Detailed information
Bioinformatically predicted
Overview
| Name | pilD | Type | Machinery gene |
| Locus tag | KKK_RS03310 | Genome accession | NZ_CP015202 |
| Coordinates | 724050..724916 (+) | Length | 288 a.a. |
| NCBI ID | WP_019750377.1 | Uniprot ID | - |
| Organism | Pseudomonas putida B6-2 | ||
| 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 | 695059..727022 | 724050..724916 | within | 0 |
Gene organization within MGE regions
Location: 695059..727022
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| KKK_RS03150 (KKK_03150) | - | 695059..698202 (-) | 3144 | WP_019750406.1 | metallophosphoesterase | - |
| KKK_RS03155 (KKK_03155) | - | 698332..699079 (+) | 748 | Protein_622 | IS3 family transposase | - |
| KKK_RS03160 (KKK_03160) | - | 699087..699891 (+) | 805 | Protein_623 | IS3 family transposase | - |
| KKK_RS03165 (KKK_03165) | - | 700067..702025 (-) | 1959 | WP_110096672.1 | hypothetical protein | - |
| KKK_RS03170 (KKK_03170) | - | 702022..702900 (-) | 879 | WP_019750403.1 | TRAFAC clade GTPase domain-containing protein | - |
| KKK_RS03175 (KKK_03175) | - | 702901..703827 (-) | 927 | WP_019750402.1 | TRAFAC clade GTPase domain-containing protein | - |
| KKK_RS03180 (KKK_03180) | - | 703827..704897 (-) | 1071 | WP_019750401.1 | GTPase-associated system all-helical protein GASH | - |
| KKK_RS29000 | - | 704909..706183 (-) | 1275 | WP_019750400.1 | metallophosphoesterase | - |
| KKK_RS03190 (KKK_03190) | - | 706418..706926 (-) | 509 | Protein_629 | integrase | - |
| KKK_RS03195 (KKK_03195) | - | 708091..709245 (-) | 1155 | WP_019750399.1 | Fic family protein | - |
| KKK_RS03200 (KKK_03200) | - | 709669..710880 (+) | 1212 | WP_019750398.1 | site-specific integrase | - |
| KKK_RS03205 (KKK_03205) | - | 710869..711789 (-) | 921 | WP_163002514.1 | hypothetical protein | - |
| KKK_RS03210 (KKK_03210) | - | 711951..712151 (+) | 201 | WP_019750396.1 | helix-turn-helix domain-containing protein | - |
| KKK_RS30645 | - | 712358..712525 (+) | 168 | WP_177412729.1 | hypothetical protein | - |
| KKK_RS03220 (KKK_03220) | - | 712612..712881 (+) | 270 | WP_019750394.1 | helix-turn-helix domain-containing protein | - |
| KKK_RS03225 (KKK_03225) | - | 712943..713344 (+) | 402 | WP_029380510.1 | helix-turn-helix domain-containing protein | - |
| KKK_RS03230 (KKK_03230) | - | 713680..714396 (-) | 717 | WP_019750392.1 | hypothetical protein | - |
| KKK_RS03235 (KKK_03235) | - | 714393..714698 (-) | 306 | WP_019750391.1 | hypothetical protein | - |
| KKK_RS03240 (KKK_03240) | - | 714836..715063 (-) | 228 | WP_019750390.1 | hypothetical protein | - |
| KKK_RS03245 (KKK_03245) | - | 715183..715530 (+) | 348 | WP_199880460.1 | hypothetical protein | - |
| KKK_RS03250 (KKK_03250) | - | 716240..716425 (+) | 186 | WP_019750388.1 | hypothetical protein | - |
| KKK_RS03255 (KKK_03255) | - | 716457..716843 (+) | 387 | WP_019750387.1 | hypothetical protein | - |
| KKK_RS29010 | - | 717243..717452 (+) | 210 | WP_033723533.1 | hypothetical protein | - |
| KKK_RS03265 (KKK_03265) | - | 717443..718288 (+) | 846 | WP_019750384.1 | hypothetical protein | - |
| KKK_RS03270 (KKK_03270) | - | 718288..718629 (+) | 342 | WP_019750383.1 | hypothetical protein | - |
| KKK_RS03275 (KKK_03275) | - | 718629..719249 (+) | 621 | WP_019750382.1 | tail assembly protein | - |
| KKK_RS03280 (KKK_03280) | - | 719395..720498 (-) | 1104 | WP_029380509.1 | TIR domain-containing protein | - |
| KKK_RS03285 (KKK_03285) | - | 720676..721290 (+) | 615 | WP_019750380.1 | recombinase family protein | - |
| KKK_RS03290 (KKK_03290) | - | 721291..721896 (-) | 606 | WP_019750379.1 | hypothetical protein | - |
| KKK_RS03300 (KKK_03300) | - | 722212..722622 (-) | 411 | WP_012051131.1 | pilin | - |
| KKK_RS03305 (KKK_03305) | - | 722839..724047 (+) | 1209 | WP_019750378.1 | type II secretion system F family protein | - |
| KKK_RS03310 (KKK_03310) | pilD | 724050..724916 (+) | 867 | WP_019750377.1 | prepilin peptidase | Machinery gene |
| KKK_RS03315 (KKK_03315) | coaE | 724916..725539 (+) | 624 | WP_004575721.1 | dephospho-CoA kinase | - |
| KKK_RS03320 (KKK_03320) | yacG | 725536..725736 (+) | 201 | WP_010951889.1 | DNA gyrase inhibitor YacG | - |
| KKK_RS03325 (KKK_03325) | - | 726072..727022 (+) | 951 | WP_004577666.1 | IS110 family transposase | - |
Sequence
Protein
Download Length: 288 a.a. Molecular weight: 31912.97 Da Isoelectric Point: 7.9101
>NTDB_id=177481 KKK_RS03310 WP_019750377.1 724050..724916(+) (pilD) [Pseudomonas putida B6-2]
MTFWAFLAEQPAYFLTLATVLGLLVGSFINVLVYRLPIMLERQWQREAQEVLGLPTTQHPRFDLCLPASRCPHCAHRIRA
WENIPVISYLALGGRCSSCKNRISLRYPVVEVASALLSLVVAWRFGASVEALLALPLTWCLLALSLIDADHQLLPDVLVL
PTMWLGLIVNAFGIHVPLADALWGAVAGYLSLWTVYWVFRLVTGKEGMGYGDFKLMALIGAWGGWQVLPLTLLLSSVVGA
LVGLCLLRFRRHAMGTAIPFGPYLAIAGWIAVLWGDEIYASYMQLLGY
MTFWAFLAEQPAYFLTLATVLGLLVGSFINVLVYRLPIMLERQWQREAQEVLGLPTTQHPRFDLCLPASRCPHCAHRIRA
WENIPVISYLALGGRCSSCKNRISLRYPVVEVASALLSLVVAWRFGASVEALLALPLTWCLLALSLIDADHQLLPDVLVL
PTMWLGLIVNAFGIHVPLADALWGAVAGYLSLWTVYWVFRLVTGKEGMGYGDFKLMALIGAWGGWQVLPLTLLLSSVVGA
LVGLCLLRFRRHAMGTAIPFGPYLAIAGWIAVLWGDEIYASYMQLLGY
Nucleotide
Download Length: 867 bp
>NTDB_id=177481 KKK_RS03310 WP_019750377.1 724050..724916(+) (pilD) [Pseudomonas putida B6-2]
ATGACTTTTTGGGCTTTTCTGGCTGAACAGCCAGCGTATTTCCTCACCCTTGCCACGGTGCTCGGCCTGCTGGTGGGCAG
CTTTATCAACGTGCTGGTGTATCGCCTGCCGATCATGCTGGAGCGGCAATGGCAGCGTGAGGCGCAAGAGGTATTGGGGC
TGCCGACCACGCAGCACCCGCGTTTCGACCTGTGCCTGCCCGCCTCCCGGTGCCCACACTGCGCGCACCGGATTCGTGCG
TGGGAGAACATTCCGGTCATCAGCTACCTGGCCTTGGGCGGGCGCTGTTCGTCCTGCAAAAACCGCATCAGCCTGCGTTA
CCCGGTAGTGGAAGTGGCCAGCGCGCTGCTGTCGCTGGTAGTGGCCTGGCGCTTCGGCGCTTCGGTAGAGGCGTTGCTGG
CGTTGCCGCTGACCTGGTGCCTGCTGGCGCTGAGCCTGATCGATGCGGACCACCAGCTGCTGCCGGATGTGCTGGTGCTG
CCGACCATGTGGCTAGGGCTGATCGTCAATGCCTTTGGCATCCATGTGCCCCTGGCCGACGCACTGTGGGGCGCAGTGGC
CGGGTATCTCAGCCTGTGGACGGTGTACTGGGTGTTCAGGCTGGTCACCGGCAAGGAAGGCATGGGCTATGGCGATTTCA
AGCTGATGGCACTGATCGGGGCGTGGGGGGGTTGGCAGGTGCTGCCGTTGACGCTGCTGTTGTCGTCAGTGGTGGGGGCG
CTTGTTGGCCTGTGCCTGCTGCGTTTTCGCCGGCATGCCATGGGCACGGCAATCCCGTTTGGCCCTTATCTGGCAATTGC
GGGGTGGATTGCCGTGCTCTGGGGTGATGAAATATACGCCTCATACATGCAACTGCTTGGATACTGA
ATGACTTTTTGGGCTTTTCTGGCTGAACAGCCAGCGTATTTCCTCACCCTTGCCACGGTGCTCGGCCTGCTGGTGGGCAG
CTTTATCAACGTGCTGGTGTATCGCCTGCCGATCATGCTGGAGCGGCAATGGCAGCGTGAGGCGCAAGAGGTATTGGGGC
TGCCGACCACGCAGCACCCGCGTTTCGACCTGTGCCTGCCCGCCTCCCGGTGCCCACACTGCGCGCACCGGATTCGTGCG
TGGGAGAACATTCCGGTCATCAGCTACCTGGCCTTGGGCGGGCGCTGTTCGTCCTGCAAAAACCGCATCAGCCTGCGTTA
CCCGGTAGTGGAAGTGGCCAGCGCGCTGCTGTCGCTGGTAGTGGCCTGGCGCTTCGGCGCTTCGGTAGAGGCGTTGCTGG
CGTTGCCGCTGACCTGGTGCCTGCTGGCGCTGAGCCTGATCGATGCGGACCACCAGCTGCTGCCGGATGTGCTGGTGCTG
CCGACCATGTGGCTAGGGCTGATCGTCAATGCCTTTGGCATCCATGTGCCCCTGGCCGACGCACTGTGGGGCGCAGTGGC
CGGGTATCTCAGCCTGTGGACGGTGTACTGGGTGTTCAGGCTGGTCACCGGCAAGGAAGGCATGGGCTATGGCGATTTCA
AGCTGATGGCACTGATCGGGGCGTGGGGGGGTTGGCAGGTGCTGCCGTTGACGCTGCTGTTGTCGTCAGTGGTGGGGGCG
CTTGTTGGCCTGTGCCTGCTGCGTTTTCGCCGGCATGCCATGGGCACGGCAATCCCGTTTGGCCCTTATCTGGCAATTGC
GGGGTGGATTGCCGTGCTCTGGGGTGATGAAATATACGCCTCATACATGCAACTGCTTGGATACTGA
3D structure
| Source | ID | Structure |
|---|
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| pilD | Vibrio cholerae strain A1552 |
51.986 |
96.181 |
0.5 |
| pilD | Acinetobacter baumannii D1279779 |
49.286 |
97.222 |
0.479 |
| pilD | Acinetobacter nosocomialis M2 |
48.571 |
97.222 |
0.472 |
| pilD | Vibrio campbellii strain DS40M4 |
48.913 |
95.833 |
0.469 |
| pilD | Neisseria gonorrhoeae MS11 |
48.327 |
93.403 |
0.451 |