Protein Info for Sama_2124 in Shewanella amazonensis SB2B

Annotation: pseudouridine synthase, Rsu (RefSeq)

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 50 100 150 200 250 295 PF01479: S4" amino acids 4 to 45 (42 residues), 40.7 bits, see alignment 1.5e-14 PF00849: PseudoU_synth_2" amino acids 67 to 198 (132 residues), 70.9 bits, see alignment E=1.5e-23 TIGR00093: pseudouridine synthase" amino acids 71 to 230 (160 residues), 180.5 bits, see alignment E=9.9e-58

Best Hits

Swiss-Prot: 65% identical to RLUB_SHIFL: Ribosomal large subunit pseudouridine synthase B (rluB) from Shigella flexneri

KEGG orthology group: K06178, ribosomal large subunit pseudouridine synthase B [EC: 5.4.99.12] (inferred from 100% identity to saz:Sama_2124)

MetaCyc: 66% identical to 23S rRNA pseudouridine2605 synthase (Escherichia coli K-12 substr. MG1655)
RXN-11836 [EC: 5.4.99.22]

Predicted SEED Role

"Ribosomal large subunit pseudouridine synthase B (EC 4.2.1.70)" in subsystem Two cell division clusters relating to chromosome partitioning (EC 4.2.1.70)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.2.1.70, 5.4.99.12

Use Curated BLAST to search for 4.2.1.70 or 5.4.99.12 or 5.4.99.22

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

See A1S7H3 at UniProt or InterPro

Protein Sequence (295 amino acids)

>Sama_2124 pseudouridine synthase, Rsu (RefSeq) (Shewanella amazonensis SB2B)
MSEKLQKVLARAGHGSRREMEAWIAAGRVSINGEIANLGDRVDADAKVRLDGRLVSIKSA
DDIICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKLRDARWVAVGRLDINTSGLLLFTSD
GELANRLMHPSNEVDREYAVRTFGEVNDFTIQKLRTGVMLEDGPAQFDYVKAAGGEGVNQ
WWHVGLREGRNREVRRLWESQEVQVSRLIRVRYGMIELPKTLPRGGWIELPLEQVNYLRQ
LAGMDPETRSMIGTDKHSVARASQVRSAKIRRAVRKSKVGAATGSKRPKPTRTRS