Protein Info for GFF2971 in Pseudomonas sp. DMC3

Annotation: 23S rRNA 5-hydroxycytidine synthase

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 50 100 150 200 250 300 350 400 450 500 550 600 662 PF01136: Peptidase_U32" amino acids 79 to 304 (226 residues), 241.5 bits, see alignment E=7.3e-76 PF12392: DUF3656" amino acids 399 to 512 (114 residues), 68 bits, see alignment E=1.1e-22

Best Hits

Swiss-Prot: 70% identical to RLHA_ECOLI: 23S rRNA 5-hydroxycytidine C2501 synthase (rlhA) from Escherichia coli (strain K12)

KEGG orthology group: K08303, putative protease [EC: 3.4.-.-] (inferred from 95% identity to pfo:Pfl01_2383)

MetaCyc: 70% identical to 23S rRNA 5-hydroxycytidine C2501 synthase (Escherichia coli K-12 substr. MG1655)
RXN-21990

Predicted SEED Role

"Putative collagenase"

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 3.4.-.-

Use Curated BLAST to search for 3.4.-.-

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 (662 amino acids)

>GFF2971 23S rRNA 5-hydroxycytidine synthase (Pseudomonas sp. DMC3)
MSLPKHHLELLSPARDVAIAREAILHGADAVYIGGPSFGARHNACNEVSEIAELVEFARR
YHARIFTTINTILHDNELEPARKLIHQLYDAGVDALIVQDLGVMELDIPPIELHASTQTD
IRTLERAKFLDQAGFSQLVLARELNLKEIRAIADETDAAIEFFIHGALCVAFSGQCNISH
AQTGRSANRGDCSQACRLPYTLKDEKGGVIAYEKHLLSMKDNNQSANIRALVEAGVRSFK
IEGRYKDMGYVKNITAYYRQRLDDVLEDRPDLARASSGRTVHFFLPDPEKTFHRGSTDYF
VTDRKIDIGAFDSPTFTGLPVGTVEKVGKRDMQVVTHEPLSNGDGLNVLVKREVVGFRAN
IAEAKGEFEEDGEKRYRYRVEPNEMPEGLFKLRPSHPLNRNLDHNWQQALQKTSSERRVA
LSWFARLREEQLEVTATSEEGISASVTLSGPFGVANKPEQALEQLRDLLGQLGTTQYHAT
DIKLDAPQAFFIPNSQLKSLRREVIEALTAARVAAHPRGSRKAETTPPPVYPDSHLTFLA
NVYNQKARDFYHRHGVKLIDAAYEAHEEPGEVPVMITKHCLRFSFNLCPKQAKGVTGVRT
KVAPMQLIHGDEVLTLKFDCKPCEMHIIGKMKGHILNLPQPGSVVGHISPEDLMKTIPRA
PH