Detailed information
Bioinformatically predicted
Overview
| Name | pilD | Type | Machinery gene |
| Locus tag | APT59_RS17770 | Genome accession | NZ_CP013987 |
| Coordinates | 3900073..3900945 (-) | Length | 290 a.a. |
| NCBI ID | WP_059316073.1 | Uniprot ID | A0A0U4VS76 |
| Organism | Pseudomonas oryzihabitans strain USDA-ARS-USMARC-56511 | ||
| 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 | 3861073..3899206 | 3900073..3900945 | flank | 867 |
Gene organization within MGE regions
Location: 3861073..3900945
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| APT59_RS17605 (APT59_17605) | recJ | 3861169..3862890 (-) | 1722 | WP_059316043.1 | single-stranded-DNA-specific exonuclease RecJ | - |
| APT59_RS17610 (APT59_17610) | - | 3862890..3863429 (-) | 540 | WP_059316044.1 | YaeQ family protein | - |
| APT59_RS17615 (APT59_17615) | thrC | 3863616..3865025 (-) | 1410 | WP_059316045.1 | threonine synthase | - |
| APT59_RS17620 (APT59_17620) | - | 3865072..3866376 (-) | 1305 | WP_059316046.1 | homoserine dehydrogenase | - |
| APT59_RS17625 (APT59_17625) | - | 3866484..3867209 (-) | 726 | WP_059316047.1 | thioredoxin fold domain-containing protein | - |
| APT59_RS17630 (APT59_17630) | xerD | 3867435..3868325 (-) | 891 | WP_017640793.1 | site-specific tyrosine recombinase XerD | - |
| APT59_RS17635 (APT59_17635) | - | 3868322..3868735 (-) | 414 | WP_059316048.1 | acyl-CoA thioesterase | - |
| APT59_RS17640 (APT59_17640) | rplS | 3868801..3869151 (-) | 351 | WP_007160957.1 | 50S ribosomal protein L19 | - |
| APT59_RS17645 (APT59_17645) | trmD | 3869194..3869931 (-) | 738 | WP_059316049.1 | tRNA (guanosine(37)-N1)-methyltransferase TrmD | - |
| APT59_RS17650 (APT59_17650) | rimM | 3869935..3870471 (-) | 537 | WP_059316050.1 | ribosome maturation factor RimM | - |
| APT59_RS17655 (APT59_17655) | rpsP | 3870477..3870725 (-) | 249 | WP_059316051.1 | 30S ribosomal protein S16 | - |
| APT59_RS17660 (APT59_17660) | ffh | 3870975..3872354 (-) | 1380 | WP_059316052.1 | signal recognition particle protein | - |
| APT59_RS17665 (APT59_17665) | - | 3872774..3873574 (+) | 801 | WP_059316053.1 | cytochrome C assembly family protein | - |
| APT59_RS17670 (APT59_17670) | - | 3873763..3875067 (+) | 1305 | WP_059316054.1 | MFS transporter | - |
| APT59_RS17675 (APT59_17675) | purT | 3875126..3876307 (-) | 1182 | WP_059316055.1 | formate-dependent phosphoribosylglycinamide formyltransferase | - |
| APT59_RS17680 (APT59_17680) | - | 3876329..3876526 (-) | 198 | WP_059316056.1 | DUF1289 domain-containing protein | - |
| APT59_RS17685 (APT59_17685) | - | 3876604..3877191 (-) | 588 | WP_059316057.1 | CoA pyrophosphatase | - |
| APT59_RS17690 (APT59_17690) | - | 3877319..3877873 (+) | 555 | WP_059316058.1 | NUDIX hydrolase | - |
| APT59_RS17695 (APT59_17695) | - | 3877897..3878433 (+) | 537 | WP_059316059.1 | L,D-transpeptidase family protein | - |
| APT59_RS17700 (APT59_17700) | - | 3878673..3879827 (-) | 1155 | WP_059316060.1 | ABC transporter ATP-binding protein | - |
| APT59_RS17705 (APT59_17705) | - | 3879838..3880497 (-) | 660 | WP_059316061.1 | ABC transporter permease | - |
| APT59_RS17710 (APT59_17710) | - | 3880501..3881403 (-) | 903 | WP_059316062.1 | glycine betaine ABC transporter substrate-binding protein | - |
| APT59_RS17715 (APT59_17715) | - | 3881413..3882123 (-) | 711 | WP_059316063.1 | ABC transporter permease | - |
| APT59_RS22485 | - | 3882843..3883034 (+) | 192 | WP_156428972.1 | hypothetical protein | - |
| APT59_RS17720 (APT59_17720) | - | 3883349..3884398 (+) | 1050 | WP_059316064.1 | glycoside hydrolase family 5 protein | - |
| APT59_RS17725 (APT59_17725) | - | 3884696..3885871 (+) | 1176 | WP_059316065.1 | acyltransferase family protein | - |
| APT59_RS17730 (APT59_17730) | - | 3885968..3887551 (+) | 1584 | WP_059316066.1 | peptide chain release factor 3 | - |
| APT59_RS17735 (APT59_17735) | rmuC | 3887632..3889197 (-) | 1566 | WP_059316067.1 | DNA recombination protein RmuC | - |
| APT59_RS17740 (APT59_17740) | recD | 3889271..3891352 (-) | 2082 | WP_059316068.1 | exodeoxyribonuclease V subunit alpha | - |
| APT59_RS17745 (APT59_17745) | recB | 3891345..3895007 (-) | 3663 | WP_059316069.1 | exodeoxyribonuclease V subunit beta | - |
| APT59_RS17750 (APT59_17750) | recC | 3895004..3898435 (-) | 3432 | WP_059316070.1 | exodeoxyribonuclease V subunit gamma | - |
| APT59_RS17755 (APT59_17755) | - | 3898618..3899115 (+) | 498 | WP_059316071.1 | hypothetical protein | - |
| APT59_RS17760 (APT59_17760) | yacG | 3899271..3899468 (-) | 198 | WP_007160931.1 | DNA gyrase inhibitor YacG | - |
| APT59_RS17765 (APT59_17765) | coaE | 3899465..3900076 (-) | 612 | WP_059316072.1 | dephospho-CoA kinase | - |
| APT59_RS17770 (APT59_17770) | pilD | 3900073..3900945 (-) | 873 | WP_059316073.1 | prepilin peptidase | Machinery gene |
Sequence
Protein
Download Length: 290 a.a. Molecular weight: 31502.54 Da Isoelectric Point: 8.2337
>NTDB_id=166871 APT59_RS17770 WP_059316073.1 3900073..3900945(-) (pilD) [Pseudomonas oryzihabitans strain USDA-ARS-USMARC-56511]
MALLELLASAPLAGALCALVLGLLVGSFLNVVVYRLPVMLRRDWQSEAREVLELPPEPAGAPFNLARPASRCPHCQRAVR
PLENVPVLSYLLLRGRCKGCQASISLRYPLVELACGLLSAWVIWHLGVTWQGGAFLLLTWGLLAASLIDADHQLLPDVIV
LPLLWLGLIANQFGLFTTLGDAVWGAVAGYLSLWLVFQLFRLLTGKEGMGYGDFKLLALLGAWGGWQILPLTILLSSLVG
AVLGVITLRLRRAETSTPLPFGPYLAVAGWIALLWGDQITGLYLNFAGFR
MALLELLASAPLAGALCALVLGLLVGSFLNVVVYRLPVMLRRDWQSEAREVLELPPEPAGAPFNLARPASRCPHCQRAVR
PLENVPVLSYLLLRGRCKGCQASISLRYPLVELACGLLSAWVIWHLGVTWQGGAFLLLTWGLLAASLIDADHQLLPDVIV
LPLLWLGLIANQFGLFTTLGDAVWGAVAGYLSLWLVFQLFRLLTGKEGMGYGDFKLLALLGAWGGWQILPLTILLSSLVG
AVLGVITLRLRRAETSTPLPFGPYLAVAGWIALLWGDQITGLYLNFAGFR
Nucleotide
Download Length: 873 bp
>NTDB_id=166871 APT59_RS17770 WP_059316073.1 3900073..3900945(-) (pilD) [Pseudomonas oryzihabitans strain USDA-ARS-USMARC-56511]
ATGGCGCTGCTGGAACTATTGGCCAGCGCGCCGCTAGCCGGGGCGTTGTGCGCGCTGGTGCTGGGGCTGCTGGTAGGTAG
CTTTCTCAATGTGGTGGTCTATCGGCTGCCGGTGATGCTGAGGCGGGATTGGCAGTCGGAGGCGCGTGAGGTGCTGGAAT
TGCCGCCCGAGCCGGCGGGAGCGCCTTTCAACCTGGCGCGACCTGCTTCCCGCTGCCCCCATTGCCAGCGTGCCGTACGG
CCCTTGGAAAACGTGCCGGTGCTGAGTTATCTGCTCCTGCGCGGTCGCTGCAAGGGGTGTCAGGCCTCCATCAGCCTGCG
TTATCCGCTGGTGGAGCTGGCCTGTGGACTGCTGTCCGCCTGGGTCATCTGGCATCTGGGCGTGACCTGGCAGGGCGGGG
CCTTCCTGCTGCTGACCTGGGGGCTGCTGGCGGCCAGTCTGATTGATGCCGATCATCAGCTGCTGCCGGACGTGATCGTC
CTGCCGTTGTTGTGGCTGGGGTTGATCGCCAATCAATTCGGGCTGTTCACCACCCTCGGCGATGCCGTCTGGGGGGCGGT
GGCGGGCTATCTGAGTCTCTGGCTTGTGTTCCAGCTGTTCCGCCTGCTTACTGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAGCTGCTGGCGCTGCTTGGCGCCTGGGGTGGTTGGCAGATCCTGCCCCTGACCATCCTGCTGTCGTCGCTGGTGGGT
GCCGTCCTGGGCGTCATCACCCTGCGTCTGCGGCGGGCGGAAACCAGCACGCCCTTGCCCTTTGGTCCCTATCTCGCCGT
AGCGGGGTGGATTGCCTTGCTCTGGGGTGATCAAATAACCGGCTTGTACCTGAACTTCGCCGGATTCCGATGA
ATGGCGCTGCTGGAACTATTGGCCAGCGCGCCGCTAGCCGGGGCGTTGTGCGCGCTGGTGCTGGGGCTGCTGGTAGGTAG
CTTTCTCAATGTGGTGGTCTATCGGCTGCCGGTGATGCTGAGGCGGGATTGGCAGTCGGAGGCGCGTGAGGTGCTGGAAT
TGCCGCCCGAGCCGGCGGGAGCGCCTTTCAACCTGGCGCGACCTGCTTCCCGCTGCCCCCATTGCCAGCGTGCCGTACGG
CCCTTGGAAAACGTGCCGGTGCTGAGTTATCTGCTCCTGCGCGGTCGCTGCAAGGGGTGTCAGGCCTCCATCAGCCTGCG
TTATCCGCTGGTGGAGCTGGCCTGTGGACTGCTGTCCGCCTGGGTCATCTGGCATCTGGGCGTGACCTGGCAGGGCGGGG
CCTTCCTGCTGCTGACCTGGGGGCTGCTGGCGGCCAGTCTGATTGATGCCGATCATCAGCTGCTGCCGGACGTGATCGTC
CTGCCGTTGTTGTGGCTGGGGTTGATCGCCAATCAATTCGGGCTGTTCACCACCCTCGGCGATGCCGTCTGGGGGGCGGT
GGCGGGCTATCTGAGTCTCTGGCTTGTGTTCCAGCTGTTCCGCCTGCTTACTGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAGCTGCTGGCGCTGCTTGGCGCCTGGGGTGGTTGGCAGATCCTGCCCCTGACCATCCTGCTGTCGTCGCTGGTGGGT
GCCGTCCTGGGCGTCATCACCCTGCGTCTGCGGCGGGCGGAAACCAGCACGCCCTTGCCCTTTGGTCCCTATCTCGCCGT
AGCGGGGTGGATTGCCTTGCTCTGGGGTGATCAAATAACCGGCTTGTACCTGAACTTCGCCGGATTCCGATGA
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| pilD | Vibrio cholerae strain A1552 |
50 |
97.931 |
0.49 |
| pilD | Neisseria gonorrhoeae MS11 |
50 |
95.172 |
0.476 |
| pilD | Acinetobacter baumannii D1279779 |
51.685 |
92.069 |
0.476 |
| pilD | Vibrio campbellii strain DS40M4 |
48.239 |
97.931 |
0.472 |
| pilD | Acinetobacter nosocomialis M2 |
50.936 |
92.069 |
0.469 |