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Table 1 The specifics of all large putative horizontally acquired gene clusters from chromosome I of V. vulnificus CMCP6, including their δ* (against V. vulnificus chromosome I) and GC composition values compared with chromosome I of V. vulnificus CMCP6. Vv5%, Vv10% and Vv10% are non-anomalous genomic fragments used as a reference clade. Ct1 and Ct2 represent Chlamydia trachomatis genomic fragments and are used as outgroups. The three V. vulnificus CMCP6 islands identified by Zhang and Zhang [22] are included in the last column. The presence of the V. vulnificus CMCP6 putative GIs in V. vulnificus YJ016 is verified by Web-ACT analysis [15].

From: An acquisition account of genomic islands based on genome signature comparisons

Locus Coordinates Size (bp) Presence in V. vulnificus YJ016 chromosome I (fraction bp similar) GI characteristics δ* (× 1000) genomic fragments with a lower δ* GC% genomic fragments with a lower GC% Islands identified by [22].
VvI-1 6115–17532 11417 Partially present (3': 2325/11417) Preceeded by a transposase (VV10005) 59.4 89.6% 41.3% 5.57%  
VvI-2 355728–393737 38010 Partially present (3': 2343/38010) Bordered by phage integrase (VV10372) 87.0 100% 37.8% 1.16% VVGI-2
VvI-3 1094281–1109572 15292 Entirely present - 42.7 81.3% 49.7% 95.3%  
inter 1109572–1122005 12433 Entirely present - 48.4 82.9% 49.6% 95.1%  
VvI-4 1122005–1138423 16419 Entirely present - 40.4 80.9% 50.7% 99.5%  
VvI-5 1749663–1764864 15202 Entirely present - 46.9 85.6% 50.5% 98.6%  
VvI-6 2017768–2042744 24976 Partially present(3': 50/24976) Putative integrase (VV12048) 74.4 98.5% 40.3% 2.29%  
VvI-7 2437730–2603335 165606 Highly dispersed Superintegron integrase (VV12401), plasmid stabilisation protein encoding genes (VV12410)) 57.8 100% 41.1% 5.26% VVGI-1
VvI-8 2649661–2664017 14357 Entirely present - 27.0 41.7% 42.8% 8.33%  
VvI-9 3033569–3043967 10399 Largely present (3': 6834/10399) Preceded by a transposase (VV12969) 51.5 82.5% 42.1% 7.94%  
VvI-10 3260213–3279905 19692 Largely absent (few limited blocks of identity) Putative transposase (VV13182) 64.6 95.8% 39.8% 1.81% VVG1-3
VvI-7a 2437730–2519809 82080 Similar as VvI-7 See VVI-7 62.4 100% 40.8% 2.56% Similar as VvI-7
VvI-7b 2519810–2603335 83526 Similar as VvI-7 See VVI-7 53.1 100% 41.4% 2.56% Similar as VvI-7
VvI-5% 1155000–1170000 15001 Entirely present - 14.0 6.0% 47.3% 59.6%  
VvI-10% 570000–585000 15001 Entirely present - 17.2 10.6% 46.4% 54.1%  
VvI-25% 270000–285000 15001 Entirely present - 21.2 24.3% 46.5% 38.5%  
Ct1 270000–285000# 15001 NR& NR 167 NR 40% NR  
Ct2 305000–320000 15001 NR NR 169 NR 39% NR  
  1. ˆ) Coordinates from the V. vulnificus YJ016 chromosome I (note; the intergenic space beteen VVI0525-VV10526 in V. vulnificus YJ016 chromosome 1 was not included)
  2. #) Coordinates for the C. trachomatis sequences are related to their respective genome sequence (Accession number AE001273).
  3. &) NR denotes not relevant