEQDPEVWWDAVCEIIRELVAKAGVDP---SEIKAIGVSGQGP 80
Query: 98 TTVVWDLNTGEPLYNAIEQG 117
T V D + G PL AI
Sbjct: 81 TVVPVDKD-GRPLRPAIIYM 99
>gnl|CDD|198371 cd07803, FGGY_D-XK, D-xylulose kinases; a subgroup of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial D-xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. Some uncharacterized
sequences are also included in this subfamily. The
prototypical member of this subfamily is Escherichia
coli xylulokinase (EcXK), which exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. XKs do not have any known allosteric
regulators, and they may have weak but significant
activity in the absence of substrate. The presence of
Mg2+ or Mn2+ is required for catalytic activity. Members
of this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 482
Score = 46.6 bits (111), Expect = 5e-07
Identities = 30/82 (36%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 33 LTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGI 92
L E V S + +T SP GW+EQDP + AVQ ++ L G S +DI +G+
Sbjct: 19 LDGELVAFASREYTTSSPHPGWSEQDPADWWDAVQRALEAL---LDQAGDSAEDIAAIGV 75
Query: 93 TNQRETTVVWDLNTGEPLYNAI 114
T Q V+ D G L AI
Sbjct: 76 TGQMHGAVLLD-QQGRVLRPAI 96
>gnl|CDD|212659 cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of a group of gluconate kinases (GntK, also
known as gluconokinase; EC 2.7.1.12) encoded by the gntK
gene, which catalyzes the ATP-dependent phosphorylation
of D-gluconate and produce 6-phospho-D-gluconate and
ADP. The presence of Mg2+ might be required for
catalytic activity. The prototypical member of this
subfamily is GntK from Lactobacillus acidophilus. Unlike
Escherichia coli GntK, which belongs to the superfamily
of P-loop containing nucleoside triphosphate hydrolases,
members in this subfamily are homologous to glycerol
kinase, xylulose kinase, and rhamnulokinase from
Escherichia coli. They have been classified as members
of the FGGY family of carbohydrate kinases, which
contain two large domains separated by a deep cleft that
forms the active site. This model spans both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Some uncharacterized homologous sequences are also
included in this subfamily. The Lactobacillus gnt operon
contains a single gntK gene. The gnt operons of some
bacteria, such as Corynebacterium glutamicum, have two
gntK genes. For example, the C. glutamicum gnt operon
has both a gluconate kinase gntV gene (also known as
gntK) and a second hypothetical gntK gene (also known as
gntK2). Both gluconate kinases encoded by these genes
belong to this family, however the protein encoded by C.
glutamicum gntV is not included in this model as it is
truncated in the C-terminal domain.
Length = 440
Score = 44.1 bits (105), Expect = 4e-06
Identities = 22/79 (27%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 36 EEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQ 95
V S +P +G AEQDP EI AV +D + K I + ++
Sbjct: 22 RIVAGVSKRYPLETPPDGAAEQDPDEIFDAVLEILDEVVAKALG-----GRIAAVSFSSA 76
Query: 96 RETTVVWDLNTGEPLYNAI 114
+ + D + GEPL I
Sbjct: 77 MHSLIALDED-GEPLTPVI 94
>gnl|CDD|198346 cd07768, FGGY_RBK_like, Ribulokinase-like carbohydrate kinases; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is composed of ribulokinases (RBKs) and
similar proteins from bacteria and eukaryota. RBKs
catalyze the MgATP-dependent phosphorylation of a
variety of sugar substrates including L- and/or
D-ribulose. Members of this subfamily contain two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. Members of this
subfamily belong to the FGGY family of carbohydrate
kinases.
Length = 465
Score = 40.6 bits (95), Expect = 7e-05
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 33 LTQEEVVSHSMDISTISPQE-GWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLG 91
L E+ S S P GWAEQDP + AV+T + A+ +A G+ D + LG
Sbjct: 20 LNGRELASASRPYPVPVPYGAGWAEQDPEDWWPAVRTAVRAAV---AAAGVDPDQVAALG 76
Query: 92 ITNQRETTVVWDLNTGEPLYNAI 114
+ T V D G+PL A+
Sbjct: 77 VDATSCTVVPLDAE-GQPLTPAL 98
>gnl|CDD|198360 cd07783, FGGY_CarbK-RPE_like, Carbohydrate kinase and
ribulose-phosphate 3-epimerase fusion proteins-like;
belongs to the FGGY family of carbohydrate kinases.
This subgroup is composed of uncharacterized proteins
with similarity to carbohydrate kinases. Some members
are carbohydrate kinase and ribulose-phosphate
3-epimerase fusion proteins. Carbohydrate kinases
catalyze the ATP-dependent phosphorylation of their
carbohydrate substrate to produce phosphorylated sugar
and ADP. The presence of Mg2+ is required for catalytic
activity. This subgroup shows high homology to
characterized ribulokinases and belongs to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 484
Score = 38.1 bits (89), Expect = 5e-04
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 47 TISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNT 106
T P+ GWAEQ+P + +A+ + A L+ G++ D+ L T V D
Sbjct: 34 TTHPRPGWAEQNPEDWWEALGAAVREA---LAEAGIAAPDVAALCCDTTCCTVVALDAA- 89
Query: 107 GEPLYNAI 114
G PL AI
Sbjct: 90 GTPLRPAI 97
>gnl|CDD|198358 cd07781, FGGY_RBK, Ribulokinases; belongs to the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial ribulokinases (RBK) which
catalyze the MgATP-dependent phosphorylation of L(or
D)-ribulose to produce L(or D)-ribulose 5-phosphate and
ADP. RBK also phosphorylates a variety of other sugar
substrates including ribitol and arabitol. The reason
why L-RBK can phosphorylate so many different
substrates is not yet clear. The presence of Mg2+ is
required for catalytic activity. This group belongs to
the FGGY family of carbohydrate kinases, the monomers
of which contain two large domains, which are separated
by a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 498
Score = 38.0 bits (89), Expect = 6e-04
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 26 RVLIISALTQEEVVSH-------SMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLS 78
R L++ T E+ S M A Q P + ++ ++T + +++
Sbjct: 14 RALLVDTETGAELASAVVEYPHGVMGEYLPDLPPNQALQHPADYIEGLETAIPEVLKEA- 72
Query: 79 AHGLSRDDIVTLGI 92
G+ DD+V +G+
Sbjct: 73 --GVDPDDVVGIGV 84
>gnl|CDD|184987 PRK15027, PRK15027, xylulokinase; Provisional.
Length = 484
Score = 35.7 bits (82), Expect = 0.004
Identities = 28/81 (34%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 24 TSRVLIISALTQEEVV-SHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGL 82
TS V +I Q EVV S + ++ P W+EQDP + QA DRA++ L
Sbjct: 9 TSGVKVILLNEQGEVVASQTEKLTVSRPHPLWSEQDPEQWWQAT----DRAMKALGDQH- 63
Query: 83 SRDDIVTLGITNQRETTVVWD 103
S D+ LGI Q + D
Sbjct: 64 SLQDVKALGIAGQMHGATLLD 84
>gnl|CDD|212661 cd07777, FGGY_SHK_like, sedoheptulokinase-like proteins; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is predominantly composed of
uncharacterized bacterial and eukaryotic proteins with
similarity to human sedoheptulokinase (SHK, also known
as D-altro-heptulose or heptulokinase, EC 2.7.1.14)
encoded by the carbohydrate kinase-like (CARKL/SHPK)
gene. SHK catalyzes the ATP-dependent phosphorylation of
sedoheptulose to produce sedoheptulose 7-phosphate and
ADP. The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subfamily belong to
the FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 448
Score = 33.1 bits (76), Expect = 0.024
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 40 SHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETT 99
S ++ + P EQD +IL T+D +++L L + +G+T Q
Sbjct: 32 PTSANVPSDGPLGS--EQDVDKILS----TLDSCLKRLPKELLK--KVKAIGVTGQMHGI 83
Query: 100 VVWDLNTGEPLYNAIE 115
V+W + + I
Sbjct: 84 VLWKQDQSCEDGDLIS 99
>gnl|CDD|198375 cd07809, FGGY_D-XK_1, D-xylulose kinases, subgroup 1; members of
the FGGY family of carbohydrate kinases. This subgroup
is composed of D-xylulose kinases (XK, also known as
xylulokinase; EC 2.7.1.17) from bacteria and eukaryota.
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. Some uncharacterized sequences are also
included in this subfamily. EcXK exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of Mg2+ or Mn2+ might be
required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 487
Score = 32.3 bits (74), Expect = 0.052
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 4/89 (4%)
Query: 25 SRVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSR 84
++V+++ A T E + S IS G EQ P + A+ +A+ G+
Sbjct: 12 TKVIVLDAETGEVLAEGSAPHELISGSNGRREQQPQWWIDALVEAFRQALADA---GIDP 68
Query: 85 DDIVTLGITNQRETTVVWDLNTGEPLYNA 113
++ +G++ Q+ V D GE L A
Sbjct: 69 KEVRAIGVSGQQHGLVPLD-AQGEVLRPA 96
>gnl|CDD|223995 COG1069, AraB, Ribulose kinase [Energy production and
conversion].
Length = 544
Score = 30.8 bits (70), Expect = 0.16
Identities = 13/67 (19%), Positives = 23/67 (34%), Gaps = 3/67 (4%)
Query: 26 RVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRD 85
R + T + P AEQ + +AV + + K G+
Sbjct: 16 RAGVFDCQTGTLLARAVRPYPMWQPGSNLAEQHSRDYWEAVCAAVRDVVAKA---GVDPA 72
Query: 86 DIVTLGI 92
D+V +G+
Sbjct: 73 DVVGIGV 79
>gnl|CDD|198377 cd07811, FGGY_D-XK_3, D-xylulose kinases, subgroup 3; members of
the FGGY family of carbohydrate kinases. This subgroup
is composed of proteobacterial D-xylulose kinases (XK,
also known as xylulokinase; EC 2.7.1.17). They share
high sequence similarity with Escherichia coli
xylulokinase (EcXK), which catalyzes the rate-limiting
step in the ATP-dependent phosphorylation of D-xylulose
to produce D-xylulose 5-phosphate (X5P) and ADP. Some
uncharacterized sequences are also included in this
subfamily. EcXK exists as a dimer. Each monomer consists
of two large domains separated by an open cleft that
forms an active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 493
Score = 31.0 bits (70), Expect = 0.16
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 48 ISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWD 103
PQ GW+EQ P++ Q + + ++ + + I +G Q TV+ D
Sbjct: 34 TVPQFGWSEQRPLDWWQGACDCIREVLARVPG---AAERIAVIGACGQMHGTVLLD 86
>gnl|CDD|130381 TIGR01314, gntK_FGGY, gluconate kinase, FGGY type. Gluconate is
derived from glucose in two steps. This model describes
one form of gluconate kinase, belonging to the FGGY
family of carbohydrate kinases. Gluconate kinase
phosphoryates gluconate for entry into the
Entner-Douderoff pathway [Energy metabolism, Sugars].
Length = 505
Score = 30.6 bits (69), Expect = 0.18
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 38 VVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRE 97
V S+ +P G AE++P EI +AV T+ L D+I+ + + Q
Sbjct: 24 VAKSSIGYPLYTPASGMAEENPEEIFEAVLVTIREVSINLE----DEDEILFVSFSTQMH 79
Query: 98 TTVVWDLNTGEPLYNAI 114
+ + +D N +PL I
Sbjct: 80 SLIAFDENW-QPLTRLI 95
>gnl|CDD|236363 PRK09029, PRK09029, O-succinylbenzoic acid--CoA ligase;
Provisional.
Length = 458
Score = 29.1 bits (66), Expect = 0.58
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 43 MDISTISPQEGWAEQDPMEIL----------QAVQTTMDRAIEKLSAHGLSRDDIVTLGI 92
M I + P WA+ P I Q + +D+ + G+ V L
Sbjct: 1 MMIFSDWPWRHWAQVRPQAIALRLNDEVLTWQQLCARIDQLAAGFAQQGVVEGSGVALRG 60
Query: 93 TNQRETTVVW 102
N ET + +
Sbjct: 61 KNSPETLLAY 70
>gnl|CDD|198353 cd07775, FGGY_AI-2K, Autoinducer-2 kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial autoinducer-2 (AI-2) kinases and
similar proteins. AI-2 is a small chemical
quorum-sensing signal involved in interspecies
communication in bacteria. Cytoplasmic autoinducer-2
kinase, encoded by the lsrK gene from Salmonella
enterica serovar Typhimurium lsr (luxS regulated)
operon, is the prototypical member of this subfamily.
AI-2 kinase catalyzes the phosphorylation of
intracellular AI-2 to phospho-AI-2, which leads to the
inactivation of lsrR, the repressor of the lsr operon.
Members of this family are homologs of glycerol
kinase-like proteins and belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 452
Score = 28.6 bits (64), Expect = 0.92
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 16/76 (21%)
Query: 36 EEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQ 95
E SMD PQ W + + L+ G++ DI + T+
Sbjct: 36 EPRYPGSMDFD---PQVNW------------KLVCRCIRQALARSGIAPIDIAAVSATSM 80
Query: 96 RETTVVWDLNTGEPLY 111
RE V++D G ++
Sbjct: 81 REGIVLYD-QNGNEIW 95
>gnl|CDD|185143 PRK15221, PRK15221, Saf-pilin pilus formation protein SafA;
Provisional.
Length = 165
Score = 28.2 bits (63), Expect = 0.94
Identities = 26/88 (29%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 42 SMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQR--ETT 99
S+DI+ SPQ+ DP+ L+A + D AI KL+ S + G N
Sbjct: 34 SVDINFASPQQLTVSLDPVSGLKAGKNKSDTAIAKLTVSSTSAKEFGVRGDANAVVDNAG 93
Query: 100 VVWDLNTGEPLYNAIEQGLRIVDCGSGR 127
VW + TG+ N I+ G C +
Sbjct: 94 DVWTV-TGKNTGNGIKVGFSGEACTRSK 120
>gnl|CDD|227286 COG4950, COG4950, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 193
Score = 27.5 bits (61), Expect = 1.6
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 72 RAIEKLSAHGLSRDDIVTL 90
A+E+L GL+ DIVTL
Sbjct: 138 EALERLYDVGLTARDIVTL 156
>gnl|CDD|237859 PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional.
Length = 1000
Score = 27.7 bits (62), Expect = 1.8
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 1/57 (1%)
Query: 53 GWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNTGEP 109
G E + +Q E L+ L + + LG T +R +V D+ EP
Sbjct: 319 GSEELPATFVPIGIQQLESALRELLADTRLGYEKLEVLG-TPRRLALLVEDVAPREP 374
>gnl|CDD|215358 PLN02666, PLN02666, 5-oxoprolinase.
Length = 1275
Score = 27.8 bits (62), Expect = 2.1
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 51 QEGWAEQDPMEILQAVQTTMD----RAIEKLSAHGLSRDDIVTLGITNQR 96
QE +A E L D + +KL G D+I T N R
Sbjct: 538 QEPYAAVYGPESLAEASRREDALAEKVRQKLQEQGFREDNITTETYLNLR 587
>gnl|CDD|225414 COG2859, COG2859, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 237
Score = 27.5 bits (61), Expect = 2.1
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 26 RVLIISALTQEEVVSHSMDISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRD 85
R +I+ L++ EV + D + Q ++ ++ L A G+
Sbjct: 38 RYVIVKGLSEREVTA---DTIIWGISFSSQGNTLQALYQDLEQQTEKIQAFLQAQGIPEA 94
Query: 86 DI 87
+I
Sbjct: 95 EI 96
>gnl|CDD|183117 PRK11397, dacD, D-alanyl-D-alanine carboxypeptidase; Provisional.
Length = 388
Score = 27.1 bits (60), Expect = 2.9
Identities = 11/22 (50%), Positives = 17/22 (77%), Gaps = 3/22 (13%)
Query: 70 MDRAIEKLSAHGLSRDDIVTLG 91
+DRAI+ +H ++ DDIVT+G
Sbjct: 73 VDRAID---SHRITPDDIVTVG 91
>gnl|CDD|216816 pfam01968, Hydantoinase_A, Hydantoinase/oxoprolinase. This family
includes the enzymes hydantoinase and oxoprolinase
EC:3.5.2.9. Both reactions involve the hydrolysis of
5-membered rings via hydrolysis of their internal imide
bonds.
Length = 285
Score = 26.9 bits (60), Expect = 3.7
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 56 EQDPMEILQAVQTTMDRAIEKLS-AHGLSRDDIVTLGI 92
E+ IL+ TM A+ LS GL D +
Sbjct: 205 EEVAEGILRIANETMADAVRLLSVERGLDPRDFPLVVF 242
>gnl|CDD|218067 pfam04402, SIMPL, Protein of unknown function (DUF541). Members
of this family have so far been found in bacteria and
mouse SwissProt or TrEMBL entries. However possible
family members have also been identified in translated
rat (Genbank:AW144450) and human (Genbank:AI478629)
ESTs. A mouse family member has been named SIMPL
(signalling molecule that associates with mouse
pelle-like kinase). SIMPL appears to facilitate and/or
regulate complex formation between IRAK/mPLK (IL-1
receptor-associated kinase) and IKK (inhibitor of
kappa-B kinase) containing complexes, and thus regulate
NF-kappa-B activity. Separate experiments demonstrate
that a mouse family member (named LaXp180) binds the
Listeria monocytogenes surface protein ActA, which is a
virulence factor that induces actin polymerisation. It
may also bind stathmin, a protein involved in signal
transduction and in the regulation of microtubule
dynamics. In bacteria its function is unknown, but it
is thought to be located in the periplasm or outer
membrane.
Length = 210
Score = 26.6 bits (59), Expect = 4.0
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 61 EILQAVQTTMDRAIEKLSAHGLSRDDIVTLGIT 93
E L+ V M+ + L G+ DI T ++
Sbjct: 31 EALEEVNERMNAVLAALKKAGIPDKDIQTSSLS 63
>gnl|CDD|234565 PRK00002, aroB, 3-dehydroquinate synthase; Reviewed.
Length = 358
Score = 26.2 bits (59), Expect = 6.2
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 69 TMDRAIEKLSAHGLSRDD-IVTLG 91
T+++ + L GL R D ++ LG
Sbjct: 77 TLEKIYDALLEAGLDRSDTLIALG 100
>gnl|CDD|239382 cd03108, AdSS, Adenylosuccinate synthetase (AdSS) catalyzes the
first step in the de novo biosynthesis of AMP. IMP and
L-aspartate are conjugated in a two-step reaction
accompanied by the hydrolysis of GTP to GDP in the
presence of Mg2+. In the first step, the r-phosphate
group of GTP is transferred to the 6-oxygen atom of IMP.
An aspartate then displaces this 6-phosphate group to
form the product adenylosuccinate. Because of its
critical role in purine biosynthesis, AdSS is a target
of antibiotics, herbicides and antitumor drugs.
Length = 363
Score = 25.9 bits (58), Expect = 7.1
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 103 DLNTGEPLYNAIEQGLRI 120
DL+T + AI+ G ++
Sbjct: 148 DLDTSYLINEAIQAGKKV 165
>gnl|CDD|212663 cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis
carbohydrate kinase-like subgroup; belongs to the FGGY
family of carbohydrate kinases. This subgroup is
composed of the uncharacterized Yersinia
Pseudotuberculosis carbohydrate kinase that has been
named glyerol/xylulose kinase and similar
uncharacterized proteins from bacteria and eukaryota.
Carbohydrate kinases catalyze the ATP-dependent
phosphorylation of their carbohydrate substrate to
produce phosphorylated sugar and ADP. The presence of
Mg2+ is required for catalytic activity. This subgroup
shows high homology to characterized ribulokinases and
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 536
Score = 26.0 bits (58), Expect = 7.5
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 44 DISTISPQEGWAEQDPMEILQAVQTTMDRAIEKLSAHGLSRDDIVTLG 91
I PQ + EQ +I QAV + AI + G+ + + +G
Sbjct: 31 PIQIWHPQPDFVEQSSDDIWQAVCQAVKAAI---AGAGVDPEQVKGIG 75
>gnl|CDD|238969 cd02011, TPP_PK, Thiamine pyrophosphate (TPP) family,
Phosphoketolase (PK) subfamily, TPP-binding module; PK
catalyzes the conversion of D-xylulose 5-phosphate and
phosphate to acetyl phosphate,
D-glyceraldehyde-3-phosphate and H2O. This enzyme
requires divalent magnesium ions and TPP for activity.
Length = 227
Score = 25.8 bits (57), Expect = 8.3
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 58 DPMEILQAVQTTMDRAIEKLSA 79
DP + QA+ T+D AIE++ A
Sbjct: 158 DPETMHQAMAATLDWAIEEIKA 179
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 25.7 bits (57), Expect = 8.9
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 9/34 (26%)
Query: 15 RDRLSATYHTSRVLIISALTQEEVVSHSMDISTI 48
RDRL A Y + VL VVSH I T+
Sbjct: 303 RDRLIAEYPGATVL---------VVSHVTPIKTL 327
>gnl|CDD|212500 cd11641, Precorrin-4_C11-MT, Precorrin-4 C11-methyltransferase
(CbiF/CobM). Precorrin-4 C11-methyltransferase
participates in the pathway toward the biosynthesis of
cobalamin (vitamin B12). There are two distinct
cobalamin biosynthetic pathways in bacteria. The aerobic
pathway requires oxygen, and cobalt is inserted late in
the pathway; the anaerobic pathway does not require
oxygen, and cobalt insertion is the first committed step
towards cobalamin synthesis. In the aerobic pathway,
CobM catalyzes the methylation of precorrin-4 at C-11 to
yield precorrin-5. In the anaerobic pathway, CibF
catalyzes the methylation of cobalt-precorrin-4 to
cobalt-precorrin-5. Both CibF and CobM, which are
homologous, are included in this model. There are about
30 enzymes involved in vitamin B12 synthetic pathway.
The enzymes involved in the aerobic pathway are prefixed
Cob and those of the anaerobic pathway Cbi. Most of the
enzymes are shared in both pathways and several of these
enzymes are pathway-specific.
Length = 228
Score = 25.5 bits (57), Expect = 9.2
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 75 EKLSAHGLSRDDIVTLGITNQRETTVVWDLNTGEP-LYNAI-EQ 116
E + ++ ++I+ L RE V L+TG+P LY AI EQ
Sbjct: 48 EIYDSASMTLEEIIALMKEAAREGKDVVRLHTGDPSLYGAIREQ 91
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 25.8 bits (56), Expect = 9.3
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 55 AEQDPMEILQAVQT------TMDRAIEKLSAHGLSRDDIVTLGITNQRETTVVWDLNTGE 108
A D I AVQ T++ K A LSRD +GI++ TT NTGE
Sbjct: 117 AASDGKSIGSAVQLPSMSGGTINSNYTKEGAKLLSRDANGNIGISSNPNTTPGTKTNTGE 176
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
0.316 0.130 0.371
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,346,570
Number of extensions: 535992
Number of successful extensions: 729
Number of sequences better than 10.0: 1
Number of HSP's gapped: 712
Number of HSP's successfully gapped: 65
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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: 53 (24.2 bits)