Table 1

Identification of sequences homologous to plasmids in human gut metagenomes

Plasmid

Homologous metagenome sequence(s)1

Corresponding region of plasmid2

Identity

e-value


pTRACA10

Human 7

    gb|AAQK01004081.1
(899)

4113 - 4577 (1)

91% (431/473)

6e-177

Human F2-W

    dbj|BAAY01023134.1
(1097)

3346 - 3966 (2)

82% (524/633)

6e-152

Human In-D

    dbj|BABD01003016.1
(1881)

3296 - 4096 (3)

82% (652/790)

0.0

pTRACA18

Human 8

gb|AAQL01009878.1 (2291)

47-209

90% (151/166)

3e-54

pTRACA22

Human 7

    gb|AAQK01007350.1
(851)

    gb|AAQK01007351.1
(885)

    gb|AAQK01007353.1
(952)

    gb|AAQK01007354.1
(764)

96 - 942 (1)

1106 - 1941 (2)

3021 - 3967 (3)

4421 - 5183 (4)

83% (716/855)

88% (748/843)

91% (882/966)

89% (690/768)

0.0

0.0

0.0

0.0

Human8

    gb|AAQL01008280.1
(1257)

    gb|AAQL01008281.1
(3107)

    gb|AAQL01008279.1
(997)

846 -1941 (5)

2183 - 5503 (6)

5547 - 5744 (7)

89% (984/1104)

89% (2436/2733)

92% (185/201)

0.0

0.0

5e-72

Human In-R

    dbj|BABG01020620.1
(940)

    dbj|BABG01024736.1
(979)

    dbj|BABG01024737.1
(921)

    dbj|BABG01020619.1
(910)

162 - 1102 (8)

3377 - 4334 (9)

4293 - 5209 (9)

5503 - 5903 (10)

94% (890/946)

95% (915/960)

94% (872/922)

91% (376/411)

0.0

0.0

0.0

3e-154

Human F2-W

    dbj|BAAY01022991.1
(1098)

    dbj|BAAY01017891.1
(946)

    dbj|BAAY01006494.1
(1365)

    dbj|BAAY01019825.1
(1034)

    dbj|BAAY01002412.1
(1906)

1 - 602 (11)

479 - 945 (12)*

1390 - 1940 (13)

2813 - 3123 (14)

3865 - 5751 (15)

95% (578/603)

83% (795/950)

92% (512/552)

86% (272/314)

93% (1780/1897)

0.0

0.0

0.0

7e-91

0.0

Human F2-V

    dbj|BAAX01003632.1
(1386)

2718 - 4071 (16)

96% (1318/1362)

0.0

Human F2-Y

    dbj|BABA01021839.1
(940)

4042 - 4710 (17)

80% (550/682)

1e-132

Human In-E

    dbj|BABE01009723.1
(975)

3858 - 4653 (18)

83% (678/810)

0.0

Human In-D

    dbj|BABD01025538.1
(985)

3049 - 3966 (19)

94% (871/921)

0.0

Human In-M

    dbj|BABF01004953.1
(1116)

1310 - 1411 (20)

89% (95/106)

2e-27


Human gut [9,10], murine gut [11], marine and soil [30,31] metagenomes were searched for sequences homologous to plasmid recovered from the human gut using Blastn. No significant homology was found for any plasmid in the non-human metagenomes. For plasmids pTRACA10, 18 and 22 homologous sequences were identified in human gut metagenomes. 1) Homologous sequences identified in each human metagenome to plasmids. Accession numbers for individual metagenomic sequences are provided and figures in parentheses indicate the total length of each metagenomic sequence. 2) Provides coordinates for the corresponding region of homology on relevant plasmids. Figures in parentheses indicate the corresponding fragment mapped onto plasmid sequences in Figure 2. *For region 12 (479-945 on plasmid pTRACA22) only the region from 602-945 bp on plasmid pTRACA22 was represented in Figure 3 due to overlap with region 11 (bp 1-602 on pTRACA22).

Jones et al. BMC Genomics 2010 11:46   doi:10.1186/1471-2164-11-46

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