YFGM - ECOLI - GREMLIN Contacts

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YFGM - UPF0070 protein YfgM

UniProt:	P76576	Sequences: MEIYENENDQVEAVKRFFAENGKALAVGVILGVGALIGWRYWNSHQVDSARSASLAYQNAVTAVSEGKPDSIPAAEKFAAENKNTYGALASLELAQQFVDKNELEKAAAQLQQGLADTSDENLKAVINLRLARVQVQLKQADAALKTLDTIKGEGWAAIVADLRGEALLSKGDKQGARSAWEAGVKSDVTPALSEMMQMKINNLSI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14209
Length:	206 (162)
Sequences:	6873 (6408)
Seq/√Len:	503.4

ECOLI - YFGM NRFG LPSRP NLPI YBGF HEMY BAMD YGEG
BACSU - YSOA RAPB YVCD RAPA
HALSA - Q9HMM8
SULSO - Q97WM3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_Q	143_A	4.227	1.00
173_D	176_G	4.190	1.00
103_E	106_K	3.663	1.00
91_S	110_Q	2.886	1.00
165_G	181_W	2.832	1.00
161_A	180_A	2.746	1.00
128_N	147_T	2.621	1.00
149_D	164_R	2.555	1.00
95_A	111_L	2.486	1.00
164_R	180_A	2.477	1.00
131_L	147_T	2.477	1.00
112_Q	131_L	2.397	1.00
132_A	148_L	2.273	1.00
111_L	130_R	2.241	1.00
148_L	163_L	2.159	1.00
168_L	176_G	2.153	1.00
94_L	110_Q	2.063	1.00
168_L	180_A	1.877	1.00
75_A	93_E	1.803	1.00
98_F	106_K	1.775	1.00
76_E	94_L	1.771	1.00
145_L	149_D	1.721	1.00
108_A	112_Q	1.712	1.00
135_Q	143_A	1.705	1.00
98_F	110_Q	1.668	1.00
142_D	171_K	1.652	1.00
178_R	182_E	1.614	1.00
60_A	75_A	1.589	1.00
135_Q	147_T	1.583	1.00
108_A	134_V	1.551	1.00
131_L	135_Q	1.527	1.00
113_Q	116_A	1.498	1.00
115_L	127_I	1.460	1.00
161_A	183_A	1.426	1.00
84_N	87_G	1.425	1.00
164_R	168_L	1.422	1.00
168_L	173_D	1.419	1.00
145_L	171_K	1.415	1.00
183_A	186_K	1.408	1.00
145_L	167_A	1.373	1.00
108_A	131_L	1.359	1.00
69_P	101_K	1.348	1.00
135_Q	140_Q	1.343	1.00
39_W	42_W	1.322	1.00
129_L	163_L	1.321	1.00
124_K	127_I	1.309	1.00
151_I	160_V	1.273	1.00
108_A	138_L	1.265	1.00
169_L	181_W	1.265	1.00
125_A	151_I	1.249	1.00
98_F	103_E	1.248	1.00
188_D	191_P	1.247	1.00
63_A	74_A	1.247	1.00
114_G	127_I	1.243	1.00
88_A	114_G	1.240	1.00
143_A	146_K	1.231	1.00
94_L	98_F	1.230	1.00
118_T	124_K	1.226	1.00
145_L	164_R	1.226	1.00
158_A	184_G	1.210	1.00
56_A	74_A	1.188	1.00
105_E	138_L	1.188	1.00
133_R	163_L	1.187	1.00
176_G	179_S	1.182	1.00
92_L	130_R	1.168	1.00
154_E	157_A	1.155	1.00
145_L	168_L	1.150	1.00
134_V	138_L	1.118	1.00
167_A	171_K	1.111	1.00
128_N	150_T	1.086	1.00
95_A	114_G	1.072	1.00
165_G	184_G	1.063	1.00
72_I	76_E	1.050	1.00
72_I	97_Q	1.038	1.00
79_A	90_A	1.037	1.00
97_Q	101_K	1.029	1.00
136_V	148_L	1.008	1.00
162_D	184_G	1.002	1.00
59_N	63_A	0.995	1.00
99_V	111_L	0.995	1.00
136_V	163_L	0.981	1.00
115_L	128_N	0.979	1.00
183_A	187_S	0.976	1.00
63_A	70_D	0.973	1.00
57_Y	61_V	0.959	1.00
162_D	166_E	0.953	1.00
182_E	186_K	0.937	1.00
158_A	188_D	0.937	1.00
92_L	96_Q	0.936	1.00
104_L	134_V	0.932	1.00
136_V	167_A	0.921	1.00
96_Q	111_L	0.914	1.00
72_I	98_F	0.903	1.00
77_K	81_E	0.902	1.00
36_L	39_W	0.899	1.00
88_A	118_T	0.898	1.00
110_Q	114_G	0.896	1.00
72_I	101_K	0.893	1.00
92_L	127_I	0.891	1.00
129_L	157_A	0.885	1.00
73_P	77_K	0.883	1.00
108_A	135_Q	0.882	1.00
129_L	160_V	0.881	1.00
77_K	80_A	0.881	1.00
60_A	78_F	0.875	1.00
79_A	91_S	0.871	1.00
87_G	90_A	0.867	1.00
114_G	117_D	0.861	1.00
128_N	151_I	0.858	1.00
157_A	160_V	0.856	1.00
179_S	182_E	0.850	1.00
78_F	90_A	0.845	1.00
144_A	148_L	0.839	1.00
99_V	134_V	0.827	1.00
70_D	73_P	0.822	1.00
166_E	181_W	0.819	1.00
96_Q	130_R	0.819	1.00
145_L	173_D	0.816	1.00
129_L	151_I	0.811	1.00
129_L	133_R	0.808	1.00
54_S	58_Q	0.806	1.00
180_A	183_A	0.797	1.00
40_R	43_N	0.791	1.00
177_A	181_W	0.790	1.00
132_A	151_I	0.785	1.00
142_D	145_L	0.779	1.00
78_F	81_E	0.773	1.00
161_A	184_G	0.770	1.00
107_A	111_L	0.769	1.00
63_A	68_K	0.769	1.00
106_K	109_A	0.767	1.00
169_L	174_K	0.759	1.00
91_S	113_Q	0.755	1.00
64_V	75_A	0.751	1.00
40_R	44_S	0.747	1.00
76_E	110_Q	0.746	1.00
96_Q	100_D	0.744	1.00
99_V	104_L	0.744	1.00
147_T	150_T	0.742	1.00
113_Q	117_D	0.740	1.00
166_E	169_L	0.737	1.00
112_Q	116_A	0.737	1.00
91_S	114_G	0.734	1.00
112_Q	147_T	0.733	1.00
111_L	134_V	0.732	1.00
72_I	94_L	0.730	1.00
136_V	141_A	0.728	1.00
124_K	128_N	0.728	1.00
180_A	184_G	0.725	1.00
59_N	74_A	0.724	1.00
74_A	77_K	0.709	1.00
71_S	75_A	0.708	1.00
61_V	75_A	0.700	1.00
142_D	146_K	0.697	1.00
88_A	124_K	0.693	1.00
146_K	150_T	0.689	1.00
141_A	167_A	0.681	1.00
61_V	93_E	0.681	1.00
92_L	124_K	0.680	1.00
136_V	170_S	0.678	1.00
76_E	106_K	0.674	1.00
56_A	81_E	0.673	1.00
184_G	187_S	0.673	1.00
174_K	178_R	0.671	1.00
175_Q	179_S	0.671	1.00
99_V	137_Q	0.669	1.00
143_A	147_T	0.662	1.00
149_D	180_A	0.659	1.00
162_D	191_P	0.657	1.00
149_D	168_L	0.655	1.00
79_A	94_L	0.654	1.00
56_A	59_N	0.648	1.00
161_A	187_S	0.643	1.00
112_Q	135_Q	0.639	1.00
90_A	93_E	0.630	1.00
108_A	140_Q	0.629	1.00
52_S	56_A	0.628	1.00
73_P	76_E	0.626	1.00
104_L	138_L	0.626	1.00
128_N	153_G	0.622	1.00
144_A	167_A	0.618	1.00
110_Q	113_Q	0.615	1.00
146_K	149_D	0.612	1.00
71_S	97_Q	0.607	0.99
125_A	154_E	0.606	0.99
37_I	40_R	0.604	0.99
181_W	185_V	0.598	0.99
60_A	71_S	0.596	0.99
76_E	80_A	0.595	0.99
69_P	72_I	0.593	0.99
166_E	170_S	0.588	0.99
42_W	45_H	0.588	0.99
158_A	162_D	0.586	0.99
104_L	137_Q	0.582	0.99
71_S	78_F	0.577	0.99
64_V	93_E	0.576	0.99
163_L	166_E	0.574	0.99
179_S	183_A	0.574	0.99
72_I	75_A	0.574	0.99
132_A	144_A	0.573	0.99
165_G	177_A	0.572	0.99
132_A	147_T	0.571	0.99
129_L	159_I	0.570	0.99
105_E	108_A	0.569	0.99
92_L	114_G	0.569	0.99
158_A	191_P	0.569	0.99
148_L	164_R	0.567	0.99
99_V	130_R	0.564	0.99
109_A	112_Q	0.563	0.99
112_Q	143_A	0.563	0.99
182_E	185_V	0.561	0.99
69_P	73_P	0.559	0.99
141_A	171_K	0.556	0.99
39_W	43_N	0.552	0.99
53_A	56_A	0.550	0.99
138_L	141_A	0.541	0.99
133_R	148_L	0.540	0.99
153_G	157_A	0.540	0.99
147_T	151_I	0.538	0.99
93_E	96_Q	0.534	0.99
164_R	171_K	0.532	0.99
118_T	127_I	0.530	0.99
114_G	118_T	0.529	0.99
176_G	180_A	0.527	0.99
67_G	71_S	0.526	0.99
102_N	139_K	0.524	0.99
74_A	78_F	0.520	0.98
115_L	131_L	0.519	0.98
109_A	113_Q	0.519	0.98
130_R	163_L	0.518	0.98
56_A	60_A	0.516	0.98
132_A	160_V	0.516	0.98
124_K	157_A	0.515	0.98
76_E	79_A	0.514	0.98
99_V	107_A	0.511	0.98
105_E	109_A	0.511	0.98
61_V	65_S	0.509	0.98
171_K	174_K	0.508	0.98
41_Y	44_S	0.506	0.98
53_A	78_F	0.505	0.98
104_L	108_A	0.504	0.98
52_S	55_L	0.502	0.98
150_T	153_G	0.500	0.98

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
3dssA	1	0.9417	99.6	0.455	Contact Map
2pziA	1	0.9175	99.6	0.455	Contact Map
2vsyA	1	0.5728	99.6	0.46	Contact Map
1dceA	1	0.9757	99.6	0.461	Contact Map
2e2eA	2	0.7427	99.6	0.461	Contact Map
4gywA	2	0.7379	99.6	0.462	Contact Map
3qkyA	1	0.7573	99.6	0.466	Contact Map
3q7aA	1	0.9126	99.6	0.47	Contact Map
5aioA	1	0.7087	99.6	0.472	Contact Map
4l9pA	1	0.966	99.6	0.474	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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