Protein Info for DDA3937_RS12270 in Dickeya dadantii 3937

Annotation: ATP-dependent RNA helicase HrpA

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 1295 TIGR01967: RNA helicase HrpA" amino acids 11 to 1291 (1281 residues), 2164.1 bits, see alignment E=0 PF00270: DEAD" amino acids 80 to 229 (150 residues), 30.2 bits, see alignment E=1.1e-10 PF00271: Helicase_C" amino acids 277 to 399 (123 residues), 45.4 bits, see alignment E=2.6e-15 PF21010: HA2_C" amino acids 494 to 552 (59 residues), 38.8 bits, see alignment 3.2e-13 PF07717: OB_NTP_bind" amino acids 617 to 693 (77 residues), 52.1 bits, see alignment 1.8e-17 PF11898: DUF3418" amino acids 708 to 1292 (585 residues), 796.9 bits, see alignment E=3.9e-243

Best Hits

Swiss-Prot: 80% identical to HRPA_ECOLI: ATP-dependent RNA helicase HrpA (hrpA) from Escherichia coli (strain K12)

KEGG orthology group: K03578, ATP-dependent helicase HrpA [EC: 3.6.4.13] (inferred from 69% identity to aat:D11S_1569)

MetaCyc: 80% identical to ATP-dependent 3'->5' RNA helicase HrpA (Escherichia coli K-12 substr. MG1655)
5.6.2.e [EC: 5.6.2.e]

Predicted SEED Role

"ATP-dependent RNA helicase HrpA (EC 3.6.4.13)" (EC 3.6.4.13)

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.13

Use Curated BLAST to search for 3.6.4.13 or 5.6.2.e

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 E0SF71 at UniProt or InterPro

Protein Sequence (1295 amino acids)

>DDA3937_RS12270 ATP-dependent RNA helicase HrpA (Dickeya dadantii 3937)
MTSPLHALEPQLNVLMLRDRQRLRRRLQGAMKVGNPQAQVSIAQEIGQEIEAARLRVEQR
RASLPAIRYPEALPVSQKREAILSAIRDHQVVIVAGETGSGKTTQLPKMCLELGRGVTGL
IGHTQPRRLAARSVADRIAAELETPLGSTVGYKVRFNDQVGDNTLVKLMTDGILLAEIQQ
DRLLMQYDTLIIDEAHERSLNIDFILGYLKQLLPRRPDLKVIITSATIDPQRFSRHFSNA
PIIEVSGRTYPVDVRYRPVVEDAQDSDRDQLQAILDAVDELCREGPGDILVFMSGEREIR
DTADALNKQDLPHTEILPLYARLSNQEQNRVFQSHHGRRIVLATNVAETSLTVPGIRYVI
DPGTARISRYSYRTKVQRLPIEPVSQASANQRKGRCGRVAAGICIRLYSEQDFLSRPPFT
DPEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQDGVRLLEELSALQSSEDGHYR
LTPQGRQLAQLPIDPRLARMVLEARQTSCVREVMVITAALSIQDPRERPVEKKQAAEEKH
RRFADKESDFLAFVNLWDYLQEQQKALSSSQFRKLCRSDYLNYLRVREWQDIYTQLRQVV
KELGFPVNSEPADYRSLHGALLTGLLSHIGQKDVEKQEFSGARNTRFAIFPGSGLFKKPP
KWTIVAELVETSRLWGRIAARIEPEWVEPLAQHLIKRSYSEPHWEKAQGAVMAQEKVTLY
GLPLVAARKVNYGATDPVVSRELFIRHALVEGDWQTQHAFFRANQKLRSEVEELENKSRR
RDILVDDETLFAFYDQRLPHDVVSSRHFDNWWKQASKTDSDQLNFEKAMLIKDGAERVSA
LDYPNHWQQGELRLRLTYQFEPGADADGVTVHIPLPVLNQVKEDGFEWQIPGLRSEVVVA
LIKSLPKPIRRNFVPAPNYAEAFLARVTPLEKGLLDALERELRLMTGVTVDREAWQWEQV
PDHLKMTFRVVDEKSRALREGKSLRALKDQLQEKVQQTLSAVADDGIEQRDLHIWSFGDL
PERYEQKRGGYAVKAYPALVDEKDSVAIRLFDTPHQQQQMMWRGQRRLLLLNIPSPIKYL
HEKLPNKAKLGLYFNPYGKVLELIDDCIACGVDQLMTVAGGPVWQEDAFRQLHERVRAEL
NDTVVDIARQVEQILTTVFNINKRLKGRVDMALALALSDIKSQMSGLVFRGFVTDNGWKR
LPDVLRYLQAIERRLDKLAQDVHRDRAQMLKVEQVQQAWQQWLNKLPPERREDDDVKAIR
WMIEELRVSYFAQQLGTPYPVSDKRILQAMAQIEG