Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   At1D1108_RS17880 Genome accession   NZ_CP032922
Coordinates   896490..896981 (+) Length   163 a.a.
NCBI ID   WP_121557264.1    Uniprot ID   -
Organism   Agrobacterium tumefaciens strain 1D1108     
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 855894..901675 896490..896981 within 0


Gene organization within MGE regions


Location: 855894..901675
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  At1D1108_RS17635 (At1D1108_34260) - 855894..856601 (-) 708 WP_121557220.1 N-acetylmuramoyl-L-alanine amidase -
  At1D1108_RS17640 (At1D1108_34270) - 856723..857730 (-) 1008 WP_121557221.1 FkbM family methyltransferase -
  At1D1108_RS17645 (At1D1108_34280) - 857837..858376 (-) 540 WP_121557222.1 hypothetical protein -
  At1D1108_RS17650 (At1D1108_34290) - 858373..859434 (-) 1062 WP_121557223.1 hypothetical protein -
  At1D1108_RS17655 (At1D1108_34300) - 859450..860154 (-) 705 WP_162995265.1 putative phage tail protein -
  At1D1108_RS17660 (At1D1108_34310) - 860144..861229 (-) 1086 WP_121557225.1 baseplate J/gp47 family protein -
  At1D1108_RS17665 (At1D1108_34320) - 861201..861737 (-) 537 WP_121557226.1 phage GP46 family protein -
  At1D1108_RS17670 (At1D1108_34330) - 861748..862236 (-) 489 WP_121557227.1 phage baseplate assembly protein domain-containing protein -
  At1D1108_RS17675 (At1D1108_34340) - 862233..863297 (-) 1065 WP_121557228.1 phage baseplate assembly protein -
  At1D1108_RS17680 (At1D1108_34350) - 863297..863920 (-) 624 WP_121557229.1 hypothetical protein -
  At1D1108_RS17685 (At1D1108_34360) - 863920..864378 (-) 459 WP_121557230.1 DNA circularization N-terminal domain-containing protein -
  At1D1108_RS17690 (At1D1108_34370) - 864377..864973 (+) 597 WP_162995266.1 hypothetical protein -
  At1D1108_RS17695 (At1D1108_34380) - 864983..866944 (-) 1962 WP_121557232.1 phage tail tape measure protein -
  At1D1108_RS17700 (At1D1108_34390) - 866954..867496 (-) 543 WP_153314865.1 hypothetical protein -
  At1D1108_RS17705 (At1D1108_34400) - 867621..867941 (-) 321 WP_121557234.1 hypothetical protein -
  At1D1108_RS17710 (At1D1108_34410) - 867951..868322 (-) 372 WP_121557235.1 phage tail tube protein -
  At1D1108_RS17715 (At1D1108_34420) - 868372..869850 (-) 1479 WP_121557236.1 hypothetical protein -
  At1D1108_RS17720 (At1D1108_34430) - 869855..870037 (-) 183 WP_121557237.1 hypothetical protein -
  At1D1108_RS17725 (At1D1108_34440) - 870050..870781 (-) 732 WP_121557238.1 hypothetical protein -
  At1D1108_RS17730 (At1D1108_34450) - 870768..871169 (-) 402 WP_121557239.1 hypothetical protein -
  At1D1108_RS17735 (At1D1108_34460) - 871174..871500 (-) 327 WP_121557240.1 hypothetical protein -
  At1D1108_RS17740 (At1D1108_34470) - 871502..872557 (-) 1056 WP_121557241.1 major capsid protein -
  At1D1108_RS17745 (At1D1108_34480) - 872582..872923 (-) 342 WP_121557242.1 hypothetical protein -
  At1D1108_RS17750 (At1D1108_34490) - 872925..873974 (-) 1050 WP_121557243.1 head maturation protease, ClpP-related -
  At1D1108_RS17755 (At1D1108_34500) - 874016..874285 (-) 270 WP_121557244.1 hypothetical protein -
  At1D1108_RS17760 (At1D1108_34510) - 874285..875898 (-) 1614 WP_121557592.1 phage portal protein -
  At1D1108_RS17765 (At1D1108_34520) - 875895..877874 (-) 1980 WP_233283705.1 terminase gpA endonuclease subunit -
  At1D1108_RS17770 (At1D1108_34530) - 877877..878482 (-) 606 WP_121557246.1 hypothetical protein -
  At1D1108_RS17775 (At1D1108_34540) - 878837..879613 (-) 777 WP_121557247.1 hypothetical protein -
  At1D1108_RS17780 (At1D1108_34550) - 880037..881857 (-) 1821 WP_121557248.1 DNA primase family protein -
  At1D1108_RS17785 (At1D1108_34560) - 881858..882955 (-) 1098 WP_233283678.1 hypothetical protein -
  At1D1108_RS17790 (At1D1108_34570) - 883175..884386 (-) 1212 WP_121557249.1 phosphoadenosine phosphosulfate reductase family protein -
  At1D1108_RS17795 (At1D1108_34580) - 884383..886476 (-) 2094 WP_233283679.1 DNA cytosine methyltransferase -
  At1D1108_RS27945 - 886514..886930 (-) 417 WP_162995240.1 hypothetical protein -
  At1D1108_RS17800 (At1D1108_34590) - 886930..887508 (-) 579 WP_121557251.1 hypothetical protein -
  At1D1108_RS17805 (At1D1108_34600) - 887505..887855 (-) 351 WP_121557252.1 hypothetical protein -
  At1D1108_RS17810 (At1D1108_34610) - 887852..890461 (-) 2610 WP_121557253.1 DNA methyltransferase -
  At1D1108_RS17815 (At1D1108_34620) - 890461..890646 (-) 186 WP_121557254.1 hypothetical protein -
  At1D1108_RS17820 (At1D1108_34630) - 890643..891092 (-) 450 WP_121557255.1 GNAT family N-acetyltransferase -
  At1D1108_RS17825 (At1D1108_34640) - 891089..891589 (-) 501 WP_121557256.1 hypothetical protein -
  At1D1108_RS17830 (At1D1108_34650) - 891735..892031 (+) 297 WP_121557257.1 hypothetical protein -
  At1D1108_RS17840 (At1D1108_34660) - 892304..892549 (-) 246 WP_121557593.1 hypothetical protein -
  At1D1108_RS17845 (At1D1108_34670) - 892636..893337 (+) 702 WP_121557258.1 S24 family peptidase -
  At1D1108_RS17855 (At1D1108_34690) - 893899..894093 (+) 195 WP_121557260.1 hypothetical protein -
  At1D1108_RS17860 (At1D1108_34700) - 894161..894346 (+) 186 WP_121557261.1 hypothetical protein -
  At1D1108_RS17865 (At1D1108_34710) - 894346..895053 (+) 708 WP_174075465.1 hypothetical protein -
  At1D1108_RS17870 (At1D1108_34720) - 895050..895340 (+) 291 WP_121557262.1 helix-turn-helix domain-containing protein -
  At1D1108_RS17875 (At1D1108_34730) - 895333..896490 (+) 1158 WP_121557263.1 DUF5131 family protein -
  At1D1108_RS17880 (At1D1108_34740) ssb 896490..896981 (+) 492 WP_121557264.1 single-stranded DNA-binding protein Machinery gene
  At1D1108_RS17885 (At1D1108_34750) - 897017..897373 (+) 357 WP_121557265.1 hypothetical protein -
  At1D1108_RS17890 (At1D1108_34760) - 897524..898327 (+) 804 WP_233283680.1 DUF2303 family protein -
  At1D1108_RS17895 (At1D1108_34770) - 898327..898851 (+) 525 WP_121557267.1 hypothetical protein -
  At1D1108_RS17900 (At1D1108_34780) dnaN 898854..899966 (+) 1113 WP_121557268.1 DNA polymerase III subunit beta -
  At1D1108_RS17905 (At1D1108_34790) - 899977..900204 (+) 228 WP_162995267.1 hypothetical protein -
  At1D1108_RS28135 (At1D1108_34800) - 900191..901159 (+) 969 WP_174075467.1 hypothetical protein -
  At1D1108_RS17915 (At1D1108_34810) - 901163..901675 (+) 513 WP_121557270.1 hypothetical protein -

Sequence

Protein


Download         Length: 163 a.a.        Molecular weight: 17837.70 Da        Isoelectric Point: 6.4882

>NTDB_id=320399 At1D1108_RS17880 WP_121557264.1 896490..896981(+) (ssb) [Agrobacterium tumefaciens strain 1D1108]
MAGSVNKVILIGHLGADPEIRQTQAGAGIASLRLATSESWRDKESGERKERTEWHSVVVFTEGLVKVCEQYLKKGAKVYI
EGKLQTRKWQHSDGGDRYTTEVVLNGFNATLTMLDSQGGGNRPPPASDPDQYGRQPSRQSGSSGSNPSTGRDFSHDMDDD
IPF

Nucleotide


Download         Length: 492 bp        

>NTDB_id=320399 At1D1108_RS17880 WP_121557264.1 896490..896981(+) (ssb) [Agrobacterium tumefaciens strain 1D1108]
ATGGCCGGCTCGGTCAACAAAGTCATTCTCATCGGACACCTCGGCGCCGATCCGGAAATCCGACAGACACAGGCGGGTGC
CGGAATTGCGAGCCTACGCCTCGCCACATCCGAAAGCTGGCGGGACAAGGAAAGCGGAGAGCGCAAAGAGCGCACCGAGT
GGCACAGCGTCGTCGTCTTTACTGAAGGTCTCGTCAAGGTGTGCGAGCAGTACCTCAAGAAGGGCGCCAAGGTTTACATC
GAAGGCAAACTGCAAACCCGAAAATGGCAGCACTCCGACGGCGGAGACCGATACACAACCGAAGTAGTGCTCAACGGTTT
CAACGCGACACTAACGATGCTCGATAGCCAGGGCGGCGGCAACCGGCCACCGCCGGCGTCCGATCCCGATCAATACGGGC
GGCAGCCGAGCCGGCAATCTGGCTCCAGCGGTTCAAACCCGAGCACCGGCCGCGATTTCAGCCACGACATGGATGACGAC
ATTCCGTTCTGA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(5-105)


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 Vibrio cholerae strain A1552

46.821

100

0.497
  ssb Glaesserella parasuis strain SC1401

42.473

100

0.485
  ssb Neisseria meningitidis MC58

37.714

100

0.405
  ssb Neisseria gonorrhoeae MS11

37.714

100

0.405

Multiple sequence alignment