Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS00590

Experiment: Arabinoxylan (Rye Flour) 2.5 mg/ml (C)

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Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

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500 ntHMPREF1058_RS00600 and HMPREF1058_RS00595 are separated by 175 nucleotidesHMPREF1058_RS00595 and HMPREF1058_RS00590 are separated by 87 nucleotidesHMPREF1058_RS00590 and HMPREF1058_RS00585 are separated by 433 nucleotides HMPREF1058_RS00600: HMPREF1058_RS00600 - diaminopimelate dehydrogenase, at 37,881 to 38,780 _RS00600 HMPREF1058_RS00595: HMPREF1058_RS00595 - Holliday junction branch migration protein RuvA, at 38,956 to 39,549 _RS00595 HMPREF1058_RS00590: HMPREF1058_RS00590 - hypothetical protein, at 39,637 to 40,461 _RS00590 HMPREF1058_RS00585: HMPREF1058_RS00585 - PAS domain-containing hybrid sensor histidine kinase/response regulator, at 40,895 to 43,669 _RS00585 Position (kb) 39 40 41Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 38.728 kb on - strandat 38.893 kb on + strandat 38.960 kb on + strandat 39.054 kb on + strand, within HMPREF1058_RS00595at 39.085 kb on - strand, within HMPREF1058_RS00595at 39.096 kb on + strand, within HMPREF1058_RS00595at 39.124 kb on + strand, within HMPREF1058_RS00595at 39.128 kb on + strand, within HMPREF1058_RS00595at 39.129 kb on - strand, within HMPREF1058_RS00595at 39.326 kb on + strand, within HMPREF1058_RS00595at 39.327 kb on - strand, within HMPREF1058_RS00595at 39.548 kb on - strandat 39.548 kb on - strandat 39.556 kb on + strandat 39.557 kb on - strandat 39.638 kb on + strandat 39.639 kb on - strandat 39.639 kb on - strandat 39.705 kb on + strandat 39.801 kb on - strand, within HMPREF1058_RS00590at 39.855 kb on + strand, within HMPREF1058_RS00590at 40.024 kb on - strand, within HMPREF1058_RS00590at 40.029 kb on + strand, within HMPREF1058_RS00590at 40.115 kb on + strand, within HMPREF1058_RS00590at 40.120 kb on - strand, within HMPREF1058_RS00590at 40.133 kb on + strand, within HMPREF1058_RS00590at 40.134 kb on - strand, within HMPREF1058_RS00590at 40.318 kb on + strand, within HMPREF1058_RS00590at 40.442 kb on - strandat 40.444 kb on + strandat 40.444 kb on + strandat 40.464 kb on - strandat 40.476 kb on + strandat 40.476 kb on + strandat 40.476 kb on + strandat 40.477 kb on - strandat 40.570 kb on + strandat 40.657 kb on - strandat 40.693 kb on - strandat 40.693 kb on - strandat 40.697 kb on + strandat 40.697 kb on + strandat 40.697 kb on + strandat 40.698 kb on - strandat 40.698 kb on - strandat 40.698 kb on - strandat 40.729 kb on - strandat 40.741 kb on - strandat 40.770 kb on - strandat 40.842 kb on - strandat 40.842 kb on - strandat 40.844 kb on - strandat 40.866 kb on + strandat 40.869 kb on - strandat 40.894 kb on + strandat 40.904 kb on + strandat 40.910 kb on - strandat 40.910 kb on - strandat 40.929 kb on - strandat 40.944 kb on + strandat 40.944 kb on + strandat 40.944 kb on + strandat 40.944 kb on + strandat 41.000 kb on - strandat 41.012 kb on - strandat 41.021 kb on + strandat 41.022 kb on - strandat 41.072 kb on - strandat 41.078 kb on - strandat 41.107 kb on + strandat 41.110 kb on + strandat 41.110 kb on + strandat 41.111 kb on - strandat 41.137 kb on - strandat 41.179 kb on + strand, within HMPREF1058_RS00585at 41.197 kb on + strand, within HMPREF1058_RS00585at 41.198 kb on - strand, within HMPREF1058_RS00585at 41.226 kb on + strand, within HMPREF1058_RS00585at 41.229 kb on + strand, within HMPREF1058_RS00585at 41.266 kb on + strand, within HMPREF1058_RS00585at 41.299 kb on - strand, within HMPREF1058_RS00585at 41.299 kb on - strand, within HMPREF1058_RS00585at 41.299 kb on - strand, within HMPREF1058_RS00585at 41.299 kb on - strand, within HMPREF1058_RS00585at 41.322 kb on + strand, within HMPREF1058_RS00585at 41.323 kb on - strand, within HMPREF1058_RS00585at 41.338 kb on + strand, within HMPREF1058_RS00585at 41.338 kb on + strand, within HMPREF1058_RS00585at 41.339 kb on - strand, within HMPREF1058_RS00585at 41.376 kb on + strand, within HMPREF1058_RS00585at 41.377 kb on - strand, within HMPREF1058_RS00585at 41.380 kb on + strand, within HMPREF1058_RS00585at 41.381 kb on - strand, within HMPREF1058_RS00585at 41.381 kb on - strand, within HMPREF1058_RS00585at 41.381 kb on - strand, within HMPREF1058_RS00585at 41.402 kb on + strand, within HMPREF1058_RS00585

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Per-strain Table

Position Strand Gene LocusTag Fraction Arabinoxylan (Rye Flour) 2.5 mg/ml (C)
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38,728 - -3.5
38,893 + -1.4
38,960 + -0.6
39,054 + HMPREF1058_RS00595 0.16 -1.7
39,085 - HMPREF1058_RS00595 0.22 -0.3
39,096 + HMPREF1058_RS00595 0.24 -2.1
39,124 + HMPREF1058_RS00595 0.28 -0.1
39,128 + HMPREF1058_RS00595 0.29 -0.7
39,129 - HMPREF1058_RS00595 0.29 -1.5
39,326 + HMPREF1058_RS00595 0.62 +0.1
39,327 - HMPREF1058_RS00595 0.62 -1.4
39,548 - +3.7
39,548 - -0.4
39,556 + -0.2
39,557 - -0.1
39,638 + +0.1
39,639 - +1.1
39,639 - +0.1
39,705 + -0.1
39,801 - HMPREF1058_RS00590 0.20 -0.6
39,855 + HMPREF1058_RS00590 0.26 +2.5
40,024 - HMPREF1058_RS00590 0.47 -1.9
40,029 + HMPREF1058_RS00590 0.48 -1.1
40,115 + HMPREF1058_RS00590 0.58 -1.9
40,120 - HMPREF1058_RS00590 0.59 -0.3
40,133 + HMPREF1058_RS00590 0.60 -2.7
40,134 - HMPREF1058_RS00590 0.60 -2.8
40,318 + HMPREF1058_RS00590 0.83 -1.1
40,442 - -1.7
40,444 + -1.7
40,444 + +0.1
40,464 - -1.0
40,476 + -0.8
40,476 + +0.0
40,476 + -2.1
40,477 - +1.7
40,570 + -2.5
40,657 - +2.5
40,693 - +1.4
40,693 - -0.1
40,697 + -0.8
40,697 + -0.3
40,697 + -0.5
40,698 - +0.3
40,698 - +0.9
40,698 - +0.5
40,729 - +1.5
40,741 - +0.7
40,770 - +1.1
40,842 - +1.7
40,842 - -0.0
40,844 - +0.3
40,866 + -1.1
40,869 - -1.2
40,894 + -1.7
40,904 + -0.5
40,910 - +1.3
40,910 - +0.1
40,929 - +0.9
40,944 + -2.3
40,944 + -1.3
40,944 + -0.1
40,944 + +0.4
41,000 - -2.3
41,012 - +0.0
41,021 + -0.9
41,022 - -1.2
41,072 - -3.2
41,078 - +0.2
41,107 + -2.8
41,110 + -1.0
41,110 + -0.2
41,111 - -0.7
41,137 - -0.7
41,179 + HMPREF1058_RS00585 0.10 -3.5
41,197 + HMPREF1058_RS00585 0.11 +0.9
41,198 - HMPREF1058_RS00585 0.11 -1.0
41,226 + HMPREF1058_RS00585 0.12 -1.7
41,229 + HMPREF1058_RS00585 0.12 +0.2
41,266 + HMPREF1058_RS00585 0.13 +0.5
41,299 - HMPREF1058_RS00585 0.15 +0.5
41,299 - HMPREF1058_RS00585 0.15 +1.7
41,299 - HMPREF1058_RS00585 0.15 +0.1
41,299 - HMPREF1058_RS00585 0.15 +1.5
41,322 + HMPREF1058_RS00585 0.15 -0.8
41,323 - HMPREF1058_RS00585 0.15 +0.1
41,338 + HMPREF1058_RS00585 0.16 -0.2
41,338 + HMPREF1058_RS00585 0.16 -0.2
41,339 - HMPREF1058_RS00585 0.16 +0.8
41,376 + HMPREF1058_RS00585 0.17 -0.2
41,377 - HMPREF1058_RS00585 0.17 -0.9
41,380 + HMPREF1058_RS00585 0.17 -1.0
41,381 - HMPREF1058_RS00585 0.18 +0.9
41,381 - HMPREF1058_RS00585 0.18 -2.7
41,381 - HMPREF1058_RS00585 0.18 +0.3
41,402 + HMPREF1058_RS00585 0.18 +0.3

Or see this region's nucleotide sequence