Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   RHM61_RS08900 Genome accession   NZ_CP133779
Coordinates   1936845..1937696 (-) Length   283 a.a.
NCBI ID   WP_322250761.1    Uniprot ID   -
Organism   Undibacterium sp. CCC3.4     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1931845..1942696
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RHM61_RS08875 (RHM61_08875) - 1933010..1933576 (+) 567 WP_322250756.1 hypothetical protein -
  RHM61_RS08880 (RHM61_08880) - 1933616..1935166 (+) 1551 WP_322250757.1 sigma 54-interacting transcriptional regulator -
  RHM61_RS08885 (RHM61_08885) - 1935179..1935355 (-) 177 WP_322250758.1 DNA gyrase inhibitor YacG -
  RHM61_RS08890 (RHM61_08890) zapD 1935358..1936113 (-) 756 WP_322250759.1 cell division protein ZapD -
  RHM61_RS08895 (RHM61_08895) coaE 1936220..1936837 (-) 618 WP_322250760.1 dephospho-CoA kinase -
  RHM61_RS08900 (RHM61_08900) pilD 1936845..1937696 (-) 852 WP_322250761.1 A24 family peptidase Machinery gene
  RHM61_RS08905 (RHM61_08905) pilC 1937696..1938922 (-) 1227 WP_322250762.1 type II secretion system F family protein Machinery gene
  RHM61_RS08910 (RHM61_08910) pilB 1938937..1940664 (-) 1728 WP_322250763.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RHM61_RS08915 (RHM61_08915) ispB 1940854..1941783 (-) 930 WP_322251074.1 octaprenyl diphosphate synthase -
  RHM61_RS08920 (RHM61_08920) rplU 1942119..1942430 (+) 312 WP_322250764.1 50S ribosomal protein L21 -

Sequence

Protein


Download         Length: 283 a.a.        Molecular weight: 30289.09 Da        Isoelectric Point: 7.6148

>NTDB_id=876694 RHM61_RS08900 WP_322250761.1 1936845..1937696(-) (pilD) [Undibacterium sp. CCC3.4]
MNSEIFFNLPGNLLSTVCAAVFGLMIGSFLNVVIYRLPKMMQRESDNYVASESGLPLPHTDQFNLMLPRSACPHCGHQIG
AMENIPVLSYLAIGGKCRGCKAAISPRYPVVELLTGALSAAMVWHFGSGVAGLAALVFGFILIALTFIDADTQLLPDDLT
LPLLWLGLLVNLNGTFTSLSSAVIGAVAGYLCLWSIYWLFKLTTGKEGMGYGDFKLLAALGAWMGWAMLPIIILLSSVVA
AVIGLAMMALRKIGRDTPLPFGPYLAGAGLIALFWGPQLSKLF

Nucleotide


Download         Length: 852 bp        

>NTDB_id=876694 RHM61_RS08900 WP_322250761.1 1936845..1937696(-) (pilD) [Undibacterium sp. CCC3.4]
ATGAATAGCGAAATTTTCTTCAACTTACCGGGCAATCTGCTCAGCACTGTGTGCGCGGCGGTTTTCGGCCTGATGATAGG
CAGCTTTCTCAATGTCGTCATTTATCGGCTGCCGAAAATGATGCAGCGCGAATCGGATAATTACGTCGCCAGCGAGAGCG
GCTTGCCGCTGCCGCACACCGACCAGTTCAATCTGATGCTGCCGCGTTCAGCGTGTCCGCACTGCGGCCACCAGATTGGC
GCAATGGAAAATATCCCGGTGCTCAGCTATCTGGCAATCGGCGGCAAATGCCGCGGCTGCAAAGCAGCGATTTCACCGCG
CTATCCGGTGGTGGAGTTATTGACCGGTGCCTTGTCGGCAGCCATGGTCTGGCACTTCGGCAGCGGTGTGGCCGGCTTGG
CCGCGCTGGTATTCGGTTTTATTCTCATTGCCCTGACTTTCATCGATGCCGATACCCAGCTCTTGCCCGACGATTTGACG
CTGCCGCTGCTATGGCTGGGCTTGCTGGTCAATCTCAACGGCACCTTTACCTCGCTGTCGTCGGCAGTCATCGGGGCCGT
CGCCGGTTACCTGTGCCTATGGTCGATTTACTGGCTCTTCAAGCTGACTACCGGCAAAGAGGGCATGGGCTATGGCGATT
TCAAACTGCTCGCGGCACTCGGGGCTTGGATGGGCTGGGCGATGTTGCCGATCATCATACTGTTGTCTTCGGTGGTAGCG
GCCGTGATCGGCTTGGCCATGATGGCCTTGCGTAAGATCGGGCGCGATACCCCACTGCCATTCGGCCCTTACTTAGCCGG
TGCCGGCTTGATCGCCTTGTTCTGGGGTCCCCAGTTAAGCAAGCTTTTTTAG

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-126)

Type IV leader peptidase family (Peptidase_A24)

(136-245)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  pilD Vibrio cholerae strain A1552

57.857

98.94

0.572
  pilD Vibrio campbellii strain DS40M4

54.643

98.94

0.541
  pilD Acinetobacter baumannii D1279779

51.292

95.76

0.491
  pilD Acinetobacter nosocomialis M2

50.554

95.76

0.484
  pilD Neisseria gonorrhoeae MS11

50.588

90.106

0.456