CIDA - BACSU - GREMLIN Contacts

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CIDA - Holin-like protein CidA

UniProt:	P39591	Sequences: MKKLLLTVIQIALLFIFARLINWVTALLHINIPGSIIGIVILFTLLHFNIIKLEWIELGAAWLLGELLLFFIPSAVGVIEYGDIMSKFGVSILLVVIISTFVVMVSTGTLTQLIAKRKEKKHTCSSEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	128 (112)
Sequences:	1803 (1374)
Seq/√Len:	129.8

ECOLI - YOHJ
BACSU - CIDA LRGA YXZK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_F	45_L	4.581	1.00
106_S	110_L	2.748	1.00
109_T	112_Q	2.747	1.00
44_T	48_F	2.596	1.00
108_G	112_Q	2.461	1.00
105_V	109_T	2.430	1.00
40_V	44_T	2.381	1.00
25_T	37_I	2.139	1.00
16_I	20_L	2.124	1.00
98_I	102_V	1.976	1.00
21_I	34_G	1.970	1.00
91_S	95_V	1.879	1.00
85_M	92_I	1.870	1.00
37_I	41_I	1.838	1.00
88_F	91_S	1.825	1.00
17_F	41_I	1.817	1.00
20_L	45_L	1.789	1.00
79_I	82_G	1.756	1.00
22_N	26_A	1.724	1.00
10_Q	59_G	1.710	1.00
9_I	55_W	1.706	1.00
18_A	22_N	1.704	1.00
35_S	70_F	1.677	1.00
18_A	35_S	1.640	1.00
110_L	113_L	1.580	1.00
23_W	27_L	1.538	1.00
52_K	55_W	1.535	1.00
109_T	113_L	1.516	1.00
24_V	27_L	1.437	1.00
33_P	74_S	1.421	1.00
39_I	75_A	1.392	1.00
78_V	81_Y	1.376	1.00
41_I	45_L	1.360	1.00
57_E	61_A	1.359	1.00
53_L	56_I	1.338	1.00
113_L	117_R	1.295	1.00
83_D	86_S	1.280	1.00
49_N	52_K	1.274	1.00
53_L	57_E	1.222	1.00
81_Y	84_I	1.212	0.99
94_L	98_I	1.173	0.99
24_V	41_I	1.171	0.99
17_F	21_I	1.131	0.99
114_I	117_R	1.122	0.99
111_T	115_A	1.119	0.99
25_T	29_H	1.101	0.99
39_I	111_T	1.078	0.99
40_V	62_W	1.074	0.99
25_T	34_G	1.070	0.99
83_D	87_K	1.069	0.99
82_G	86_S	1.047	0.98
96_V	103_V	1.042	0.98
84_I	88_F	1.029	0.98
21_I	37_I	1.024	0.98
113_L	116_K	0.997	0.98
11_I	59_G	0.989	0.98
68_L	72_I	0.977	0.98
14_L	59_G	0.974	0.98
103_V	107_T	0.971	0.98
45_L	51_I	0.949	0.97
65_G	74_S	0.943	0.97
45_L	50_I	0.941	0.97
36_I	68_L	0.936	0.97
24_V	37_I	0.934	0.97
79_I	97_I	0.932	0.97
9_I	12_A	0.928	0.97
42_L	51_I	0.926	0.97
10_Q	17_F	0.920	0.97
107_T	111_T	0.917	0.97
25_T	28_L	0.911	0.96
24_V	29_H	0.900	0.96
101_F	105_V	0.887	0.96
22_N	34_G	0.884	0.96
21_I	77_G	0.877	0.96
23_W	26_A	0.872	0.95
50_I	53_L	0.866	0.95
51_I	56_I	0.846	0.95
13_L	16_I	0.837	0.94
24_V	57_E	0.830	0.94
34_G	37_I	0.828	0.94
39_I	56_I	0.824	0.94
15_F	77_G	0.823	0.94
100_T	103_V	0.815	0.93
11_I	21_I	0.812	0.93
36_I	64_L	0.790	0.92
88_F	92_I	0.790	0.92
15_F	107_T	0.789	0.92
57_E	77_G	0.783	0.92
20_L	41_I	0.783	0.92
43_F	47_H	0.766	0.91
51_I	55_W	0.763	0.91
45_L	48_F	0.756	0.91
10_Q	62_W	0.754	0.90
25_T	30_I	0.749	0.90
18_A	33_P	0.739	0.90
76_V	79_I	0.734	0.89
71_F	74_S	0.733	0.89
64_L	67_L	0.726	0.89
11_I	99_S	0.726	0.89
80_E	83_D	0.716	0.88
40_V	43_F	0.711	0.88
68_L	75_A	0.710	0.88
7_T	58_L	0.708	0.87
35_S	104_M	0.708	0.87
32_I	38_G	0.697	0.87
96_V	100_T	0.693	0.86
44_T	110_L	0.690	0.86
111_T	114_I	0.687	0.86
63_L	68_L	0.681	0.85
31_N	36_I	0.675	0.85
54_E	63_L	0.674	0.85
28_L	37_I	0.669	0.84
24_V	28_L	0.664	0.84
75_A	78_V	0.663	0.84
108_G	117_R	0.655	0.83
56_I	64_L	0.655	0.83
53_L	60_A	0.648	0.82
14_L	55_W	0.647	0.82
66_E	69_L	0.639	0.82
42_L	56_I	0.638	0.81
29_H	40_V	0.633	0.81
9_I	54_E	0.624	0.80
75_A	82_G	0.622	0.80
67_L	103_V	0.622	0.80
95_V	104_M	0.620	0.80
110_L	117_R	0.619	0.79
75_A	81_Y	0.617	0.79
57_E	103_V	0.611	0.79
100_T	104_M	0.610	0.78
51_I	67_L	0.609	0.78
69_L	72_I	0.605	0.78
9_I	13_L	0.605	0.78
87_K	98_I	0.595	0.77
112_Q	117_R	0.593	0.77
8_V	118_K	0.593	0.77
68_L	99_S	0.587	0.76
15_F	21_I	0.587	0.76
26_A	85_M	0.570	0.74
32_I	77_G	0.565	0.73
69_L	84_I	0.565	0.73
103_V	111_T	0.561	0.73
53_L	88_F	0.560	0.72
36_I	76_V	0.560	0.72
60_A	101_F	0.557	0.72
14_L	99_S	0.552	0.71
27_L	97_I	0.551	0.71
19_R	101_F	0.551	0.71
67_L	71_F	0.546	0.70
9_I	59_G	0.546	0.70
19_R	22_N	0.537	0.69
88_F	98_I	0.534	0.69
55_W	59_G	0.528	0.68
62_W	67_L	0.528	0.68
54_E	113_L	0.528	0.68
50_I	54_E	0.527	0.68
45_L	49_N	0.527	0.68
35_S	43_F	0.526	0.68
35_S	96_V	0.519	0.67
35_S	64_L	0.518	0.67
47_H	50_I	0.517	0.66
49_N	53_L	0.511	0.65
23_W	97_I	0.511	0.65
52_K	98_I	0.510	0.65
41_I	112_Q	0.507	0.65
84_I	92_I	0.505	0.65
13_L	17_F	0.503	0.64
11_I	15_F	0.501	0.64
110_L	114_I	0.500	0.64

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
2kv5A	1	0.2578	56.2	0.902	Contact Map
3w9iA	3	0.9375	53.8	0.904	Contact Map
4dx5A	3	0.9922	49.3	0.906	Contact Map
4cz8A	2	0.9531	46.3	0.908	Contact Map
4czbA	2	0.9609	46.3	0.908	Contact Map
3ne5A	3	0.9219	37.4	0.913	Contact Map
4k0jA	3	0.8828	33.1	0.915	Contact Map
4mt1A	3	0.8984	32.5	0.916	Contact Map
2m20A	2	0.3203	29.2	0.917	Contact Map
2kncA	1	0.3984	27.7	0.918	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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