DUF2236 - PFAM28P - GREMLIN Contacts

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DUF2236 - Uncharacterized protein conserved in bacteria (DUF2236)

PFAM:	PF09995	Sequences: WRVHGDEAALLLGGLRALLLQAAHPLVAAGVAEHSDFADPWGRLRRTARFVATTTFGTREEAEAAAARVRRIHARVRGTLDGRPYSAIDPELLLWVHATLVDSFLRAYERFRPLSPAERDAYYAEWRRVGRLLGVPAEDLPATRAEFRAYLDAMLRPELRVTPAARELARPLYRLLRAAAVGLLPPWLRELLGLPRPWSPRRERARAALRALARALRW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	218 (206)
Sequences:	14909 (9613)
Seq/√Len:	669.8
META:	0.749

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_S	118_E	3.831	1.00
143_T	146_E	3.743	1.00
109_E	119_R	3.602	1.00
58_T	61_E	2.870	1.00
39_D	42_G	2.796	1.00
119_R	144_R	2.698	1.00
199_S	202_R	2.643	1.00
161_V	166_R	2.581	1.00
16_R	102_D	2.560	1.00
91_E	158_E	2.422	1.00
144_R	148_R	2.410	1.00
121_A	125_E	2.400	1.00
136_P	139_D	2.378	1.00
74_A	88_I	2.267	1.00
63_E	67_A	2.066	1.00
131_R	137_A	2.062	1.00
120_D	124_A	2.041	1.00
187_W	191_L	1.988	1.00
209_L	213_A	1.961	1.00
53_T	65_A	1.955	1.00
149_A	153_A	1.923	1.00
59_R	63_E	1.909	1.00
80_L	83_R	1.903	1.00
127_R	142_A	1.878	1.00
77_R	86_S	1.873	1.00
94_L	150_Y	1.834	1.00
29_A	33_E	1.811	1.00
70_R	88_I	1.800	1.00
16_R	103_S	1.797	1.00
162_T	165_A	1.794	1.00
124_A	127_R	1.768	1.00
105_L	119_R	1.767	1.00
128_R	131_R	1.745	1.00
102_D	106_R	1.735	1.00
198_W	202_R	1.729	1.00
50_F	69_V	1.689	1.00
63_E	132_L	1.623	1.00
128_R	132_L	1.605	1.00
71_R	74_A	1.592	1.00
98_A	147_F	1.589	1.00
163_P	167_E	1.579	1.00
42_G	46_R	1.556	1.00
156_R	159_L	1.554	1.00
116_P	119_R	1.551	1.00
142_A	146_E	1.546	1.00
153_A	157_P	1.516	1.00
203_E	210_R	1.498	1.00
50_F	65_A	1.473	1.00
98_A	150_Y	1.471	1.00
105_L	144_R	1.463	1.00
97_H	130_G	1.419	1.00
156_R	187_W	1.399	1.00
181_V	194_L	1.395	1.00
53_T	61_E	1.393	1.00
101_V	126_W	1.348	1.00
116_P	144_R	1.336	1.00
123_Y	147_F	1.327	1.00
150_Y	154_M	1.326	1.00
116_P	120_D	1.316	1.00
202_R	205_A	1.311	1.00
130_G	140_L	1.302	1.00
148_R	152_D	1.298	1.00
164_A	167_E	1.297	1.00
120_D	144_R	1.294	1.00
198_W	201_R	1.284	1.00
131_R	142_A	1.264	1.00
145_A	149_A	1.259	1.00
186_P	190_E	1.254	1.00
116_P	145_A	1.252	1.00
90_P	136_P	1.244	1.00
117_A	121_A	1.232	1.00
106_R	109_E	1.226	1.00
200_P	204_R	1.224	1.00
102_D	148_R	1.206	1.00
161_V	165_A	1.189	1.00
72_I	75_R	1.189	1.00
26_L	92_L	1.181	1.00
70_R	134_G	1.169	1.00
118_E	121_A	1.166	1.00
151_L	155_L	1.159	1.00
188_L	191_L	1.133	1.00
29_A	164_A	1.107	1.00
163_P	166_R	1.097	1.00
181_V	189_R	1.071	1.00
198_W	203_E	1.069	1.00
210_R	213_A	1.060	1.00
201_R	205_A	1.059	1.00
182_G	198_W	1.050	1.00
24_H	28_A	1.050	1.00
16_R	106_R	1.047	1.00
8_A	12_L	1.046	1.00
127_R	140_L	1.043	1.00
108_Y	112_R	1.043	1.00
199_S	203_E	1.036	1.00
154_M	158_E	1.035	1.00
8_A	11_L	1.035	1.00
106_R	110_R	1.035	1.00
26_L	80_L	1.034	1.00
165_A	168_L	1.032	1.00
107_A	110_R	1.026	1.00
30_G	35_S	1.024	1.00
109_E	113_P	1.021	1.00
94_L	139_D	1.019	1.00
161_V	191_L	1.006	1.00
120_D	145_A	1.006	1.00
198_W	204_R	0.992	1.00
32_A	164_A	0.972	1.00
105_L	122_Y	0.970	1.00
121_A	124_A	0.967	1.00
114_L	118_E	0.954	1.00
26_L	30_G	0.948	1.00
65_A	68_R	0.940	1.00
66_A	132_L	0.939	1.00
200_P	205_A	0.931	1.00
60_E	63_E	0.924	1.00
89_D	92_L	0.920	1.00
107_A	111_F	0.915	1.00
77_R	88_I	0.908	1.00
36_D	39_D	0.903	1.00
9_A	12_L	0.892	1.00
171_P	174_R	0.886	1.00
50_F	66_A	0.880	1.00
26_L	29_A	0.880	1.00
30_G	34_H	0.877	1.00
20_L	188_L	0.876	1.00
64_A	68_R	0.876	1.00
26_L	89_D	0.875	1.00
44_L	48_A	0.874	1.00
93_L	135_V	0.871	1.00
126_W	129_V	0.870	1.00
27_V	30_G	0.867	1.00
130_G	135_V	0.863	1.00
124_A	142_A	0.861	1.00
32_A	35_S	0.859	1.00
15_L	19_L	0.858	1.00
127_R	131_R	0.856	1.00
185_P	188_L	0.854	1.00
205_A	211_A	0.850	1.00
135_V	140_L	0.840	1.00
174_R	177_R	0.838	1.00
103_S	106_R	0.837	1.00
94_L	140_L	0.834	1.00
120_D	123_Y	0.833	1.00
184_L	188_L	0.831	1.00
24_H	154_M	0.831	1.00
3_V	6_D	0.829	1.00
152_D	156_R	0.829	1.00
71_R	75_R	0.825	1.00
200_P	203_E	0.824	1.00
67_A	71_R	0.822	1.00
48_A	52_A	0.814	1.00
67_A	70_R	0.811	1.00
14_G	18_L	0.811	1.00
76_V	87_A	0.809	1.00
16_R	19_L	0.808	1.00
189_R	196_R	0.808	1.00
98_A	151_L	0.808	1.00
181_V	190_E	0.807	1.00
201_R	204_R	0.801	1.00
177_R	180_A	0.801	1.00
59_R	62_A	0.799	1.00
53_T	68_R	0.794	1.00
19_L	22_A	0.792	1.00
102_D	151_L	0.788	1.00
68_R	71_R	0.786	1.00
49_R	53_T	0.786	1.00
26_L	83_R	0.782	1.00
47_T	96_V	0.780	1.00
109_E	112_R	0.780	1.00
123_Y	144_R	0.776	1.00
4_H	122_Y	0.771	1.00
27_V	96_V	0.767	1.00
61_E	64_A	0.762	1.00
23_A	28_A	0.757	1.00
34_H	85_Y	0.757	1.00
173_Y	176_L	0.757	1.00
177_R	181_V	0.757	1.00
185_P	189_R	0.755	1.00
18_L	21_Q	0.749	1.00
22_A	168_L	0.746	1.00
105_L	109_E	0.741	1.00
160_R	165_A	0.739	1.00
68_R	72_I	0.737	1.00
31_V	35_S	0.733	1.00
111_F	179_A	0.727	1.00
50_F	68_R	0.726	1.00
186_P	196_R	0.725	1.00
50_F	133_L	0.725	1.00
28_A	31_V	0.724	1.00
114_L	119_R	0.721	1.00
106_R	148_R	0.719	1.00
135_V	139_D	0.718	1.00
51_V	100_L	0.717	1.00
173_Y	177_R	0.715	1.00
51_V	54_T	0.715	1.00
60_E	64_A	0.714	1.00
57_G	61_E	0.711	1.00
176_L	180_A	0.704	1.00
31_V	34_H	0.702	1.00
176_L	179_A	0.700	1.00
149_A	152_D	0.700	1.00
28_A	168_L	0.695	1.00
127_R	137_A	0.691	1.00
22_A	31_V	0.690	1.00
62_A	132_L	0.688	1.00
209_L	212_L	0.685	1.00
147_F	151_L	0.685	1.00
184_L	192_L	0.684	1.00
116_P	148_R	0.680	1.00
205_A	209_L	0.678	1.00
174_R	178_A	0.678	1.00
187_W	190_E	0.677	1.00
25_P	28_A	0.676	1.00
160_R	191_L	0.674	1.00
151_L	154_M	0.674	1.00
146_E	149_A	0.672	1.00
45_R	49_R	0.672	1.00
33_E	164_A	0.669	1.00
180_A	184_L	0.668	1.00
190_E	196_R	0.666	1.00
166_R	193_G	0.666	1.00
24_H	27_V	0.665	1.00
152_D	155_L	0.663	1.00
23_A	188_L	0.661	1.00
119_R	148_R	0.661	1.00
29_A	162_T	0.657	1.00
108_Y	114_L	0.656	1.00
153_A	158_E	0.655	1.00
54_T	69_V	0.648	1.00
100_L	126_W	0.647	1.00
137_A	142_A	0.644	1.00
70_R	74_A	0.643	1.00
101_V	123_Y	0.642	1.00
25_P	31_V	0.641	1.00
91_E	139_D	0.640	1.00
91_E	94_L	0.638	1.00
145_A	148_R	0.632	1.00
199_S	205_A	0.631	1.00
103_S	107_A	0.624	1.00
150_Y	153_A	0.621	1.00
155_L	159_L	0.617	1.00
147_F	150_Y	0.617	1.00
164_A	168_L	0.613	1.00
14_G	19_L	0.612	1.00
198_W	205_A	0.611	1.00
69_V	133_L	0.608	1.00
63_E	70_R	0.608	1.00
178_A	202_R	0.608	1.00
110_R	183_L	0.607	1.00
54_T	129_V	0.606	1.00
109_E	144_R	0.600	1.00
178_A	182_G	0.600	1.00
12_L	16_R	0.600	1.00
16_R	183_L	0.599	1.00
67_A	132_L	0.597	1.00
23_A	27_V	0.597	1.00
203_E	209_L	0.597	1.00
13_G	17_A	0.595	1.00
6_D	10_L	0.594	1.00
189_R	198_W	0.592	1.00
24_H	29_A	0.590	1.00
66_A	133_L	0.584	1.00
28_A	165_A	0.583	1.00
108_Y	111_F	0.582	1.00
123_Y	142_A	0.581	1.00
59_R	132_L	0.581	1.00
30_G	76_V	0.580	1.00
94_L	138_E	0.578	1.00
146_E	150_Y	0.578	1.00
78_G	85_Y	0.574	1.00
26_L	91_E	0.574	1.00
64_A	71_R	0.567	1.00
78_G	84_P	0.562	1.00
95_W	99_T	0.559	1.00
74_A	86_S	0.555	1.00
28_A	32_A	0.554	1.00
18_L	22_A	0.553	1.00
189_R	194_L	0.551	1.00
43_R	47_T	0.551	1.00
6_D	9_A	0.544	1.00
199_S	204_R	0.542	1.00
175_L	179_A	0.542	1.00
26_L	31_V	0.540	1.00
86_S	89_D	0.539	1.00
14_G	21_Q	0.537	1.00
172_L	176_L	0.536	1.00
4_H	10_L	0.534	1.00
15_L	180_A	0.531	1.00
155_L	158_E	0.531	1.00
13_G	103_S	0.529	1.00
79_T	84_P	0.528	1.00
91_E	154_M	0.527	1.00
41_W	45_R	0.526	0.99
27_V	31_V	0.522	0.99
165_A	169_A	0.521	0.99
160_R	164_A	0.521	0.99
97_H	123_Y	0.517	0.99
101_V	105_L	0.516	0.99
106_R	151_L	0.515	0.99
204_R	211_A	0.509	0.99
123_Y	127_R	0.508	0.99
55_T	125_E	0.508	0.99
178_A	205_A	0.506	0.99
5_G	8_A	0.505	0.99
17_A	20_L	0.504	0.99
66_A	70_R	0.503	0.99
88_I	93_L	0.501	0.99
198_W	209_L	0.501	0.99
180_A	183_L	0.500	0.99

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
3ubcA	3	0.5459	15.4	0.939	Contact Map
1tu9A	1	0.5596	12.8	0.941	Contact Map
3g46A	2	0.5321	12.1	0.942	Contact Map
4hrrA	1	0.5459	8.4	0.946	Contact Map
3wfwA	2	0.578	8.2	0.946	Contact Map
1hlbA	1	0.5642	8.1	0.946	Contact Map
4hrrB	2	0.5459	7.6	0.947	Contact Map
1binA	1	0.555	6.5	0.948	Contact Map
1hlmA	2	0.5688	6	0.949	Contact Map
3vfzA	2	0.2615	5.2	0.951	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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