Detailed information
Bioinformatically predicted
Overview
| Name | pilD | Type | Machinery gene |
| Locus tag | AB8617_RS11245 | Genome accession | NZ_CP166995 |
| Coordinates | 2456955..2457827 (+) | Length | 290 a.a. |
| NCBI ID | WP_409438964.1 | Uniprot ID | - |
| Organism | Psychromonas sp. GE-S-Ul-11 | ||
| 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 | 2457343..2499172 | 2456955..2457827 | flank | -484 |
Gene organization within MGE regions
Location: 2456955..2499172
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AB8617_RS11245 (AB8617_11240) | pilD | 2456955..2457827 (+) | 873 | WP_409438964.1 | prepilin peptidase | Machinery gene |
| AB8617_RS11250 (AB8617_11245) | tadA | 2457832..2458308 (+) | 477 | WP_418135121.1 | tRNA adenosine(34) deaminase TadA | - |
| AB8617_RS11255 (AB8617_11250) | - | 2458324..2458494 (+) | 171 | WP_169727660.1 | hypothetical protein | - |
| AB8617_RS11260 (AB8617_11255) | - | 2458579..2459520 (-) | 942 | WP_290041207.1 | DMT family transporter | - |
| AB8617_RS11265 (AB8617_11260) | - | 2459742..2460158 (-) | 417 | WP_409438965.1 | CBS domain-containing protein | - |
| AB8617_RS11270 (AB8617_11265) | mltF | 2460351..2462183 (-) | 1833 | WP_409438966.1 | membrane-bound lytic murein transglycosylase MltF | - |
| AB8617_RS11275 (AB8617_11270) | purL | 2462376..2466269 (+) | 3894 | WP_418135122.1 | phosphoribosylformylglycinamidine synthase | - |
| AB8617_RS11280 (AB8617_11275) | - | 2466415..2469120 (+) | 2706 | WP_409438968.1 | EAL and GGDEF domain-containing protein | - |
| AB8617_RS11285 (AB8617_11280) | cls | 2469310..2470767 (+) | 1458 | WP_409438969.1 | cardiolipin synthase | - |
| AB8617_RS11290 (AB8617_11285) | - | 2471213..2471653 (+) | 441 | WP_290041195.1 | hypothetical protein | - |
| AB8617_RS11295 (AB8617_11290) | - | 2471669..2471854 (+) | 186 | WP_409438970.1 | DUF1289 domain-containing protein | - |
| AB8617_RS11300 (AB8617_11295) | - | 2472113..2472568 (-) | 456 | WP_290041191.1 | MerR family transcriptional regulator | - |
| AB8617_RS11305 (AB8617_11300) | - | 2472822..2473073 (+) | 252 | WP_290041189.1 | hypothetical protein | - |
| AB8617_RS11310 (AB8617_11305) | adhE | 2473167..2475851 (-) | 2685 | WP_418135123.1 | bifunctional acetaldehyde-CoA/alcohol dehydrogenase | - |
| AB8617_RS11315 (AB8617_11310) | - | 2476203..2477324 (+) | 1122 | WP_290041185.1 | AI-2E family transporter | - |
| AB8617_RS11320 (AB8617_11315) | - | 2477326..2478255 (+) | 930 | WP_290041183.1 | class I SAM-dependent methyltransferase | - |
| AB8617_RS11325 (AB8617_11320) | - | 2478370..2478972 (-) | 603 | WP_409438971.1 | hypothetical protein | - |
| AB8617_RS11330 (AB8617_11325) | pta | 2479243..2481408 (-) | 2166 | WP_290041179.1 | phosphate acetyltransferase | - |
| AB8617_RS11335 (AB8617_11330) | - | 2481471..2482670 (-) | 1200 | WP_290041178.1 | acetate kinase | - |
| AB8617_RS11340 (AB8617_11335) | yfbV | 2482950..2483399 (+) | 450 | WP_290041176.1 | terminus macrodomain insulation protein YfbV | - |
| AB8617_RS11345 (AB8617_11340) | rlmA | 2483396..2484211 (-) | 816 | WP_409438972.1 | 23S rRNA (guanine(745)-N(1))-methyltransferase | - |
| AB8617_RS11350 (AB8617_11345) | pflA | 2484315..2485055 (-) | 741 | WP_290041171.1 | pyruvate formate lyase 1-activating protein | - |
| AB8617_RS11355 (AB8617_11350) | pflB | 2485239..2487524 (-) | 2286 | WP_290041169.1 | formate C-acetyltransferase | - |
| AB8617_RS11360 (AB8617_11355) | - | 2488000..2488503 (+) | 504 | WP_409438973.1 | glycine cleavage system protein R | - |
| AB8617_RS11365 (AB8617_11360) | - | 2488612..2490132 (-) | 1521 | WP_409438974.1 | DUF3360 family protein | - |
| AB8617_RS11370 (AB8617_11365) | fldB | 2490574..2491092 (-) | 519 | WP_290041163.1 | flavodoxin FldB | - |
| AB8617_RS11375 (AB8617_11370) | xerD | 2491150..2492046 (+) | 897 | WP_409438975.1 | site-specific tyrosine recombinase XerD | - |
| AB8617_RS11380 (AB8617_11375) | dsbC | 2492178..2492933 (+) | 756 | WP_290041160.1 | bifunctional protein-disulfide isomerase/oxidoreductase DsbC | - |
| AB8617_RS11385 (AB8617_11380) | recJ | 2492990..2494723 (+) | 1734 | WP_409438976.1 | single-stranded-DNA-specific exonuclease RecJ | - |
| AB8617_RS11390 (AB8617_11385) | trmL | 2494774..2495238 (-) | 465 | WP_409438977.1 | tRNA (uridine(34)/cytosine(34)/5- carboxymethylaminomethyluridine(34)-2'-O)- methyltransferase TrmL | - |
| AB8617_RS11395 (AB8617_11390) | - | 2495584..2496519 (+) | 936 | WP_290041155.1 | cation diffusion facilitator family transporter | - |
| AB8617_RS11400 (AB8617_11395) | cysE | 2496547..2497326 (+) | 780 | WP_290041154.1 | serine O-acetyltransferase | - |
| AB8617_RS11405 (AB8617_11400) | - | 2497346..2497579 (-) | 234 | WP_290041153.1 | DUF1653 domain-containing protein | - |
| AB8617_RS11410 (AB8617_11405) | - | 2497752..2497985 (+) | 234 | WP_290041151.1 | cell division protein ZapB | - |
| AB8617_RS11415 (AB8617_11410) | rraA | 2498093..2498608 (-) | 516 | WP_290041149.1 | ribonuclease E activity regulator RraA | - |
Sequence
Protein
Download Length: 290 a.a. Molecular weight: 32284.43 Da Isoelectric Point: 4.7567
>NTDB_id=1036651 AB8617_RS11245 WP_409438964.1 2456955..2457827(+) (pilD) [Psychromonas sp. GE-S-Ul-11]
MSDVITLMEQVPSFYFGLVLVLGLLVGSFLNVVIYRLPVMMQRSWEADCAETFPDSNIKVDDSTFNLVLPRSRCPKCNHL
IGSLENIPLVSWLLQKGRCKHCDCNIPARYPSIELLTGLMSLAVAYVIPFGWPVLFALLFTWTLISLTFIDVDTMLLPDQ
LTLPLVWLGLLVNMSDTFIGLQDAVLGAVFGYLTLWSVYWAFKLLTGKEGMGYGDFKLLAALGAWFGWQALPLIIILSSF
AGAILGIIMIALSKDKQSKPMPFGPYLAIAGWVYLVYGAELTDLYYSLIL
MSDVITLMEQVPSFYFGLVLVLGLLVGSFLNVVIYRLPVMMQRSWEADCAETFPDSNIKVDDSTFNLVLPRSRCPKCNHL
IGSLENIPLVSWLLQKGRCKHCDCNIPARYPSIELLTGLMSLAVAYVIPFGWPVLFALLFTWTLISLTFIDVDTMLLPDQ
LTLPLVWLGLLVNMSDTFIGLQDAVLGAVFGYLTLWSVYWAFKLLTGKEGMGYGDFKLLAALGAWFGWQALPLIIILSSF
AGAILGIIMIALSKDKQSKPMPFGPYLAIAGWVYLVYGAELTDLYYSLIL
Nucleotide
Download Length: 873 bp
>NTDB_id=1036651 AB8617_RS11245 WP_409438964.1 2456955..2457827(+) (pilD) [Psychromonas sp. GE-S-Ul-11]
ATGAGTGACGTGATCACATTGATGGAACAAGTTCCCTCTTTTTATTTTGGGCTTGTTTTAGTCTTAGGCTTATTGGTTGG
TTCATTTTTAAATGTGGTGATTTATCGCTTGCCTGTGATGATGCAACGTAGTTGGGAAGCTGATTGTGCAGAAACATTTC
CTGACAGTAATATTAAAGTTGACGATTCCACCTTCAATTTAGTACTACCTCGTTCGCGTTGCCCTAAATGTAATCATTTG
ATTGGTTCACTTGAAAATATTCCATTAGTCAGCTGGTTGCTACAAAAAGGTCGTTGCAAGCATTGTGATTGCAATATCCC
TGCTCGTTACCCAAGCATAGAGTTATTGACTGGTTTAATGTCATTAGCTGTTGCTTATGTCATTCCGTTTGGTTGGCCTG
TTTTATTTGCACTATTGTTCACTTGGACCTTGATTAGTTTAACCTTTATTGATGTAGATACTATGTTACTGCCGGATCAG
TTAACTTTACCATTGGTTTGGTTAGGTTTACTGGTGAATATGTCTGATACCTTCATAGGGCTTCAGGATGCGGTTTTAGG
CGCTGTTTTCGGTTACTTGACCCTTTGGTCAGTTTACTGGGCGTTTAAGCTCCTGACGGGCAAGGAGGGCATGGGATACG
GTGACTTTAAATTATTAGCTGCGTTAGGTGCATGGTTTGGTTGGCAAGCGCTGCCTTTAATTATTATTCTCTCTTCATTT
GCTGGTGCCATTTTGGGCATTATTATGATCGCTTTATCTAAGGATAAACAAAGCAAACCAATGCCTTTTGGCCCATATTT
AGCGATAGCAGGTTGGGTTTATTTAGTCTACGGTGCAGAATTAACTGACCTCTATTACTCTTTGATTCTTTAG
ATGAGTGACGTGATCACATTGATGGAACAAGTTCCCTCTTTTTATTTTGGGCTTGTTTTAGTCTTAGGCTTATTGGTTGG
TTCATTTTTAAATGTGGTGATTTATCGCTTGCCTGTGATGATGCAACGTAGTTGGGAAGCTGATTGTGCAGAAACATTTC
CTGACAGTAATATTAAAGTTGACGATTCCACCTTCAATTTAGTACTACCTCGTTCGCGTTGCCCTAAATGTAATCATTTG
ATTGGTTCACTTGAAAATATTCCATTAGTCAGCTGGTTGCTACAAAAAGGTCGTTGCAAGCATTGTGATTGCAATATCCC
TGCTCGTTACCCAAGCATAGAGTTATTGACTGGTTTAATGTCATTAGCTGTTGCTTATGTCATTCCGTTTGGTTGGCCTG
TTTTATTTGCACTATTGTTCACTTGGACCTTGATTAGTTTAACCTTTATTGATGTAGATACTATGTTACTGCCGGATCAG
TTAACTTTACCATTGGTTTGGTTAGGTTTACTGGTGAATATGTCTGATACCTTCATAGGGCTTCAGGATGCGGTTTTAGG
CGCTGTTTTCGGTTACTTGACCCTTTGGTCAGTTTACTGGGCGTTTAAGCTCCTGACGGGCAAGGAGGGCATGGGATACG
GTGACTTTAAATTATTAGCTGCGTTAGGTGCATGGTTTGGTTGGCAAGCGCTGCCTTTAATTATTATTCTCTCTTCATTT
GCTGGTGCCATTTTGGGCATTATTATGATCGCTTTATCTAAGGATAAACAAAGCAAACCAATGCCTTTTGGCCCATATTT
AGCGATAGCAGGTTGGGTTTATTTAGTCTACGGTGCAGAATTAACTGACCTCTATTACTCTTTGATTCTTTAG
3D structure
| Source | ID | Structure |
|---|
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| pilD | Vibrio cholerae strain A1552 |
56.458 |
93.448 |
0.528 |
| pilD | Vibrio campbellii strain DS40M4 |
52.265 |
98.966 |
0.517 |
| pilD | Acinetobacter nosocomialis M2 |
49.301 |
98.621 |
0.486 |
| pilD | Acinetobacter baumannii D1279779 |
48.951 |
98.621 |
0.483 |
| pilD | Neisseria gonorrhoeae MS11 |
51.154 |
89.655 |
0.459 |