Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   LQE85_RS15495 Genome accession   NZ_CP088000
Coordinates   3365839..3366702 (+) Length   287 a.a.
NCBI ID   WP_068853817.1    Uniprot ID   A0AAP6GZC8
Organism   Stenotrophomonas rhizophila strain Bl2-2     
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 3335551..3373259 3365839..3366702 within 0


Gene organization within MGE regions


Location: 3335551..3373259
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LQE85_RS15350 (LQE85_15350) - 3335551..3336474 (-) 924 WP_249832990.1 hypothetical protein -
  LQE85_RS15355 (LQE85_15355) - 3336583..3338217 (-) 1635 WP_249832991.1 NAD+ synthase -
  LQE85_RS15360 (LQE85_15360) sucD 3338355..3339230 (-) 876 WP_093533719.1 succinate--CoA ligase subunit alpha -
  LQE85_RS15365 (LQE85_15365) sucC 3339252..3340421 (-) 1170 WP_068853794.1 ADP-forming succinate--CoA ligase subunit beta -
  LQE85_RS15370 (LQE85_15370) - 3340665..3342278 (+) 1614 WP_184126716.1 HAMP domain-containing sensor histidine kinase -
  LQE85_RS15375 (LQE85_15375) pilR 3342343..3343728 (+) 1386 WP_249832992.1 sigma-54 dependent transcriptional regulator Regulator
  LQE85_RS15380 (LQE85_15380) - 3344218..3344766 (+) 549 WP_249832993.1 SymE family type I addiction module toxin -
  LQE85_RS19750 - 3345345..3345467 (-) 123 WP_283938960.1 hypothetical protein -
  LQE85_RS15385 (LQE85_15385) - 3345625..3346101 (-) 477 WP_249832994.1 hypothetical protein -
  LQE85_RS15390 (LQE85_15390) - 3346489..3346971 (-) 483 WP_249832995.1 hypothetical protein -
  LQE85_RS15395 (LQE85_15395) - 3347182..3347544 (-) 363 WP_249832996.1 hypothetical protein -
  LQE85_RS15400 (LQE85_15400) - 3348190..3348462 (-) 273 WP_157771757.1 hypothetical protein -
  LQE85_RS15405 (LQE85_15405) - 3349427..3349723 (-) 297 WP_249832997.1 hypothetical protein -
  LQE85_RS15410 (LQE85_15410) - 3350320..3350676 (-) 357 WP_249832998.1 hypothetical protein -
  LQE85_RS15415 (LQE85_15415) - 3350788..3350937 (-) 150 WP_217538604.1 hypothetical protein -
  LQE85_RS15420 (LQE85_15420) - 3350930..3351412 (-) 483 WP_249832999.1 hypothetical protein -
  LQE85_RS15425 (LQE85_15425) - 3351445..3351717 (-) 273 WP_249833000.1 hypothetical protein -
  LQE85_RS15430 (LQE85_15430) - 3351981..3352355 (-) 375 WP_249833001.1 DUF6869 domain-containing protein -
  LQE85_RS15435 (LQE85_15435) - 3352472..3352681 (-) 210 WP_210130936.1 hypothetical protein -
  LQE85_RS15440 (LQE85_15440) - 3352817..3353518 (-) 702 WP_249833002.1 hypothetical protein -
  LQE85_RS15445 (LQE85_15445) - 3354717..3355064 (-) 348 WP_249833003.1 hypothetical protein -
  LQE85_RS15450 (LQE85_15450) - 3355331..3355819 (-) 489 WP_249833004.1 hypothetical protein -
  LQE85_RS15455 (LQE85_15455) - 3355957..3356337 (-) 381 WP_249833005.1 hypothetical protein -
  LQE85_RS15460 (LQE85_15460) - 3356667..3357197 (-) 531 WP_157771765.1 hypothetical protein -
  LQE85_RS15465 (LQE85_15465) - 3357261..3357992 (-) 732 WP_249833006.1 hypothetical protein -
  LQE85_RS15470 (LQE85_15470) - 3358171..3361209 (-) 3039 WP_249833007.1 spermine synthase -
  LQE85_RS15475 (LQE85_15475) pilB 3361493..3363226 (-) 1734 WP_068853813.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LQE85_RS15480 (LQE85_15480) - 3363283..3363693 (-) 411 WP_249833008.1 pilin -
  LQE85_RS15485 (LQE85_15485) pilA/pilAI 3363812..3364219 (-) 408 WP_068853815.1 pilin Machinery gene
  LQE85_RS15490 (LQE85_15490) pilC 3364576..3365832 (+) 1257 WP_068853816.1 type II secretion system F family protein Machinery gene
  LQE85_RS15495 (LQE85_15495) pilD 3365839..3366702 (+) 864 WP_068853817.1 A24 family peptidase Machinery gene
  LQE85_RS15500 (LQE85_15500) coaE 3366710..3367318 (+) 609 WP_249833009.1 dephospho-CoA kinase -
  LQE85_RS15505 (LQE85_15505) - 3367405..3368769 (-) 1365 WP_095363631.1 HAMP domain-containing sensor histidine kinase -
  LQE85_RS15510 (LQE85_15510) - 3368732..3369409 (-) 678 WP_017356179.1 response regulator transcription factor -
  LQE85_RS15515 (LQE85_15515) - 3369417..3369887 (-) 471 WP_095363630.1 hypothetical protein -
  LQE85_RS15520 (LQE85_15520) rimK 3370120..3371025 (-) 906 WP_249833010.1 30S ribosomal protein S6--L-glutamate ligase -
  LQE85_RS15525 (LQE85_15525) - 3371244..3372023 (+) 780 WP_249833011.1 histidine phosphatase family protein -
  LQE85_RS15530 (LQE85_15530) - 3372025..3372897 (+) 873 WP_093533699.1 NAD(P)H-hydrate dehydratase -
  LQE85_RS15535 (LQE85_15535) - 3372900..3373259 (-) 360 WP_184126692.1 nuclear transport factor 2 family protein -

Sequence

Protein


Download         Length: 287 a.a.        Molecular weight: 31733.82 Da        Isoelectric Point: 8.4749

>NTDB_id=632242 LQE85_RS15495 WP_068853817.1 3365839..3366702(+) (pilD) [Stenotrophomonas rhizophila strain Bl2-2]
MAFLDQHPGLGYPAAAALGLLIGSFLNVVILRLPKRLEWQWKRDAREVLELPDIYEPPPPGIVVEPSHCPHCKHKLSWYE
NIPLFSWLVLGGKCRHCHAPISIQYPLVELLTGLLVVASVWQFGFGWQGFGAIVLSCFLVALSGIDLRTQLLPDQLTLPL
MWLGLIGSIDNLYMPAKPALLGAIAGYLLLWSVWWLFKQITGKEGIGHGDFKLLAALGAWCGLKGILPIILLSSVLGAII
GSIWLYSRGRDRATPIPFGPYLALAGWIVFMWGEPLINAYLRVSGLR

Nucleotide


Download         Length: 864 bp        

>NTDB_id=632242 LQE85_RS15495 WP_068853817.1 3365839..3366702(+) (pilD) [Stenotrophomonas rhizophila strain Bl2-2]
ATGGCATTTCTCGACCAGCATCCCGGCCTCGGCTATCCGGCCGCGGCCGCACTGGGGTTGCTGATTGGCAGCTTCCTCAA
TGTGGTGATCCTGCGCCTGCCCAAGCGGCTGGAGTGGCAGTGGAAGCGCGACGCCCGCGAGGTGCTCGAGCTTCCGGACA
TCTACGAACCACCCCCGCCCGGGATCGTGGTCGAGCCGTCGCACTGCCCGCACTGCAAGCACAAGCTGTCCTGGTACGAG
AACATCCCGCTGTTCAGCTGGCTGGTCCTAGGCGGCAAGTGCCGCCACTGCCATGCGCCGATCTCCATCCAGTACCCGCT
GGTCGAGCTGTTGACCGGCTTGCTGGTGGTAGCCAGCGTCTGGCAGTTCGGCTTCGGCTGGCAGGGCTTCGGCGCCATCG
TGCTGAGCTGCTTCCTGGTGGCCTTGTCCGGTATCGACCTGCGCACCCAGTTGTTGCCTGACCAGCTCACCCTGCCGCTG
ATGTGGCTGGGCCTGATAGGCAGCATCGACAACCTGTACATGCCGGCCAAGCCTGCCCTGCTGGGCGCGATAGCCGGCTA
CCTGCTGCTGTGGTCGGTATGGTGGCTGTTCAAGCAGATCACCGGCAAGGAAGGCATTGGTCACGGCGATTTCAAGCTGC
TGGCCGCGCTGGGCGCCTGGTGCGGGTTGAAGGGCATCCTGCCGATCATCCTGCTCTCGTCGGTGCTTGGGGCGATCATC
GGTTCGATCTGGCTTTACTCGCGCGGCCGCGACCGTGCCACGCCGATTCCGTTCGGGCCCTACCTGGCCCTGGCGGGCTG
GATCGTGTTCATGTGGGGCGAGCCGTTGATCAACGCGTATCTGCGGGTGTCCGGCCTGCGCTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(133-241)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-123)


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 Acinetobacter baumannii D1279779

48.264

100

0.484
  pilD Acinetobacter nosocomialis M2

48.41

98.606

0.477
  pilD Vibrio campbellii strain DS40M4

46.479

98.955

0.46
  pilD Vibrio cholerae strain A1552

47.292

96.516

0.456
  pilD Neisseria gonorrhoeae MS11

44.043

96.516

0.425