YBCI - BACSU - GREMLIN Contacts

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YBCI - Uncharacterized protein YbcI

UniProt:	O34380	Sequences: MKKSKGSIESEISKSITQWEKDYLGRGSVSVKTDILRDMIIVNLKGILTPAEYVVCGSKEGMLSIKQTRSELVESGIEGLKDIILKITGEKVKSFHTDLSSRTGERVMVFKLCNDLEKNLEKIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	124 (117)
Sequences:	140 (97)
Seq/√Len:	9.0

BACSU - YBCI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_D	118_K	3.156	0.93
33_T	58_S	2.961	0.90
10_S	38_D	2.659	0.84
16_I	55_V	2.410	0.77
95_F	108_M	2.409	0.77
73_V	95_F	2.329	0.75
23_Y	38_D	2.321	0.74
77_I	81_K	2.265	0.73
10_S	40_I	2.161	0.69
100_S	103_T	2.135	0.68
34_D	37_R	2.101	0.67
38_D	43_N	2.099	0.66
55_V	101_S	1.887	0.58
18_Q	22_D	1.807	0.54
94_S	100_S	1.754	0.52
17_T	31_V	1.751	0.52
58_S	70_S	1.739	0.51
57_G	67_Q	1.734	0.51
19_W	43_N	1.576	0.44
112_L	120_L	1.567	0.44
73_V	108_M	1.492	0.41
66_K	104_G	1.486	0.41
107_V	119_N	1.459	0.39
19_W	34_D	1.434	0.38
97_T	106_R	1.431	0.38
49_T	96_H	1.428	0.38
4_S	7_S	1.419	0.38
55_V	77_I	1.415	0.38
8_I	102_R	1.393	0.37
8_I	16_I	1.369	0.36
18_Q	65_I	1.367	0.36
39_M	92_V	1.349	0.35
33_T	70_S	1.340	0.35
79_G	107_V	1.340	0.35
22_D	45_K	1.325	0.34
116_L	120_L	1.303	0.33
84_I	87_I	1.302	0.33
16_I	71_E	1.287	0.33
58_S	86_K	1.273	0.32
81_K	94_S	1.273	0.32
8_I	85_L	1.258	0.31
14_K	111_K	1.242	0.31
17_T	24_L	1.225	0.30
45_K	56_C	1.218	0.30
82_D	86_K	1.214	0.30
12_I	84_I	1.209	0.30
40_I	87_I	1.190	0.29
13_S	108_M	1.153	0.28
6_G	44_L	1.148	0.28
96_H	100_S	1.147	0.27
67_Q	102_R	1.133	0.27
11_E	83_I	1.128	0.27
64_S	108_M	1.114	0.26
22_D	79_G	1.113	0.26
96_H	99_L	1.079	0.25
18_Q	34_D	1.069	0.25
51_A	73_V	1.067	0.25
11_E	53_Y	1.064	0.25
74_E	100_S	1.060	0.25
21_K	110_F	1.053	0.24
23_Y	97_T	1.052	0.24
22_D	43_N	1.044	0.24
5_K	50_P	1.029	0.24
15_S	45_K	1.025	0.23
30_S	56_C	1.021	0.23
20_E	23_Y	1.019	0.23
22_D	65_I	1.016	0.23
39_M	87_I	1.010	0.23
20_E	108_M	1.007	0.23
43_N	62_M	1.000	0.23
47_I	109_V	0.999	0.23
6_G	20_E	0.991	0.22
33_T	74_E	0.986	0.22
55_V	71_E	0.983	0.22
116_L	119_N	0.979	0.22
10_S	101_S	0.977	0.22
8_I	79_G	0.963	0.22
11_E	14_K	0.947	0.21
51_A	95_F	0.937	0.21
65_I	68_T	0.932	0.21
94_S	103_T	0.929	0.21
21_K	32_K	0.912	0.20
51_A	110_F	0.906	0.20
60_E	96_H	0.901	0.20
17_T	30_S	0.887	0.19
56_C	77_I	0.866	0.19
88_T	116_L	0.855	0.19
44_L	50_P	0.854	0.19
35_I	40_I	0.850	0.18
84_I	119_N	0.831	0.18
24_L	75_S	0.830	0.18
88_T	110_F	0.826	0.18
81_K	86_K	0.813	0.17
33_T	71_E	0.809	0.17
79_G	96_H	0.808	0.17
14_K	19_W	0.806	0.17
40_I	54_V	0.804	0.17
89_G	106_R	0.796	0.17
6_G	76_G	0.789	0.17
36_L	53_Y	0.788	0.17
63_L	88_T	0.750	0.16
41_I	83_I	0.746	0.16
38_D	91_K	0.745	0.16
91_K	113_C	0.742	0.16
28_S	53_Y	0.740	0.16
31_V	64_S	0.734	0.16
11_E	41_I	0.724	0.15
8_I	87_I	0.722	0.15
18_Q	71_E	0.721	0.15
93_K	113_C	0.712	0.15
18_Q	58_S	0.708	0.15
17_T	106_R	0.708	0.15
16_I	80_L	0.705	0.15
54_V	96_H	0.705	0.15
65_I	82_D	0.704	0.15
20_E	51_A	0.703	0.15
24_L	63_L	0.677	0.14
99_L	115_D	0.668	0.14
19_W	63_L	0.655	0.14
46_G	107_V	0.647	0.14
69_R	98_D	0.643	0.14
51_A	112_L	0.643	0.14
59_K	99_L	0.641	0.14
35_I	116_L	0.633	0.13
79_G	83_I	0.626	0.13
14_K	22_D	0.623	0.13
18_Q	70_S	0.622	0.13
98_D	104_G	0.613	0.13
43_N	67_Q	0.612	0.13
60_E	67_Q	0.612	0.13
39_M	111_K	0.612	0.13
21_K	28_S	0.609	0.13
33_T	46_G	0.609	0.13
29_V	120_L	0.603	0.13
58_S	85_L	0.600	0.13
28_S	64_S	0.595	0.13
40_I	84_I	0.595	0.13
44_L	76_G	0.593	0.13
26_R	98_D	0.592	0.13
51_A	106_R	0.586	0.12
56_C	85_L	0.584	0.12
92_V	107_V	0.582	0.12
58_S	118_K	0.582	0.12
60_E	84_I	0.581	0.12
43_N	79_G	0.581	0.12
14_K	18_Q	0.580	0.12
27_G	98_D	0.580	0.12
18_Q	68_T	0.576	0.12
66_K	74_E	0.573	0.12
40_I	91_K	0.570	0.12
17_T	75_S	0.570	0.12
6_G	51_A	0.561	0.12
35_I	65_I	0.554	0.12
46_G	106_R	0.552	0.12
17_T	51_A	0.552	0.12
74_E	104_G	0.551	0.12
17_T	73_V	0.550	0.12
64_S	68_T	0.546	0.12
79_G	111_K	0.540	0.12
12_I	35_I	0.533	0.12
57_G	60_E	0.533	0.12
36_L	56_C	0.529	0.11
51_A	80_L	0.525	0.11
17_T	95_F	0.523	0.11
18_Q	38_D	0.522	0.11
47_I	110_F	0.521	0.11
83_I	109_V	0.521	0.11
20_E	80_L	0.520	0.11
90_E	95_F	0.520	0.11
49_T	110_F	0.517	0.11
90_E	93_K	0.512	0.11
17_T	110_F	0.512	0.11
32_K	35_I	0.504	0.11
112_L	119_N	0.504	0.11
78_E	117_E	0.502	0.11
34_D	106_R	0.500	0.11

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
2qq8A	1	0.7742	21	0.946	Contact Map
2j85A	2	0.75	9.7	0.953	Contact Map
1avyA	3	0.4113	8.9	0.954	Contact Map
2bsgA	3	0.3871	5.2	0.959	Contact Map
2nz7A	2	0.5161	4.8	0.959	Contact Map
1vlcA	2	0.3871	4	0.961	Contact Map
3t98A	4	0.121	3.9	0.961	Contact Map
3tejA	1	0.4516	3.6	0.962	Contact Map
4j3hA	4	0.1452	3.5	0.962	Contact Map
3crdA	1	0.621	3.4	0.962	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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