Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   RB214_RS14865 Genome accession   NZ_CP133569
Coordinates   3209672..3210565 (+) Length   297 a.a.
NCBI ID   WP_309169028.1    Uniprot ID   -
Organism   Pseudoalteromonas sp. HL-AS1     
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)
ICE 3192192..3258234 3209672..3210565 within 0


Gene organization within MGE regions


Location: 3192192..3258234
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RB214_RS14795 (RB214_14795) - 3192192..3193160 (-) 969 WP_309167684.1 IS30 family transposase -
  RB214_RS14800 (RB214_14800) - 3193327..3193842 (+) 516 WP_309167685.1 hypothetical protein -
  RB214_RS14805 (RB214_14805) - 3193853..3194533 (-) 681 WP_309167686.1 tRNA-uridine aminocarboxypropyltransferase -
  RB214_RS14810 (RB214_14810) lpdA 3194670..3196094 (-) 1425 WP_002957761.1 dihydrolipoyl dehydrogenase -
  RB214_RS14815 (RB214_14815) aceF 3196300..3198216 (-) 1917 WP_309167687.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  RB214_RS14820 (RB214_14820) aceE 3198227..3200893 (-) 2667 WP_002957763.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  RB214_RS14825 (RB214_14825) pdhR 3200984..3201733 (-) 750 WP_002957764.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  RB214_RS14830 (RB214_14830) - 3202371..3202823 (+) 453 WP_309167688.1 transposase -
  RB214_RS14835 (RB214_14835) ampE 3202975..3203826 (-) 852 WP_309167689.1 beta-lactamase regulator AmpE -
  RB214_RS14840 (RB214_14840) ampD 3203840..3204394 (-) 555 WP_309167690.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  RB214_RS14845 (RB214_14845) nadC 3204722..3205567 (+) 846 WP_309167691.1 carboxylating nicotinate-nucleotide diphosphorylase -
  RB214_RS14850 (RB214_14850) pilA/pilAI 3206108..3206536 (+) 429 WP_309167692.1 pilin Machinery gene
  RB214_RS14855 (RB214_14855) - 3206588..3208261 (+) 1674 WP_309167693.1 Wzy polymerase domain-containing protein -
  RB214_RS14860 (RB214_14860) pilC 3208271..3209500 (+) 1230 WP_309167694.1 type II secretion system F family protein Machinery gene
  RB214_RS14865 (RB214_14865) pilD 3209672..3210565 (+) 894 WP_309169028.1 A24 family peptidase Machinery gene
  RB214_RS14870 (RB214_14870) coaE 3210567..3211220 (+) 654 WP_309167695.1 dephospho-CoA kinase -
  RB214_RS14875 (RB214_14875) pilB 3211314..3212990 (+) 1677 WP_309167696.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RB214_RS14880 (RB214_14880) yacG 3213102..3213332 (+) 231 WP_024597564.1 DNA gyrase inhibitor YacG -
  RB214_RS14885 (RB214_14885) - 3213405..3213893 (-) 489 WP_309167697.1 periplasmic heavy metal sensor -
  RB214_RS14890 (RB214_14890) - 3214322..3215011 (+) 690 WP_197098823.1 response regulator -
  RB214_RS14895 (RB214_14895) - 3214989..3216404 (+) 1416 WP_309167698.1 ATP-binding protein -
  RB214_RS14900 (RB214_14900) - 3216408..3217355 (+) 948 WP_309167699.1 alpha/beta fold hydrolase -
  RB214_RS14905 (RB214_14905) - 3217315..3218181 (-) 867 WP_081709160.1 cation diffusion facilitator family transporter -
  RB214_RS14910 (RB214_14910) trmL 3218343..3218807 (+) 465 WP_309167700.1 tRNA (uridine(34)/cytosine(34)/5- carboxymethylaminomethyluridine(34)-2'-O)- methyltransferase TrmL -
  RB214_RS14915 (RB214_14915) gpsA 3218876..3219883 (-) 1008 WP_309167701.1 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase -
  RB214_RS14920 (RB214_14920) secB 3219887..3220372 (-) 486 WP_309167702.1 protein-export chaperone SecB -
  RB214_RS14925 (RB214_14925) grxC 3220407..3220664 (-) 258 WP_002957783.1 glutaredoxin 3 -
  RB214_RS14930 (RB214_14930) - 3220696..3221127 (-) 432 WP_007376037.1 rhodanese-like domain-containing protein -
  RB214_RS14935 (RB214_14935) gpmM 3221465..3223009 (+) 1545 WP_007582830.1 2,3-bisphosphoglycerate-independent phosphoglycerate mutase -
  RB214_RS14940 (RB214_14940) - 3223013..3224152 (+) 1140 WP_197098828.1 murein hydrolase activator EnvC -
  RB214_RS14945 (RB214_14945) - 3224187..3225452 (+) 1266 WP_309167703.1 S41 family peptidase -
  RB214_RS14950 (RB214_14950) - 3225503..3226264 (+) 762 WP_309167704.1 divergent polysaccharide deacetylase family protein -
  RB214_RS14955 (RB214_14955) rpoH 3226607..3227470 (-) 864 WP_002957791.1 RNA polymerase sigma factor RpoH -
  RB214_RS14960 (RB214_14960) ftsX 3227785..3228771 (-) 987 WP_165744576.1 permease-like cell division protein FtsX -
  RB214_RS14965 (RB214_14965) ftsE 3228768..3229445 (-) 678 WP_002957793.1 cell division ATP-binding protein FtsE -
  RB214_RS14970 (RB214_14970) ftsY 3229533..3231464 (-) 1932 WP_309167705.1 signal recognition particle-docking protein FtsY -
  RB214_RS14975 (RB214_14975) rsmD 3231672..3232277 (+) 606 WP_165744710.1 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD -
  RB214_RS14980 (RB214_14980) rpsU 3232423..3232638 (+) 216 WP_002957797.1 30S ribosomal protein S21 -
  RB214_RS14985 (RB214_14985) - 3232658..3233104 (+) 447 WP_007376027.1 GatB/YqeY domain-containing protein -
  RB214_RS14990 (RB214_14990) dnaG 3233349..3235100 (+) 1752 WP_165744708.1 DNA primase -
  RB214_RS14995 (RB214_14995) rpoD 3235491..3237341 (+) 1851 WP_309167706.1 RNA polymerase sigma factor RpoD -
  RB214_RS15000 (RB214_15000) prmA 3237409..3238290 (+) 882 WP_002957801.1 50S ribosomal protein L11 methyltransferase -
  RB214_RS15005 (RB214_15005) dusB 3238573..3239544 (+) 972 WP_024603689.1 tRNA dihydrouridine synthase DusB -
  RB214_RS15010 (RB214_15010) fis 3239564..3239854 (+) 291 WP_002957804.1 DNA-binding transcriptional regulator Fis -
  RB214_RS15015 (RB214_15015) purH 3240180..3241766 (+) 1587 WP_309167707.1 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase -
  RB214_RS15020 (RB214_15020) - 3241873..3242694 (+) 822 WP_309167708.1 methyltransferase -
  RB214_RS15025 (RB214_15025) purD 3242710..3243993 (+) 1284 WP_165744701.1 phosphoribosylamine--glycine ligase -
  RB214_RS15030 (RB214_15030) - 3244106..3246646 (+) 2541 WP_309167709.1 EAL domain-containing protein -
  RB214_RS15035 (RB214_15035) - 3246669..3247478 (+) 810 WP_024597548.1 DUF2797 domain-containing protein -
  RB214_RS15040 (RB214_15040) - 3247485..3247778 (+) 294 WP_002957811.1 hypothetical protein -
  RB214_RS15045 (RB214_15045) - 3247792..3248709 (-) 918 WP_309167710.1 histone deacetylase family protein -
  RB214_RS15050 (RB214_15050) - 3248810..3250351 (-) 1542 WP_309167711.1 serine hydrolase -
  RB214_RS15055 (RB214_15055) - 3250367..3250861 (-) 495 WP_182747947.1 gamma-glutamylcyclotransferase family protein -
  RB214_RS15060 (RB214_15060) - 3250888..3251526 (-) 639 WP_197111575.1 LysE family translocator -
  RB214_RS15065 (RB214_15065) - 3251538..3252311 (-) 774 WP_002957816.1 hypothetical protein -
  RB214_RS15070 (RB214_15070) - 3252359..3252844 (-) 486 WP_002957817.1 CreA family protein -
  RB214_RS15075 (RB214_15075) - 3253052..3253381 (+) 330 WP_002957818.1 5-carboxymethyl-2-hydroxymuconate Delta-isomerase -
  RB214_RS15080 (RB214_15080) - 3253983..3254282 (-) 300 WP_309167712.1 HigA family addiction module antitoxin -
  RB214_RS15085 (RB214_15085) - 3254354..3254659 (-) 306 WP_309167713.1 type II toxin-antitoxin system RelE/ParE family toxin -
  RB214_RS15090 (RB214_15090) - 3255257..3255436 (+) 180 WP_309167714.1 hypothetical protein -
  RB214_RS15095 (RB214_15095) - 3255429..3256310 (+) 882 WP_309167715.1 site-specific integrase -
  RB214_RS15100 (RB214_15100) - 3256352..3256714 (-) 363 WP_309167716.1 hypothetical protein -
  RB214_RS15105 (RB214_15105) - 3256766..3257038 (-) 273 WP_309167717.1 hypothetical protein -
  RB214_RS15110 (RB214_15110) - 3257181..3257768 (-) 588 WP_309167718.1 hypothetical protein -

Sequence

Protein


Download         Length: 297 a.a.        Molecular weight: 32794.05 Da        Isoelectric Point: 7.4655

>NTDB_id=874972 RB214_RS14865 WP_309169028.1 3209672..3210565(+) (pilD) [Pseudoalteromonas sp. HL-AS1]
MQSIIEVMQSQLWFYLTTVGLISLCIGSFLNVVIYRLPLMMQREWQSECRLLLEDELTANKSKQANTSEPFNLVKPNSTC
PKCKTAIKPWQNIPIISWLILKGKCASCSNPISARYPAVELITAVLSLIVAYSFGTTEQALLYIFVTWILVALTFIDIDH
MLLPDQLTLPLVWLALIASVLGYTITPTDAIIGAACGYLSLWSVFWLFKLLTGKEGMGYGDFKLLAVFGALLGWQSLLTI
ILLSSVVGAIIGIALLSIQGKDKATPIPFGPYLAIAGWIAMLWGNQIQGAYFNLIGY

Nucleotide


Download         Length: 894 bp        

>NTDB_id=874972 RB214_RS14865 WP_309169028.1 3209672..3210565(+) (pilD) [Pseudoalteromonas sp. HL-AS1]
ATGCAAAGTATTATTGAAGTAATGCAAAGCCAATTGTGGTTTTATTTAACCACAGTTGGCTTAATTAGTTTATGTATCGG
TAGCTTTTTAAATGTGGTTATTTATCGCTTACCGCTAATGATGCAACGTGAGTGGCAAAGCGAATGCAGACTACTGTTGG
AAGATGAACTTACAGCTAATAAATCTAAACAAGCCAACACCAGCGAACCTTTCAACTTAGTAAAACCCAACTCTACCTGC
CCTAAATGTAAAACTGCCATTAAGCCTTGGCAGAATATTCCTATTATTAGTTGGTTAATACTTAAAGGTAAATGTGCAAG
CTGCAGTAACCCTATTTCTGCTCGCTACCCTGCTGTAGAGCTAATTACTGCCGTATTAAGTTTAATTGTTGCCTACAGCT
TTGGTACGACCGAGCAAGCCCTTTTATATATTTTTGTAACGTGGATTTTAGTAGCACTAACCTTTATTGATATTGATCAC
ATGTTACTGCCAGACCAGCTTACATTACCGCTTGTATGGCTTGCACTTATTGCCTCGGTATTAGGTTACACAATTACGCC
TACTGATGCCATTATTGGCGCTGCTTGTGGTTATTTAAGCTTATGGAGCGTATTTTGGTTATTTAAGCTATTGACCGGCA
AAGAAGGCATGGGCTATGGCGATTTTAAATTGCTCGCTGTATTTGGGGCGTTACTTGGCTGGCAGTCATTGCTTACTATT
ATTCTGCTTTCGAGCGTAGTAGGTGCCATAATAGGTATTGCACTGTTGAGCATACAAGGTAAAGACAAAGCGACCCCTAT
CCCTTTTGGCCCTTATTTAGCGATAGCTGGCTGGATTGCAATGCTTTGGGGCAACCAAATTCAAGGCGCTTATTTTAATT
TAATAGGTTATTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(145-253)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-134)


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

52.234

97.98

0.512
  pilD Acinetobacter nosocomialis M2

51.877

98.653

0.512
  pilD Vibrio cholerae strain A1552

51.89

97.98

0.508
  pilD Vibrio campbellii strain DS40M4

51.712

98.316

0.508
  pilD Neisseria gonorrhoeae MS11

46.241

89.562

0.414