GapMind for catabolism of small carbon sources

 

Clusters of Characterized Proteins

Clustering the characterized proteins for xylF (ABC transporter for xylose, substrate binding component xylF) in D-xylose catabolism

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Definition of xylF

Fetched 4 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 3 of these sequences

Found 1 clusters of similar sequences. Another 1 sequences are not clustered. Download as table or as draft rules or view by organism

Cluster 1 330-359 amino acids (heteromeric)

The first sequence in each cluster is the seed.

b3566 xylose ABC transporter periplasmic binding protein (EC 7.5.2.13; EC 7.5.2.10) from Escherichia coli K-12 substr. MG1655
TC 3.A.1.2.4 / P37387 XylF aka XYLT aka B3566, component of Xylose porter from Escherichia coli
P37387 xylose ABC transporter periplasmic binding protein (EC 7.5.2.13) from Escherichia coli (strain K12)
GB|AAC76590.1 D-xylose ABC transporter, periplasmic D-xylose-binding protein from Escherichia coli K12
PFams: Peripla_BP_4, Peripla_BP_1
Heteromeric, 330 amino acids: PaperBLAST, CDD, Compare to cluster

TC 3.A.1.2.26 / A6LW10 D-xylose ABC transporter, periplasmic substrate-binding protein, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)
PFams: Peripla_BP_4, Peripla_BP_1
Heteromeric, 359 amino acids: PaperBLAST, CDD, Compare to cluster

TC 3.A.1.2.5 / P25548 CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter from Agrobacterium tumefaciens
PFams: Peripla_BP_1, Peripla_BP_4
Heteromeric, 354 amino acids: PaperBLAST, CDD, Compare to cluster

Singletons (1/1 heteromeric)

TC 3.A.1.2.20 / G4FGN5 LacI family transcriptional regulator, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
PFams: Peripla_BP_1, Peripla_BP_4, ABC_sub_bind
Heteromeric, 343 amino acids: PaperBLAST, CDD