ABC2_membrane - PFAM28P - GREMLIN Contacts

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ABC2_membrane - ABC-2 type transporter

PFAM:	PF01061	Sequences: TQIWALVRRELKRRYRNPVLGLLWSLLQPLLFLLVFGFVFGGLGSSSGGVNYPGLLAGLVLFTAFSSLTSISLVSERERGTLERLLVTPLYSRPAILLGKVLAALLIALLQLLLVLLVALLLFGLPISSFLLLLLLLLLLALAFLGLGLLLSALAVSFRDAQQIVNFVLLPLFFLSGVFYPISSLPGWLQWIAYLNPLTYAVEALRAALF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	210 (204)
Sequences:	99551 (65267)
Seq/√Len:	4569.6
META:	0.709

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_L	204_A	4.901	1.00
8_R	12_K	3.889	1.00
140_L	201_A	3.720	1.00
7_V	106_L	3.536	1.00
92_S	95_A	3.300	1.00
187_G	191_W	3.199	1.00
188_W	191_W	3.000	1.00
4_W	8_R	2.861	1.00
191_W	194_Y	2.848	1.00
190_Q	194_Y	2.796	1.00
187_G	190_Q	2.629	1.00
140_L	144_F	2.295	1.00
54_G	58_G	2.218	1.00
131_L	134_L	2.165	1.00
136_L	208_A	2.006	1.00
191_W	195_L	1.881	1.00
47_S	50_V	1.835	1.00
72_S	148_G	1.821	1.00
140_L	205_L	1.805	1.00
10_E	100_K	1.786	1.00
45_S	48_G	1.710	1.00
182_I	193_A	1.709	1.00
54_G	62_F	1.691	1.00
49_G	52_Y	1.680	1.00
113_L	134_L	1.673	1.00
4_W	7_V	1.659	1.00
193_A	199_T	1.652	1.00
182_I	194_Y	1.648	1.00
15_Y	18_P	1.631	1.00
46_S	49_G	1.609	1.00
25_S	29_P	1.607	1.00
5_A	8_R	1.582	1.00
66_S	70_S	1.582	1.00
132_L	135_L	1.569	1.00
203_E	207_A	1.540	1.00
7_V	102_L	1.529	1.00
29_P	33_L	1.516	1.00
178_V	202_V	1.504	1.00
132_L	208_A	1.495	1.00
118_V	122_L	1.493	1.00
12_K	15_Y	1.492	1.00
135_L	139_L	1.481	1.00
58_G	62_F	1.479	1.00
46_S	50_V	1.474	1.00
199_T	203_E	1.463	1.00
131_L	135_L	1.459	1.00
67_S	71_I	1.451	1.00
157_S	160_D	1.407	1.00
194_Y	199_T	1.388	1.00
194_Y	200_Y	1.371	1.00
108_A	111_Q	1.369	1.00
58_G	61_L	1.361	1.00
45_S	50_V	1.357	1.00
85_L	88_T	1.352	1.00
75_S	79_R	1.339	1.00
53_P	57_A	1.318	1.00
57_A	61_L	1.309	1.00
181_P	184_S	1.308	1.00
167_F	171_P	1.303	1.00
53_P	58_G	1.295	1.00
45_S	49_G	1.289	1.00
87_V	90_L	1.285	1.00
48_G	51_N	1.280	1.00
94_P	98_L	1.253	1.00
166_N	170_L	1.250	1.00
186_P	190_Q	1.237	1.00
196_N	199_T	1.233	1.00
74_V	78_E	1.231	1.00
156_V	160_D	1.215	1.00
185_L	193_A	1.203	1.00
55_L	59_L	1.198	1.00
107_I	111_Q	1.193	1.00
200_Y	204_A	1.184	1.00
54_G	57_A	1.183	1.00
76_E	81_T	1.181	1.00
118_V	121_L	1.175	1.00
114_L	117_L	1.173	1.00
172_L	198_L	1.172	1.00
7_V	99_G	1.167	1.00
133_L	205_L	1.166	1.00
28_Q	32_F	1.143	1.00
18_P	21_G	1.124	1.00
111_Q	115_V	1.119	1.00
59_L	63_T	1.117	1.00
48_G	52_Y	1.115	1.00
202_V	206_R	1.081	1.00
76_E	80_G	1.071	1.00
190_Q	193_A	1.070	1.00
57_A	60_V	1.068	1.00
85_L	89_P	1.068	1.00
172_L	196_N	1.060	1.00
76_E	100_K	1.058	1.00
124_G	127_I	1.057	1.00
117_L	121_L	1.051	1.00
182_I	199_T	1.050	1.00
185_L	189_L	1.043	1.00
126_P	129_S	1.036	1.00
11_L	15_Y	1.028	1.00
133_L	208_A	1.021	1.00
182_I	190_Q	1.018	1.00
62_F	65_F	1.016	1.00
173_F	179_F	1.013	1.00
6_L	99_G	1.004	1.00
119_A	123_F	1.001	1.00
14_R	18_P	0.991	1.00
73_L	76_E	0.990	1.00
188_W	192_I	0.987	1.00
74_V	77_R	0.986	1.00
143_A	146_G	0.979	1.00
47_S	51_N	0.974	1.00
177_G	199_T	0.972	1.00
107_I	110_L	0.969	1.00
9_R	13_R	0.966	1.00
34_L	38_F	0.965	1.00
55_L	58_G	0.965	1.00
75_S	78_E	0.963	1.00
80_G	84_R	0.962	1.00
182_I	203_E	0.960	1.00
203_E	206_R	0.959	1.00
177_G	182_I	0.955	1.00
10_E	13_R	0.954	1.00
109_L	113_L	0.948	1.00
32_F	36_F	0.946	1.00
144_F	148_G	0.934	1.00
136_L	140_L	0.929	1.00
69_T	165_V	0.915	1.00
84_R	87_V	0.912	1.00
201_A	204_A	0.907	1.00
129_S	132_L	0.902	1.00
110_L	114_L	0.900	1.00
78_E	158_F	0.896	1.00
134_L	138_L	0.893	1.00
24_W	28_Q	0.884	1.00
106_L	110_L	0.869	1.00
168_V	171_P	0.866	1.00
171_P	175_L	0.865	1.00
103_A	106_L	0.857	1.00
67_S	70_S	0.854	1.00
54_G	64_A	0.851	1.00
116_L	120_L	0.851	1.00
66_S	69_T	0.850	1.00
102_L	106_L	0.849	1.00
56_L	59_L	0.843	1.00
46_S	52_Y	0.842	1.00
156_V	159_R	0.842	1.00
46_S	51_N	0.842	1.00
81_T	85_L	0.837	1.00
83_E	86_L	0.837	1.00
99_G	103_A	0.835	1.00
77_R	82_L	0.825	1.00
114_L	118_V	0.823	1.00
155_A	161_A	0.820	1.00
117_L	120_L	0.819	1.00
86_L	89_P	0.819	1.00
12_K	16_R	0.815	1.00
143_A	201_A	0.814	1.00
109_L	138_L	0.813	1.00
155_A	160_D	0.813	1.00
31_L	34_L	0.812	1.00
88_T	93_R	0.811	1.00
105_L	109_L	0.800	1.00
150_L	153_A	0.798	1.00
53_P	56_L	0.795	1.00
189_L	193_A	0.788	1.00
83_E	87_V	0.783	1.00
38_F	41_G	0.782	1.00
204_A	207_A	0.781	1.00
153_A	156_V	0.781	1.00
137_L	205_L	0.775	1.00
73_L	77_R	0.772	1.00
7_V	11_L	0.771	1.00
84_R	88_T	0.766	1.00
105_L	112_L	0.762	1.00
56_L	60_V	0.759	1.00
53_P	65_F	0.757	1.00
11_L	103_A	0.754	1.00
135_L	138_L	0.746	1.00
160_D	163_Q	0.746	1.00
23_L	27_L	0.745	1.00
53_P	61_L	0.737	1.00
176_S	198_L	0.734	1.00
104_A	107_I	0.732	1.00
138_L	142_L	0.731	1.00
101_V	146_G	0.731	1.00
93_R	97_L	0.730	1.00
177_G	180_Y	0.730	1.00
123_F	127_I	0.727	1.00
119_A	122_L	0.726	1.00
132_L	136_L	0.725	1.00
33_L	37_G	0.722	1.00
58_G	64_A	0.719	1.00
112_L	116_L	0.718	1.00
77_R	156_V	0.717	1.00
110_L	113_L	0.715	1.00
81_T	84_R	0.713	1.00
96_I	99_G	0.712	1.00
111_Q	114_L	0.711	1.00
155_A	164_I	0.710	1.00
58_G	63_T	0.708	1.00
113_L	117_L	0.706	1.00
204_A	208_A	0.706	1.00
37_G	41_G	0.704	1.00
200_Y	203_E	0.701	1.00
98_L	102_L	0.700	1.00
60_V	64_A	0.689	1.00
100_K	104_A	0.685	1.00
146_G	150_L	0.685	1.00
120_L	127_I	0.684	1.00
97_L	101_V	0.682	1.00
34_L	37_G	0.680	1.00
151_L	161_A	0.674	1.00
182_I	185_L	0.673	1.00
86_L	93_R	0.672	1.00
150_L	154_L	0.669	1.00
201_A	205_L	0.658	1.00
121_L	124_G	0.658	1.00
98_L	101_V	0.657	1.00
25_S	28_Q	0.655	1.00
77_R	81_T	0.650	1.00
193_A	196_N	0.646	1.00
146_G	153_A	0.645	1.00
120_L	123_F	0.642	1.00
151_L	155_A	0.639	1.00
61_L	65_F	0.634	1.00
108_A	112_L	0.633	1.00
116_L	119_A	0.633	1.00
170_L	173_F	0.632	1.00
41_G	44_G	0.631	1.00
159_R	163_Q	0.631	1.00
95_A	98_L	0.628	1.00
85_L	90_L	0.627	1.00
79_R	83_E	0.626	1.00
78_E	81_T	0.622	1.00
57_A	62_F	0.618	1.00
146_G	149_L	0.614	1.00
73_L	165_V	0.614	1.00
68_L	144_F	0.612	1.00
61_L	64_A	0.611	1.00
162_Q	166_N	0.609	1.00
65_F	69_T	0.609	1.00
83_E	90_L	0.608	1.00
141_A	145_L	0.605	1.00
24_W	29_P	0.604	1.00
105_L	142_L	0.599	1.00
165_V	168_V	0.598	1.00
15_Y	19_V	0.598	1.00
76_E	82_L	0.595	1.00
106_L	109_L	0.594	1.00
80_G	83_E	0.592	1.00
68_L	71_I	0.589	1.00
95_A	99_G	0.588	1.00
94_P	97_L	0.585	1.00
103_A	107_I	0.585	1.00
184_S	187_G	0.583	1.00
7_V	103_A	0.579	1.00
83_E	89_P	0.575	1.00
136_L	205_L	0.573	1.00
168_V	172_L	0.573	1.00
186_P	189_L	0.571	1.00
53_P	63_T	0.569	1.00
124_G	128_S	0.563	1.00
147_L	168_V	0.563	1.00
159_R	162_Q	0.563	1.00
65_F	70_S	0.559	1.00
60_V	63_T	0.559	1.00
93_R	96_I	0.551	1.00
127_I	130_F	0.550	1.00
64_A	141_A	0.549	1.00
57_A	63_T	0.549	1.00
14_R	17_N	0.548	1.00
53_P	60_V	0.547	1.00
14_R	21_G	0.547	1.00
13_R	17_N	0.545	1.00
163_Q	167_F	0.539	1.00
7_V	10_E	0.537	1.00
90_L	93_R	0.537	1.00
66_S	71_I	0.535	1.00
189_L	192_I	0.534	1.00
151_L	165_V	0.533	1.00
142_L	146_G	0.532	1.00
137_L	201_A	0.531	1.00
125_L	128_S	0.529	1.00
78_E	100_K	0.524	1.00
139_L	143_A	0.524	1.00
81_T	86_L	0.524	1.00
113_L	116_L	0.523	1.00
149_L	153_A	0.519	1.00
104_A	108_A	0.519	1.00
194_Y	203_E	0.516	1.00
74_V	162_Q	0.516	1.00
83_E	88_T	0.515	1.00
96_I	100_K	0.514	1.00
77_R	159_R	0.514	1.00
195_L	200_Y	0.514	1.00
85_L	96_I	0.514	1.00
177_G	203_E	0.513	1.00
45_S	51_N	0.512	1.00
205_L	208_A	0.511	1.00
188_W	193_A	0.510	1.00
69_T	73_L	0.507	1.00
45_S	52_Y	0.505	1.00
59_L	64_A	0.504	1.00
75_S	81_T	0.502	1.00
19_V	23_L	0.501	1.00
185_L	190_Q	0.500	1.00
185_L	188_W	0.500	1.00

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
2a65A	2	0.3857	3.2	0.927	Contact Map
2kogA	1	0.1952	0.9	0.946	Contact Map
2m8rA	1	0.1857	0.9	0.948	Contact Map
4b19A	1	0.1429	0.7	0.95	Contact Map
2zy9A	2	0.4952	0.7	0.951	Contact Map
4mbsA	1	0.0571	0.7	0.952	Contact Map
3rqwA	4	0.6286	0.6	0.952	Contact Map
3echC	1	0.0952	0.6	0.952	Contact Map
4i0uA	4	0.3429	0.6	0.953	Contact Map
4ev6A	3	0.3524	0.6	0.953	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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