Protein Info for LRK54_RS00495 in Rhodanobacter denitrificans FW104-10B01

Annotation: ribonuclease R

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 897 TIGR02063: ribonuclease R" amino acids 60 to 759 (700 residues), 857.9 bits, see alignment E=6.3e-262 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 117 to 759 (643 residues), 715.7 bits, see alignment E=5.2e-219 PF08206: OB_RNB" amino acids 128 to 185 (58 residues), 73.4 bits, see alignment 2.3e-24 PF17876: CSD2" amino acids 206 to 279 (74 residues), 73.1 bits, see alignment E=4.1e-24 PF00773: RNB" amino acids 301 to 629 (329 residues), 360 bits, see alignment E=3.1e-111 PF00575: S1" amino acids 677 to 756 (80 residues), 45.2 bits, see alignment E=2.5e-15

Best Hits

Swiss-Prot: 50% identical to RNR_ECOLI: Ribonuclease R (rnr) from Escherichia coli (strain K12)

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 62% identity to psu:Psesu_0923)

MetaCyc: 50% identical to RNase R (Escherichia coli K-12 substr. MG1655)
3.1.13.-

Predicted SEED Role

"3'-to-5' exoribonuclease RNase R" in subsystem RNA processing and degradation, bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.1.-.-

Use Curated BLAST to search for 3.1.-.-

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Search 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 (897 amino acids)

>LRK54_RS00495 ribonuclease R (Rhodanobacter denitrificans FW104-10B01)
MTRKTPPHSGNSQDSRSAKKPAKRAPRAAAAPDKRNKAAAGAVRDPHADREAQRYARPIP
SREAILALLEERGELLTEARIAEALDIHDETDLEALRKRLAAMVRDGQLLLGRRGGYAPT
QKLDLIAGVVLANAEGYGFLRPDEGGDDLYLSPQQMRAVMHGDRVLASVVGIDRRGRRQG
AIAEVLQRRSPRLVGRVVIDDGVTLVTPDDRRLNQDVMIKPGRELGARSGQIVVAEITDP
PTLQRGPIGEIRAVLGERLQPSLVVEMAIASHDLPHDWPAEVLRDAAQVESTVTAAEREG
RTDLRKLPLVTIDGADARDFDDAVYAEPRRGGGWRLIVAIADVSHYVQVGNALDREAFER
STSTYFPGFVVPMLPETLSNGICSLNPKVERLCMVCDMQVDAEGSVVKSRFYDAVMLSHA
RLTYDKVWQAVGLREQDARHEVADVLPQLEHLHALYKAMAGQRRRRGAIDFETPEVKFRL
DQTGGVESMGATERNDAHKLIEECMIAANVQAALFLEKKKIPALFRAHEPPPAEKYEDLQ
QFLREFKLRMPPVDEVTPGDFSEILRMVHDRPERELIQSVLLRSQSMAAYQPDNRGHFGL
SLQAYAHFTSPIRRYPDLLVHRAIRHALTGRKPADYAYTPAEMAAMAVHCSQRERRAEEA
ERDVDERFKCAWMEKHIGSEFDGVVTGVTSFGLFVELDESKVSGLVHISQLMNDYYHFDA
TRKLLKGERTGAQFRLGDHVRIQVLRASLEDRKIDFRLVSPRTSAPAPTGSGKAYDYAAA
GERYSLPKKAAATTKAPGMFGRAAKAIGRAFGRKEVEVAAPAPAPRKAAVSDNPPPRAQP
AAARQHAGGQHQGRRVESSSDRRPRKEGSARRGPAPAATSPAPKKHGGRKPKPKGKP