GLNH - ECOLI - GREMLIN Contacts

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GLNH - Glutamine-binding periplasmic protein

UniProt:	P0AEQ3	Sequences: MKSVLKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10386
Length:	248 (228)
Sequences:	21574 (15520)
Seq/√Len:	1027.9

ECOLI - GLNH ARGT HISJ YHDW GLTI ARTJ FLIY ARTI MLTF EVGS
BACSU - YXEM ARTP TCYJ GLNH TCYK YCKB 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
30_A	84_V	3.672	1.00
135_A	173_A	3.544	1.00
26_K	66_E	3.541	1.00
60_E	228_T	2.818	1.00
158_F	167_E	2.402	1.00
143_V	157_Q	2.397	1.00
93_I	98_K	2.364	1.00
105_D	227_K	2.290	1.00
42_Q	47_V	2.275	1.00
78_A	84_V	2.246	1.00
28_V	66_E	2.240	1.00
160_N	163_N	2.132	1.00
93_I	208_G	2.076	1.00
28_V	68_K	2.071	1.00
80_Q	100_A	2.060	1.00
58_A	65_Y	2.056	1.00
143_V	147_K	2.044	1.00
26_K	64_D	2.012	1.00
234_T	237_E	2.005	1.00
95_D	98_K	1.991	1.00
236_N	240_K	1.981	1.00
102_D	219_R	1.976	1.00
211_F	219_R	1.965	1.00
56_A	59_K	1.950	1.00
60_E	225_A	1.936	1.00
133_V	156_R	1.933	1.00
164_A	176_V	1.932	1.00
101_I	210_A	1.897	1.00
227_K	231_E	1.892	1.00
178_H	183_I	1.878	1.00
219_R	223_N	1.843	1.00
125_S	128_D	1.842	1.00
167_E	172_R	1.802	1.00
29_V	54_W	1.762	1.00
211_F	222_V	1.751	1.00
56_A	234_T	1.717	1.00
105_D	223_N	1.711	1.00
133_V	154_D	1.711	1.00
78_A	83_N	1.664	1.00
115_M	183_I	1.656	1.00
88_L	209_I	1.653	1.00
124_K	128_D	1.589	1.00
117_K	171_N	1.580	1.00
56_A	60_E	1.541	1.00
56_A	229_L	1.532	1.00
104_S	223_N	1.518	1.00
109_K	206_Q	1.509	1.00
138_S	159_P	1.488	1.00
52_D	241_K	1.436	1.00
220_D	224_G	1.435	1.00
75_I	87_A	1.429	1.00
60_E	232_N	1.403	1.00
113_L	180_T	1.401	1.00
212_P	215_S	1.397	1.00
42_Q	45_K	1.391	1.00
180_T	184_L	1.390	1.00
145_Y	149_N	1.379	1.00
221_K	224_G	1.367	1.00
61_L	225_A	1.359	1.00
40_F	47_V	1.357	1.00
144_D	148_A	1.352	1.00
19_S	23_A	1.349	1.00
51_V	55_A	1.342	1.00
29_V	86_L	1.341	1.00
216_D	220_D	1.331	1.00
57_I	225_A	1.331	1.00
169_G	194_Q	1.323	1.00
133_V	174_D	1.322	1.00
76_I	101_I	1.321	1.00
54_W	88_L	1.303	1.00
167_E	173_A	1.293	1.00
33_T	69_P	1.292	1.00
70_M	78_A	1.290	1.00
14_L	17_A	1.281	1.00
55_A	67_L	1.278	1.00
225_A	228_T	1.267	1.00
116_V	175_A	1.256	1.00
147_K	157_Q	1.242	1.00
50_D	107_Y	1.236	1.00
91_I	210_A	1.225	1.00
112_L	142_S	1.223	1.00
82_K	212_P	1.210	1.00
20_S	24_D	1.196	1.00
135_A	158_F	1.194	1.00
102_D	214_G	1.192	1.00
77_P	80_Q	1.188	1.00
230_R	235_Y	1.184	1.00
132_K	174_D	1.176	1.00
168_L	195_F	1.175	1.00
41_K	69_P	1.170	1.00
166_M	170_T	1.169	1.00
134_V	175_A	1.165	1.00
221_K	225_A	1.165	1.00
228_T	232_N	1.163	1.00
225_A	229_L	1.160	1.00
19_S	22_A	1.157	1.00
159_P	163_N	1.149	1.00
114_V	175_A	1.132	1.00
63_L	221_K	1.123	1.00
166_M	169_G	1.118	1.00
25_K	63_L	1.117	1.00
150_I	153_K	1.099	1.00
113_L	197_A	1.093	1.00
77_P	81_T	1.087	1.00
158_F	164_A	1.087	1.00
87_A	91_I	1.079	1.00
136_V	143_V	1.078	1.00
118_A	196_K	1.075	1.00
118_A	194_Q	1.052	1.00
54_W	67_L	1.049	1.00
49_F	239_Y	1.045	1.00
96_E	99_K	1.044	1.00
185_Y	189_T	1.038	1.00
119_N	196_K	1.036	1.00
49_F	238_I	1.036	1.00
70_M	84_V	1.030	1.00
234_T	238_I	1.029	1.00
102_D	213_K	1.025	1.00
138_S	157_Q	1.024	1.00
217_E	221_K	1.023	1.00
52_D	242_W	1.019	1.00
71_D	74_G	1.015	1.00
47_V	52_D	1.011	1.00
224_G	228_T	1.001	1.00
55_A	59_K	1.001	1.00
137_K	140_T	0.998	1.00
102_D	216_D	0.986	1.00
29_V	65_Y	0.986	1.00
116_V	198_V	0.969	1.00
54_W	65_Y	0.969	1.00
21_H	24_D	0.967	1.00
76_I	91_I	0.967	1.00
53_L	235_Y	0.959	1.00
49_F	243_F	0.958	1.00
21_H	63_L	0.957	1.00
168_L	173_A	0.953	1.00
46_Y	51_V	0.952	1.00
168_L	176_V	0.951	1.00
45_K	55_A	0.950	1.00
144_D	147_K	0.945	1.00
21_H	25_K	0.942	1.00
60_E	234_T	0.941	1.00
33_T	46_Y	0.933	1.00
216_D	219_R	0.933	1.00
15_A	18_V	0.933	1.00
41_K	44_D	0.929	1.00
135_A	164_A	0.928	1.00
163_N	166_M	0.927	1.00
162_D	166_M	0.922	1.00
24_D	28_V	0.921	1.00
223_N	227_K	0.919	1.00
105_D	230_R	0.917	1.00
52_D	55_A	0.913	1.00
57_I	222_V	0.911	1.00
86_L	222_V	0.909	1.00
103_F	210_A	0.904	1.00
86_L	211_F	0.898	1.00
94_T	97_R	0.893	1.00
36_V	40_F	0.887	1.00
127_K	130_D	0.887	1.00
53_L	229_L	0.887	1.00
229_L	234_T	0.884	1.00
235_Y	239_Y	0.875	1.00
104_S	222_V	0.872	1.00
98_K	213_K	0.866	1.00
239_Y	243_F	0.861	1.00
49_F	235_Y	0.860	1.00
14_L	18_V	0.857	1.00
111_G	180_T	0.856	1.00
95_D	99_K	0.853	1.00
80_Q	101_I	0.851	1.00
74_G	78_A	0.850	1.00
92_T	205_Q	0.848	1.00
161_I	178_H	0.843	1.00
156_R	167_E	0.837	1.00
54_W	209_I	0.833	1.00
237_E	241_K	0.830	1.00
237_E	240_K	0.828	1.00
223_N	226_L	0.825	1.00
217_E	220_D	0.825	1.00
145_Y	148_A	0.824	1.00
87_A	210_A	0.816	1.00
27_L	86_L	0.816	1.00
116_V	196_K	0.815	1.00
110_S	181_P	0.814	1.00
86_L	209_I	0.814	1.00
72_F	75_I	0.812	1.00
56_A	225_A	0.808	1.00
13_T	16_F	0.808	1.00
61_L	221_K	0.803	1.00
28_V	85_D	0.802	1.00
41_K	46_Y	0.800	1.00
27_L	63_L	0.800	1.00
31_T	67_L	0.790	1.00
236_N	239_Y	0.789	1.00
54_W	86_L	0.787	1.00
228_T	231_E	0.778	1.00
57_I	61_L	0.772	1.00
38_F	108_Y	0.771	1.00
26_K	63_L	0.766	1.00
31_T	51_V	0.748	1.00
109_K	204_A	0.746	1.00
184_L	188_K	0.744	1.00
115_M	195_F	0.744	1.00
229_L	232_N	0.740	1.00
22_A	25_K	0.732	1.00
129_L	175_A	0.732	1.00
57_I	88_L	0.729	1.00
27_L	58_A	0.720	1.00
40_F	242_W	0.719	1.00
149_N	153_K	0.716	1.00
29_V	67_L	0.715	1.00
114_V	177_L	0.711	1.00
79_L	101_I	0.709	1.00
229_L	233_G	0.708	1.00
123_V	128_D	0.701	1.00
68_K	83_N	0.695	1.00
110_S	180_T	0.688	1.00
163_N	167_E	0.688	1.00
60_E	229_L	0.686	1.00
229_L	235_Y	0.686	1.00
165_Y	169_G	0.685	1.00
158_F	173_A	0.685	1.00
113_L	199_G	0.682	1.00
55_A	65_Y	0.681	1.00
74_G	77_P	0.680	1.00
79_L	84_V	0.678	1.00
135_A	167_E	0.678	1.00
215_S	218_L	0.672	1.00
227_K	230_R	0.668	1.00
224_G	227_K	0.666	1.00
104_S	209_I	0.662	1.00
209_I	222_V	0.660	1.00
93_I	106_G	0.659	1.00
76_I	80_Q	0.656	1.00
56_A	238_I	0.654	1.00
103_F	208_G	0.652	1.00
82_K	214_G	0.650	1.00
220_D	223_N	0.650	1.00
70_M	75_I	0.649	1.00
130_D	152_T	0.649	1.00
79_L	87_A	0.647	1.00
32_D	72_F	0.645	1.00
97_R	103_F	0.645	1.00
104_S	211_F	0.643	1.00
32_D	39_E	0.643	1.00
111_G	204_A	0.642	1.00
31_T	89_A	0.639	1.00
47_V	242_W	0.639	1.00
156_R	173_A	0.639	1.00
133_V	173_A	0.638	1.00
185_Y	188_K	0.637	1.00
106_G	109_K	0.637	1.00
122_D	196_K	0.636	1.00
147_K	155_L	0.635	1.00
111_G	201_S	0.634	1.00
93_I	103_F	0.633	1.00
53_L	226_L	0.632	1.00
30_A	75_I	0.630	1.00
68_K	84_V	0.629	1.00
54_W	58_A	0.625	1.00
113_L	183_I	0.625	1.00
13_T	17_A	0.623	1.00
51_V	67_L	0.623	1.00
169_G	192_N	0.621	1.00
141_G	205_Q	0.620	1.00
146_A	155_L	0.620	1.00
58_A	61_L	0.617	1.00
115_M	165_Y	0.616	1.00
35_F	90_G	0.612	1.00
92_T	97_R	0.606	1.00
136_V	157_Q	0.606	1.00
50_D	90_G	0.604	1.00
72_F	91_I	0.603	1.00
165_Y	195_F	0.602	1.00
111_G	203_E	0.601	1.00
80_Q	212_P	0.598	1.00
43_G	47_V	0.595	1.00
20_S	23_A	0.594	1.00
184_L	197_A	0.594	1.00
35_F	72_F	0.593	1.00
192_N	195_F	0.591	1.00
36_V	189_T	0.590	1.00
117_K	194_Q	0.586	1.00
104_S	226_L	0.584	1.00
31_T	46_Y	0.584	1.00
58_A	63_L	0.581	1.00
91_I	101_I	0.579	1.00
178_H	182_N	0.579	1.00
195_F	198_V	0.576	1.00
39_E	89_A	0.575	1.00
24_D	85_D	0.575	1.00
72_F	97_R	0.573	1.00
229_L	238_I	0.572	1.00
102_D	215_S	0.570	1.00
104_S	219_R	0.569	1.00
13_T	18_V	0.567	1.00
112_L	177_L	0.567	1.00
233_G	236_N	0.565	1.00
27_L	218_L	0.562	1.00
108_Y	207_Y	0.561	1.00
33_T	39_E	0.559	1.00
61_L	218_L	0.557	1.00
183_I	187_I	0.555	1.00
79_L	212_P	0.554	1.00
169_G	195_F	0.550	1.00
137_K	161_I	0.546	1.00
60_E	221_K	0.546	1.00
30_A	87_A	0.544	1.00
186_F	189_T	0.542	1.00
167_E	170_T	0.542	1.00
146_A	177_L	0.541	1.00
54_W	57_I	0.538	1.00
32_D	89_A	0.538	1.00
32_D	137_K	0.536	1.00
114_V	129_L	0.535	1.00
233_G	237_E	0.533	1.00
36_V	185_Y	0.528	1.00
22_A	221_K	0.526	1.00
33_T	41_K	0.526	1.00
37_P	40_F	0.526	1.00
68_K	78_A	0.525	1.00
156_R	172_R	0.524	1.00
25_K	221_K	0.522	1.00
52_D	238_I	0.521	1.00
83_N	172_R	0.520	1.00
115_M	187_I	0.520	1.00
59_K	234_T	0.518	1.00
92_T	141_G	0.518	1.00
136_V	155_L	0.517	1.00
146_A	150_I	0.513	1.00
148_A	151_K	0.512	1.00
98_K	102_D	0.512	1.00
105_D	226_L	0.510	1.00
110_S	207_Y	0.510	1.00
30_A	78_A	0.510	1.00
58_A	62_K	0.507	1.00
57_I	209_I	0.506	1.00
70_M	74_G	0.505	1.00
134_V	146_A	0.503	1.00
138_S	143_V	0.501	1.00
180_T	201_S	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
4powA	1	0.9032	100	0.239	Contact Map
3hv1A	2	0.9677	100	0.244	Contact Map
3kbrA	4	0.9073	100	0.245	Contact Map
3k4uA	5	0.9153	100	0.247	Contact Map
1pb7A	1	0.9435	100	0.248	Contact Map
1wdnA	1	0.8992	100	0.249	Contact Map
2vhaA	2	0.9556	100	0.251	Contact Map
4ohnA	1	0.9476	100	0.252	Contact Map
1xt8A	1	0.9153	100	0.252	Contact Map
2ylnA	1	0.9194	100	0.254	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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