Protein Info for GFF5235 in Variovorax sp. SCN45

Annotation: General secretion pathway protein D / Type II secretion outermembrane pore forming protein (PulD)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 763 signal peptide" amino acids 1 to 33 (33 residues), see Phobius details TIGR02517: type II secretion system protein D" amino acids 46 to 671 (626 residues), 588 bits, see alignment E=1e-180 PF21305: type_II_gspD_N0" amino acids 46 to 115 (70 residues), 83.9 bits, see alignment E=8.5e-28 PF03958: Secretin_N" amino acids 145 to 204 (60 residues), 50.4 bits, see alignment 3.3e-17 amino acids 208 to 288 (81 residues), 53 bits, see alignment E=4.9e-18 amino acids 300 to 413 (114 residues), 47.6 bits, see alignment E=2.4e-16 PF00263: Secretin" amino acids 499 to 664 (166 residues), 160.9 bits, see alignment E=3.4e-51

Best Hits

KEGG orthology group: K02453, general secretion pathway protein D (inferred from 85% identity to vpe:Varpa_1156)

Predicted SEED Role

"General secretion pathway protein D / Type II secretion outermembrane pore forming protein (PulD)"

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 (763 amino acids)

>GFF5235 General secretion pathway protein D / Type II secretion outermembrane pore forming protein (PulD) (Variovorax sp. SCN45)
MMKPLFSTGTVALAVRVLIAATFLQAAPAAFAQTSDAPRRGEPITLNFANADIEAVARTM
AVVTGRDVVVDPRVKGTMNLVTDRAIQPAAAFNQFASALRLQGFAVVEADGLYKVVPEAD
AKLQSSAVNTSIGAVSSSGSNQIVTQIFRLNYESPNSLLPVLRPLIPPNNTINVNPGNNS
LVITDYADNMRRLARIIASLDVPNASDVEVIQLKHSIASDMVPLISRLIEGSGSGAPGTA
AAPGATDASFRTTLLADPRSNSLILRAANPARVQLVRTLVEKLDRQPAEGSNGAAGNIYV
VYLKNADAVRLAATLRAAMAANQQTSASGQPGAAGSSPVPQQSAPQAMQVNLSGGQNGGS
AAASAPLNNANQPSTGGQIQADPTTNSLIITAPEPQYRQMRAVIDKLDGRRAQVMIEALI
VEVSAKKAANFGVQWQSALGNNAVIGTNSSLASANILALTQALATKNVAGITPSPGLNLG
IAGKIGGQYILGAIANFFNSDGDANVLSTPNLLTLDNEEAKIVIGQNVPFVTGQYASTSG
SVGINPFTTVERKDVGLTLRVRPTINENGTVKMTIFQETSTVDQNTAKDPNGPTTNKRSI
ESSVLVEDGGLVMLGGLLSDDYGNTVEKVPVAGDIPVLGNLFKNEVRTRNKSNLMMFLRP
AVMRDGASTQAFAYDRYDEIRGMQQRTQPSTDNIMLRGVDSAPVLPEVPLVRAAPNAPGS
ERIGGTQLIPPPRAAADNRKLAPSPLRGTLPPTDDPASAREMP