Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS00560

Experiment: Rhamnogalacturonan from soy bean pectic fibre 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_RS00570 and HMPREF1058_RS00565 are separated by 4 nucleotidesHMPREF1058_RS00565 and HMPREF1058_RS00560 are separated by 294 nucleotidesHMPREF1058_RS00560 and HMPREF1058_RS00555 are separated by 5 nucleotides HMPREF1058_RS00570: HMPREF1058_RS00570 - HD domain-containing protein, at 49,403 to 50,884 _RS00570 HMPREF1058_RS00565: HMPREF1058_RS00565 - hemolysin III family protein, at 50,889 to 51,524 _RS00565 HMPREF1058_RS00560: HMPREF1058_RS00560 - anaerobic ribonucleoside triphosphate reductase, at 51,819 to 54,095 _RS00560 HMPREF1058_RS00555: HMPREF1058_RS00555 - anaerobic ribonucleoside-triphosphate reductase activating protein, at 54,101 to 54,559 _RS00555 Position (kb) 51 52 53 54 55Strain fitness (log2 ratio) -2 -1 0 1 2 3at 50.865 kb on + strandat 50.865 kb on + strandat 50.897 kb on - strandat 50.956 kb on + strand, within HMPREF1058_RS00565at 50.957 kb on - strand, within HMPREF1058_RS00565at 51.041 kb on - strand, within HMPREF1058_RS00565at 51.060 kb on + strand, within HMPREF1058_RS00565at 51.061 kb on - strand, within HMPREF1058_RS00565at 51.162 kb on + strand, within HMPREF1058_RS00565at 51.162 kb on + strand, within HMPREF1058_RS00565at 51.221 kb on + strand, within HMPREF1058_RS00565at 51.259 kb on + strand, within HMPREF1058_RS00565at 51.307 kb on - strand, within HMPREF1058_RS00565at 51.308 kb on + strand, within HMPREF1058_RS00565at 51.308 kb on + strandat 51.309 kb on - strand, within HMPREF1058_RS00565at 51.309 kb on - strand, within HMPREF1058_RS00565at 51.311 kb on - strand, within HMPREF1058_RS00565at 51.374 kb on + strand, within HMPREF1058_RS00565at 51.405 kb on + strand, within HMPREF1058_RS00565at 51.406 kb on - strand, within HMPREF1058_RS00565at 51.406 kb on - strand, within HMPREF1058_RS00565at 51.449 kb on + strand, within HMPREF1058_RS00565at 51.754 kb on + strandat 51.754 kb on + strandat 52.043 kb on - strandat 52.065 kb on + strand, within HMPREF1058_RS00560at 52.068 kb on - strand, within HMPREF1058_RS00560at 52.251 kb on - strand, within HMPREF1058_RS00560at 52.254 kb on + strandat 52.403 kb on + strand, within HMPREF1058_RS00560at 52.562 kb on - strand, within HMPREF1058_RS00560at 52.780 kb on + strand, within HMPREF1058_RS00560at 52.878 kb on + strand, within HMPREF1058_RS00560at 53.036 kb on + strand, within HMPREF1058_RS00560at 53.150 kb on - strand, within HMPREF1058_RS00560at 53.993 kb on + strandat 53.993 kb on + strandat 53.994 kb on - strandat 53.994 kb on - strandat 54.594 kb on + strandat 54.596 kb on + strandat 54.733 kb on + strandat 54.755 kb on + strandat 54.755 kb on + strandat 54.756 kb on - strandat 54.764 kb on - strandat 54.769 kb on + strandat 54.797 kb on + strandat 54.798 kb on - strandat 54.798 kb on - strandat 54.804 kb on - strandat 54.806 kb on + strandat 54.814 kb on - strandat 54.855 kb on + strandat 54.856 kb on - strandat 54.859 kb on + strandat 54.859 kb on + strandat 54.974 kb on + strandat 54.997 kb on - strandat 55.029 kb on - strandat 55.030 kb on + strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Rhamnogalacturonan from soy bean pectic fibre 5 mg/ml (C)
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50,865 + -0.3
50,865 + +0.2
50,897 - +0.9
50,956 + HMPREF1058_RS00565 0.11 -0.1
50,957 - HMPREF1058_RS00565 0.11 -0.3
51,041 - HMPREF1058_RS00565 0.24 +0.6
51,060 + HMPREF1058_RS00565 0.27 -0.4
51,061 - HMPREF1058_RS00565 0.27 -0.8
51,162 + HMPREF1058_RS00565 0.43 -1.1
51,162 + HMPREF1058_RS00565 0.43 +0.3
51,221 + HMPREF1058_RS00565 0.52 -0.1
51,259 + HMPREF1058_RS00565 0.58 -1.6
51,307 - HMPREF1058_RS00565 0.66 +0.6
51,308 + HMPREF1058_RS00565 0.66 -1.3
51,308 + +0.4
51,309 - HMPREF1058_RS00565 0.66 +0.8
51,309 - HMPREF1058_RS00565 0.66 +0.3
51,311 - HMPREF1058_RS00565 0.66 -0.1
51,374 + HMPREF1058_RS00565 0.76 -1.0
51,405 + HMPREF1058_RS00565 0.81 -0.9
51,406 - HMPREF1058_RS00565 0.81 +0.4
51,406 - HMPREF1058_RS00565 0.81 +0.7
51,449 + HMPREF1058_RS00565 0.88 -1.5
51,754 + -0.2
51,754 + -1.1
52,043 - -1.2
52,065 + HMPREF1058_RS00560 0.11 -2.7
52,068 - HMPREF1058_RS00560 0.11 -2.4
52,251 - HMPREF1058_RS00560 0.19 -1.3
52,254 + +0.4
52,403 + HMPREF1058_RS00560 0.26 +0.1
52,562 - HMPREF1058_RS00560 0.33 -1.0
52,780 + HMPREF1058_RS00560 0.42 -2.2
52,878 + HMPREF1058_RS00560 0.47 -1.3
53,036 + HMPREF1058_RS00560 0.53 -1.5
53,150 - HMPREF1058_RS00560 0.58 -1.3
53,993 + -0.2
53,993 + -0.4
53,994 - -1.7
53,994 - -0.4
54,594 + -1.8
54,596 + -0.5
54,733 + +3.2
54,755 + +0.5
54,755 + -0.9
54,756 - -0.5
54,764 - -1.3
54,769 + +0.8
54,797 + -0.5
54,798 - -1.3
54,798 - +1.2
54,804 - +0.6
54,806 + -1.6
54,814 - +0.4
54,855 + +0.6
54,856 - +0.2
54,859 + +0.4
54,859 + +0.3
54,974 + +2.4
54,997 - +0.4
55,029 - -0.3
55,030 + +0.9

Or see this region's nucleotide sequence