Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   M5M_RS17565 Genome accession   NC_018868
Coordinates   3939252..3940076 (-) Length   274 a.a.
NCBI ID   WP_338057834.1    Uniprot ID   -
Organism   Simiduia agarivorans SA1 = DSM 21679     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3934252..3945076
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  M5M_RS17545 (M5M_17855) argJ 3936219..3937439 (+) 1221 WP_015048852.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  M5M_RS17550 (M5M_17860) - 3937439..3938392 (+) 954 WP_024330114.1 Nudix family hydrolase -
  M5M_RS17555 (M5M_17865) yacG 3938414..3938614 (-) 201 WP_015048854.1 DNA gyrase inhibitor YacG -
  M5M_RS17560 (M5M_17870) coaE 3938662..3939255 (-) 594 WP_015048855.1 dephospho-CoA kinase -
  M5M_RS17565 (M5M_17875) pilD 3939252..3940076 (-) 825 WP_338057834.1 A24 family peptidase Machinery gene
  M5M_RS17570 (M5M_17880) pilC 3940149..3941384 (-) 1236 WP_015048857.1 type II secretion system F family protein Machinery gene
  M5M_RS17575 (M5M_17885) pilB 3941391..3943121 (-) 1731 WP_015048858.1 type IV-A pilus assembly ATPase PilB Machinery gene
  M5M_RS17580 (M5M_17890) - 3943458..3943898 (+) 441 WP_015048859.1 pilin -
  M5M_RS17585 (M5M_17895) - 3943993..3944706 (+) 714 WP_016389906.1 hypothetical protein -

Sequence

Protein


Download         Length: 274 a.a.        Molecular weight: 30065.47 Da        Isoelectric Point: 7.0186

>NTDB_id=54095 M5M_RS17565 WP_338057834.1 3939252..3940076(-) (pilD) [Simiduia agarivorans SA1 = DSM 21679]
MLGLTVGSFLNVVIYRLPKILEANWRSECCELMGQSEHSKPEASFNLAFPASHCPSCKAPIKAWQNIPVISWLILRGRCS
NCKASISVRYPLVEITSGLLSLLIALQFGASLQALFLLGFTWTLICLTLIDADTMLLPDSLTLPLMWAGLVVNYFGYVTD
FDSAFWGAIAGYGVLWLVFWGFKLLTGKDGMGYGDFKLLAALGAWLGWQALPLIILLSSFVGAAWGISQIVLKGRDNQQP
MPFGPYLAVAGWIAMMWGEQITNLYLNLSGINNG

Nucleotide


Download         Length: 825 bp        

>NTDB_id=54095 M5M_RS17565 WP_338057834.1 3939252..3940076(-) (pilD) [Simiduia agarivorans SA1 = DSM 21679]
GTGCTGGGACTTACAGTTGGTAGCTTTTTAAATGTGGTAATTTACCGGCTGCCTAAAATTTTAGAGGCTAACTGGCGGAG
CGAATGTTGTGAGTTAATGGGGCAAAGCGAGCATTCAAAACCCGAGGCATCTTTTAATCTCGCTTTTCCTGCCTCGCACT
GCCCATCGTGTAAAGCCCCCATTAAAGCCTGGCAAAACATTCCGGTTATCAGCTGGTTGATACTGCGCGGTAGGTGCAGC
AATTGTAAAGCCTCAATCTCAGTACGTTATCCTCTCGTTGAAATTACTTCCGGCCTGCTAAGTCTGTTAATTGCCCTTCA
GTTCGGTGCCAGTTTACAAGCTCTTTTTCTACTTGGTTTCACCTGGACGCTCATCTGCCTGACCCTCATCGACGCAGACA
CCATGCTCCTGCCCGACAGTCTGACCCTGCCACTTATGTGGGCGGGCCTGGTGGTCAATTACTTTGGTTATGTGACTGAT
TTCGACAGTGCGTTCTGGGGCGCCATTGCCGGCTACGGCGTCTTGTGGCTGGTGTTCTGGGGCTTTAAATTACTCACCGG
CAAAGATGGCATGGGTTACGGCGACTTCAAGCTGCTGGCCGCCTTGGGCGCCTGGCTGGGTTGGCAAGCGCTGCCATTGA
TCATTTTGCTGTCGTCTTTCGTTGGCGCCGCCTGGGGTATCAGCCAGATTGTGCTCAAGGGGCGTGACAACCAACAACCC
ATGCCGTTTGGCCCCTATCTGGCGGTCGCCGGCTGGATTGCCATGATGTGGGGTGAACAGATCACCAATCTTTACCTGAA
TCTGTCTGGTATCAACAACGGGTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(2-108)

Type IV leader peptidase family (Peptidase_A24)

(120-227)


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 campbellii strain DS40M4

54.478

97.81

0.533
  pilD Vibrio cholerae strain A1552

53.358

97.81

0.522
  pilD Acinetobacter baumannii D1279779

53.383

97.08

0.518
  pilD Acinetobacter nosocomialis M2

52.632

97.08

0.511
  pilD Neisseria gonorrhoeae MS11

50.575

95.255

0.482

Multiple sequence alignment