Detailed information
Bioinformatically predicted
Overview
| Name | ssb | Type | Machinery gene |
| Locus tag | SD438_RS04020 | Genome accession | NZ_CP138454 |
| Coordinates | 834044..834481 (+) | Length | 145 a.a. |
| NCBI ID | WP_005686916.1 | Uniprot ID | - |
| Organism | Lacticaseibacillus rhamnosus strain SN21-1 | ||
| 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 | 826778..867605 | 834044..834481 | within | 0 |
Gene organization within MGE regions
Location: 826778..867605
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SD438_RS03960 (SD438_03960) | - | 826778..827905 (-) | 1128 | WP_005686887.1 | site-specific integrase | - |
| SD438_RS03965 (SD438_03965) | - | 828080..828757 (-) | 678 | WP_005686889.1 | hypothetical protein | - |
| SD438_RS03970 (SD438_03970) | - | 828814..829488 (-) | 675 | WP_005686890.1 | LexA family transcriptional regulator | - |
| SD438_RS03975 (SD438_03975) | - | 829650..829895 (+) | 246 | WP_005686894.1 | helix-turn-helix transcriptional regulator | - |
| SD438_RS03980 (SD438_03980) | - | 829892..830617 (+) | 726 | WP_005686896.1 | phage regulatory protein | - |
| SD438_RS03985 (SD438_03985) | - | 830665..831021 (+) | 357 | WP_003572199.1 | DUF771 domain-containing protein | - |
| SD438_RS03990 (SD438_03990) | - | 831106..831258 (+) | 153 | WP_005686904.1 | hypothetical protein | - |
| SD438_RS03995 (SD438_03995) | - | 831263..831466 (+) | 204 | WP_005686906.1 | hypothetical protein | - |
| SD438_RS04000 (SD438_04000) | - | 831484..831975 (+) | 492 | WP_005686909.1 | siphovirus Gp157 family protein | - |
| SD438_RS04005 (SD438_04005) | - | 831986..832741 (+) | 756 | WP_005686911.1 | ERF family protein | - |
| SD438_RS04010 (SD438_04010) | - | 832744..833406 (+) | 663 | WP_048516655.1 | putative HNHc nuclease | - |
| SD438_RS04015 (SD438_04015) | - | 833420..833968 (+) | 549 | WP_005686914.1 | NUMOD4 domain-containing protein | - |
| SD438_RS04020 (SD438_04020) | ssb | 834044..834481 (+) | 438 | WP_005686916.1 | single-stranded DNA-binding protein | Machinery gene |
| SD438_RS04025 (SD438_04025) | - | 834498..835331 (+) | 834 | WP_005686918.1 | helix-turn-helix domain-containing protein | - |
| SD438_RS04030 (SD438_04030) | - | 835328..836590 (+) | 1263 | WP_005686920.1 | DnaB-like helicase C-terminal domain-containing protein | - |
| SD438_RS04035 (SD438_04035) | - | 836592..836936 (+) | 345 | WP_005686922.1 | hypothetical protein | - |
| SD438_RS04040 (SD438_04040) | - | 836949..837227 (+) | 279 | WP_005686924.1 | helix-turn-helix domain-containing protein | - |
| SD438_RS04045 (SD438_04045) | - | 837224..837673 (+) | 450 | WP_005686926.1 | hypothetical protein | - |
| SD438_RS04050 (SD438_04050) | - | 837676..838059 (+) | 384 | WP_005686928.1 | DUF1064 domain-containing protein | - |
| SD438_RS04055 (SD438_04055) | - | 838071..838181 (+) | 111 | WP_005686930.1 | hypothetical protein | - |
| SD438_RS04060 (SD438_04060) | - | 838273..839028 (+) | 756 | WP_005686931.1 | site-specific DNA-methyltransferase | - |
| SD438_RS04065 (SD438_04065) | - | 839113..839556 (+) | 444 | WP_373879533.1 | DUF1642 domain-containing protein | - |
| SD438_RS04070 (SD438_04070) | - | 839546..839917 (+) | 372 | WP_005686935.1 | hypothetical protein | - |
| SD438_RS04075 (SD438_04075) | - | 839914..840303 (+) | 390 | WP_005686937.1 | hypothetical protein | - |
| SD438_RS04080 (SD438_04080) | - | 840300..840488 (+) | 189 | WP_005686939.1 | hypothetical protein | - |
| SD438_RS04085 (SD438_04085) | - | 840554..840973 (+) | 420 | WP_319071685.1 | YopX family protein | - |
| SD438_RS04090 (SD438_04090) | - | 841403..841846 (+) | 444 | WP_005686946.1 | ArpU family phage packaging/lysis transcriptional regulator | - |
| SD438_RS04095 (SD438_04095) | - | 842134..842994 (+) | 861 | WP_005686948.1 | hypothetical protein | - |
| SD438_RS04100 (SD438_04100) | - | 843535..844683 (+) | 1149 | WP_005686951.1 | GcrA family cell cycle regulator | - |
| SD438_RS04105 (SD438_04105) | - | 844696..845226 (+) | 531 | WP_005686953.1 | NUMOD4 domain-containing protein | - |
| SD438_RS04110 (SD438_04110) | - | 845230..845550 (+) | 321 | WP_005686955.1 | hypothetical protein | - |
| SD438_RS04115 (SD438_04115) | - | 845553..845876 (+) | 324 | WP_005686957.1 | hypothetical protein | - |
| SD438_RS04120 (SD438_04120) | - | 845894..846058 (+) | 165 | WP_005686959.1 | hypothetical protein | - |
| SD438_RS04125 (SD438_04125) | - | 846095..846889 (+) | 795 | WP_005686961.1 | HNH endonuclease | - |
| SD438_RS04130 (SD438_04130) | - | 847089..847544 (+) | 456 | WP_005686963.1 | P27 family phage terminase small subunit | - |
| SD438_RS04135 (SD438_04135) | - | 847566..849278 (+) | 1713 | WP_005686965.1 | terminase large subunit | - |
| SD438_RS04140 (SD438_04140) | - | 849290..849481 (+) | 192 | WP_003661399.1 | hypothetical protein | - |
| SD438_RS04145 (SD438_04145) | - | 849487..850740 (+) | 1254 | WP_005686969.1 | phage portal protein | - |
| SD438_RS04150 (SD438_04150) | - | 850694..851323 (+) | 630 | WP_015764348.1 | HK97 family phage prohead protease | - |
| SD438_RS04155 (SD438_04155) | - | 851365..852567 (+) | 1203 | WP_005686973.1 | phage major capsid protein | - |
| SD438_RS04160 (SD438_04160) | - | 852585..852824 (+) | 240 | WP_005686975.1 | Ig-like domain-containing protein | - |
| SD438_RS04165 (SD438_04165) | - | 852835..853194 (+) | 360 | WP_005686976.1 | head-tail connector protein | - |
| SD438_RS04170 (SD438_04170) | - | 853184..853513 (+) | 330 | WP_005686978.1 | head-tail adaptor protein | - |
| SD438_RS04175 (SD438_04175) | - | 853513..853899 (+) | 387 | WP_005686980.1 | HK97-gp10 family putative phage morphogenesis protein | - |
| SD438_RS04180 (SD438_04180) | - | 853899..854285 (+) | 387 | WP_005686982.1 | hypothetical protein | - |
| SD438_RS04185 (SD438_04185) | - | 854319..854939 (+) | 621 | WP_005686984.1 | major tail protein | - |
| SD438_RS04190 (SD438_04190) | - | 854996..855181 (+) | 186 | WP_005686987.1 | Ig-like domain-containing protein | - |
| SD438_RS04195 (SD438_04195) | gpG | 855252..855665 (+) | 414 | WP_003661382.1 | phage tail assembly chaperone G | - |
| SD438_RS04200 (SD438_04200) | - | 855788..860650 (+) | 4863 | WP_005686989.1 | phage tail tape measure protein | - |
| SD438_RS04205 (SD438_04205) | - | 860651..862573 (+) | 1923 | WP_005686991.1 | distal tail protein Dit | - |
| SD438_RS04210 (SD438_04210) | - | 862573..865080 (+) | 2508 | WP_005686993.1 | phage tail protein | - |
| SD438_RS04215 (SD438_04215) | - | 865090..865413 (+) | 324 | WP_005686996.1 | hypothetical protein | - |
| SD438_RS04220 (SD438_04220) | - | 865406..865537 (+) | 132 | WP_014569499.1 | XkdX family protein | - |
| SD438_RS04225 (SD438_04225) | - | 865567..865857 (+) | 291 | WP_005686998.1 | hypothetical protein | - |
| SD438_RS04230 (SD438_04230) | - | 865850..866296 (+) | 447 | WP_005687000.1 | phage holin | - |
| SD438_RS04235 (SD438_04235) | - | 866307..867605 (+) | 1299 | WP_005687002.1 | LysM peptidoglycan-binding domain-containing protein | - |
Sequence
Protein
Download Length: 145 a.a. Molecular weight: 15964.61 Da Isoelectric Point: 5.1662
>NTDB_id=902840 SD438_RS04020 WP_005686916.1 834044..834481(+) (ssb) [Lacticaseibacillus rhamnosus strain SN21-1]
MLNTVALTGRLTKDVDLRYTQSGTAVGSFTIAVDRQFRSANGERETDFINCAIWRKSAENFANFTHKGSLVGIEGHIQTR
TYDNAQGQKVFVTEVIVENFALLEPRQASQDGQQRSANNPAAAIQGNSFANNGQPVDIRDDDLPF
MLNTVALTGRLTKDVDLRYTQSGTAVGSFTIAVDRQFRSANGERETDFINCAIWRKSAENFANFTHKGSLVGIEGHIQTR
TYDNAQGQKVFVTEVIVENFALLEPRQASQDGQQRSANNPAAAIQGNSFANNGQPVDIRDDDLPF
Nucleotide
Download Length: 438 bp
>NTDB_id=902840 SD438_RS04020 WP_005686916.1 834044..834481(+) (ssb) [Lacticaseibacillus rhamnosus strain SN21-1]
ATGTTAAACACAGTTGCTTTAACAGGTCGATTAACCAAAGATGTTGATCTTCGCTATACACAAAGCGGAACAGCAGTTGG
CTCATTTACGATTGCTGTTGATCGCCAATTTCGCAGCGCAAACGGCGAACGTGAAACTGACTTCATCAATTGTGCCATCT
GGCGTAAGTCTGCTGAGAACTTTGCCAACTTCACGCACAAGGGTTCACTTGTTGGCATCGAAGGCCATATCCAAACGCGT
ACGTATGATAACGCGCAAGGGCAGAAAGTATTCGTGACCGAGGTAATCGTTGAGAATTTTGCTTTGCTTGAGCCACGGCA
AGCGTCTCAGGATGGTCAACAACGATCGGCTAATAACCCAGCGGCCGCAATCCAAGGCAACAGTTTTGCCAACAATGGTC
AGCCAGTCGATATCAGGGATGATGATCTTCCATTCTAA
ATGTTAAACACAGTTGCTTTAACAGGTCGATTAACCAAAGATGTTGATCTTCGCTATACACAAAGCGGAACAGCAGTTGG
CTCATTTACGATTGCTGTTGATCGCCAATTTCGCAGCGCAAACGGCGAACGTGAAACTGACTTCATCAATTGTGCCATCT
GGCGTAAGTCTGCTGAGAACTTTGCCAACTTCACGCACAAGGGTTCACTTGTTGGCATCGAAGGCCATATCCAAACGCGT
ACGTATGATAACGCGCAAGGGCAGAAAGTATTCGTGACCGAGGTAATCGTTGAGAATTTTGCTTTGCTTGAGCCACGGCA
AGCGTCTCAGGATGGTCAACAACGATCGGCTAATAACCCAGCGGCCGCAATCCAAGGCAACAGTTTTGCCAACAATGGTC
AGCCAGTCGATATCAGGGATGATGATCTTCCATTCTAA
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 |
57.059 |
100 |
0.669 |
| ssbA | Bacillus subtilis subsp. subtilis str. 168 |
46.857 |
100 |
0.566 |
| ssbB | Bacillus subtilis subsp. subtilis str. 168 |
53.774 |
73.103 |
0.393 |
| ssb | Neisseria meningitidis MC58 |
32.37 |
100 |
0.386 |
| ssb | Neisseria gonorrhoeae MS11 |
32.37 |
100 |
0.386 |
| ssb | Vibrio cholerae strain A1552 |
31.214 |
100 |
0.372 |
| ssbB/cilA | Streptococcus pneumoniae TIGR4 |
37.241 |
100 |
0.372 |
| ssbB | Streptococcus sobrinus strain NIDR 6715-7 |
37.241 |
100 |
0.372 |
| ssbB/cilA | Streptococcus mitis NCTC 12261 |
37.241 |
100 |
0.372 |
| ssbB/cilA | Streptococcus pneumoniae Rx1 |
36.552 |
100 |
0.366 |
| ssbB/cilA | Streptococcus mitis SK321 |
36.552 |
100 |
0.366 |
| ssbB/cilA | Streptococcus pneumoniae D39 |
36.552 |
100 |
0.366 |
| ssbB/cilA | Streptococcus pneumoniae R6 |
36.552 |
100 |
0.366 |