Protein Info for DDA3937_RS01425 in Dickeya dadantii 3937

Annotation: RNase E specificity factor CsrD

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 50 100 150 200 250 300 350 400 450 500 550 600 648 transmembrane" amino acids 6 to 33 (28 residues), see Phobius details amino acids 137 to 159 (23 residues), see Phobius details PF17157: GAPES4" amino acids 33 to 130 (98 residues), 108.5 bits, see alignment E=2.9e-35 PF00990: GGDEF" amino acids 225 to 382 (158 residues), 66.7 bits, see alignment E=3.3e-22 PF00563: EAL" amino acids 406 to 630 (225 residues), 127.8 bits, see alignment E=6.9e-41

Best Hits

Swiss-Prot: 59% identical to CSRD_ECOLI: RNase E specificity factor CsrD (csrD) from Escherichia coli (strain K12)

KEGG orthology group: None (inferred from 100% identity to ddd:Dda3937_00661)

Predicted SEED Role

"RNase E specificity factor CsrD"

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

See E0SHA1 at UniProt or InterPro

Protein Sequence (648 amino acids)

>DDA3937_RS01425 RNase E specificity factor CsrD (Dickeya dadantii 3937)
MGLTVRISILMTMLTTLAVVLMLVSSIFSFVCYSQQRMEHQLRAVAASIDQALLVQPPDS
IQFWLPAVMKAAGIVELEIRDGHESLYLLRLPEMLSDGADRALLYRHTRLSLLHHTDVKV
NVTYVDPLFGTPRYLKSTLSIVLVILVIAVTVFHGVRWLRRQMAGQEQLERRARRILAGE
RDTVMHGSVHEWPATASGALDQLLLDLAEAREARSRVDTLIRSFAAQDAQTGLNNRLFFE
NQLATQLEDPEDVGTHGVVMMIRLPDFDTLQETHGYGGVLEEYRNTLINLLSTFVLRYPA
ALLARYYHSDFTVLLPHRTLKEADSIASQLVKAIDILPVTPLIDREDILHIGISAYHGGQ
TTEQVMESVEDATRNAVLQGGNGWCVYDRRVPEKGRGSVKWRTLLEHTLLRGGPRLYQKP
AITRDGEVHHREMFSRIYDGTQELLEAEYMPLVRQLGLTSGYDRQLINRVIALTVSWQDS
VLAFPITVDSLLQRPFLRWLRETLLQCPKRQRERLLFELAEADVCQYIGRLRPILAMITG
LGCRLAVTQAGLTLVSTAYIKSLQVEVIKLHPGLVRSLDKRPENQLFVSSLTEACKGTHA
QVFAAGVRTREEWQTLLDKGVCGGQGDLFAASEPVSNTLKKYSPRTYV