Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   C7M42_RS07910 Genome accession   NZ_CP028249
Coordinates   1648668..1649093 (-) Length   141 a.a.
NCBI ID   WP_128211868.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain SRCM102732     
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 1619416..1658110 1648668..1649093 within 0


Gene organization within MGE regions


Location: 1619416..1658110
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  C7M42_RS07710 (C7M42_01564) - 1619416..1620537 (-) 1122 WP_128211675.1 peptidoglycan recognition family protein -
  C7M42_RS07715 (C7M42_01565) - 1620521..1620763 (-) 243 WP_128211673.1 phage holin -
  C7M42_RS07720 (C7M42_01566) - 1620763..1621146 (-) 384 WP_229092876.1 hypothetical protein -
  C7M42_RS10540 (C7M42_01567) - 1621097..1621243 (-) 147 WP_075139822.1 XkdX family protein -
  C7M42_RS07730 (C7M42_01568) - 1621243..1621521 (-) 279 WP_128211671.1 hypothetical protein -
  C7M42_RS07735 (C7M42_01569) - 1621521..1622480 (-) 960 WP_128211669.1 hypothetical protein -
  C7M42_RS07740 (C7M42_01570) - 1622473..1624206 (-) 1734 WP_128211667.1 BppU family phage baseplate upper protein -
  C7M42_RS07745 (C7M42_01571) - 1624206..1624517 (-) 312 WP_128211665.1 hypothetical protein -
  C7M42_RS07750 (C7M42_01572) - 1624518..1624838 (-) 321 WP_128211663.1 hypothetical protein -
  C7M42_RS07755 (C7M42_01573) - 1624828..1626042 (-) 1215 WP_128211660.1 phage tail protein -
  C7M42_RS07760 (C7M42_01574) - 1625972..1626805 (-) 834 WP_128211658.1 phage tail domain-containing protein -
  C7M42_RS07765 (C7M42_01575) - 1626818..1631932 (-) 5115 WP_128211656.1 tape measure protein -
  C7M42_RS10245 (C7M42_01576) - 1631936..1632106 (-) 171 WP_164873654.1 hypothetical protein -
  C7M42_RS07770 (C7M42_01577) - 1632139..1632543 (-) 405 WP_128211654.1 phage tail tube assembly chaperone -
  C7M42_RS07775 (C7M42_01578) - 1632680..1633282 (-) 603 WP_159215558.1 phage tail protein -
  C7M42_RS07780 (C7M42_01579) - 1633295..1633669 (-) 375 WP_159215557.1 DUF806 family protein -
  C7M42_RS07785 (C7M42_01580) - 1633672..1634085 (-) 414 WP_128211804.1 HK97 gp10 family phage protein -
  C7M42_RS07790 (C7M42_01581) - 1634085..1634444 (-) 360 WP_128211806.1 phage head closure protein -
  C7M42_RS07795 (C7M42_01582) - 1634422..1634745 (-) 324 WP_128211808.1 head-tail connector protein -
  C7M42_RS07800 (C7M42_01583) - 1634761..1635231 (-) 471 WP_128211810.1 Ig-like domain-containing protein -
  C7M42_RS07805 (C7M42_01584) - 1635314..1636648 (-) 1335 WP_230312668.1 phage major capsid protein -
  C7M42_RS07810 (C7M42_01585) - 1636649..1637239 (-) 591 WP_128211820.1 HK97 family phage prohead protease -
  C7M42_RS07815 (C7M42_01586) - 1637223..1638335 (-) 1113 WP_128211812.1 phage portal protein -
  C7M42_RS07820 (C7M42_01587) - 1638536..1640410 (-) 1875 WP_128211814.1 terminase TerL endonuclease subunit -
  C7M42_RS07825 (C7M42_01588) - 1640410..1640874 (-) 465 WP_128211816.1 phage terminase small subunit P27 family -
  C7M42_RS07830 (C7M42_01589) - 1641073..1641372 (-) 300 WP_128212003.1 hypothetical protein -
  C7M42_RS07835 (C7M42_01590) - 1641369..1641824 (-) 456 WP_128212001.1 HNH endonuclease -
  C7M42_RS07840 (C7M42_01591) - 1641909..1642229 (-) 321 WP_159215554.1 bacteriocin immunity protein -
  C7M42_RS07845 (C7M42_01592) - 1642451..1642885 (-) 435 WP_128211997.1 ArpU family phage packaging/lysis transcriptional regulator -
  C7M42_RS07850 (C7M42_01594) - 1643222..1643485 (-) 264 WP_128211995.1 hypothetical protein -
  C7M42_RS07855 (C7M42_01595) - 1643499..1643807 (-) 309 WP_200834124.1 hypothetical protein -
  C7M42_RS07860 (C7M42_01596) - 1643811..1644176 (-) 366 WP_159215553.1 hypothetical protein -
  C7M42_RS07865 (C7M42_01597) - 1644193..1644393 (-) 201 WP_128211852.1 hypothetical protein -
  C7M42_RS07870 (C7M42_01598) - 1644393..1644533 (-) 141 WP_159215552.1 hypothetical protein -
  C7M42_RS07875 (C7M42_01599) - 1644536..1644907 (-) 372 WP_128211854.1 N-acetylmuramoyl-L-alanine amidase -
  C7M42_RS10250 (C7M42_01600) - 1644894..1645043 (-) 150 WP_164873659.1 hypothetical protein -
  C7M42_RS07880 (C7M42_01601) - 1645040..1645441 (-) 402 WP_128211856.1 RusA family crossover junction endodeoxyribonuclease -
  C7M42_RS07885 (C7M42_01602) - 1645422..1646054 (-) 633 WP_128211858.1 RNA polymerase subunit sigma-70 -
  C7M42_RS07890 (C7M42_01604) - 1646172..1646816 (-) 645 WP_229092964.1 ATP-binding protein -
  C7M42_RS07895 (C7M42_01605) - 1646968..1647720 (-) 753 WP_128211862.1 conserved phage C-terminal domain-containing protein -
  C7M42_RS07900 (C7M42_01606) - 1647759..1647989 (-) 231 WP_128211864.1 hypothetical protein -
  C7M42_RS07905 (C7M42_01607) - 1647973..1648656 (-) 684 WP_128211866.1 putative HNHc nuclease -
  C7M42_RS07910 (C7M42_01608) ssb 1648668..1649093 (-) 426 WP_128211868.1 single-stranded DNA-binding protein Machinery gene
  C7M42_RS07915 (C7M42_01609) - 1649086..1649784 (-) 699 WP_128211870.1 ERF family protein -
  C7M42_RS07920 (C7M42_01610) - 1649785..1650240 (-) 456 WP_128211872.1 chromosome segregation protein SMC -
  C7M42_RS07925 (C7M42_01612) - 1650464..1651126 (+) 663 WP_159215551.1 hypothetical protein -
  C7M42_RS07930 (C7M42_01613) - 1651236..1651490 (-) 255 WP_128211987.1 hypothetical protein -
  C7M42_RS07935 (C7M42_01614) - 1651591..1651920 (-) 330 WP_128211985.1 DUF771 domain-containing protein -
  C7M42_RS07940 (C7M42_01616) - 1652217..1652999 (-) 783 WP_128211989.1 phage antirepressor -
  C7M42_RS07945 (C7M42_01617) - 1653105..1653299 (+) 195 WP_128211983.1 hypothetical protein -
  C7M42_RS07950 (C7M42_01618) - 1653291..1653428 (-) 138 WP_159215550.1 hypothetical protein -
  C7M42_RS07955 (C7M42_01619) - 1653442..1653660 (-) 219 WP_235016628.1 helix-turn-helix transcriptional regulator -
  C7M42_RS07960 (C7M42_01620) - 1653719..1654027 (+) 309 WP_128211981.1 hypothetical protein -
  C7M42_RS07965 (C7M42_01621) - 1654017..1654223 (-) 207 WP_159215549.1 hypothetical protein -
  C7M42_RS07970 (C7M42_01622) - 1654480..1654821 (+) 342 WP_002831842.1 helix-turn-helix domain-containing protein -
  C7M42_RS07975 (C7M42_01623) - 1654830..1655237 (+) 408 WP_128212081.1 ImmA/IrrE family metallo-endopeptidase -
  C7M42_RS07980 (C7M42_01624) - 1655300..1656427 (+) 1128 WP_159215548.1 hypothetical protein -
  C7M42_RS07985 (C7M42_01625) - 1656574..1656771 (+) 198 WP_053905909.1 hypothetical protein -
  C7M42_RS07990 (C7M42_01626) - 1656995..1658110 (+) 1116 WP_128212073.1 site-specific integrase -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15657.41 Da        Isoelectric Point: 7.9971

>NTDB_id=283705 C7M42_RS07910 WP_128211868.1 1648668..1649093(-) (ssb) [Pediococcus acidilactici strain SRCM102732]
MINRTVLIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFAKYTQKGSLVGIDGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNARQASTPGDLFANGGQSIDISDDQLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=283705 C7M42_RS07910 WP_128211868.1 1648668..1649093(-) (ssb) [Pediococcus acidilactici strain SRCM102732]
ATGATTAATCGAACAGTCCTAATAGGACGCCTAACTAAAGATGTTGAACTTCGCCACACAGCTAAAGGTGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGCGAAGCGGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCCAAGTACACACAAAAAGGTTCGTTGGTAGGCATTGACGGTCGAATTCAAACCCGT
TCGTACGAAAACCAACAAGGACAACGAGTTTATGTAACTGAGGTTGTAGCTGATAACTTCTCGTTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAATGCACGGCAAGCATCAACGCCGGGAGATCTGTTCGCCAATGGTGGTCAATCAATCGACA
TTTCAGATGATCAGCTCCCCTTTTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-102)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  ssb Latilactobacillus sakei subsp. sakei 23K

58.824

100

0.709
  ssbA Bacillus subtilis subsp. subtilis str. 168

54.07

100

0.66
  ssbB Bacillus subtilis subsp. subtilis str. 168

62.037

76.596

0.475
  ssbB Streptococcus sobrinus strain NIDR 6715-7

43.662

100

0.44
  ssbB/cilA Streptococcus pneumoniae TIGR4

42.958

100

0.433
  ssbB/cilA Streptococcus mitis NCTC 12261

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/cilA Streptococcus mitis SK321

42.254

100

0.426
  ssbA Streptococcus mutans UA159

39.007

100

0.39

Multiple sequence alignment