COX4 - BACSU - GREMLIN Contacts

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COX4 - Cytochrome c oxidase subunit 4B

UniProt:	P24013	Sequences: MVDKKSRGHINSDLEFKKKKHAREMKYQVLSFGLMIGLTIVAFLTVATDGVGSWFTIPFIILLAAIQVIFQLYYFMHMNQKGHEAPALFLYSGVFVAFITVLAFVTIIWW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	110 (101)
Sequences:	182 (131)
Seq/√Len:	13.1

BACSU - COX4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_Q	75_F	2.976	0.96
30_L	45_T	2.473	0.91
94_V	98_F	2.459	0.90
27_Y	80_Q	2.457	0.90
36_I	61_I	2.233	0.85
33_G	36_I	2.226	0.85
104_F	107_I	2.164	0.83
56_T	108_I	2.098	0.81
35_M	75_F	2.091	0.81
94_V	97_A	2.002	0.78
41_V	52_G	1.950	0.76
65_A	69_I	1.929	0.75
98_F	102_L	1.751	0.68
27_Y	30_L	1.725	0.67
102_L	106_T	1.718	0.66
38_L	45_T	1.658	0.63
26_K	62_L	1.651	0.63
19_K	38_L	1.610	0.61
73_Y	91_Y	1.561	0.58
46_V	56_T	1.560	0.58
14_L	98_F	1.498	0.55
28_Q	37_G	1.481	0.54
30_L	54_W	1.464	0.53
96_V	103_A	1.409	0.51
60_I	72_L	1.383	0.49
59_F	85_A	1.369	0.48
79_N	83_H	1.368	0.48
60_I	90_L	1.341	0.47
19_K	92_S	1.340	0.47
38_L	57_I	1.316	0.46
62_L	66_I	1.311	0.45
18_K	84_E	1.294	0.45
51_V	62_L	1.266	0.43
16_F	25_M	1.219	0.41
40_I	48_T	1.205	0.40
85_A	105_V	1.181	0.39
41_V	59_F	1.172	0.38
53_S	57_I	1.159	0.38
40_I	51_V	1.154	0.37
83_H	86_P	1.141	0.37
52_G	108_I	1.123	0.36
20_K	55_F	1.100	0.35
62_L	106_T	1.099	0.35
33_G	75_F	1.096	0.35
19_K	78_M	1.075	0.34
96_V	99_I	1.068	0.33
79_N	82_G	1.059	0.33
19_K	96_V	1.059	0.33
75_F	107_I	1.047	0.32
78_M	93_G	1.039	0.32
23_R	74_Y	1.015	0.31
45_T	59_F	1.011	0.31
25_M	107_I	1.000	0.30
48_T	64_A	0.999	0.30
41_V	97_A	0.995	0.30
88_L	96_V	0.993	0.30
52_G	56_T	0.982	0.29
49_D	98_F	0.978	0.29
26_K	70_F	0.977	0.29
72_L	103_A	0.974	0.29
47_A	52_G	0.966	0.29
17_K	57_I	0.965	0.29
62_L	65_A	0.965	0.29
47_A	57_I	0.953	0.28
32_F	41_V	0.952	0.28
25_M	28_Q	0.936	0.28
81_K	90_L	0.927	0.27
17_K	63_L	0.926	0.27
26_K	60_I	0.923	0.27
74_Y	83_H	0.915	0.27
92_S	100_T	0.913	0.27
26_K	34_L	0.911	0.26
35_M	107_I	0.887	0.26
31_S	99_I	0.883	0.25
38_L	66_I	0.870	0.25
40_I	44_L	0.864	0.25
17_K	21_H	0.863	0.25
20_K	24_E	0.861	0.24
18_K	94_V	0.842	0.24
36_I	94_V	0.826	0.23
11_N	40_I	0.825	0.23
34_L	56_T	0.820	0.23
81_K	94_V	0.818	0.23
72_L	91_Y	0.814	0.23
28_Q	107_I	0.803	0.22
30_L	34_L	0.797	0.22
45_T	95_F	0.792	0.22
23_R	60_I	0.791	0.22
47_A	61_I	0.788	0.22
78_M	94_V	0.775	0.21
26_K	48_T	0.769	0.21
58_P	75_F	0.767	0.21
31_S	101_V	0.763	0.21
35_M	73_Y	0.744	0.20
29_V	56_T	0.731	0.20
30_L	55_F	0.729	0.20
58_P	63_L	0.729	0.20
15_E	29_V	0.720	0.19
16_F	102_L	0.720	0.19
36_I	97_A	0.699	0.19
28_Q	35_M	0.694	0.19
44_L	55_F	0.692	0.19
31_S	50_G	0.685	0.18
80_Q	99_I	0.684	0.18
15_E	86_P	0.684	0.18
48_T	61_I	0.681	0.18
41_V	68_V	0.680	0.18
32_F	58_P	0.674	0.18
21_H	108_I	0.671	0.18
15_E	53_S	0.671	0.18
81_K	101_V	0.668	0.18
30_L	95_F	0.661	0.18
99_I	103_A	0.655	0.17
55_F	86_P	0.654	0.17
100_T	108_I	0.647	0.17
98_F	105_V	0.640	0.17
69_I	88_L	0.638	0.17
56_T	102_L	0.638	0.17
45_T	80_Q	0.627	0.17
21_H	95_F	0.624	0.16
94_V	99_I	0.624	0.16
18_K	22_A	0.619	0.16
12_S	56_T	0.619	0.16
18_K	29_V	0.617	0.16
52_G	80_Q	0.614	0.16
9_H	13_D	0.614	0.16
103_A	108_I	0.613	0.16
26_K	49_D	0.605	0.16
30_L	33_G	0.598	0.16
33_G	84_E	0.596	0.16
75_F	89_F	0.586	0.15
24_E	35_M	0.586	0.15
25_M	75_F	0.580	0.15
84_E	87_A	0.578	0.15
74_Y	86_P	0.572	0.15
30_L	53_S	0.571	0.15
26_K	63_L	0.565	0.15
74_Y	90_L	0.555	0.15
19_K	55_F	0.553	0.15
18_K	78_M	0.552	0.15
9_H	14_L	0.549	0.14
13_D	17_K	0.548	0.14
89_F	97_A	0.546	0.14
68_V	82_G	0.544	0.14
24_E	107_I	0.538	0.14
25_M	73_Y	0.535	0.14
58_P	62_L	0.523	0.14
10_I	13_D	0.521	0.14
69_I	103_A	0.510	0.13
31_S	34_L	0.503	0.13
12_S	18_K	0.500	0.13
36_I	100_T	0.500	0.13

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4q2eA	2	0.6818	38.5	0.929	Contact Map
4cofA	3	0.7818	22.3	0.937	Contact Map
2xq2A	2	0.6636	6.9	0.95	Contact Map
4c7rA	3	0.2545	5.6	0.952	Contact Map
2m20A	2	0.2273	5.2	0.953	Contact Map
2axcA	1	0.2636	4.9	0.953	Contact Map
4il3A	1	1	4.7	0.954	Contact Map
2kluA	1	0.2636	4.1	0.955	Contact Map
2kncB	1	0.2909	4.1	0.955	Contact Map
4aw6A	2	0.9909	4	0.955	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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