Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   PM1_RS25520 Genome accession   NZ_CP094343
Coordinates   5774836..5775708 (+) Length   290 a.a.
NCBI ID   WP_009617626.1    Uniprot ID   -
Organism   Pseudomonas sp. M1     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Genomic island 5763639..5777553 5774836..5775708 within 0


Gene organization within MGE regions


Location: 5763639..5777553
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PM1_RS25455 (MRY70_25455) - 5763639..5763890 (+) 252 WP_009617650.1 helix-turn-helix domain-containing protein -
  PM1_RS25460 (MRY70_25460) - 5763890..5765086 (+) 1197 WP_009617648.1 type II toxin-antitoxin system HipA family toxin -
  PM1_RS25465 (MRY70_25465) - 5765274..5765501 (-) 228 WP_009617646.1 DUF433 domain-containing protein -
  PM1_RS25470 (MRY70_25470) - 5765567..5765908 (-) 342 WP_009617644.1 type II toxin-antitoxin system HicB family antitoxin -
  PM1_RS25475 (MRY70_25475) - 5765905..5766156 (-) 252 WP_009617642.1 type II toxin-antitoxin system HicA family toxin -
  PM1_RS25480 (MRY70_25480) - 5766260..5766406 (+) 147 WP_024128154.1 hypothetical protein -
  PM1_RS25485 (MRY70_25485) - 5766403..5767476 (-) 1074 WP_009617639.1 diguanylate cyclase -
  PM1_RS25495 (MRY70_25495) - 5767752..5769305 (-) 1554 WP_009617637.1 O-antigen ligase family protein -
  PM1_RS25500 (MRY70_25500) - 5769319..5771154 (-) 1836 WP_161788510.1 sulfatase-like hydrolase/transferase -
  PM1_RS25505 (MRY70_25505) comP 5771276..5771680 (-) 405 WP_009617631.1 pilin Machinery gene
  PM1_RS25510 (MRY70_25510) pilB 5771909..5773612 (+) 1704 WP_009617629.1 type IV-A pilus assembly ATPase PilB Machinery gene
  PM1_RS25515 (MRY70_25515) pilC 5773616..5774833 (+) 1218 WP_009617627.1 type II secretion system F family protein Machinery gene
  PM1_RS25520 (MRY70_25520) pilD 5774836..5775708 (+) 873 WP_009617626.1 A24 family peptidase Machinery gene
  PM1_RS25525 (MRY70_25525) coaE 5775782..5776390 (+) 609 WP_009617624.1 dephospho-CoA kinase -
  PM1_RS25530 (MRY70_25530) yacG 5776387..5776596 (+) 210 WP_009617622.1 DNA gyrase inhibitor YacG -
  PM1_RS25535 (MRY70_25535) - 5776862..5777056 (+) 195 WP_009617620.1 hypothetical protein -
  PM1_RS25540 (MRY70_25540) - 5777056..5777331 (+) 276 WP_024128153.1 type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family -
  PM1_RS25545 (MRY70_25545) - 5777338..5777553 (-) 216 WP_009617618.1 hypothetical protein -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 32060.99 Da        Isoelectric Point: 6.6244

>NTDB_id=669102 PM1_RS25520 WP_009617626.1 5774836..5775708(+) (pilD) [Pseudomonas sp. M1]
MPVLDFLASYELAFVLCAALLGLLVGSFLNVVIHRLPKMMELEWQQQARDALSLPQPEQKATYNLVLPNSQCPHCGHEIR
AWENIPVISYLALRGKCSACKAPISARYPLVELATALLSGFVAWHFGFTWQAGAMLLLTWGLLAMSLIDVDHQLLPDALV
LPLLWLGLIVNYFGLFTSLGDALWGAVFGYLSLWSVYWLFKLLTGKEGMGYGDFKLLAMLGAWGGWQVLPLTILFSSLVG
AVLGVILLRLRNAETSTPIPFGPYLAIAGWIALLWGDQITTTYLQFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=669102 PM1_RS25520 WP_009617626.1 5774836..5775708(+) (pilD) [Pseudomonas sp. M1]
ATGCCTGTACTCGACTTCCTGGCCAGCTACGAGCTGGCCTTTGTTTTATGCGCCGCCCTGCTCGGCCTTCTGGTCGGTAG
CTTCCTCAACGTGGTCATCCATCGCCTGCCGAAGATGATGGAGCTGGAATGGCAACAGCAGGCACGTGATGCGCTTTCCC
TGCCCCAGCCCGAGCAAAAGGCCACCTACAACCTGGTTCTGCCCAACTCCCAGTGCCCGCATTGCGGTCATGAAATCCGT
GCCTGGGAGAACATCCCCGTCATCAGCTACCTGGCCTTGCGCGGCAAGTGCTCGGCCTGTAAGGCGCCGATCAGTGCGCG
TTATCCGCTGGTCGAGCTGGCCACCGCTCTACTCTCCGGTTTCGTTGCCTGGCACTTCGGCTTTACCTGGCAGGCTGGGG
CCATGCTGTTGCTGACCTGGGGGCTGTTGGCCATGAGCCTGATCGATGTCGATCACCAGTTGCTGCCGGATGCGTTGGTG
CTGCCGCTGCTCTGGCTGGGCTTGATCGTCAATTACTTCGGGCTTTTCACCAGCCTGGGCGATGCGCTCTGGGGTGCGGT
GTTCGGTTACCTGAGCCTGTGGTCGGTGTACTGGCTGTTCAAGCTGCTGACCGGCAAGGAAGGCATGGGTTATGGCGACT
TCAAGCTGCTGGCCATGCTCGGCGCCTGGGGTGGCTGGCAGGTGTTGCCGCTGACCATCCTGTTCTCGTCCCTGGTCGGG
GCCGTGCTGGGCGTCATTCTGCTGCGTCTGCGCAATGCCGAGACCAGCACGCCGATCCCCTTCGGGCCCTATCTGGCCAT
CGCCGGCTGGATTGCGCTGCTCTGGGGTGATCAAATAACCACTACCTATCTGCAGTTCGCCGGTTTCCGGTAG

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)

Type IV leader peptidase family (Peptidase_A24)

(137-245)


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

58.363

96.897

0.566
  pilD Vibrio campbellii strain DS40M4

55.477

97.586

0.541
  pilD Acinetobacter baumannii D1279779

55.636

94.828

0.528
  pilD Acinetobacter nosocomialis M2

55.273

94.828

0.524
  pilD Neisseria gonorrhoeae MS11

50.57

90.69

0.459

Multiple sequence alignment