Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   HV561_RS07960 Genome accession   NZ_CP055302
Coordinates   1561653..1562105 (-) Length   150 a.a.
NCBI ID   WP_176808457.1    Uniprot ID   -
Organism   Mannheimia pernigra strain 16CN0041     
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 1550059..1595729 1561653..1562105 within 0


Gene organization within MGE regions


Location: 1550059..1595729
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HV561_RS07890 (HV561_07885) csrA 1550059..1550238 (-) 180 WP_176808447.1 carbon storage regulator CsrA -
  HV561_RS07895 (HV561_07890) alaS 1550316..1552940 (-) 2625 WP_176808448.1 alanine--tRNA ligase -
  HV561_RS07900 (HV561_07895) - 1553134..1553559 (-) 426 WP_176808449.1 universal stress protein -
  HV561_RS07905 (HV561_07900) - 1553798..1554571 (+) 774 WP_159630157.1 FNR family transcription factor -
  HV561_RS07910 (HV561_07905) - 1554711..1555502 (+) 792 WP_159630155.1 enoyl-ACP reductase FabI -
  HV561_RS07915 (HV561_07910) - 1555602..1557578 (+) 1977 WP_176808450.1 exoribonuclease II -
  HV561_RS07920 (HV561_07915) apaH 1557651..1558463 (+) 813 WP_176808451.1 bis(5'-nucleosyl)-tetraphosphatase (symmetrical) ApaH -
  HV561_RS07930 (HV561_07925) - 1558828..1559826 (+) 999 WP_176808452.1 tyrosine-type recombinase/integrase -
  HV561_RS07935 (HV561_07930) - 1560104..1560286 (+) 183 WP_176808453.1 ribbon-helix-helix protein, CopG family -
  HV561_RS07940 (HV561_07935) - 1560566..1560751 (+) 186 WP_159630147.1 ribbon-helix-helix protein, CopG family -
  HV561_RS07945 (HV561_07940) - 1560769..1561062 (-) 294 WP_176808454.1 hypothetical protein -
  HV561_RS07950 (HV561_07945) - 1561062..1561319 (-) 258 WP_176808455.1 DUF6378 domain-containing protein -
  HV561_RS07955 (HV561_07950) - 1561306..1561608 (-) 303 WP_176808456.1 hypothetical protein -
  HV561_RS07960 (HV561_07955) ssb 1561653..1562105 (-) 453 WP_176808457.1 single-stranded DNA-binding protein Machinery gene
  HV561_RS07965 (HV561_07960) - 1562293..1564704 (-) 2412 WP_176808458.1 replication endonuclease -
  HV561_RS07970 (HV561_07965) - 1564701..1565033 (-) 333 WP_176808459.1 hypothetical protein -
  HV561_RS07975 (HV561_07970) - 1565017..1565271 (-) 255 WP_176808460.1 hypothetical protein -
  HV561_RS07980 (HV561_07975) - 1565332..1565625 (-) 294 WP_159630132.1 hypothetical protein -
  HV561_RS07985 (HV561_07980) - 1565635..1565964 (-) 330 WP_176808461.1 hypothetical protein -
  HV561_RS07990 (HV561_07985) - 1566047..1566319 (-) 273 WP_159630130.1 hypothetical protein -
  HV561_RS07995 (HV561_07990) - 1566456..1566857 (+) 402 WP_176808462.1 hypothetical protein -
  HV561_RS08000 (HV561_07995) - 1567078..1567317 (+) 240 WP_176808463.1 hypothetical protein -
  HV561_RS08005 (HV561_08000) - 1567474..1568019 (-) 546 WP_176808464.1 hypothetical protein -
  HV561_RS08010 (HV561_08005) - 1568044..1568238 (-) 195 WP_176808465.1 hypothetical protein -
  HV561_RS08015 (HV561_08010) - 1568382..1568825 (+) 444 WP_272955591.1 helix-turn-helix domain-containing protein -
  HV561_RS08020 (HV561_08015) - 1568859..1569212 (+) 354 WP_176808467.1 hypothetical protein -
  HV561_RS08025 (HV561_08020) - 1569264..1570403 (+) 1140 WP_176808468.1 hypothetical protein -
  HV561_RS08030 (HV561_08025) - 1570406..1570732 (+) 327 WP_176808469.1 STAS-like domain-containing protein -
  HV561_RS08035 (HV561_08030) - 1570736..1571140 (+) 405 WP_176808470.1 hypothetical protein -
  HV561_RS08040 (HV561_08035) - 1571144..1572382 (-) 1239 WP_176808471.1 phage late control D family protein -
  HV561_RS08045 (HV561_08040) - 1572382..1572819 (-) 438 WP_176808472.1 phage tail protein -
  HV561_RS08050 (HV561_08045) - 1572884..1573051 (-) 168 WP_420371406.1 GpE family phage tail protein -
  HV561_RS08055 (HV561_08050) - 1573024..1573335 (-) 312 WP_176808473.1 phage tail assembly protein -
  HV561_RS08060 (HV561_08055) - 1573401..1573907 (-) 507 WP_176808474.1 phage major tail tube protein -
  HV561_RS08065 (HV561_08060) - 1573917..1575098 (-) 1182 WP_176808475.1 phage tail sheath protein -
  HV561_RS08070 (HV561_08065) - 1575206..1575478 (-) 273 WP_176808476.1 hypothetical protein -
  HV561_RS08075 (HV561_08070) - 1575462..1576103 (-) 642 WP_337795462.1 DUF4376 domain-containing protein -
  HV561_RS08080 (HV561_08075) - 1576094..1578466 (-) 2373 WP_176808477.1 phage tail protein -
  HV561_RS08085 (HV561_08080) - 1578468..1579010 (-) 543 WP_176808478.1 phage tail protein I -
  HV561_RS08090 (HV561_08085) - 1579000..1579917 (-) 918 WP_176808479.1 baseplate J/gp47 family protein -
  HV561_RS08095 (HV561_08090) - 1579914..1580249 (-) 336 WP_176808480.1 GPW/gp25 family protein -
  HV561_RS08100 (HV561_08095) - 1580249..1580818 (-) 570 WP_176808481.1 phage baseplate assembly protein V -
  HV561_RS08105 (HV561_08100) - 1580945..1581232 (-) 288 WP_176808482.1 type II toxin-antitoxin system RelE/ParE family toxin -
  HV561_RS08110 (HV561_08105) - 1581225..1581404 (-) 180 WP_176808483.1 hypothetical protein -
  HV561_RS08115 (HV561_08110) - 1581544..1581975 (-) 432 WP_176808484.1 type II toxin-antitoxin system HicB family antitoxin -
  HV561_RS08120 (HV561_08115) - 1582036..1582209 (-) 174 WP_176808485.1 type II toxin-antitoxin system HicA family toxin -
  HV561_RS08125 (HV561_08120) - 1582379..1582792 (-) 414 WP_176808486.1 type II toxin-antitoxin system HicB family antitoxin -
  HV561_RS08130 (HV561_08125) - 1582815..1583000 (-) 186 WP_272955592.1 type II toxin-antitoxin system HicA family toxin -
  HV561_RS08135 (HV561_08130) - 1583143..1586121 (-) 2979 WP_176808487.1 phage tail tape measure protein -
  HV561_RS08140 (HV561_08135) - 1586158..1586409 (+) 252 WP_176808488.1 hypothetical protein -
  HV561_RS08145 (HV561_08140) - 1586524..1586802 (+) 279 WP_176808489.1 hypothetical protein -
  HV561_RS08150 (HV561_08145) - 1586830..1587294 (-) 465 WP_176808490.1 phage virion morphogenesis protein -
  HV561_RS08155 (HV561_08150) - 1587287..1587772 (-) 486 WP_176808491.1 phage tail protein -
  HV561_RS08160 (HV561_08155) - 1587769..1587990 (-) 222 WP_176808492.1 TraR/DksA family transcriptional regulator -
  HV561_RS11675 lysC 1588015..1588245 (-) 231 WP_371739895.1 Rz1-like lysis system protein LysC -
  HV561_RS08165 (HV561_08160) - 1588139..1588594 (-) 456 WP_176808493.1 hypothetical protein -
  HV561_RS08170 (HV561_08165) - 1588596..1589123 (-) 528 WP_176808494.1 lysozyme -
  HV561_RS08175 (HV561_08170) - 1589123..1589326 (-) 204 WP_176808495.1 HP1 family phage holin -
  HV561_RS08180 (HV561_08175) - 1589348..1589560 (-) 213 WP_176808496.1 tail protein X -
  HV561_RS08185 (HV561_08180) - 1589560..1590075 (-) 516 WP_176808497.1 head completion/stabilization protein -
  HV561_RS08190 (HV561_08185) - 1590185..1590844 (-) 660 WP_176808498.1 terminase endonuclease subunit -
  HV561_RS08195 (HV561_08190) - 1590846..1591904 (-) 1059 WP_176808499.1 phage major capsid protein, P2 family -
  HV561_RS08200 (HV561_08195) - 1591915..1592724 (-) 810 WP_176808500.1 GPO family capsid scaffolding protein -
  HV561_RS08205 (HV561_08200) - 1592878..1594680 (+) 1803 WP_176809026.1 terminase ATPase subunit family protein -
  HV561_RS08210 (HV561_08205) - 1594689..1595729 (+) 1041 WP_176808501.1 phage portal protein -

Sequence

Protein


Download         Length: 150 a.a.        Molecular weight: 17066.43 Da        Isoelectric Point: 8.4532

>NTDB_id=457485 HV561_RS07960 WP_176808457.1 1561653..1562105(-) (ssb) [Mannheimia pernigra strain 16CN0041]
MNLVTLIGRLGQDPDIRTMQNGEKVAVLSVATTEKWTDKQTGVKKESTEWHRVVLYRRLAEIAELYIRKGMLVSVVGKIK
SRKWTDSNGVERNITEIIAEQVQMLSSGEKNTPNTPNKAENKPQPKQKNQDVMTADEQKDIPQFDDDIPF

Nucleotide


Download         Length: 453 bp        

>NTDB_id=457485 HV561_RS07960 WP_176808457.1 1561653..1562105(-) (ssb) [Mannheimia pernigra strain 16CN0041]
ATGAATTTAGTTACATTAATCGGTCGATTGGGGCAAGACCCTGATATTAGAACAATGCAAAACGGTGAGAAAGTTGCGGT
TTTATCGGTAGCAACAACAGAAAAATGGACGGATAAGCAAACGGGCGTGAAGAAAGAAAGCACTGAATGGCATAGAGTAG
TGCTTTATCGCCGATTAGCCGAAATTGCGGAATTGTACATTAGAAAAGGGATGTTGGTGTCTGTTGTCGGGAAAATTAAA
AGCCGAAAATGGACGGATAGCAACGGCGTTGAGCGAAATATTACTGAAATTATTGCAGAGCAGGTGCAAATGCTCAGTAG
TGGTGAGAAAAATACGCCAAATACGCCAAATAAGGCAGAAAATAAACCGCAACCAAAGCAGAAAAATCAAGACGTGATGA
CGGCGGACGAGCAGAAAGATATTCCGCAGTTTGATGATGATATACCGTTCTGA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(1-105)


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 Glaesserella parasuis strain SC1401

44.199

100

0.533
  ssb Vibrio cholerae strain A1552

41.279

100

0.473
  ssb Neisseria meningitidis MC58

38.728

100

0.447
  ssb Neisseria gonorrhoeae MS11

38.728

100

0.447