Protein Info for GFF4164 in Variovorax sp. SCN45

Annotation: Thymidine phosphorylase (EC 2.4.2.4)

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 439 TIGR02643: thymidine phosphorylase" amino acids 1 to 436 (436 residues), 620 bits, see alignment E=2.3e-190 PF02885: Glycos_trans_3N" amino acids 4 to 66 (63 residues), 55.6 bits, see alignment E=5.5e-19 TIGR02644: pyrimidine-nucleoside phosphorylase" amino acids 4 to 421 (418 residues), 497.3 bits, see alignment E=3.3e-153 PF00591: Glycos_transf_3" amino acids 78 to 309 (232 residues), 153.9 bits, see alignment E=9.7e-49 PF07831: PYNP_C" amino acids 349 to 422 (74 residues), 62 bits, see alignment E=5.1e-21

Best Hits

Swiss-Prot: 55% identical to TYPH_AGRFC: Thymidine phosphorylase (deoA) from Agrobacterium fabrum (strain C58 / ATCC 33970)

KEGG orthology group: K00758, thymidine phosphorylase [EC: 2.4.2.4] (inferred from 62% identity to rce:RC1_2274)

MetaCyc: 51% identical to thymidine phosphorylase (Escherichia coli K-12 substr. MG1655)
Pyrimidine-nucleoside phosphorylase. [EC: 2.4.2.2, 2.4.2.3]; Thymidine phosphorylase. [EC: 2.4.2.2, 2.4.2.3, 2.4.2.4]

Predicted SEED Role

"Thymidine phosphorylase (EC 2.4.2.4)" in subsystem Deoxyribose and Deoxynucleoside Catabolism (EC 2.4.2.4)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.4.2.4

Use Curated BLAST to search for 2.4.2.2 or 2.4.2.3 or 2.4.2.4

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (439 amino acids)

>GFF4164 Thymidine phosphorylase (EC 2.4.2.4) (Variovorax sp. SCN45)
MLAQEIIRLKRDRATLDAAHIDAFVQGLVDASWSEAQAASMAMAIYLNGMTAAETVALTR
AMTRSGDLLDWAGANLDGPILDKHSTGGVGDKVSLALAPIVAACGGYVPMISGRGLGHTG
GTLDKLDSIPGYDSSPSTARLHRAVRDAGCAIVGQTARLAPADRRLYAVRDVTATVESVP
LITASILSKKLAAGLQGLVMDVKTGNGAFAAGRSEADTLARSLASVARGAGLPTQVWITD
MNQVLGHACGNALEVAEAIALLRDARGEPRLLEITRMLGAEMLLLGRLAASLEEALAKVD
AALSSGRALERWARMVSALGGPTDLAERPERHLPSAPVQRAVLAARGGWVSHLQTRDIGL
LLIELGGGRRQASDAVDPRVGFSGIASVGQRVEAGDVLAHVHAAHAADAEMAQQKMAEWI
HVADTPASASPVLLERLEG