DUF2284 - PFAM28P - GREMLIN Contacts

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DUF2284 - Predicted metal-binding protein (DUF2284)

PFAM:	PF10050	Sequences: KIIDPSDIVVDERVRLKCRFGCGNYGKNWTCPPAVPSPEECREILKEYSRALLFQTEGPLEDSFDRKEGMREAKRKHNEILLELEREAFLDGYYKAFALGAGSCKLCEECAYPDGEPCRFPEKARPSMEACGIDVFKTARKAGLPIEVGKDKDNTVTYYGLVLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	164 (159)
Sequences:	5629 (4183)
Seq/√Len:	331.7
META:	0.918

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_T	124_A	3.768	1.00
42_R	46_K	3.183	1.00
137_K	141_K	2.649	1.00
34_A	112_Y	2.571	1.00
4_D	7_D	2.528	1.00
7_D	142_A	2.399	1.00
134_D	137_K	2.395	1.00
85_E	125_R	2.355	1.00
37_S	40_E	2.347	1.00
16_L	19_R	2.340	1.00
120_F	123_K	2.333	1.00
7_D	141_K	2.317	1.00
81_L	98_A	2.305	1.00
56_T	77_H	2.305	1.00
54_F	81_L	2.303	1.00
29_W	112_Y	2.161	1.00
10_V	45_L	2.114	1.00
39_E	43_E	1.998	1.00
128_M	133_I	1.965	1.00
111_A	119_R	1.955	1.00
8_I	133_I	1.859	1.00
41_C	131_C	1.818	1.00
86_R	123_K	1.808	1.00
4_D	50_R	1.800	1.00
79_E	123_K	1.777	1.00
38_P	132_G	1.721	1.00
109_E	114_D	1.715	1.00
150_K	154_N	1.676	1.00
9_V	137_K	1.586	1.00
86_R	90_L	1.585	1.00
133_I	138_T	1.563	1.00
99_L	131_C	1.558	1.00
11_D	134_D	1.532	1.00
57_E	155_T	1.522	1.00
12_E	42_R	1.490	1.00
139_A	159_Y	1.480	1.00
55_Q	144_L	1.478	1.00
128_M	135_V	1.446	1.00
47_E	95_K	1.397	1.00
12_E	47_E	1.388	1.00
83_E	87_E	1.379	1.00
81_L	160_G	1.376	1.00
137_K	140_R	1.371	1.00
9_V	141_K	1.367	1.00
53_L	142_A	1.348	1.00
78_N	100_G	1.333	1.00
26_G	33_P	1.332	1.00
72_E	76_K	1.308	1.00
12_E	16_L	1.308	1.00
145_P	159_Y	1.305	1.00
55_Q	157_T	1.278	1.00
9_V	138_T	1.253	1.00
106_L	123_K	1.242	1.00
12_E	43_E	1.225	1.00
35_V	130_A	1.222	1.00
24_N	27_K	1.210	1.00
129_E	135_V	1.182	1.00
74_K	78_N	1.178	1.00
79_E	83_E	1.169	1.00
88_A	162_V	1.167	1.00
128_M	161_L	1.165	1.00
111_A	116_E	1.164	1.00
19_R	25_Y	1.158	1.00
126_P	131_C	1.153	1.00
29_W	111_A	1.114	1.00
51_A	161_L	1.113	1.00
87_E	91_D	1.099	1.00
75_R	79_E	1.094	1.00
15_R	38_P	1.082	1.00
11_D	137_K	1.066	1.00
17_K	20_F	1.026	1.00
114_D	119_R	1.023	1.00
147_E	154_N	1.017	1.00
77_H	101_A	1.005	1.00
58_G	73_A	0.996	1.00
29_W	113_P	0.992	1.00
29_W	34_A	0.989	1.00
78_N	82_L	0.988	1.00
43_E	46_K	0.985	1.00
16_L	44_I	0.982	1.00
55_Q	159_Y	0.977	1.00
57_E	157_T	0.972	1.00
144_L	159_Y	0.969	1.00
102_G	127_S	0.959	1.00
13_R	95_K	0.955	1.00
85_E	98_A	0.955	1.00
94_Y	137_K	0.948	1.00
15_R	37_S	0.934	1.00
15_R	19_R	0.929	1.00
85_E	96_A	0.926	1.00
98_A	125_R	0.921	1.00
76_K	79_E	0.905	1.00
56_T	80_I	0.905	1.00
39_E	42_R	0.905	1.00
53_L	128_M	0.904	1.00
74_K	105_K	0.901	1.00
84_L	162_V	0.899	1.00
89_F	92_G	0.899	1.00
111_A	117_P	0.896	1.00
66_R	71_R	0.895	1.00
81_L	162_V	0.890	1.00
14_V	129_E	0.881	1.00
13_R	16_L	0.880	1.00
109_E	113_P	0.877	1.00
136_F	148_V	0.868	1.00
35_V	131_C	0.865	1.00
82_L	85_E	0.862	1.00
12_E	39_E	0.859	1.00
28_N	105_K	0.852	1.00
45_L	133_I	0.851	1.00
146_I	149_G	0.850	1.00
106_L	120_F	0.848	1.00
14_V	134_D	0.839	1.00
5_P	50_R	0.839	1.00
24_N	103_S	0.838	1.00
87_E	90_L	0.833	1.00
106_L	124_A	0.830	1.00
156_V	160_G	0.827	1.00
138_T	141_K	0.827	1.00
102_G	129_E	0.826	1.00
89_F	93_Y	0.826	1.00
24_N	105_K	0.822	1.00
13_R	134_D	0.819	1.00
82_L	123_K	0.818	1.00
12_E	38_P	0.808	1.00
54_F	98_A	0.803	1.00
69_G	72_E	0.795	1.00
77_H	160_G	0.795	1.00
40_E	43_E	0.795	1.00
135_V	138_T	0.792	1.00
44_I	97_F	0.786	1.00
76_K	80_I	0.782	1.00
10_V	46_K	0.777	1.00
55_Q	145_P	0.775	1.00
24_N	28_N	0.771	1.00
27_K	113_P	0.769	1.00
85_E	89_F	0.762	1.00
8_I	138_T	0.756	1.00
148_V	157_T	0.754	1.00
81_L	85_E	0.747	0.99
8_I	51_A	0.746	0.99
23_G	122_E	0.740	0.99
18_C	22_C	0.740	0.99
62_D	65_D	0.737	0.99
53_L	138_T	0.733	0.99
62_D	68_E	0.731	0.99
61_E	65_D	0.729	0.99
14_V	17_K	0.725	0.99
29_W	117_P	0.724	0.99
40_E	44_I	0.716	0.99
77_H	81_L	0.715	0.99
90_L	150_K	0.707	0.99
30_T	126_P	0.698	0.99
107_C	110_C	0.697	0.99
70_M	73_A	0.680	0.99
5_P	51_A	0.675	0.99
22_C	31_C	0.674	0.99
77_H	80_I	0.674	0.99
149_G	154_N	0.674	0.99
53_L	139_A	0.666	0.99
54_F	160_G	0.665	0.99
57_E	148_V	0.664	0.99
71_R	74_K	0.663	0.99
107_C	118_C	0.661	0.99
26_G	32_P	0.659	0.99
26_G	34_A	0.657	0.99
55_Q	139_A	0.655	0.99
140_R	146_I	0.650	0.99
41_C	99_L	0.644	0.98
98_A	162_V	0.644	0.98
72_E	75_R	0.641	0.98
11_D	47_E	0.641	0.98
104_C	118_C	0.641	0.98
156_V	159_Y	0.641	0.98
61_E	68_E	0.640	0.98
136_F	140_R	0.638	0.98
82_L	125_R	0.638	0.98
37_S	41_C	0.637	0.98
118_C	121_P	0.634	0.98
103_S	127_S	0.631	0.98
71_R	75_R	0.629	0.98
80_I	84_L	0.624	0.98
106_L	109_E	0.619	0.98
26_G	112_Y	0.613	0.98
116_E	119_R	0.612	0.98
38_P	42_R	0.603	0.98
146_I	159_Y	0.597	0.97
69_G	73_A	0.596	0.97
149_G	156_V	0.596	0.97
5_P	46_K	0.594	0.97
61_E	64_F	0.592	0.97
151_D	154_N	0.591	0.97
156_V	161_L	0.590	0.97
56_T	76_K	0.586	0.97
154_N	157_T	0.586	0.97
59_P	155_T	0.581	0.97
21_G	97_F	0.581	0.97
94_Y	140_R	0.574	0.97
78_N	105_K	0.572	0.97
28_N	113_P	0.571	0.97
147_E	155_T	0.570	0.97
34_A	113_P	0.569	0.97
58_G	77_H	0.568	0.97
2_I	52_L	0.564	0.96
140_R	147_E	0.563	0.96
61_E	69_G	0.562	0.96
126_P	130_A	0.560	0.96
112_Y	115_G	0.558	0.96
31_C	103_S	0.553	0.96
68_E	71_R	0.549	0.96
157_T	160_G	0.548	0.96
10_V	13_R	0.548	0.96
10_V	133_I	0.547	0.96
15_R	25_Y	0.546	0.96
58_G	76_K	0.545	0.96
43_E	47_E	0.545	0.96
88_A	93_Y	0.544	0.96
85_E	88_A	0.543	0.96
48_Y	95_K	0.542	0.96
8_I	45_L	0.538	0.95
64_F	69_G	0.534	0.95
2_I	5_P	0.532	0.95
4_D	51_A	0.531	0.95
10_V	41_C	0.527	0.95
41_C	45_L	0.525	0.95
63_S	69_G	0.525	0.95
36_P	40_E	0.525	0.95
10_V	42_R	0.524	0.95
155_T	159_Y	0.522	0.95
14_V	136_F	0.522	0.95
28_N	124_A	0.515	0.94
155_T	158_Y	0.506	0.94
101_A	160_G	0.506	0.94
99_L	128_M	0.505	0.94
96_A	162_V	0.504	0.93
28_N	103_S	0.504	0.93
48_Y	97_F	0.502	0.93
60_L	66_R	0.500	0.93

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
1ercA	1	0.2073	4.3	0.948	Contact Map
2l9zA	1	0.2378	3.2	0.951	Contact Map
4fw2A	2	0.25	2.8	0.952	Contact Map
4nfnA	1	0.8232	2.8	0.952	Contact Map
2apoB	1	0.3354	2.6	0.953	Contact Map
4udxX	2	0.5671	2.5	0.954	Contact Map
2jiiA	1	0.8537	2.3	0.955	Contact Map
3dinD	1	0.1585	2.2	0.955	Contact Map
2lzyA	1	0.1768	2.2	0.955	Contact Map
3dl8C	1	0.0488	2.2	0.955	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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