Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilU   Type   Machinery gene
Locus tag   GDM11_RS19055 Genome accession   NZ_AP019684
Coordinates   4232865..4233998 (+) Length   377 a.a.
NCBI ID   WP_012439300.1    Uniprot ID   Q93S76
Organism   Xanthomonas campestris pv. campestris strain MAFF302021     
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 4198547..4241219 4232865..4233998 within 0


Gene organization within MGE regions


Location: 4198547..4241219
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GDM11_RS18905 (Xcc3_36760) - 4200214..4200855 (-) 642 WP_012439272.1 succinyl-CoA--3-ketoacid CoA transferase subunit B -
  GDM11_RS18910 (Xcc3_36770) - 4200855..4201583 (-) 729 WP_012439273.1 succinyl-CoA--3-ketoacid CoA transferase subunit A -
  GDM11_RS18915 (Xcc3_36780) - 4201718..4203064 (+) 1347 WP_014506571.1 phosphohexose mutase -
  GDM11_RS18920 (Xcc3_36790) - 4203110..4204513 (+) 1404 WP_012439275.1 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase -
  GDM11_RS18925 (Xcc3_36800) rfbD 4204635..4205543 (-) 909 WP_050912436.1 dTDP-4-dehydrorhamnose reductase -
  GDM11_RS18930 (Xcc3_36810) rfbC 4205540..4206097 (-) 558 WP_011035866.1 dTDP-4-dehydrorhamnose 3,5-epimerase -
  GDM11_RS18935 (Xcc3_36820) rfbA 4206094..4206981 (-) 888 WP_012439277.1 glucose-1-phosphate thymidylyltransferase RfbA -
  GDM11_RS18940 (Xcc3_36840) rfbB 4207045..4208099 (-) 1055 Protein_3565 dTDP-glucose 4,6-dehydratase -
  GDM11_RS18945 (Xcc3_36850) - 4208328..4209074 (+) 747 WP_011035863.1 electron transfer flavoprotein subunit beta/FixA family protein -
  GDM11_RS18950 (Xcc3_36860) - 4209074..4210018 (+) 945 WP_012439279.1 electron transfer flavoprotein subunit alpha/FixB family protein -
  GDM11_RS18955 (Xcc3_36870) - 4210105..4210425 (+) 321 WP_230439256.1 hypothetical protein -
  GDM11_RS18960 (Xcc3_36880) - 4210474..4211577 (+) 1104 WP_011035860.1 DegT/DnrJ/EryC1/StrS family aminotransferase -
  GDM11_RS18965 (Xcc3_36890) - 4211562..4212533 (+) 972 WP_070691767.1 glycosyltransferase family 2 protein -
  GDM11_RS18970 (Xcc3_36900) - 4212530..4213459 (+) 930 WP_019237976.1 WxcM-like domain-containing protein -
  GDM11_RS18975 (Xcc3_36910) - 4213446..4213883 (+) 438 WP_100666050.1 GtrA family protein -
  GDM11_RS18980 (Xcc3_36920) - 4213978..4216230 (+) 2253 WP_100666048.1 sugar translocase -
  GDM11_RS18985 (Xcc3_36930) - 4216415..4217353 (-) 939 WP_100666046.1 NAD-dependent epimerase/dehydratase family protein -
  GDM11_RS18990 (Xcc3_36940) gmd 4217337..4218371 (-) 1035 WP_100666044.1 GDP-mannose 4,6-dehydratase -
  GDM11_RS18995 (Xcc3_36950) - 4218453..4219052 (-) 600 WP_019237979.1 hypothetical protein -
  GDM11_RS19000 - 4219088..4220828 (-) 1741 Protein_3577 glycosyltransferase -
  GDM11_RS19005 (Xcc3_36980) - 4220849..4221928 (-) 1080 WP_011035847.1 glycosyltransferase family 4 protein -
  GDM11_RS19010 (Xcc3_36990) - 4221963..4224467 (-) 2505 WP_100666427.1 methyltransferase domain-containing protein -
  GDM11_RS19015 (Xcc3_37010) - 4224508..4225794 (-) 1287 WP_011035845.1 ABC transporter ATP-binding protein -
  GDM11_RS19020 (Xcc3_37020) - 4225791..4226576 (-) 786 WP_040942391.1 ABC transporter permease -
  GDM11_RS19025 (Xcc3_37030) - 4226660..4228045 (-) 1386 WP_100666428.1 glycosyltransferase family 4 protein -
  GDM11_RS19030 (Xcc3_37040) - 4228042..4229241 (-) 1200 WP_011035842.1 cystathionine gamma-synthase -
  GDM11_RS19035 (Xcc3_37050) - 4229335..4230705 (-) 1371 WP_050911712.1 pyridoxal-phosphate dependent enzyme -
  GDM11_RS19040 (Xcc3_37060) - 4230937..4231155 (-) 219 WP_012439297.1 YdcH family protein -
  GDM11_RS19045 (Xcc3_37070) - 4231496..4232386 (-) 891 WP_012439298.1 membrane protein -
  GDM11_RS19050 (Xcc3_37080) - 4232383..4232766 (-) 384 WP_040941833.1 DUF4398 domain-containing protein -
  GDM11_RS19055 (Xcc3_37090) pilU 4232865..4233998 (+) 1134 WP_012439300.1 PilT/PilU family type 4a pilus ATPase Machinery gene
  GDM11_RS23715 - 4234106..4234317 (-) 212 Protein_3589 hypothetical protein -
  GDM11_RS19065 (Xcc3_37100) maiA 4234518..4235180 (-) 663 WP_012439301.1 maleylacetoacetate isomerase -
  GDM11_RS19070 (Xcc3_37110) - 4235224..4236213 (-) 990 WP_011035835.1 fumarylacetoacetate hydrolase family protein -
  GDM11_RS19080 (Xcc3_37120) - 4236593..4237981 (+) 1389 WP_050912442.1 DEAD/DEAH box helicase -
  GDM11_RS19085 (Xcc3_37130) queD 4238097..4238450 (+) 354 WP_008576903.1 6-carboxytetrahydropterin synthase QueD -
  GDM11_RS19090 (Xcc3_37140) - 4238640..4238975 (+) 336 WP_011035833.1 phasin family protein -
  GDM11_RS19095 (Xcc3_37150) bioD 4239132..4239806 (-) 675 WP_012439302.1 dethiobiotin synthase -
  GDM11_RS19100 (Xcc3_37160) - 4240078..4240560 (+) 483 WP_019237988.1 GAF domain-containing protein -
  GDM11_RS19105 (Xcc3_37170) - 4240557..4240949 (+) 393 WP_011035830.1 TfoX/Sxy family protein -

Sequence

Protein


Download         Length: 377 a.a.        Molecular weight: 41799.10 Da        Isoelectric Point: 6.1401

>NTDB_id=73233 GDM11_RS19055 WP_012439300.1 4232865..4233998(+) (pilU) [Xanthomonas campestris pv. campestris strain MAFF302021]
MDIGYFLKLMTEKNASDMFLTTGAPVYIKIEGKLYPLGNTGLPPGMVKKIAYSLMDEGQVPQFERELELNMAIALSDAGR
FRVNVFKQRGEVGMVIRAIRSRIPSIEELNLPQVLKDVIMTPRGLVLVVGSTGSGKSTSLASMIDHRNSTTTGHILTIED
PIEYLHKHKMSIVNQREVGLDTHAFQSALKNAMREAPDVILIGEILDAETMEAAIAFAETGHLCLATLHSNNADQTIERI
LNFFPESAHKNVLMNLALNLRAVVSQRLVKGLDGRRRPATEVLLNTPMIRDLLRRGQVHEVKQAMEESLEEGMQTFDQCL
FRMVKTGEIEQEEALRAADSRDGLALKFRLSEGGSGEHDPYADYESASAPKISHGFI

Nucleotide


Download         Length: 1134 bp        

>NTDB_id=73233 GDM11_RS19055 WP_012439300.1 4232865..4233998(+) (pilU) [Xanthomonas campestris pv. campestris strain MAFF302021]
ATGGATATCGGCTACTTCCTGAAGCTGATGACCGAAAAGAATGCCTCGGACATGTTCTTGACCACCGGCGCGCCGGTGTA
CATCAAGATCGAAGGCAAGCTTTACCCGCTCGGCAATACGGGGTTGCCGCCGGGGATGGTCAAGAAAATCGCTTACTCAT
TGATGGACGAAGGCCAGGTGCCGCAGTTCGAGCGCGAGCTGGAACTCAACATGGCCATCGCTCTGTCCGACGCCGGGCGC
TTCCGCGTGAACGTGTTCAAGCAGCGCGGCGAAGTGGGCATGGTGATCCGTGCCATCCGCAGCCGGATCCCGAGCATCGA
GGAGCTCAACCTGCCGCAGGTGCTCAAGGACGTCATCATGACCCCGCGCGGGCTGGTGCTGGTGGTCGGTTCGACCGGTT
CGGGCAAGTCGACCTCGCTGGCCTCGATGATCGACCACCGCAACAGCACCACGACCGGGCACATCCTCACCATCGAGGAC
CCGATCGAGTACCTGCACAAGCACAAGATGTCGATCGTGAACCAGCGCGAGGTGGGCCTGGACACGCACGCCTTCCAGAG
CGCGCTGAAGAACGCGATGCGCGAGGCGCCCGACGTGATCCTGATCGGCGAGATCCTGGACGCCGAGACCATGGAGGCGG
CGATCGCCTTCGCTGAAACCGGCCATCTGTGCCTGGCGACGCTGCACTCCAACAACGCCGACCAGACCATCGAGCGCATC
CTCAACTTCTTCCCGGAAAGCGCGCACAAGAACGTGCTGATGAACCTGGCACTGAATCTGCGCGCAGTGGTGTCCCAGCG
CCTGGTCAAGGGACTGGACGGGCGCCGCCGCCCGGCCACCGAGGTGCTGCTCAACACGCCGATGATCCGCGACCTGCTGC
GTCGCGGGCAGGTGCACGAGGTCAAGCAGGCGATGGAGGAGTCGCTGGAAGAAGGCATGCAGACCTTCGACCAGTGCCTG
TTCCGGATGGTCAAGACCGGCGAGATCGAGCAGGAGGAAGCGCTGCGCGCGGCCGACTCGCGCGACGGCCTGGCGCTGAA
ATTCCGTCTTTCCGAAGGCGGCTCCGGCGAGCACGATCCGTATGCCGACTACGAGTCGGCCTCGGCGCCGAAGATCAGCC
ATGGGTTTATTTAG

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(76-270)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q93S76

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
  pilU Pseudomonas stutzeri DSM 10701

52.368

95.225

0.499
  pilU Vibrio cholerae strain A1552

49.167

95.491

0.469
  pilU Acinetobacter baylyi ADP1

49.435

93.899

0.464
  pilT Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

44.764

100

0.454
  pilT Pseudomonas aeruginosa PAK

42.604

89.655

0.382
  pilT Legionella pneumophila strain ERS1305867

41.42

89.655

0.371
  pilT Legionella pneumophila strain Lp02

41.42

89.655

0.371
  pilT Acinetobacter baumannii D1279779

41.124

89.655

0.369
  pilT Acinetobacter nosocomialis M2

41.124

89.655

0.369
  pilT Acinetobacter baumannii strain A118

41.124

89.655

0.369
  pilT Acinetobacter baylyi ADP1

40.588

90.186

0.366
  pilT Pseudomonas stutzeri DSM 10701

41.018

88.594

0.363

Multiple sequence alignment