CbbQ_C - PFAM28P - GREMLIN Contacts

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CbbQ_C - CbbQ/NirQ/NorQ C-terminal

PFAM:	PF08406	Sequences: EAEIVAHESGVDEETAAKLVKLAEKIRNLKGHGLEEGASTRLLVYAARLIAAGIPPREACRAAIVEPLTDDPDVRAALDELVDAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (84)
Sequences:	8905 (4754)
Seq/√Len:	518.7
META:	0.918

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_R	79_D	3.471	1.00
2_A	17_A	2.881	1.00
6_A	13_E	2.393	1.00
12_D	15_T	2.243	1.00
11_V	15_T	2.029	1.00
13_E	17_A	2.012	1.00
2_A	13_E	2.002	1.00
50_I	56_P	1.941	1.00
2_A	6_A	1.930	1.00
57_R	83_D	1.868	1.00
26_I	38_A	1.811	1.00
11_V	16_A	1.758	1.00
21_K	25_K	1.742	1.00
9_S	47_A	1.721	1.00
19_L	43_L	1.637	1.00
22_L	82_V	1.598	1.00
23_A	43_L	1.597	1.00
25_K	28_N	1.478	1.00
19_L	46_A	1.467	1.00
3_E	6_A	1.406	1.00
6_A	16_A	1.398	1.00
3_E	7_H	1.386	1.00
46_A	63_A	1.369	1.00
26_I	37_G	1.346	1.00
3_E	13_E	1.332	1.00
55_P	58_E	1.301	1.00
20_V	24_E	1.264	1.00
80_E	83_D	1.241	1.00
65_V	82_V	1.218	1.00
14_E	18_K	1.211	1.00
46_A	60_C	1.196	1.00
26_I	78_L	1.192	1.00
5_V	43_L	1.185	1.00
66_E	75_R	1.182	1.00
79_D	83_D	1.158	1.00
58_E	62_A	1.140	1.00
61_R	66_E	1.133	1.00
15_T	18_K	1.103	1.00
28_N	32_H	1.100	1.00
74_V	77_A	1.091	1.00
66_E	79_D	1.079	1.00
17_A	21_K	1.066	1.00
2_A	20_V	1.059	1.00
21_K	24_E	1.048	1.00
5_V	9_S	1.028	1.00
22_L	81_L	1.000	1.00
80_E	84_A	0.998	1.00
76_A	80_E	0.998	1.00
15_T	50_I	0.978	1.00
16_A	20_V	0.972	1.00
14_E	17_A	0.965	1.00
42_L	45_Y	0.924	1.00
48_R	51_A	0.922	1.00
5_V	20_V	0.914	1.00
10_G	51_A	0.907	1.00
22_L	26_I	0.892	1.00
65_V	79_D	0.868	1.00
58_E	61_R	0.860	1.00
65_V	75_R	0.848	1.00
18_K	21_K	0.846	1.00
43_L	64_I	0.845	1.00
46_A	64_I	0.838	1.00
30_K	37_G	0.838	1.00
40_T	44_V	0.836	1.00
61_R	83_D	0.824	1.00
69_T	75_R	0.817	1.00
38_A	42_L	0.816	1.00
19_L	23_A	0.795	1.00
49_L	63_A	0.793	1.00
79_D	82_V	0.786	1.00
6_A	9_S	0.772	1.00
32_H	45_Y	0.767	1.00
75_R	79_D	0.763	1.00
48_R	52_A	0.752	1.00
1_E	27_R	0.725	1.00
8_E	44_V	0.722	1.00
29_L	32_H	0.720	1.00
4_I	8_E	0.716	1.00
21_K	28_N	0.715	1.00
35_E	45_Y	0.711	1.00
65_V	78_L	0.709	1.00
50_I	53_G	0.699	1.00
19_L	50_I	0.695	1.00
45_Y	48_R	0.689	1.00
9_S	51_A	0.688	1.00
72_P	75_R	0.679	1.00
36_E	39_S	0.676	1.00
27_R	40_T	0.676	1.00
60_C	82_V	0.673	1.00
26_I	68_L	0.667	1.00
76_A	79_D	0.661	1.00
36_E	42_L	0.660	1.00
73_D	76_A	0.659	1.00
11_V	47_A	0.659	1.00
62_A	66_E	0.655	1.00
25_K	80_E	0.646	1.00
76_A	83_D	0.641	1.00
38_A	64_I	0.634	1.00
26_I	81_L	0.615	1.00
64_I	67_P	0.605	1.00
63_A	67_P	0.600	1.00
31_G	35_E	0.598	0.99
35_E	74_V	0.597	0.99
47_A	50_I	0.593	0.99
25_K	81_L	0.588	0.99
5_V	47_A	0.586	0.99
59_A	70_D	0.583	0.99
12_D	18_K	0.580	0.99
50_I	59_A	0.578	0.99
60_C	64_I	0.573	0.99
15_T	56_P	0.571	0.99
24_E	28_N	0.568	0.99
9_S	48_R	0.564	0.99
33_G	74_V	0.563	0.99
57_R	61_R	0.559	0.99
72_P	76_A	0.557	0.99
74_V	78_L	0.550	0.99
32_H	81_L	0.545	0.99
5_V	8_E	0.529	0.99
25_K	32_H	0.522	0.99
9_S	44_V	0.520	0.99
56_P	60_C	0.515	0.98
36_E	69_T	0.513	0.98
18_K	84_A	0.505	0.98
26_I	34_L	0.501	0.98
28_N	31_G	0.500	0.98

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
4akgA	2	0.9765	63.4	0.811	Contact Map
3vkgA	2	0.9765	54.9	0.82	Contact Map
2r44A	1	1	42.6	0.833	Contact Map
4r7yA	3	0.8353	31.8	0.845	Contact Map
1tr2A	1	0.9529	23.8	0.854	Contact Map
3nbxX	1	0.9412	22.6	0.855	Contact Map
1g8pA	1	0.8	20.8	0.857	Contact Map
3ja87	1	0.8235	19.8	0.859	Contact Map
3vf0A	1	0.8588	17.6	0.862	Contact Map
3ja83	1	0.8706	16.9	0.864	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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