ARTI - ECOLI - GREMLIN Contacts

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ARTI - Putative ABC transporter arginine-binding protein 2

UniProt:	P30859	Sequences: MKKVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11625
Length:	243 (224)
Sequences:	21080 (15099)
Seq/√Len:	1008.8

ECOLI - ARTI ARTJ YHDW GLNH ARGT HISJ GLTI FLIY EVGS MLTF
BACSU - GLNH TCYJ ARTP TCYK YCKB YXEM TCYA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_A	81_V	3.662	1.00
130_G	168_I	3.569	1.00
22_T	63_T	3.507	1.00
57_E	226_K	2.842	1.00
153_Y	162_D	2.421	1.00
90_I	95_E	2.402	1.00
138_Q	152_P	2.360	1.00
102_T	225_E	2.267	1.00
24_R	63_T	2.241	1.00
75_S	81_V	2.186	1.00
90_I	206_G	2.106	1.00
155_S	158_N	2.083	1.00
55_C	62_C	2.052	1.00
24_R	65_S	2.052	1.00
138_Q	142_M	2.041	1.00
22_T	61_T	2.037	1.00
77_K	97_Q	2.027	1.00
98_V	208_A	2.020	1.00
38_D	44_V	1.997	1.00
232_T	235_T	1.986	1.00
53_A	56_K	1.965	1.00
99_L	217_Q	1.944	1.00
209_V	217_Q	1.935	1.00
159_A	171_V	1.931	1.00
92_P	95_E	1.917	1.00
128_K	151_V	1.901	1.00
234_E	238_N	1.876	1.00
57_E	223_A	1.869	1.00
225_E	229_K	1.866	1.00
173_G	178_V	1.859	1.00
217_Q	221_N	1.823	1.00
162_D	167_R	1.811	1.00
120_S	123_Q	1.790	1.00
128_K	149_T	1.764	1.00
25_F	51_A	1.735	1.00
102_T	221_N	1.721	1.00
209_V	220_L	1.707	1.00
111_F	178_V	1.670	1.00
53_A	232_T	1.658	1.00
75_S	80_R	1.644	1.00
85_M	207_I	1.635	1.00
53_A	57_E	1.609	1.00
53_A	227_V	1.594	1.00
119_T	123_Q	1.571	1.00
101_T	221_N	1.568	1.00
106_D	204_G	1.546	1.00
214_T	218_Q	1.521	1.00
113_G	166_G	1.499	1.00
140_F	144_K	1.498	1.00
113_G	116_G	1.481	1.00
133_N	154_D	1.477	1.00
210_R	213_N	1.476	1.00
67_Q	75_S	1.453	1.00
57_E	230_D	1.415	1.00
49_D	239_K	1.411	1.00
37_I	66_N	1.408	1.00
72_L	84_V	1.393	1.00
25_F	83_A	1.373	1.00
36_S	44_V	1.369	1.00
54_L	223_A	1.349	1.00
218_Q	222_T	1.345	1.00
58_I	223_A	1.330	1.00
15_L	19_A	1.329	1.00
128_K	169_D	1.329	1.00
175_T	179_T	1.327	1.00
38_D	42_Q	1.327	1.00
219_K	222_T	1.325	1.00
99_L	212_G	1.311	1.00
109_A	175_T	1.306	1.00
139_K	143_D	1.306	1.00
52_Q	64_F	1.288	1.00
48_V	52_Q	1.288	1.00
223_A	226_K	1.271	1.00
51_A	85_M	1.265	1.00
127_K	169_D	1.264	1.00
29_A	66_N	1.258	1.00
88_M	208_A	1.246	1.00
162_D	168_I	1.241	1.00
114_Q	187_K	1.234	1.00
73_I	98_V	1.229	1.00
142_M	152_P	1.208	1.00
130_G	153_Y	1.204	1.00
164_Q	187_K	1.204	1.00
16_S	20_A	1.196	1.00
74_P	77_K	1.193	1.00
79_R	210_R	1.189	1.00
163_L	188_L	1.171	1.00
46_F	237_Y	1.170	1.00
223_A	227_V	1.169	1.00
129_V	170_G	1.165	1.00
112_V	170_G	1.163	1.00
228_K	233_Y	1.163	1.00
219_K	223_A	1.147	1.00
114_Q	189_A	1.145	1.00
60_A	219_K	1.144	1.00
47_D	104_Y	1.143	1.00
161_L	164_Q	1.140	1.00
161_L	165_N	1.129	1.00
99_L	214_T	1.128	1.00
226_K	230_D	1.116	1.00
115_Q	189_A	1.110	1.00
153_Y	159_A	1.090	1.00
74_P	78_F	1.087	1.00
154_D	158_N	1.081	1.00
21_E	60_A	1.078	1.00
110_L	170_G	1.078	1.00
131_V	138_Q	1.076	1.00
84_V	88_M	1.074	1.00
99_L	211_Q	1.071	1.00
15_L	18_T	1.070	1.00
133_N	152_P	1.049	1.00
214_T	217_Q	1.046	1.00
163_L	171_V	1.046	1.00
46_F	236_I	1.036	1.00
163_L	168_I	1.029	1.00
68_A	71_S	1.024	1.00
51_A	64_F	1.018	1.00
67_Q	81_V	1.009	1.00
44_V	49_D	1.007	1.00
180_E	184_D	1.004	1.00
37_I	41_N	1.001	1.00
93_E	96_K	0.997	1.00
12_G	215_E	0.984	1.00
50_L	233_Y	0.984	1.00
57_E	232_T	0.979	1.00
83_A	220_L	0.978	1.00
109_A	190_A	0.972	1.00
49_D	52_Q	0.972	1.00
25_F	62_C	0.972	1.00
145_H	148_I	0.972	1.00
73_I	88_M	0.970	1.00
215_E	219_K	0.966	1.00
101_T	220_L	0.964	1.00
222_T	226_K	0.953	1.00
132_Q	135_T	0.952	1.00
130_G	159_A	0.947	1.00
112_V	191_V	0.946	1.00
139_K	142_M	0.943	1.00
52_Q	56_K	0.938	1.00
102_T	228_K	0.938	1.00
51_A	62_C	0.934	1.00
43_I	48_V	0.933	1.00
112_V	116_G	0.932	1.00
221_N	225_E	0.928	1.00
232_T	236_I	0.923	1.00
83_A	209_V	0.913	1.00
227_V	232_T	0.912	1.00
151_V	162_D	0.912	1.00
157_Q	161_L	0.911	1.00
158_N	161_L	0.904	1.00
100_F	208_A	0.901	1.00
164_Q	185_N	0.898	1.00
54_L	220_L	0.883	1.00
77_K	98_V	0.879	1.00
20_A	24_R	0.877	1.00
91_T	94_R	0.876	1.00
49_D	240_W	0.870	1.00
118_Y	123_Q	0.868	1.00
50_L	227_V	0.865	1.00
32_P	36_S	0.863	1.00
108_S	175_T	0.857	1.00
42_Q	52_Q	0.855	1.00
13_F	16_S	0.851	1.00
221_N	224_L	0.845	1.00
140_F	143_D	0.844	1.00
71_S	75_S	0.840	1.00
92_P	96_K	0.839	1.00
17_A	21_E	0.837	1.00
233_Y	237_Y	0.835	1.00
95_E	211_Q	0.834	1.00
156_Y	173_G	0.833	1.00
46_F	233_Y	0.831	1.00
29_A	43_I	0.830	1.00
17_A	60_A	0.830	1.00
89_D	203_T	0.826	1.00
14_S	17_A	0.826	1.00
37_I	43_I	0.825	1.00
107_N	176_A	0.821	1.00
234_E	237_Y	0.820	1.00
23_I	60_A	0.818	1.00
12_G	16_S	0.812	1.00
235_T	238_N	0.809	1.00
51_A	207_I	0.804	1.00
12_G	15_L	0.803	1.00
27_T	64_F	0.802	1.00
23_I	83_A	0.797	1.00
84_V	208_A	0.796	1.00
69_F	72_L	0.790	1.00
53_A	223_A	0.786	1.00
227_V	230_D	0.784	1.00
58_I	219_K	0.783	1.00
124_L	170_G	0.773	1.00
18_T	21_E	0.772	1.00
51_A	83_A	0.766	1.00
17_A	20_A	0.765	1.00
34_F	105_Y	0.759	1.00
215_E	218_Q	0.752	1.00
57_E	227_V	0.751	1.00
83_A	207_I	0.751	1.00
24_R	82_E	0.749	1.00
73_I	77_K	0.748	1.00
117_K	189_A	0.746	1.00
226_K	229_K	0.739	1.00
111_F	188_L	0.735	1.00
22_T	60_A	0.734	1.00
122_D	125_K	0.733	1.00
54_L	58_I	0.731	1.00
23_I	55_C	0.724	1.00
110_L	172_F	0.724	1.00
227_V	231_G	0.723	1.00
112_V	189_A	0.719	1.00
235_T	239_K	0.712	1.00
76_L	98_V	0.711	1.00
151_V	168_I	0.708	1.00
107_N	175_T	0.706	1.00
101_T	207_I	0.705	1.00
222_T	225_E	0.704	1.00
227_V	233_Y	0.698	1.00
27_T	48_V	0.698	1.00
52_Q	62_C	0.698	1.00
14_S	18_T	0.689	1.00
65_S	80_R	0.688	1.00
158_N	162_D	0.685	1.00
142_M	150_T	0.684	1.00
179_T	183_K	0.683	1.00
53_A	236_I	0.681	1.00
130_G	162_D	0.679	1.00
76_L	84_V	0.676	1.00
76_L	81_V	0.675	1.00
71_S	74_P	0.674	1.00
141_I	150_T	0.665	1.00
94_R	100_F	0.663	1.00
79_R	212_G	0.658	1.00
67_Q	72_L	0.657	1.00
160_K	164_Q	0.656	1.00
28_E	35_E	0.655	1.00
25_F	64_F	0.653	1.00
26_A	72_L	0.647	1.00
103_P	106_D	0.645	1.00
13_F	17_A	0.642	1.00
54_L	85_M	0.639	1.00
207_I	220_L	0.638	1.00
90_I	103_P	0.635	1.00
14_S	20_A	0.635	1.00
27_T	86_A	0.635	1.00
225_E	228_K	0.633	1.00
213_N	216_L	0.630	1.00
128_K	168_I	0.630	1.00
180_E	183_K	0.627	1.00
125_K	147_E	0.627	1.00
101_T	209_V	0.625	1.00
218_Q	221_N	0.623	1.00
33_P	36_S	0.622	1.00
99_L	213_N	0.619	1.00
65_S	81_V	0.618	1.00
36_S	240_W	0.616	1.00
48_V	64_F	0.616	1.00
44_V	240_W	0.615	1.00
51_A	55_C	0.613	1.00
55_C	58_I	0.611	1.00
50_L	224_L	0.611	1.00
143_D	146_P	0.610	1.00
31_Y	69_F	0.610	1.00
89_D	94_R	0.606	1.00
113_G	187_K	0.605	1.00
28_E	69_F	0.604	1.00
88_M	98_V	0.603	1.00
69_F	94_R	0.599	1.00
28_E	132_Q	0.594	1.00
178_V	182_L	0.594	1.00
106_D	197_D	0.592	1.00
69_F	88_M	0.591	1.00
100_F	206_G	0.591	1.00
31_Y	87_G	0.589	1.00
55_C	60_A	0.583	1.00
153_Y	168_I	0.581	1.00
58_I	216_L	0.580	1.00
77_K	210_R	0.579	1.00
47_D	87_G	0.574	1.00
109_A	178_V	0.572	1.00
141_I	172_F	0.571	1.00
179_T	190_A	0.571	1.00
188_L	191_V	0.570	1.00
32_P	184_D	0.564	1.00
16_S	19_A	0.563	1.00
101_T	217_Q	0.563	1.00
110_L	124_L	0.562	1.00
227_V	236_I	0.562	1.00
76_L	210_R	0.562	1.00
182_L	185_N	0.562	1.00
27_T	43_I	0.560	1.00
101_T	224_L	0.560	1.00
90_I	100_F	0.560	1.00
107_N	205_L	0.560	1.00
29_A	35_E	0.559	1.00
99_L	209_V	0.558	1.00
35_E	86_A	0.556	1.00
132_Q	156_Y	0.554	1.00
136_T	203_T	0.551	1.00
173_G	177_V	0.551	1.00
108_S	196_T	0.550	1.00
132_Q	159_A	0.549	1.00
209_V	213_N	0.549	1.00
111_F	160_K	0.548	1.00
89_D	136_T	0.548	1.00
181_W	184_D	0.546	1.00
160_K	188_L	0.546	1.00
131_V	152_P	0.546	1.00
162_D	165_N	0.545	1.00
105_Y	205_L	0.542	1.00
181_W	185_N	0.540	1.00
26_A	67_Q	0.538	1.00
29_A	37_I	0.537	1.00
231_G	234_E	0.533	1.00
57_E	219_K	0.532	1.00
144_K	147_E	0.531	1.00
56_K	232_T	0.531	1.00
231_G	235_T	0.530	1.00
26_A	84_V	0.528	1.00
164_Q	188_L	0.528	1.00
115_Q	166_G	0.527	1.00
13_F	20_A	0.520	1.00
21_E	219_K	0.516	1.00
116_G	169_D	0.515	1.00
28_E	86_A	0.515	1.00
182_L	186_P	0.514	1.00
13_F	210_R	0.512	1.00
109_A	192_G	0.512	1.00
49_D	236_I	0.509	1.00
141_I	145_H	0.507	1.00
18_T	219_K	0.505	1.00
133_N	138_Q	0.505	1.00
102_T	224_L	0.504	1.00
32_P	180_E	0.503	1.00
111_F	182_L	0.500	1.00
51_A	54_L	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
3kbrA	4	0.9218	100	0.228	Contact Map
3delB	1	0.8889	100	0.237	Contact Map
4powA	1	0.9177	100	0.238	Contact Map
3hv1A	2	0.9671	100	0.238	Contact Map
1pb7A	1	0.9424	100	0.239	Contact Map
2y7iA	2	0.9342	100	0.241	Contact Map
4ohnA	1	0.9465	100	0.244	Contact Map
2vhaA	2	0.9547	100	0.245	Contact Map
3k4uA	5	0.9095	100	0.248	Contact Map
1xt8A	1	0.93	100	0.248	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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