CcmB - PFAM28P - GREMLIN Contacts

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CcmB - CcmB protein

PFAM:	PF03379	Sequences: MLALLRKDLRLELRSREALLAMLLFFLLVVVLFPFALGPDPALLRRIAPGVLWVAALFAALLGLDRLFAAEREDGTLDQLLLAPVPLEAIVLGKALAHWLLLGLPLVLLAPLFALLLNLPLAALPLLLLVLLLGTPGLSAVGTLGAALTVGLRRRGLLLPLLLLPLLVPVLIFGVGATAAALAGLPAGGWLLLLAAFDLLFLALAPLAAAAALRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	215 (205)
Sequences:	16775 (9725)
Seq/√Len:	679.2
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_R	10_R	4.553	1.00
5_L	100_L	2.970	1.00
43_L	46_R	2.943	1.00
53_W	134_G	2.811	1.00
64_L	142_G	2.672	1.00
130_V	177_A	2.631	1.00
137_G	170_V	2.555	1.00
5_L	96_L	2.502	1.00
106_L	135_T	2.485	1.00
60_A	138_L	2.427	1.00
4_L	93_G	2.406	1.00
137_G	198_D	2.329	1.00
179_A	183_A	2.207	1.00
188_G	192_L	2.139	1.00
176_G	179_A	2.104	1.00
81_L	87_L	2.102	1.00
5_L	93_G	2.064	1.00
29_V	55_A	2.052	1.00
95_A	140_A	1.998	1.00
145_G	163_L	1.985	1.00
95_A	143_T	1.954	1.00
99_W	135_T	1.911	1.00
144_L	205_A	1.892	1.00
125_P	129_L	1.871	1.00
197_F	201_F	1.830	1.00
68_F	143_T	1.686	1.00
193_L	196_A	1.681	1.00
26_F	109_L	1.667	1.00
86_P	89_A	1.655	1.00
198_D	201_F	1.638	1.00
67_L	98_H	1.623	1.00
75_G	78_D	1.613	1.00
134_G	174_G	1.609	1.00
56_A	106_L	1.599	1.00
125_P	128_L	1.593	1.00
91_V	95_A	1.570	1.00
93_G	97_A	1.558	1.00
192_L	195_A	1.537	1.00
190_W	193_L	1.522	1.00
193_L	197_F	1.508	1.00
141_V	166_L	1.496	1.00
22_M	63_G	1.495	1.00
53_W	178_T	1.492	1.00
138_L	167_L	1.490	1.00
69_A	73_E	1.488	1.00
61_L	164_L	1.466	1.00
136_P	198_D	1.464	1.00
195_A	198_D	1.463	1.00
197_F	200_L	1.453	1.00
99_W	136_P	1.414	1.00
99_W	103_G	1.403	1.00
68_F	147_A	1.400	1.00
176_G	190_W	1.394	1.00
79_Q	82_L	1.393	1.00
173_F	190_W	1.387	1.00
37_L	47_I	1.369	1.00
40_D	46_R	1.361	1.00
157_L	160_P	1.359	1.00
10_R	14_R	1.325	1.00
33_F	51_V	1.324	1.00
201_F	204_L	1.323	1.00
80_L	90_I	1.320	1.00
101_L	105_P	1.306	1.00
98_H	139_S	1.303	1.00
102_L	106_L	1.302	1.00
133_L	195_A	1.291	1.00
176_G	180_A	1.283	1.00
42_A	45_R	1.282	1.00
137_G	197_F	1.275	1.00
136_P	202_L	1.258	1.00
13_L	16_R	1.252	1.00
163_L	167_L	1.249	1.00
72_R	150_V	1.245	1.00
141_V	167_L	1.242	1.00
78_D	81_L	1.221	1.00
41_P	45_R	1.213	1.00
28_L	31_V	1.200	1.00
85_V	88_E	1.193	1.00
189_G	192_L	1.190	1.00
12_E	101_L	1.182	1.00
132_L	136_P	1.181	1.00
124_L	128_L	1.150	1.00
140_A	202_L	1.132	1.00
126_L	187_A	1.124	1.00
88_E	92_L	1.119	1.00
200_L	204_L	1.116	1.00
91_V	140_A	1.110	1.00
198_D	205_A	1.110	1.00
79_Q	83_A	1.102	1.00
53_W	174_G	1.102	1.00
33_F	54_V	1.089	1.00
130_V	174_G	1.087	1.00
121_L	124_L	1.085	1.00
65_D	154_R	1.083	1.00
3_A	6_R	1.078	1.00
93_G	96_L	1.070	1.00
149_T	152_L	1.060	1.00
42_A	46_R	1.054	1.00
126_L	130_V	1.052	1.00
196_A	200_L	1.052	1.00
145_G	166_L	1.046	1.00
108_L	111_P	1.042	1.00
25_F	29_V	1.035	1.00
201_F	205_A	1.030	1.00
130_V	181_A	1.023	1.00
175_V	178_T	1.020	1.00
107_V	111_P	1.017	1.00
5_L	97_A	1.006	1.00
199_L	203_A	1.006	1.00
103_G	132_L	1.003	1.00
84_P	87_L	0.998	1.00
49_P	178_T	0.998	1.00
185_L	189_G	0.985	1.00
98_H	143_T	0.984	1.00
187_A	190_W	0.972	1.00
65_D	69_A	0.970	1.00
193_L	201_F	0.964	1.00
31_V	34_P	0.964	1.00
173_F	193_L	0.963	1.00
192_L	196_A	0.962	1.00
21_A	24_L	0.945	1.00
191_L	198_D	0.942	1.00
127_L	130_V	0.942	1.00
179_A	182_L	0.942	1.00
122_A	125_P	0.941	1.00
191_L	195_A	0.931	1.00
40_D	43_L	0.927	1.00
103_G	107_V	0.921	1.00
110_A	131_L	0.909	1.00
203_A	206_P	0.907	1.00
180_A	190_W	0.907	1.00
91_V	143_T	0.898	1.00
102_L	139_S	0.895	1.00
123_A	126_L	0.895	1.00
193_L	200_L	0.891	1.00
185_L	188_G	0.883	1.00
60_A	102_L	0.883	1.00
65_D	156_G	0.882	1.00
170_V	194_L	0.872	1.00
51_V	54_V	0.868	1.00
112_L	115_L	0.867	1.00
186_P	189_G	0.861	1.00
145_G	159_L	0.858	1.00
70_A	73_E	0.850	1.00
107_V	128_L	0.847	1.00
10_R	13_L	0.842	1.00
190_W	198_D	0.837	1.00
43_L	47_I	0.836	1.00
133_L	198_D	0.833	1.00
103_G	135_T	0.832	1.00
192_L	199_L	0.830	1.00
15_S	18_A	0.829	1.00
188_G	191_L	0.827	1.00
46_R	179_A	0.824	1.00
200_L	203_A	0.823	1.00
81_L	84_P	0.823	1.00
177_A	180_A	0.823	1.00
196_A	201_F	0.821	1.00
76_T	79_Q	0.820	1.00
66_R	69_A	0.818	1.00
95_A	139_S	0.815	1.00
56_A	135_T	0.811	1.00
203_A	207_L	0.811	1.00
141_V	163_L	0.810	1.00
190_W	197_F	0.806	1.00
18_A	21_A	0.805	1.00
102_L	105_P	0.800	1.00
33_F	37_L	0.798	1.00
156_G	160_P	0.795	1.00
111_P	114_A	0.793	1.00
127_L	178_T	0.785	1.00
187_A	191_L	0.782	1.00
191_L	197_F	0.778	1.00
85_V	89_A	0.776	1.00
57_L	61_L	0.773	1.00
129_L	132_L	0.769	1.00
29_V	54_V	0.767	1.00
110_A	114_A	0.766	1.00
106_L	110_A	0.762	1.00
190_W	200_L	0.761	1.00
16_R	19_L	0.761	1.00
170_V	174_G	0.754	1.00
72_R	77_L	0.753	1.00
180_A	185_L	0.752	1.00
32_L	54_V	0.750	1.00
45_R	118_N	0.750	1.00
142_G	163_L	0.750	1.00
30_V	113_F	0.750	1.00
92_L	202_L	0.747	1.00
8_D	94_K	0.742	1.00
48_A	119_L	0.733	1.00
83_A	90_I	0.730	1.00
174_G	178_T	0.726	1.00
103_G	106_L	0.726	1.00
114_A	118_N	0.726	1.00
30_V	117_L	0.722	1.00
5_L	8_D	0.720	1.00
190_W	201_F	0.716	1.00
126_L	181_A	0.714	1.00
180_A	187_A	0.713	1.00
85_V	90_I	0.710	1.00
83_A	86_P	0.703	1.00
129_L	191_L	0.694	1.00
140_A	205_A	0.694	1.00
195_A	199_L	0.691	1.00
22_M	26_F	0.689	1.00
149_T	159_L	0.687	1.00
67_L	143_T	0.684	1.00
189_G	193_L	0.683	1.00
121_L	125_P	0.681	1.00
111_P	115_L	0.679	1.00
186_P	190_W	0.678	1.00
123_A	182_L	0.676	1.00
8_D	93_G	0.669	1.00
114_A	121_L	0.665	1.00
15_S	20_L	0.657	1.00
196_A	203_A	0.656	1.00
30_V	55_A	0.655	1.00
31_V	35_F	0.654	1.00
13_L	19_L	0.653	1.00
80_L	84_P	0.652	1.00
33_F	36_A	0.648	1.00
27_L	112_L	0.646	1.00
41_P	118_N	0.646	1.00
105_P	109_L	0.643	1.00
37_L	51_V	0.642	1.00
104_L	107_V	0.642	1.00
95_A	136_P	0.638	1.00
140_A	201_F	0.634	1.00
193_L	198_D	0.633	1.00
60_A	139_S	0.633	1.00
100_L	103_G	0.632	1.00
99_W	106_L	0.632	1.00
44_L	48_A	0.631	1.00
106_L	131_L	0.619	1.00
191_L	194_L	0.618	1.00
90_I	94_K	0.616	1.00
78_D	82_L	0.616	1.00
87_L	90_I	0.611	1.00
40_D	44_L	0.610	1.00
9_L	97_A	0.610	1.00
200_L	205_A	0.609	1.00
107_V	110_A	0.606	1.00
17_E	20_L	0.606	1.00
187_A	192_L	0.606	1.00
99_W	139_S	0.601	1.00
194_L	198_D	0.593	1.00
12_E	17_E	0.588	1.00
130_V	178_T	0.588	1.00
30_V	36_A	0.587	1.00
9_L	100_L	0.587	1.00
25_F	28_L	0.585	1.00
61_L	65_D	0.581	1.00
126_L	129_L	0.577	1.00
9_L	13_L	0.577	1.00
7_K	94_K	0.575	1.00
106_L	111_P	0.572	1.00
195_A	201_F	0.572	1.00
21_A	157_L	0.572	1.00
52_L	113_F	0.570	1.00
46_R	49_P	0.568	1.00
57_L	171_L	0.565	1.00
178_T	181_A	0.564	1.00
38_G	41_P	0.563	1.00
18_A	28_L	0.561	1.00
134_G	170_V	0.556	1.00
198_D	204_L	0.555	1.00
119_L	127_L	0.555	1.00
88_E	207_L	0.555	1.00
198_D	202_L	0.555	1.00
192_L	198_D	0.552	1.00
204_L	207_L	0.552	1.00
190_W	194_L	0.552	1.00
26_F	59_A	0.551	1.00
107_V	136_P	0.550	1.00
96_L	99_W	0.549	1.00
89_A	93_G	0.546	1.00
110_A	128_L	0.544	1.00
92_L	96_L	0.542	1.00
35_F	168_V	0.542	1.00
194_L	197_F	0.539	1.00
184_G	188_G	0.538	1.00
12_E	16_R	0.538	1.00
60_A	167_L	0.535	1.00
196_A	199_L	0.534	1.00
28_L	33_F	0.532	1.00
189_G	196_A	0.531	1.00
122_A	126_L	0.531	1.00
64_L	98_H	0.531	1.00
34_P	39_P	0.531	1.00
36_A	54_V	0.530	1.00
66_R	70_A	0.529	1.00
60_A	63_G	0.529	1.00
189_G	195_A	0.524	1.00
15_S	19_L	0.523	1.00
112_L	116_L	0.520	0.99
5_L	9_L	0.519	0.99
71_E	94_K	0.516	0.99
65_D	117_L	0.514	0.99
12_E	66_R	0.514	0.99
120_P	123_A	0.513	0.99
177_A	190_W	0.513	0.99
45_R	48_A	0.513	0.99
56_A	131_L	0.512	0.99
95_A	99_W	0.505	0.99
34_P	37_L	0.502	0.99
190_W	195_A	0.501	0.99
4_L	80_L	0.500	0.99

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
2onkC	2	0.586	9.3	0.935	Contact Map
2ksfA	1	0.4977	4.4	0.944	Contact Map
2wswA	3	0.3256	3	0.949	Contact Map
4c5sA	4	0.2326	2.9	0.949	Contact Map
3d31C	2	0.5721	2.9	0.949	Contact Map
2a65A	2	0.6698	2.5	0.951	Contact Map
4us3A	1	0.4837	1.5	0.957	Contact Map
3zuxA	1	0.7953	1.4	0.957	Contact Map
4c7rA	3	0.2047	1.3	0.958	Contact Map
3tx3A	2	0.2884	1.3	0.958	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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