Virulence_RhuM - PFAM28P - GREMLIN Contacts

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Virulence_RhuM - Virulence protein RhuM family

PFAM:	PF13310	Sequences: STVRKFRTVAAEGKREVTRNVKFYNLDAIISVGYRVNSKRATQFRIWATQRLKEYIIKGFVMDDERLKNGTAGGKDYFDELLERIRDIRASERRFYQKITDIYATSIDYDPKSEITKEFFATVQNKLHYAIHGHTAAEIIYERADAEKPNMGLTTWKGAKIRKSDVSIAKNYLNEDELKELNRIVSAYLDFAELQAERRIPMTMKDWIEKLDAFLKFNEREILTDAGKISHEQAKEKAESEYEKYRKQDKNY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	252 (250)
Sequences:	8454 (3587)
Seq/√Len:	226.9
META:	0.898

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_R	7_R	6.776	1.00
3_V	8_T	6.459	1.00
231_H	235_K	4.185	1.00
64_D	84_R	3.137	1.00
134_H	142_E	3.107	1.00
34_Y	49_T	2.876	1.00
51_R	61_V	2.724	1.00
186_S	190_D	2.654	1.00
63_D	66_R	2.553	1.00
5_K	22_K	2.500	1.00
79_D	98_K	2.486	1.00
179_K	197_E	2.421	1.00
5_K	20_N	2.298	1.00
144_A	151_M	2.278	1.00
194_L	220_R	2.121	1.00
213_A	216_K	2.110	1.00
40_R	43_Q	2.078	1.00
76_D	94_R	2.064	1.00
163_K	239_E	2.060	1.00
198_R	220_R	2.055	1.00
2_T	9_V	2.029	1.00
175_E	179_K	1.931	1.00
46_I	50_Q	1.900	1.00
27_D	53_K	1.898	1.00
117_K	121_A	1.862	1.00
12_E	19_R	1.849	1.00
167_S	239_E	1.840	1.00
53_K	57_I	1.836	1.00
241_E	244_K	1.835	1.00
58_K	80_E	1.810	1.00
145_D	148_K	1.794	1.00
114_E	118_E	1.777	1.00
187_A	191_F	1.691	1.00
107_I	201_P	1.679	1.00
167_S	235_K	1.663	1.00
141_Y	237_K	1.659	1.00
7_R	18_T	1.650	1.00
10_A	19_R	1.638	1.00
11_A	16_E	1.633	1.00
132_H	139_I	1.602	1.00
180_E	197_E	1.586	1.00
235_K	239_E	1.585	1.00
246_R	249_D	1.562	1.00
4_R	8_T	1.536	1.00
205_K	209_E	1.495	1.00
43_Q	46_I	1.489	1.00
103_Y	116_T	1.474	1.00
191_F	195_Q	1.468	1.00
3_V	7_R	1.450	1.00
8_T	23_F	1.444	1.00
69_N	72_A	1.444	1.00
183_R	194_L	1.441	1.00
10_A	14_K	1.439	1.00
9_V	12_E	1.432	1.00
128_H	169_A	1.429	1.00
137_A	231_H	1.422	1.00
180_E	198_R	1.421	1.00
11_A	14_K	1.412	1.00
232_E	236_E	1.409	1.00
12_E	17_V	1.399	1.00
83_E	179_K	1.397	1.00
4_R	18_T	1.395	1.00
107_I	203_T	1.377	1.00
146_A	244_K	1.376	1.00
213_A	219_E	1.359	1.00
210_K	219_E	1.333	1.00
176_D	197_E	1.330	1.00
3_V	22_K	1.328	1.00
31_S	39_K	1.328	1.00
126_K	212_D	1.323	1.00
86_R	183_R	1.319	1.00
8_T	22_K	1.316	1.00
62_M	81_L	1.315	1.00
7_R	20_N	1.310	1.00
187_A	218_N	1.309	1.00
37_N	41_A	1.308	1.00
2_T	12_E	1.306	1.00
202_M	206_D	1.300	1.00
6_F	23_F	1.281	1.00
12_E	15_R	1.280	1.00
183_R	197_E	1.276	1.00
166_V	239_E	1.262	1.00
191_F	217_F	1.261	1.00
180_E	194_L	1.259	1.00
115_I	118_E	1.254	1.00
42_T	46_I	1.248	1.00
187_A	190_D	1.246	1.00
28_A	32_V	1.235	1.00
4_R	20_N	1.233	1.00
62_M	84_R	1.232	1.00
14_K	19_R	1.231	1.00
118_E	226_A	1.231	1.00
191_F	210_K	1.229	1.00
28_A	37_N	1.226	1.00
68_K	87_D	1.197	1.00
210_K	213_A	1.190	1.00
236_E	240_S	1.187	1.00
113_S	116_T	1.186	1.00
118_E	122_T	1.185	1.00
90_A	182_N	1.172	1.00
150_N	156_W	1.171	1.00
157_K	164_S	1.162	1.00
87_D	182_N	1.159	1.00
15_R	19_R	1.145	1.00
118_E	121_A	1.140	1.00
237_K	241_E	1.138	1.00
163_K	243_E	1.104	1.00
54_E	58_K	1.103	1.00
51_R	55_Y	1.101	1.00
133_G	221_E	1.091	1.00
10_A	17_V	1.085	1.00
2_T	10_A	1.080	1.00
195_Q	200_I	1.079	1.00
8_T	21_V	1.075	1.00
86_R	193_E	1.066	1.00
179_K	183_R	1.066	1.00
203_T	206_D	1.060	1.00
213_A	217_F	1.057	1.00
234_A	238_A	1.049	1.00
60_F	84_R	1.049	1.00
191_F	218_N	1.041	1.00
209_E	213_A	1.034	1.00
233_Q	236_E	1.029	1.00
115_I	208_I	1.026	1.00
194_L	198_R	1.024	1.00
93_R	97_Q	1.013	1.00
93_R	100_T	1.009	1.00
10_A	21_V	1.003	1.00
162_R	165_D	0.988	1.00
10_A	15_R	0.988	1.00
184_I	187_A	0.980	1.00
9_V	14_K	0.979	1.00
122_T	208_I	0.978	1.00
9_V	19_R	0.977	1.00
28_A	41_A	0.974	1.00
7_R	22_K	0.964	1.00
55_Y	61_V	0.963	1.00
65_E	157_K	0.961	1.00
9_V	17_V	0.952	1.00
87_D	90_A	0.950	1.00
195_Q	210_K	0.943	1.00
208_I	212_D	0.939	1.00
60_F	64_D	0.939	1.00
156_W	161_I	0.936	1.00
198_R	219_E	0.932	1.00
146_A	241_E	0.921	1.00
225_D	228_K	0.918	1.00
195_Q	202_M	0.918	1.00
243_E	246_R	0.917	1.00
194_L	218_N	0.913	0.99
206_D	209_E	0.913	0.99
2_T	19_R	0.911	0.99
85_I	196_A	0.908	0.99
4_R	22_K	0.907	0.99
247_K	250_K	0.905	0.99
131_I	180_E	0.904	0.99
95_F	189_L	0.898	0.99
83_E	164_S	0.895	0.99
6_F	37_N	0.894	0.99
14_K	17_V	0.892	0.99
232_E	235_K	0.891	0.99
163_K	167_S	0.891	0.99
67_L	94_R	0.890	0.99
65_E	68_K	0.884	0.99
141_Y	229_I	0.882	0.99
66_R	72_A	0.878	0.99
210_K	214_F	0.877	0.99
48_A	52_L	0.875	0.99
80_E	157_K	0.869	0.99
176_D	199_R	0.867	0.99
9_V	15_R	0.864	0.99
11_A	19_R	0.863	0.99
32_V	36_V	0.859	0.99
188_Y	195_Q	0.855	0.99
233_Q	237_K	0.853	0.99
31_S	37_N	0.851	0.99
200_I	219_E	0.849	0.99
195_Q	219_E	0.848	0.99
17_V	20_N	0.847	0.99
35_R	42_T	0.844	0.99
97_Q	120_F	0.843	0.99
153_L	166_V	0.840	0.99
210_K	217_F	0.839	0.99
75_K	199_R	0.837	0.99
147_E	248_Q	0.828	0.99
176_D	180_E	0.825	0.99
240_S	244_K	0.821	0.99
143_R	177_E	0.820	0.99
2_T	17_V	0.817	0.99
30_I	37_N	0.816	0.99
30_I	49_T	0.811	0.99
90_A	186_S	0.807	0.99
187_A	214_F	0.806	0.99
166_V	238_A	0.806	0.99
39_K	43_Q	0.797	0.99
2_T	14_K	0.796	0.99
153_L	156_W	0.789	0.99
183_R	187_A	0.789	0.99
128_H	132_H	0.786	0.98
122_T	226_A	0.786	0.98
158_G	162_R	0.786	0.98
114_E	117_K	0.767	0.98
2_T	15_R	0.765	0.98
36_V	41_A	0.763	0.98
110_D	115_I	0.761	0.98
183_R	190_D	0.759	0.98
187_A	217_F	0.757	0.98
46_I	53_K	0.752	0.98
64_D	68_K	0.747	0.98
60_F	80_E	0.733	0.98
246_R	250_K	0.726	0.97
179_K	182_N	0.725	0.97
236_E	239_E	0.723	0.97
38_S	52_L	0.722	0.97
215_L	222_I	0.711	0.97
3_V	21_V	0.708	0.97
39_K	113_S	0.707	0.97
54_E	84_R	0.704	0.97
19_R	22_K	0.702	0.97
118_E	208_I	0.698	0.97
157_K	165_D	0.698	0.97
62_M	67_L	0.697	0.97
115_I	205_K	0.697	0.97
155_T	159_A	0.695	0.97
187_A	194_L	0.693	0.97
42_T	49_T	0.689	0.97
105_T	120_F	0.687	0.96
189_L	207_W	0.684	0.96
30_I	42_T	0.683	0.96
3_V	10_A	0.679	0.96
70_G	73_G	0.678	0.96
134_H	143_R	0.678	0.96
103_Y	211_L	0.677	0.96
50_Q	53_K	0.677	0.96
95_F	98_K	0.674	0.96
154_T	174_N	0.672	0.96
36_V	40_R	0.669	0.96
6_F	20_N	0.661	0.96
12_E	21_V	0.660	0.96
97_Q	101_D	0.659	0.96
111_P	116_T	0.658	0.96
12_E	16_E	0.658	0.96
219_E	222_I	0.658	0.96
125_N	136_A	0.656	0.95
199_R	219_E	0.655	0.95
17_V	21_V	0.652	0.95
57_I	61_V	0.651	0.95
4_R	21_V	0.650	0.95
13_G	17_V	0.650	0.95
217_F	220_R	0.647	0.95
103_Y	204_M	0.647	0.95
18_T	21_V	0.644	0.95
212_D	216_K	0.644	0.95
155_T	165_D	0.643	0.95
195_Q	218_N	0.641	0.95
129_Y	225_D	0.639	0.95
121_A	137_A	0.639	0.95
59_G	152_G	0.637	0.95
1_S	14_K	0.636	0.95
51_R	57_I	0.635	0.95
214_F	217_F	0.633	0.94
97_Q	100_T	0.632	0.94
67_L	74_G	0.632	0.94
94_R	97_Q	0.631	0.94
134_H	139_I	0.631	0.94
96_Y	127_L	0.630	0.94
90_A	178_L	0.630	0.94
25_N	53_K	0.629	0.94
17_V	22_K	0.629	0.94
192_A	207_W	0.627	0.94
49_T	53_K	0.626	0.94
55_Y	63_D	0.626	0.94
161_I	165_D	0.626	0.94
32_V	41_A	0.626	0.94
196_A	202_M	0.625	0.94
96_Y	129_Y	0.625	0.94
147_E	244_K	0.621	0.94
63_D	72_A	0.621	0.94
54_E	61_V	0.617	0.94
9_V	21_V	0.617	0.94
30_I	56_I	0.616	0.94
87_D	162_R	0.608	0.93
137_A	235_K	0.607	0.93
2_T	21_V	0.603	0.93
93_R	101_D	0.603	0.93
187_A	210_K	0.601	0.93
28_A	40_R	0.599	0.93
15_R	18_T	0.599	0.93
37_N	40_R	0.599	0.93
239_E	243_E	0.598	0.93
180_E	220_R	0.597	0.93
33_G	152_G	0.597	0.93
6_F	18_T	0.596	0.93
182_N	186_S	0.595	0.92
103_Y	123_V	0.594	0.92
230_S	233_Q	0.593	0.92
32_V	40_R	0.593	0.92
51_R	56_I	0.592	0.92
183_R	193_E	0.590	0.92
86_R	186_S	0.589	0.92
209_E	216_K	0.588	0.92
5_K	8_T	0.584	0.92
2_T	11_A	0.583	0.92
10_A	16_E	0.582	0.92
46_I	49_T	0.580	0.91
143_R	154_T	0.580	0.91
136_A	169_A	0.578	0.91
27_D	31_S	0.578	0.91
27_D	34_Y	0.577	0.91
16_E	19_R	0.577	0.91
30_I	46_I	0.576	0.91
237_K	240_S	0.573	0.91
127_L	131_I	0.569	0.91
5_K	37_N	0.569	0.91
180_E	184_I	0.568	0.91
167_S	231_H	0.566	0.90
140_I	231_H	0.565	0.90
58_K	76_D	0.564	0.90
231_H	234_A	0.563	0.90
244_K	247_K	0.561	0.90
6_F	41_A	0.559	0.90
122_T	212_D	0.559	0.90
100_T	104_A	0.559	0.90
225_D	233_Q	0.558	0.90
240_S	243_E	0.557	0.90
110_D	113_S	0.556	0.90
18_T	22_K	0.553	0.89
33_G	59_G	0.548	0.89
56_I	72_A	0.547	0.89
102_I	105_T	0.546	0.89
123_V	211_L	0.545	0.89
39_K	42_T	0.545	0.89
144_A	237_K	0.544	0.89
84_R	175_E	0.541	0.88
80_E	84_R	0.541	0.88
54_E	64_D	0.539	0.88
15_R	22_K	0.538	0.88
82_L	186_S	0.537	0.88
9_V	16_E	0.534	0.88
183_R	186_S	0.534	0.88
76_D	80_E	0.533	0.88
238_A	241_E	0.533	0.88
214_F	218_N	0.532	0.88
215_L	218_N	0.531	0.88
166_V	235_K	0.530	0.87
79_D	197_E	0.530	0.87
125_N	169_A	0.529	0.87
202_M	207_W	0.527	0.87
69_N	73_G	0.526	0.87
127_L	181_L	0.525	0.87
8_T	11_A	0.525	0.87
65_E	69_N	0.522	0.87
121_A	226_A	0.522	0.87
188_Y	207_W	0.521	0.87
183_R	214_F	0.520	0.86
140_I	238_A	0.519	0.86
41_A	51_R	0.519	0.86
150_N	154_T	0.518	0.86
32_V	37_N	0.517	0.86
3_V	6_F	0.516	0.86
11_A	18_T	0.515	0.86
96_Y	106_S	0.514	0.86
214_F	219_E	0.514	0.86
245_Y	249_D	0.514	0.86
50_Q	61_V	0.511	0.85
27_D	46_I	0.510	0.85
112_K	117_K	0.508	0.85
12_E	18_T	0.507	0.85
121_A	231_H	0.506	0.85
210_K	218_N	0.506	0.85
53_K	56_I	0.505	0.85
221_E	224_T	0.505	0.85
87_D	246_R	0.504	0.85
15_R	21_V	0.503	0.85
187_A	195_Q	0.500	0.84

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
2fhmA	1	0.3452	24	0.971	Contact Map
4hi1A	3	0.3373	16.2	0.973	Contact Map
2gv1A	1	0.3492	15.2	0.974	Contact Map
1ulrA	1	0.3333	14	0.974	Contact Map
1w2iA	2	0.3413	11.9	0.975	Contact Map
2bjdA	1	0.3452	11.6	0.975	Contact Map
2vh7A	1	0.3611	11.4	0.975	Contact Map
1gxuA	5	0.3452	10.4	0.976	Contact Map
1apsA	1	0.373	8.8	0.976	Contact Map
1wpiA	1	0.4643	8.1	0.977	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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