DUF2336 - PFAM28P - GREMLIN Contacts

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DUF2336 - Uncharacterized protein conserved in bacteria (DUF2336)

PFAM:	PF10098	Sequences: VAGPVLERSPRLSDADLVEIARTKSQAHLLAIARRPSLSEAVTDALVERGDREVVRALAANPGARFSEAGFARLVERAEGDDALAEPLGLRPDLPPALARRLLAKASEALRRRLLARAPLDAEEIQRALAEAAERATAELAAASRDYAAARRLVRALHRAGRLTEALLLRAARAGKFEEFVAALALLAGVPIEVVERLLHDRRGEGLLILCKAAGLSWSTFRAILAARAAARGISAADLEAALALFERLSPETAQRVLRFWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	262 (260)
Sequences:	8461 (5712)
Seq/√Len:	354.2
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_D	39_S	5.086	1.00
37_S	63_G	4.602	1.00
52_R	81_D	3.752	1.00
40_E	65_R	3.561	1.00
7_E	34_R	3.525	1.00
44_D	70_G	3.102	1.00
34_R	57_A	3.022	1.00
26_Q	51_D	3.019	1.00
155_R	186_L	2.925	1.00
158_H	186_L	2.870	1.00
47_V	70_G	2.784	1.00
13_S	16_D	2.678	1.00
3_G	7_E	2.556	1.00
165_E	217_S	2.332	1.00
176_K	179_E	2.276	1.00
25_S	28_H	2.182	1.00
44_D	67_S	2.176	1.00
21_A	32_I	2.169	1.00
59_A	74_L	2.121	1.00
33_A	57_A	2.113	1.00
46_L	54_V	2.113	1.00
211_C	224_I	2.103	1.00
6_L	32_I	2.066	1.00
10_P	36_P	2.009	1.00
67_S	70_G	1.996	1.00
38_L	63_G	1.981	1.00
43_T	66_F	1.952	1.00
75_V	98_L	1.949	1.00
172_A	180_F	1.925	1.00
164_T	167_L	1.913	1.00
21_A	45_A	1.901	1.00
56_R	83_A	1.897	1.00
30_L	57_A	1.884	1.00
29_L	49_R	1.874	1.00
181_V	199_L	1.809	1.00
68_E	97_A	1.744	1.00
29_L	51_D	1.742	1.00
38_L	43_T	1.721	1.00
251_P	255_Q	1.709	1.00
43_T	58_L	1.680	1.00
48_E	73_R	1.670	1.00
155_R	159_R	1.663	1.00
165_E	220_T	1.661	1.00
62_P	92_P	1.648	1.00
153_L	179_E	1.636	1.00
190_V	195_V	1.592	1.00
19_E	23_T	1.579	1.00
163_L	183_A	1.544	1.00
168_L	183_A	1.535	1.00
66_F	70_G	1.506	1.00
26_Q	29_L	1.489	1.00
113_R	117_R	1.481	1.00
95_P	98_L	1.470	1.00
169_L	173_R	1.450	1.00
157_L	163_L	1.446	1.00
18_V	41_A	1.444	1.00
132_A	136_A	1.437	1.00
90_L	113_R	1.413	1.00
256_R	260_F	1.406	1.00
242_A	246_F	1.401	1.00
181_V	196_E	1.390	1.00
18_V	42_V	1.389	1.00
207_L	211_C	1.378	1.00
56_R	60_A	1.365	1.00
43_T	70_G	1.349	1.00
14_D	41_A	1.333	1.00
76_E	79_E	1.321	1.00
151_R	186_L	1.307	1.00
106_A	110_L	1.305	1.00
151_R	182_A	1.305	1.00
255_Q	259_R	1.305	1.00
72_A	98_L	1.303	1.00
198_L	206_G	1.298	1.00
30_L	54_V	1.282	1.00
39_S	42_V	1.269	1.00
122_A	126_Q	1.268	1.00
185_A	188_A	1.265	1.00
124_E	127_R	1.260	1.00
211_C	221_F	1.248	1.00
185_A	192_I	1.247	1.00
66_F	71_F	1.232	1.00
253_T	260_F	1.220	1.00
37_S	65_R	1.211	1.00
6_L	28_H	1.207	1.00
40_E	67_S	1.203	1.00
58_L	66_F	1.197	1.00
30_L	33_A	1.195	1.00
71_F	95_P	1.194	1.00
242_A	245_L	1.191	1.00
245_L	248_R	1.191	1.00
50_G	77_R	1.190	1.00
21_A	29_L	1.189	1.00
30_L	53_E	1.185	1.00
30_L	34_R	1.166	1.00
188_A	195_V	1.162	1.00
116_A	119_P	1.158	1.00
30_L	51_D	1.152	1.00
60_A	87_P	1.149	1.00
156_A	160_A	1.144	1.00
157_L	162_R	1.132	1.00
55_V	77_R	1.129	1.00
56_R	81_D	1.124	1.00
154_V	183_A	1.120	1.00
38_L	58_L	1.118	1.00
1_V	4_P	1.115	1.00
61_N	64_A	1.113	1.00
43_T	64_A	1.106	1.00
180_F	224_I	1.095	1.00
52_R	83_A	1.091	1.00
73_R	76_E	1.088	1.00
151_R	155_R	1.084	1.00
22_R	48_E	1.077	1.00
192_I	196_E	1.069	1.00
24_K	28_H	1.066	1.00
59_A	87_P	1.061	1.00
22_R	45_A	1.060	1.00
121_D	124_E	1.057	1.00
181_V	192_I	1.055	1.00
253_T	257_V	1.053	1.00
257_V	260_F	1.050	1.00
89_G	110_L	1.040	1.00
5_V	9_S	1.038	1.00
79_E	105_K	1.035	1.00
153_L	157_L	1.035	1.00
111_R	115_L	1.028	1.00
85_A	110_L	1.026	1.00
154_V	182_A	1.026	1.00
12_L	16_D	1.025	1.00
107_S	133_A	1.016	1.00
26_Q	54_V	1.015	1.00
96_P	100_R	1.013	1.00
208_L	212_K	1.011	1.00
154_V	186_L	1.005	1.00
244_A	248_R	0.998	1.00
238_D	241_A	0.990	1.00
188_A	210_L	0.989	1.00
217_S	220_T	0.988	1.00
29_L	54_V	0.985	1.00
168_L	187_L	0.981	1.00
18_V	21_A	0.972	1.00
253_T	256_R	0.968	1.00
51_D	54_V	0.959	1.00
168_L	180_F	0.958	1.00
215_G	251_P	0.957	1.00
2_A	28_H	0.957	1.00
115_L	118_A	0.954	1.00
212_K	218_W	0.954	1.00
256_R	259_R	0.953	1.00
150_A	154_V	0.951	1.00
168_L	216_L	0.950	1.00
205_E	209_I	0.949	1.00
29_L	33_A	0.943	1.00
165_E	216_L	0.941	1.00
222_R	226_A	0.939	1.00
218_W	247_E	0.938	1.00
181_V	200_H	0.938	1.00
89_G	114_L	0.925	1.00
78_A	85_A	0.925	1.00
163_L	187_L	0.923	1.00
250_S	253_T	0.923	1.00
56_R	87_P	0.918	1.00
195_V	210_L	0.913	1.00
157_L	167_L	0.911	1.00
208_L	221_F	0.903	1.00
47_V	77_R	0.899	1.00
6_L	20_I	0.899	1.00
21_A	46_L	0.892	1.00
45_A	49_R	0.889	1.00
205_E	208_L	0.885	1.00
187_L	216_L	0.883	1.00
211_C	216_L	0.881	1.00
183_A	187_L	0.880	1.00
82_D	85_A	0.875	1.00
109_A	112_R	0.871	1.00
107_S	110_L	0.870	1.00
243_L	247_E	0.864	1.00
171_A	179_E	0.863	1.00
76_E	101_R	0.863	1.00
153_L	156_A	0.861	1.00
27_A	53_E	0.860	1.00
158_H	161_G	0.856	1.00
86_E	90_L	0.855	1.00
44_D	73_R	0.854	1.00
101_R	105_K	0.845	1.00
252_E	255_Q	0.845	1.00
72_A	101_R	0.833	1.00
165_E	187_L	0.833	1.00
68_E	98_L	0.829	1.00
74_L	88_L	0.829	1.00
73_R	77_R	0.829	1.00
254_A	259_R	0.829	1.00
185_A	195_V	0.828	1.00
15_A	41_A	0.827	1.00
154_V	171_A	0.824	1.00
14_D	18_V	0.824	1.00
188_A	214_A	0.823	1.00
245_L	249_L	0.821	1.00
16_D	20_I	0.816	1.00
99_A	103_L	0.816	1.00
18_V	45_A	0.813	1.00
240_E	244_A	0.807	1.00
102_L	105_K	0.804	1.00
21_A	49_R	0.800	1.00
154_V	163_L	0.800	1.00
26_Q	53_E	0.800	1.00
209_I	213_A	0.792	1.00
108_E	111_R	0.792	1.00
59_A	84_L	0.790	1.00
65_R	93_D	0.786	1.00
89_G	113_R	0.783	1.00
245_L	253_T	0.780	1.00
81_D	84_L	0.778	1.00
248_R	251_P	0.775	1.00
111_R	129_L	0.775	1.00
78_A	84_L	0.773	1.00
42_V	45_A	0.763	1.00
246_F	256_R	0.762	1.00
250_S	254_A	0.762	1.00
157_L	179_E	0.759	1.00
248_R	253_T	0.756	1.00
237_A	241_A	0.755	1.00
40_E	43_T	0.748	1.00
47_V	58_L	0.744	1.00
190_V	210_L	0.741	1.00
78_A	102_L	0.741	1.00
55_V	74_L	0.740	1.00
120_L	125_I	0.737	1.00
167_L	170_R	0.736	1.00
14_D	37_S	0.730	1.00
156_A	162_R	0.724	0.99
187_L	214_A	0.721	0.99
222_R	243_L	0.721	0.99
68_E	72_A	0.721	0.99
207_L	221_F	0.719	0.99
167_L	179_E	0.717	0.99
249_L	254_A	0.716	0.99
208_L	218_W	0.715	0.99
209_I	257_V	0.709	0.99
125_I	129_L	0.707	0.99
252_E	256_R	0.706	0.99
170_R	174_A	0.704	0.99
216_L	220_T	0.698	0.99
113_R	116_A	0.698	0.99
7_E	31_A	0.693	0.99
49_R	77_R	0.692	0.99
85_A	102_L	0.691	0.99
132_A	135_R	0.685	0.99
154_V	179_E	0.674	0.99
247_E	255_Q	0.665	0.99
115_L	119_P	0.663	0.99
168_L	184_L	0.662	0.99
250_S	256_R	0.662	0.99
118_A	125_I	0.660	0.99
251_P	257_V	0.659	0.99
201_D	204_G	0.657	0.99
216_L	224_I	0.653	0.99
242_A	250_S	0.652	0.99
130_A	133_A	0.650	0.99
165_E	168_L	0.649	0.99
182_A	186_L	0.647	0.99
218_W	243_L	0.645	0.99
173_R	223_A	0.644	0.99
45_A	48_E	0.640	0.99
237_A	242_A	0.640	0.99
247_E	251_P	0.639	0.99
244_A	253_T	0.638	0.99
146_D	149_A	0.636	0.99
217_S	221_F	0.634	0.99
75_V	102_L	0.633	0.99
244_A	247_E	0.633	0.99
221_F	246_F	0.631	0.99
130_A	134_E	0.630	0.99
56_R	59_A	0.630	0.99
52_R	56_R	0.629	0.99
246_F	253_T	0.627	0.99
9_S	20_I	0.627	0.99
247_E	252_E	0.626	0.98
3_G	27_A	0.626	0.98
223_A	227_A	0.624	0.98
14_D	42_V	0.623	0.98
38_L	44_D	0.621	0.98
236_A	239_L	0.620	0.98
240_E	243_L	0.617	0.98
209_I	214_A	0.614	0.98
157_L	171_A	0.612	0.98
17_L	32_I	0.609	0.98
225_L	229_A	0.609	0.98
161_G	164_T	0.602	0.98
234_I	237_A	0.600	0.98
18_V	22_R	0.597	0.98
194_V	197_R	0.597	0.98
75_V	105_K	0.597	0.98
149_A	152_R	0.597	0.98
53_E	83_A	0.596	0.98
55_V	84_L	0.596	0.98
82_D	86_E	0.596	0.98
131_E	135_R	0.593	0.98
146_D	178_E	0.593	0.98
158_H	182_A	0.592	0.98
5_V	12_L	0.592	0.98
153_L	167_L	0.590	0.98
215_G	255_Q	0.590	0.98
251_P	254_A	0.589	0.98
247_E	256_R	0.589	0.98
126_Q	130_A	0.589	0.98
248_R	252_E	0.588	0.98
75_V	85_A	0.588	0.98
86_E	113_R	0.587	0.98
63_G	66_F	0.587	0.98
27_A	30_L	0.587	0.98
178_E	181_V	0.587	0.98
238_D	242_A	0.586	0.98
29_L	32_I	0.585	0.98
231_A	234_I	0.584	0.98
3_G	31_A	0.583	0.98
177_F	181_V	0.583	0.98
124_E	128_A	0.583	0.98
112_R	116_A	0.582	0.98
44_D	48_E	0.579	0.98
245_L	257_V	0.579	0.98
20_I	24_K	0.576	0.97
125_I	128_A	0.575	0.97
106_A	114_L	0.573	0.97
153_L	176_K	0.572	0.97
245_L	252_E	0.572	0.97
165_E	180_F	0.569	0.97
218_W	221_F	0.568	0.97
2_A	5_V	0.568	0.97
186_L	189_G	0.566	0.97
61_N	91_R	0.566	0.97
236_A	240_E	0.565	0.97
252_E	259_R	0.565	0.97
40_E	44_D	0.563	0.97
98_L	101_R	0.563	0.97
221_F	225_L	0.562	0.97
154_V	157_L	0.561	0.97
235_S	238_D	0.561	0.97
196_E	200_H	0.560	0.97
246_F	249_L	0.557	0.97
150_A	178_E	0.554	0.97
39_S	43_T	0.554	0.97
249_L	256_R	0.554	0.97
184_L	214_A	0.553	0.97
246_F	254_A	0.552	0.97
249_L	253_T	0.551	0.97
184_L	199_L	0.551	0.97
5_V	11_R	0.548	0.97
253_T	258_L	0.548	0.97
242_A	247_E	0.547	0.96
230_A	234_I	0.541	0.96
5_V	20_I	0.540	0.96
75_V	94_L	0.539	0.96
235_S	240_E	0.538	0.96
138_A	141_A	0.537	0.96
111_R	114_L	0.537	0.96
137_T	144_S	0.536	0.96
246_F	257_V	0.535	0.96
213_A	218_W	0.534	0.96
50_G	54_V	0.533	0.96
75_V	88_L	0.533	0.96
5_V	8_R	0.532	0.96
88_L	170_R	0.531	0.96
184_L	195_V	0.531	0.96
55_V	78_A	0.529	0.96
137_T	140_L	0.528	0.96
245_L	256_R	0.526	0.96
100_R	104_A	0.525	0.96
203_R	206_G	0.524	0.96
145_R	178_E	0.524	0.96
247_E	257_V	0.523	0.95
121_D	128_A	0.523	0.95
154_V	158_H	0.522	0.95
180_F	199_L	0.520	0.95
235_S	239_L	0.518	0.95
209_I	212_K	0.517	0.95
29_L	50_G	0.516	0.95
170_R	175_G	0.515	0.95
191_P	194_V	0.514	0.95
24_K	110_L	0.514	0.95
143_A	146_D	0.514	0.95
3_G	28_H	0.513	0.95
10_P	37_S	0.510	0.95
157_L	164_T	0.509	0.95
190_V	194_V	0.506	0.95
85_A	89_G	0.504	0.95
198_L	210_L	0.504	0.95
54_V	61_N	0.503	0.94
148_A	151_R	0.502	0.94
255_Q	258_L	0.501	0.94
243_L	257_V	0.500	0.94

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
4fhrB	1	0.4809	48.6	0.929	Contact Map
4o8bA	2	0.3321	46.6	0.93	Contact Map
2ictA	2	0.3473	44.5	0.931	Contact Map
1b0nA	2	0.3511	40.7	0.932	Contact Map
2ypfA	1	0.9656	38.7	0.933	Contact Map
4ndwA	2	0.3817	36.4	0.934	Contact Map
3qwgA	2	0.2977	34.1	0.935	Contact Map
4jcyA	2	0.3244	33.6	0.936	Contact Map
1lrvA	1	0.7595	32.9	0.936	Contact Map
1xi4A	8	0.8053	31.9	0.936	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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