Detailed information
Bioinformatically predicted
Overview
| Name | ssb | Type | Machinery gene |
| Locus tag | CPU05_RS05990 | Genome accession | NZ_CP023654 |
| Coordinates | 1250600..1251025 (-) | Length | 141 a.a. |
| NCBI ID | WP_002830426.1 | Uniprot ID | - |
| Organism | Pediococcus acidilactici strain JQII-5 | ||
| Function | ssDNA binding (predicted from homology) DNA processing |
||
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) |
|---|---|---|---|---|
| Prophage | 1213104..1259703 | 1250600..1251025 | within | 0 |
Gene organization within MGE regions
Location: 1213104..1259703
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CPU05_RS05775 (CPU05_05795) | - | 1213104..1213658 (-) | 555 | WP_087116102.1 | hypothetical protein | - |
| CPU05_RS05780 (CPU05_05800) | - | 1213686..1214540 (-) | 855 | WP_087116100.1 | hypothetical protein | - |
| CPU05_RS05785 (CPU05_05805) | - | 1214886..1216076 (-) | 1191 | WP_257640360.1 | DUF262 domain-containing protein | - |
| CPU05_RS05790 (CPU05_05810) | - | 1216219..1216485 (-) | 267 | WP_141783057.1 | hypothetical protein | - |
| CPU05_RS05795 (CPU05_05815) | - | 1217053..1218021 (+) | 969 | WP_260603934.1 | site-specific integrase | - |
| CPU05_RS05800 (CPU05_05820) | - | 1219323..1219565 (-) | 243 | WP_024862287.1 | hypothetical protein | - |
| CPU05_RS05805 (CPU05_05825) | - | 1219683..1220045 (-) | 363 | WP_002830384.1 | phage holin | - |
| CPU05_RS05810 (CPU05_05830) | - | 1220058..1220321 (-) | 264 | WP_002830385.1 | hemolysin XhlA family protein | - |
| CPU05_RS05815 (CPU05_05835) | - | 1220321..1221484 (-) | 1164 | WP_002830386.1 | GH25 family lysozyme | - |
| CPU05_RS05820 (CPU05_05840) | - | 1221496..1221855 (-) | 360 | WP_002830387.1 | hypothetical protein | - |
| CPU05_RS05825 (CPU05_05845) | - | 1221870..1222118 (-) | 249 | WP_002830389.1 | hypothetical protein | - |
| CPU05_RS05830 (CPU05_05850) | - | 1222160..1222369 (-) | 210 | WP_002830391.1 | hypothetical protein | - |
| CPU05_RS05835 (CPU05_05855) | - | 1222362..1222589 (-) | 228 | WP_002830394.1 | hypothetical protein | - |
| CPU05_RS10375 | - | 1222582..1225710 (-) | 3129 | WP_002830395.1 | cell envelope integrity protein TolA | - |
| CPU05_RS05845 (CPU05_05865) | - | 1225716..1228100 (-) | 2385 | WP_002830396.1 | phage tail spike protein | - |
| CPU05_RS05850 (CPU05_05870) | - | 1228165..1229935 (-) | 1771 | Protein_1133 | phage tail domain-containing protein | - |
| CPU05_RS05855 (CPU05_05875) | - | 1230012..1234796 (-) | 4785 | WP_141783058.1 | peptidoglycan DD-metalloendopeptidase family protein | - |
| CPU05_RS05860 (CPU05_05880) | - | 1234824..1235009 (-) | 186 | WP_002830399.1 | hypothetical protein | - |
| CPU05_RS05865 (CPU05_05885) | - | 1235054..1235428 (-) | 375 | WP_002830400.1 | phage tail assembly chaperone | - |
| CPU05_RS05870 (CPU05_05890) | - | 1235504..1236193 (-) | 690 | WP_002830401.1 | phage tail protein | - |
| CPU05_RS05875 (CPU05_05895) | - | 1236207..1236587 (-) | 381 | WP_002830403.1 | DUF806 family protein | - |
| CPU05_RS05880 (CPU05_05900) | - | 1236587..1236994 (-) | 408 | WP_002830405.1 | HK97-gp10 family putative phage morphogenesis protein | - |
| CPU05_RS05885 (CPU05_05905) | - | 1236997..1237344 (-) | 348 | WP_002830406.1 | phage head closure protein | - |
| CPU05_RS05890 (CPU05_05910) | - | 1237334..1237666 (-) | 333 | WP_002830407.1 | head-tail connector protein | - |
| CPU05_RS05895 (CPU05_05915) | - | 1237739..1238971 (-) | 1233 | WP_141783059.1 | phage major capsid protein | - |
| CPU05_RS05900 (CPU05_05920) | - | 1238971..1239717 (-) | 747 | WP_036672383.1 | head maturation protease, ClpP-related | - |
| CPU05_RS05905 (CPU05_05925) | - | 1239695..1240858 (-) | 1164 | WP_002830410.1 | phage portal protein | - |
| CPU05_RS05910 (CPU05_05930) | - | 1240861..1241055 (-) | 195 | WP_036672386.1 | DUF1056 family protein | - |
| CPU05_RS05915 (CPU05_05935) | - | 1241045..1242943 (-) | 1899 | WP_087116079.1 | terminase large subunit | - |
| CPU05_RS05920 (CPU05_05940) | - | 1242946..1243404 (-) | 459 | WP_002830412.1 | phage terminase small subunit P27 family | - |
| CPU05_RS05925 (CPU05_05945) | - | 1243563..1243844 (-) | 282 | WP_036672389.1 | hypothetical protein | - |
| CPU05_RS05930 (CPU05_05950) | - | 1243911..1244375 (-) | 465 | WP_180385071.1 | HNH endonuclease | - |
| CPU05_RS05940 (CPU05_05960) | - | 1244908..1245369 (-) | 462 | WP_002830416.1 | ArpU family phage packaging/lysis transcriptional regulator | - |
| CPU05_RS10165 | - | 1245650..1245808 (-) | 159 | WP_155105540.1 | hypothetical protein | - |
| CPU05_RS05945 (CPU05_05970) | - | 1245826..1246011 (-) | 186 | WP_036672393.1 | hypothetical protein | - |
| CPU05_RS05950 (CPU05_05975) | - | 1246029..1246301 (-) | 273 | WP_036672395.1 | hypothetical protein | - |
| CPU05_RS05955 (CPU05_05985) | - | 1246485..1246856 (-) | 372 | WP_002830418.1 | hypothetical protein | - |
| CPU05_RS10170 | - | 1246856..1246993 (-) | 138 | WP_185833626.1 | hypothetical protein | - |
| CPU05_RS05960 (CPU05_05990) | - | 1246990..1247400 (-) | 411 | WP_002830420.1 | RusA family crossover junction endodeoxyribonuclease | - |
| CPU05_RS05965 (CPU05_05995) | - | 1247381..1248013 (-) | 633 | WP_036672399.1 | DNA-directed RNA polymerase sigma-70 factor | - |
| CPU05_RS05970 (CPU05_06000) | - | 1248131..1248946 (-) | 816 | WP_141783060.1 | ATP-binding protein | - |
| CPU05_RS05975 (CPU05_06005) | - | 1248927..1249667 (-) | 741 | WP_002830424.1 | conserved phage C-terminal domain-containing protein | - |
| CPU05_RS05980 (CPU05_06010) | - | 1249697..1249921 (-) | 225 | WP_036672402.1 | hypothetical protein | - |
| CPU05_RS05985 (CPU05_06015) | - | 1249911..1250588 (-) | 678 | WP_141783061.1 | putative HNHc nuclease | - |
| CPU05_RS05990 (CPU05_06020) | ssb | 1250600..1251025 (-) | 426 | WP_002830426.1 | single-stranded DNA-binding protein | Machinery gene |
| CPU05_RS05995 (CPU05_06025) | - | 1251018..1251224 (-) | 207 | WP_024863113.1 | hypothetical protein | - |
| CPU05_RS06000 (CPU05_06030) | - | 1251217..1251942 (-) | 726 | WP_050755615.1 | ERF family protein | - |
| CPU05_RS06005 (CPU05_06035) | - | 1251943..1252398 (-) | 456 | WP_230457018.1 | chromosome segregation protein SMC | - |
| CPU05_RS06010 (CPU05_06040) | - | 1252624..1252890 (+) | 267 | WP_036672405.1 | hypothetical protein | - |
| CPU05_RS06015 (CPU05_06045) | - | 1252847..1253104 (-) | 258 | WP_036672407.1 | hypothetical protein | - |
| CPU05_RS06020 (CPU05_06050) | - | 1253204..1253533 (-) | 330 | WP_002830431.1 | DUF771 domain-containing protein | - |
| CPU05_RS06025 (CPU05_06055) | - | 1253547..1254269 (-) | 723 | WP_002830432.1 | phage regulatory protein | - |
| CPU05_RS06030 (CPU05_06060) | - | 1254283..1254492 (-) | 210 | WP_065124225.1 | helix-turn-helix transcriptional regulator | - |
| CPU05_RS06035 (CPU05_06065) | - | 1254748..1255089 (+) | 342 | WP_065124226.1 | helix-turn-helix domain-containing protein | - |
| CPU05_RS06040 (CPU05_06070) | - | 1255098..1255505 (+) | 408 | WP_036672412.1 | ImmA/IrrE family metallo-endopeptidase | - |
| CPU05_RS06045 (CPU05_06075) | - | 1255568..1256695 (+) | 1128 | WP_002830434.1 | hypothetical protein | - |
| CPU05_RS06050 (CPU05_06085) | - | 1256842..1257039 (+) | 198 | WP_036672414.1 | hypothetical protein | - |
| CPU05_RS06055 (CPU05_06090) | - | 1257446..1258447 (+) | 1002 | WP_002830435.1 | Abi family protein | - |
| CPU05_RS06060 (CPU05_06095) | - | 1258588..1259703 (+) | 1116 | WP_002830436.1 | site-specific integrase | - |
Sequence
Protein
Download Length: 141 a.a. Molecular weight: 15642.35 Da Isoelectric Point: 6.9816
>NTDB_id=248900 CPU05_RS05990 WP_002830426.1 1250600..1251025(-) (ssb) [Pediococcus acidilactici strain JQII-5]
MINRTILIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFAKYTQKGSLVGIDGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNARQSTTPGDPFANGGQSIDIGDDDLPF
MINRTILIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFAKYTQKGSLVGIDGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNARQSTTPGDPFANGGQSIDIGDDDLPF
Nucleotide
Download Length: 426 bp
>NTDB_id=248900 CPU05_RS05990 WP_002830426.1 1250600..1251025(-) (ssb) [Pediococcus acidilactici strain JQII-5]
ATGATTAATCGAACGATACTAATAGGACGTTTAACTAAAGATGTTGAGCTTCGCCACACAGCTAAAGGCGACGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGCGAAGCAGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCCAAGTACACACAAAAAGGTTCGTTGGTAGGCATTGATGGACGGATCCAAACTCGT
TCCTACGAAAACCAACAAGGGCAGCGAGTTTATGTTACCGAAGTTGTTGCGGATAACTTCTCACTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAACGCACGGCAATCTACAACGCCGGGAGACCCGTTCGCTAATGGCGGGCAGTCAATCGATA
TTGGTGACGACGATTTACCGTTCTAG
ATGATTAATCGAACGATACTAATAGGACGTTTAACTAAAGATGTTGAGCTTCGCCACACAGCTAAAGGCGACGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGCGAAGCAGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCCAAGTACACACAAAAAGGTTCGTTGGTAGGCATTGATGGACGGATCCAAACTCGT
TCCTACGAAAACCAACAAGGGCAGCGAGTTTATGTTACCGAAGTTGTTGCGGATAACTTCTCACTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAACGCACGGCAATCTACAACGCCGGGAGACCCGTTCGCTAATGGCGGGCAGTCAATCGATA
TTGGTGACGACGATTTACCGTTCTAG
3D structure
| Source | ID | Structure |
|---|
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| ssb | Latilactobacillus sakei subsp. sakei 23K |
60 |
100 |
0.723 |
| ssbA | Bacillus subtilis subsp. subtilis str. 168 |
53.488 |
100 |
0.652 |
| ssbB | Bacillus subtilis subsp. subtilis str. 168 |
62.037 |
76.596 |
0.475 |
| ssbB/cilA | Streptococcus mitis NCTC 12261 |
42.958 |
100 |
0.433 |
| ssbB/cilA | Streptococcus pneumoniae TIGR4 |
42.958 |
100 |
0.433 |
| ssbB/cilA | Streptococcus pneumoniae Rx1 |
42.254 |
100 |
0.426 |
| ssbB/cilA | Streptococcus pneumoniae D39 |
42.254 |
100 |
0.426 |
| ssbB/cilA | Streptococcus pneumoniae R6 |
42.254 |
100 |
0.426 |
| ssbB | Streptococcus sobrinus strain NIDR 6715-7 |
42.254 |
100 |
0.426 |
| ssbB/cilA | Streptococcus mitis SK321 |
42.254 |
100 |
0.426 |
| ssbA | Streptococcus mutans UA159 |
38.732 |
100 |
0.39 |