Protein Info for GFF3810 in Pseudomonas sp. DMC3

Annotation: ATP-dependent RNA helicase SrmB

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

1 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1428 signal peptide" amino acids 1 to 20 (20 residues), see Phobius details PF00270: DEAD" amino acids 30 to 216 (187 residues), 99.2 bits, see alignment E=9e-32 PF04851: ResIII" amino acids 36 to 215 (180 residues), 36.2 bits, see alignment E=2.3e-12 PF00271: Helicase_C" amino acids 269 to 371 (103 residues), 66.7 bits, see alignment 8.3e-22 PF19306: WH_Lhr" amino acids 400 to 562 (163 residues), 116.8 bits, see alignment E=2.6e-37 PF08494: DEAD_assoc" amino acids 636 to 838 (203 residues), 161.4 bits, see alignment E=9.2e-51 PF23235: WH3_Lhr" amino acids 1072 to 1140 (69 residues), 47.7 bits, see alignment 6.5e-16 PF23234: WH4_Lhr" amino acids 1276 to 1360 (85 residues), 96.1 bits, see alignment 2.9e-31

Best Hits

Predicted SEED Role

"Lhr-like helicases"

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 (1428 amino acids)

>GFF3810 ATP-dependent RNA helicase SrmB (Pseudomonas sp. DMC3)
MNLPLPANSALAGFHPAVSAWFNKTFPAVTTAQARAWPLIRQRRSTLIAAPTGSGKTLTA
FLAVLDELVHRGLEQPEGLPAETLVVYVSPLKALSNDIQINLQNPLAGITAQLREMGLPE
LTITTAVRTGDTPQKDRAAMRKTAPHILVTTPESLYVLLGSESGRRMLGTTRTVIIDEIH
AMAAGKRGSHLSLSLERLQALCAEPLTRIGLSATQKPVEAVARFLVGHARPCEIVDIGHA
RPRDLGIEVPPVPLSAVMANDVWELVYERLAELAREHRTTLIFVNTRRLAERLSRHLSER
LGKQAVAAHHGSLAKEFRLDAEQRLKRGELQVLIATASLELGIDIGEVDLVCQISSPRSI
AAFLQRVGRSGHQVGGTPKGRLFATTRDDLIECAALLDCVRRGELDTLHIPEKPLDVLAQ
QIIAEVSSQEWSEDALLAMFRRAWPYRDLDEKHYQALLSMLAEGYNGRQGIRSAYLHRDA
VSRTLRGRRGAQLTAVTSGGTIPDNADYSVLLEPQGLNIGSVNEDFAVESIAGDVFQLGN
TSYRILRVESGKVRVEDAQGMPPTIPFWLGEAPGRSDELSAAVARLQAQLDELLSASPGN
LQPALDWLTTILGLNLASAEQLVEYLARARQTLGALPSQDTLLMERFFDESGGTQLIIHT
PFGSRINRAWGLALRKRFCRTFNFELQAAASEDAIVLSLSTSHSFELDEVWRYLHSNSAE
HTLIQAVLDAPLFGVRWRWNAGVALALPRFTGGRKVAPQLQRMKSEDLIASVFPDQIACL
ENLAGEREVPEHPLVEQTLDDCLHEAMDSEGWLTLLRRMERGEVRLIARDLPAPSPLAAE
ILSARPYTFLDDAPLEERRTQAVINRRWSDPQSTDDLGALDADAITAVREEAWPSPNSMD
EMHEALMSLACISDTEARANAGWPDWLQTLMASGRACLLQIDAEHQLWLARERLSCLQAL
YPQATLLTEAVALPGFDDTWAFDEALVEVIRARLGAFGPTPLPAIAEPLALPAAQVNQAL
AQLEREGYVLRGQFTPNSGIEEWCERHLLARIHRYTVKRLRREIEPVALQDFMRFLFDWQ
HLTPATQGQGSAVLPAIVGQFEGYPAAASAWDSDILPARLKDYSPSRLDDLCRNGKLVWT
RINARQKVSGSALRSTPIVLLPRSQVGLWSALAERTPVSELSPKTQKVFEALSQHGALFF
DELIHEARLLRSELEIALQELVAAGLVNADSFAGLRALITPASKRQQRSSRRGRGAFIGG
MDDAGRWALLRRGSSADAAETLEHVAMTLLRRYGVVFWRLLEREADWLPSWRELLRTFHR
LEARGEIRGGRFVNGLAGEQFALPEAIPLLREVRRRPQDGSLVAVCGVDPLNLAGTLLPG
VKVPALVSNRLVYRDGVVVAAMVAGKPQIWGEWDQVVVEQIGRKLIRN