Clusters of Characterized Proteins

GapMind for catabolism of small carbon sources

Clusters of Characterized Proteins

Clustering the characterized proteins for xdh (D-xylose dehydrogenase) in D-xylose catabolism

Or see other characterized proteins similar to xdh

Or see all steps for D-xylose catabolism

Or cluster curated proteins matching a keyword

Definition of xdh

Curated proteins or TIGRFams with EC 1.1.1.179
Curated proteins or TIGRFams with EC 1.1.1.175
UniProt sequence A0A4R8NY47: SubName: Full=NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) {ECO:0000313|EMBL:TDY98647.1};
Comment: Watanabe et al 2019 (PMC6336799) show that C785_RS00860 = WP_034330287.1 = A0A4R8NY47 is D-xylose dehydrogenase (xdh). Another issue is that xdh from Haloferax volcanii (HVO_B0028; D4GP29) is reported to form xylono-1,4-lactone, (Sutter et al 2017, PMID:28854683), but this is not reflected in the databases, and for some (many?) xylose dehydrogenases, it is uncertain which lactone they form. So, both forms of D-xylose dehydrogenase are included in "xdh."

Fetched 15 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 13 of these sequences

Found 3 clusters of similar sequences. Another 2 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 329-391 amino acids (not heteromeric)

XDH_HYPJR / A0A024SMV2 D-xylose 1-dehydrogenase (NADP(+)); XDH; D-xylose-NADP dehydrogenase; NADP(+)-dependent D-xylose dehydrogenase; EC 1.1.1.179 from Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30) (Trichoderma reesei)
PFams: GFO_IDH_MocA
391 amino acids: PaperBLAST, CDD, Compare to cluster

DHDH_MACFA / Q9TQS6 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; Cmo2DD; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; EC 1.3.1.20; EC 1.1.1.179 from Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
DHDH_MACFU / Q7JK39 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Jmo2DD; EC 1.3.1.20; EC 1.1.1.179 from Macaca fuscata fuscata (Japanese macaque)
Q9TQS6 D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179); trans-1,2-dihydrobenzene-1,2-diol dehydrogenase (EC 1.3.1.20) from Macaca fascicularis
PFams: GFO_IDH_MocA
334 amino acids: PaperBLAST, CDD, Compare to cluster

DHDH_CANLF / Q9TV68 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; Can2DD; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; EC 1.3.1.20; EC 1.1.1.179 from Canis lupus familiaris (Dog) (Canis familiaris)
PFams: GFO_IDH_MocA
335 amino acids: PaperBLAST, CDD, Compare to cluster

DHDH_PIG / Q9TV69 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Sus2DD; EC 1.3.1.20; EC 1.1.1.179 from Sus scrofa (Pig)
PFams: GFO_IDH_MocA
335 amino acids: PaperBLAST, CDD, Compare to cluster

DHDH_RABIT / Q9TV70 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Ory2DD; EC 1.3.1.20; EC 1.1.1.179 from Oryctolagus cuniculus (Rabbit)
PFams: GFO_IDH_MocA
329 amino acids: PaperBLAST, CDD, Compare to cluster

DHDH_HUMAN / Q9UQ10 Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Hum2DD; EC 1.3.1.20; EC 1.1.1.179 from Homo sapiens (Human)
PFams: GFO_IDH_MocA
334 amino acids: PaperBLAST, CDD, Compare to cluster

XDH_SCHPO / Q9UT60 Probable D-xylose 1-dehydrogenase (NADP(+)); XDH; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase homolog; NADP(+)-dependent D-xylose dehydrogenase; EC 1.1.1.179 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
PFams: GFO_IDH_MocA
368 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 2 325-390 amino acids (not heteromeric)

D4GP29 D-xylose dehydrogenase subunit (EC 1.1.1.179) from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
XDH1_HALVD / D4GP29 D-xylose 1-dehydrogenase (NADP(+)) 1; XDH 1; EC 1.1.1.179 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii)
PFams: GFO_IDH_MocA
390 amino acids: PaperBLAST, CDD, Compare to cluster

XDH2_HALVD / D4GP30 D-xylose 1-dehydrogenase (NADP(+)) 2; XDH 2; EC 1.1.1.179 from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (Halobacterium volcanii)
D4GP30 D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) from Haloferax volcanii
PFams: GFO_IDH_MocA
325 amino acids: PaperBLAST, CDD, Compare to cluster

Q5UY95 D-xylose dehydrogenase subunit (EC 1.1.1.179) from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
GFO6_HALMA / Q5UY95 Xylose dehydrogenase Gfo6; XDH; EC 1.1.1.179 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Q5UY95 D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) from Haloarcula marismortui
PFams: GFO_IDH_MocA
360 amino acids: PaperBLAST, CDD, Compare to cluster

Cluster 3 248-263 amino acids (not heteromeric)

CCNA_00864 D-xylose 1-dehydrogenase (EC 1.1.1.175) from Caulobacter crescentus NA1000
XDH_CAUVN / B8H1Z0 D-xylose 1-dehydrogenase; XDH; EC 1.1.1.175 from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus)
B8H1Z0 D-xylose 1-dehydrogenase (EC 1.1.1.175) from Caulobacter vibrioides
PFams: adh_short, adh_short_C2
248 amino acids: PaperBLAST, CDD, Compare to cluster

A0A4R8NY47 NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
263 amino acids: PaperBLAST, CDD, Compare to cluster

Ga0059261_1894 D-xylose 1-dehydrogenase (EC 1.1.1.175) from Sphingomonas koreensis DSMZ 15582
PFams: adh_short, Epimerase, adh_short_C2
259 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (0/2 heteromeric)

XDH_PAENI / Q8GAK6 D-xylose dehydrogenase; NADP-dependent D-xylose dehydrogenase; EC 1.1.1.179 from Paenarthrobacter nicotinovorans (Arthrobacter nicotinovorans)
PFams: GFO_IDH_MocA
388 amino acids: PaperBLAST, CDD

GLCDH_HALMT / Q977U7 Glucose 1-dehydrogenase; GDH; GlcDH; EC 1.1.1.47 from Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)
Q977U7 L-xylose 1-dehydrogenase (EC 1.1.1.113); glucose 1-dehydrogenase (NADP+) (EC 1.1.1.119); D-xylose 1-dehydrogenase (EC 1.1.1.175); glucose 1-dehydrogenase [NAD(P)+] (EC 1.1.1.47) from Haloferax mediterranei
PFams: ADH_N, Glu_dehyd_C
357 amino acids: PaperBLAST, CDD