Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JH290_RS16235 Genome accession   NZ_CP066978
Coordinates   3710156..3711892 (-) Length   578 a.a.
NCBI ID   WP_223646357.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. incanae strain 18048     
Function   power the 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 3702652..3754995 3710156..3711892 within 0


Gene organization within MGE regions


Location: 3702652..3754995
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH290_RS16200 (JH290_16160) - 3702652..3703062 (-) 411 WP_323549302.1 DNA-binding protein -
  JH290_RS16205 (JH290_16165) sucD 3703166..3704041 (-) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  JH290_RS16210 (JH290_16170) sucC 3704066..3705235 (-) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  JH290_RS16215 (JH290_16175) - 3705469..3707079 (+) 1611 WP_223646353.1 HAMP domain-containing sensor histidine kinase -
  JH290_RS16220 (JH290_16180) pilR 3707288..3708682 (+) 1395 WP_223646355.1 sigma-54 dependent transcriptional regulator Regulator
  JH290_RS16225 (JH290_16185) - 3708874..3709236 (+) 363 WP_217694196.1 hypothetical protein -
  JH290_RS16230 (JH290_16190) - 3709236..3709973 (+) 738 WP_070690009.1 zeta toxin family protein -
  JH290_RS16235 (JH290_16195) pilB 3710156..3711892 (-) 1737 WP_223646357.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JH290_RS16240 (JH290_16200) pilA 3711986..3712432 (-) 447 WP_274704645.1 pilin Machinery gene
  JH290_RS16250 (JH290_16205) - 3712552..3712992 (-) 441 WP_223646359.1 pilin -
  JH290_RS16255 (JH290_16210) pilC 3713346..3714605 (+) 1260 WP_223646360.1 type II secretion system F family protein Machinery gene
  JH290_RS16260 (JH290_16215) - 3714612..3715475 (+) 864 WP_223646361.1 A24 family peptidase -
  JH290_RS16265 (JH290_16220) coaE 3715489..3716112 (+) 624 WP_223646362.1 dephospho-CoA kinase -
  JH290_RS16270 (JH290_16225) - 3716643..3717044 (+) 402 WP_223646363.1 SymE family type I addiction module toxin -
  JH290_RS16275 (JH290_16230) - 3717120..3717410 (+) 291 WP_014508712.1 DUF1778 domain-containing protein -
  JH290_RS16280 (JH290_16235) - 3717407..3717898 (+) 492 WP_223646366.1 GNAT family N-acetyltransferase -
  JH290_RS16285 (JH290_16240) - 3718041..3719375 (-) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  JH290_RS16290 (JH290_16245) - 3719368..3720045 (-) 678 WP_003490678.1 response regulator transcription factor -
  JH290_RS16295 (JH290_16250) rimK 3720695..3721570 (-) 876 WP_070689999.1 30S ribosomal protein S6--L-glutamate ligase -
  JH290_RS16300 (JH290_16255) glgX 3722063..3724192 (+) 2130 WP_223646368.1 glycogen debranching protein GlgX -
  JH290_RS16305 (JH290_16260) - 3724724..3725116 (-) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  JH290_RS16310 (JH290_16265) - 3725207..3725602 (-) 396 WP_042594933.1 hypothetical protein -
  JH290_RS16315 (JH290_16270) - 3725787..3725933 (-) 147 WP_116889157.1 hypothetical protein -
  JH290_RS16320 - 3726051..3726362 (-) 312 WP_223646370.1 hypothetical protein -
  JH290_RS16325 (JH290_16280) - 3726525..3726896 (-) 372 WP_116889159.1 hypothetical protein -
  JH290_RS16330 (JH290_16285) - 3727594..3727935 (+) 342 WP_070689991.1 hypothetical protein -
  JH290_RS16335 (JH290_16290) - 3728000..3728281 (+) 282 WP_076037058.1 DUF6516 family protein -
  JH290_RS16340 (JH290_16295) - 3728289..3728657 (+) 369 WP_223646372.1 transcriptional regulator -
  JH290_RS16345 (JH290_16300) - 3728729..3730324 (-) 1596 WP_223646374.1 MobA/MobL family protein -
  JH290_RS16350 (JH290_16305) - 3730591..3730845 (+) 255 WP_223646376.1 hypothetical protein -
  JH290_RS16355 (JH290_16310) - 3730873..3732294 (-) 1422 WP_223646379.1 XVIPCD domain-containing protein -
  JH290_RS16360 (JH290_16315) - 3732287..3732976 (-) 690 WP_223646381.1 hypothetical protein -
  JH290_RS16365 (JH290_16320) - 3733073..3734410 (-) 1338 WP_223646383.1 hypothetical protein -
  JH290_RS16370 (JH290_16325) - 3734412..3736394 (-) 1983 WP_223646385.1 DUF87 domain-containing protein -
  JH290_RS16375 (JH290_16330) - 3736405..3737232 (-) 828 WP_223646387.1 Dam family site-specific DNA-(adenine-N6)-methyltransferase -
  JH290_RS16380 (JH290_16335) radC 3737376..3737855 (-) 480 WP_029219507.1 DNA repair protein RadC -
  JH290_RS16385 (JH290_16340) - 3738255..3738479 (-) 225 WP_029219506.1 hypothetical protein -
  JH290_RS16390 (JH290_16345) - 3738677..3739351 (-) 675 WP_223646389.1 Abi family protein -
  JH290_RS16395 (JH290_16350) - 3739376..3740478 (+) 1103 WP_223646391.1 IS3-like element IS1404 family transposase -
  JH290_RS16405 (JH290_16360) - 3741642..3743042 (+) 1401 WP_223646393.1 site-specific integrase -
  JH290_RS16410 (JH290_16365) - 3743124..3743507 (-) 384 WP_119129756.1 hypothetical protein -
  JH290_RS16415 (JH290_16370) - 3743557..3743781 (+) 225 WP_075287338.1 hypothetical protein -
  JH290_RS16420 (JH290_16375) - 3743814..3745343 (-) 1530 WP_075287337.1 DndE family protein -
  JH290_RS16425 - 3745345..3746118 (-) 774 WP_223648261.1 hypothetical protein -
  JH290_RS16430 (JH290_16380) - 3746022..3747422 (-) 1401 WP_223646395.1 AAA family ATPase -
  JH290_RS16435 (JH290_16385) - 3747412..3747627 (-) 216 WP_017154970.1 DNA modification system-associated small protein -
  JH290_RS16440 (JH290_16390) dndC 3747648..3748805 (-) 1158 WP_223646397.1 DNA phosphorothioation system sulfurtransferase DndC -
  JH290_RS16445 (JH290_16395) - 3748936..3749265 (-) 330 WP_075287335.1 helix-turn-helix transcriptional regulator -
  JH290_RS16450 (JH290_16400) - 3749367..3750128 (+) 762 WP_223646399.1 hypothetical protein -
  JH290_RS16455 (JH290_16405) - 3750183..3750497 (+) 315 WP_223646401.1 hypothetical protein -
  JH290_RS16460 (JH290_16410) - 3750494..3750874 (+) 381 WP_223646403.1 hypothetical protein -
  JH290_RS16465 (JH290_16415) - 3751455..3752300 (+) 846 WP_139051259.1 hypothetical protein -
  JH290_RS16470 (JH290_16420) - 3752311..3753156 (+) 846 WP_223646405.1 hypothetical protein -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62950.04 Da        Isoelectric Point: 5.6058

>NTDB_id=523777 JH290_RS16235 WP_223646357.1 3710156..3711892(-) (pilB) [Xanthomonas campestris pv. incanae strain 18048]
MNQVSSSANLVGITGIARRLVQDGALEEAAARIAMEQATAAKVPLPQWFSDKKLVSGAQLAAANAVEFGMPLMDVSAFDA
NQNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASFGSSL
GNDDDEMGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKA
PVKLNQRISARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQ
KLFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQD
PDIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTL
PEHALLAEGFTPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALM
KASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=523777 JH290_RS16235 WP_223646357.1 3710156..3711892(-) (pilB) [Xanthomonas campestris pv. incanae strain 18048]
GTGAACCAAGTATCAAGTAGCGCTAATTTGGTCGGCATCACAGGTATAGCCCGTCGGCTTGTCCAAGATGGGGCCTTAGA
AGAAGCTGCTGCACGTATTGCGATGGAGCAGGCTACTGCAGCTAAAGTTCCGTTGCCACAATGGTTTTCTGATAAAAAAC
TAGTCTCCGGGGCTCAACTCGCTGCAGCCAACGCCGTTGAGTTCGGGATGCCGCTGATGGATGTGTCGGCGTTCGACGCC
AATCAGAACGCGGTCAAGCTGGTCAGTGAGGAGTTGCTCCAGAAGTACCAGGTGCTGCCGCTGTTCAAGCGCGGCAACCG
GTTGTTCGTGGGGGTGAGCAACCCGACCCAGACCCGGGCGCTGGACGATATCAAGTTCCATACGAACCTGGTTGTCGAGC
CTATCCTGGTCGACGAGGACCAGATTCGTCGCACTTTGGAGCAGTGGCAGGCAAGTAACGCTTCGTTTGGTTCGTCGTTG
GGGAACGACGATGACGAGATGGGGGACCTGGACGTGTCGGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGT
CGATGCCAAGGGCGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGG
ACATCCATTTCGAGCCGTATGAAGACGACTACCGGGTGCGGTTGCGGATCGATGGGCTGCTGAAGAACGTGGCCAAGGCG
CCGGTGAAGCTCAACCAGCGCATCTCCGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCA
GGACGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGAGTACCTTGCCGACCCTGTTCGGCG
AGAAGGTGGTGCTGCGTATCCTGGACGCCAGTGCGGCCAAGCTCGGTATCGAGAAGCTGGGCTATGAGGCGGACCAGCAG
AAGCTGTTCCTGGATGCGATCCACAAGCCCTACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTC
GCTGTATACCGCGCTCGGGATTCTCAACGACGAGACGCGCAATATTTCCACGGCCGAGGATCCGGTCGAAATCCGGTTGC
CTGGCGTCAATCAGGTGCAGCAGAACGTCAAGCGGGGCATGACGTTTGCGGCGGCGCTGCGGTCGTTCCTGCGTCAGGAC
CCGGACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCACAT
GGTGCTGTCGACACTGCACACCAACGATGCGCCGCAAACCATTGCGCGTCTGATGAACATGGGTATCGCGCCGTACAACA
TCACCTCCTCGGTGACCCTGGTCATCGCGCAGCGTTTGGCACGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTG
CCGGAACATGCGCTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAAGCGGTCGGTTGCGA
TGAGTGCACCGAAGGCTACAAGGGCCGTACCGGCATCTATCAGGTGATGCCGATGACCGATGAAATCGGTGCGATCGTGC
TGGAAGGCGGCAATGCGATGCAGATCGCCGAGGCTGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCATTGATG
AAGGCTTCGCACGGCGTGACCAGCCTGGCCGAGATCAATCGTGTGACGAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(202-469)

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(52-153)


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
  pilB Acinetobacter baylyi ADP1

55.986

98.27

0.55
  pilB Acinetobacter baumannii D1279779

55.282

98.27

0.543
  pilB Legionella pneumophila strain ERS1305867

51.937

98.27

0.51
  pilF Neisseria gonorrhoeae MS11

48.944

98.27

0.481
  pilB Vibrio cholerae strain A1552

47.993

99.135

0.476
  pilB Vibrio campbellii strain DS40M4

46.221

98.443

0.455
  pilB Vibrio parahaemolyticus RIMD 2210633

46.512

96.713

0.45