DUF2203 - PFAM28P - GREMLIN Contacts

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DUF2203 - Uncharacterized conserved protein (DUF2203)

PFAM:	PF09969	Sequences: RLFTLEEANALLPLVRPLLEDLVELRRELRELEEELEALAARIRGNGGAELRAELERLAERLREALEELEELGVEVKDLDRGLVDFPALRDGREVYLCWKLGEDEIEFWHELDEGFAGRKPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	122 (122)
Sequences:	14028 (9360)
Seq/√Len:	847.4
META:	0.981

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_E	114_E	3.652	1.00
9_N	105_E	3.483	1.00
81_R	100_K	3.183	1.00
93_R	111_E	2.955	1.00
78_D	81_R	2.918	1.00
2_L	94_E	2.812	1.00
89_L	94_E	2.456	1.00
90_R	95_V	2.351	1.00
75_E	96_Y	2.299	1.00
26_R	30_R	2.229	1.00
25_L	61_R	2.028	1.00
26_R	80_D	1.982	1.00
13_P	17_P	1.965	1.00
23_V	101_L	1.943	1.00
88_A	95_V	1.884	1.00
5_L	9_N	1.712	1.00
14_L	18_L	1.709	1.00
18_L	68_E	1.627	1.00
28_E	58_L	1.600	1.00
21_D	65_A	1.524	1.00
107_E	121_P	1.517	1.00
19_L	23_V	1.512	1.00
63_R	67_E	1.491	1.00
114_E	118_G	1.483	1.00
69_L	74_V	1.478	1.00
18_L	65_A	1.454	1.00
2_L	89_L	1.426	1.00
25_L	58_L	1.402	1.00
85_D	98_C	1.386	1.00
77_K	85_D	1.383	1.00
11_L	72_L	1.379	1.00
16_R	20_E	1.375	1.00
68_E	72_L	1.371	1.00
16_R	104_D	1.370	1.00
20_E	101_L	1.354	1.00
115_G	118_G	1.319	1.00
88_A	97_L	1.297	1.00
9_N	106_I	1.291	1.00
48_G	52_R	1.271	1.00
85_D	110_H	1.268	1.00
77_K	83_L	1.264	1.00
21_D	61_R	1.221	1.00
14_L	72_L	1.221	1.00
3_F	73_G	1.205	1.00
15_V	69_L	1.204	1.00
87_P	94_E	1.197	1.00
14_L	17_P	1.177	1.00
16_R	102_G	1.171	1.00
65_A	68_E	1.130	1.00
114_E	120_K	1.126	1.00
5_L	106_I	1.124	1.00
14_L	68_E	1.122	1.00
74_V	84_V	1.118	1.00
96_Y	112_L	1.086	1.00
35_E	51_L	1.076	1.00
6_E	10_A	1.076	1.00
104_D	107_E	1.072	1.00
89_L	92_G	1.047	1.00
20_E	24_E	1.038	1.00
67_E	70_E	1.038	1.00
67_E	71_E	1.033	1.00
36_L	39_L	1.028	1.00
59_A	63_R	0.997	1.00
51_L	54_E	0.995	1.00
49_A	53_A	0.995	1.00
8_A	74_V	0.986	1.00
22_L	62_L	0.986	1.00
28_E	32_L	0.983	1.00
4_T	7_E	0.944	1.00
11_L	14_L	0.938	1.00
28_E	54_E	0.929	1.00
87_P	96_Y	0.921	1.00
61_R	65_A	0.917	1.00
12_L	15_V	0.915	1.00
28_E	31_E	0.915	1.00
15_V	84_V	0.914	1.00
16_R	101_L	0.908	1.00
25_L	62_L	0.903	1.00
24_E	28_E	0.895	1.00
35_E	38_A	0.894	1.00
19_L	101_L	0.891	1.00
29_L	59_A	0.886	1.00
35_E	39_L	0.885	1.00
25_L	65_A	0.875	1.00
21_D	25_L	0.861	1.00
75_E	87_P	0.846	1.00
18_L	21_D	0.842	1.00
43_I	47_G	0.841	1.00
54_E	58_L	0.837	1.00
22_L	65_A	0.835	1.00
33_E	37_E	0.813	1.00
108_F	121_P	0.810	1.00
98_C	110_H	0.809	1.00
15_V	72_L	0.808	1.00
56_E	59_A	0.806	1.00
66_L	79_L	0.793	1.00
25_L	28_E	0.788	1.00
27_R	31_E	0.781	1.00
36_L	40_A	0.773	1.00
57_R	60_E	0.771	1.00
70_E	75_E	0.770	1.00
90_R	122_L	0.763	1.00
49_A	52_R	0.762	1.00
78_D	82_G	0.755	1.00
18_L	69_L	0.755	1.00
23_V	26_R	0.748	1.00
33_E	55_L	0.747	1.00
32_L	54_E	0.745	1.00
32_L	58_L	0.734	1.00
38_A	41_A	0.731	1.00
48_G	51_L	0.725	1.00
109_W	120_K	0.715	1.00
5_L	122_L	0.714	1.00
90_R	93_R	0.706	1.00
56_E	60_E	0.704	1.00
87_P	112_L	0.699	1.00
30_R	33_E	0.697	1.00
40_A	44_R	0.690	1.00
83_L	100_K	0.680	1.00
19_L	76_V	0.679	1.00
15_V	19_L	0.676	1.00
100_K	116_F	0.673	1.00
81_R	101_L	0.671	1.00
50_E	54_E	0.668	1.00
111_E	120_K	0.665	1.00
21_D	24_E	0.664	1.00
52_R	55_L	0.659	1.00
66_L	70_E	0.647	1.00
41_A	44_R	0.640	1.00
26_R	79_L	0.634	1.00
110_H	115_G	0.628	1.00
43_I	46_N	0.623	1.00
88_A	96_Y	0.621	1.00
42_R	45_G	0.615	1.00
55_L	59_A	0.615	1.00
39_L	43_I	0.610	1.00
40_A	43_I	0.609	1.00
17_P	20_E	0.606	1.00
77_K	98_C	0.606	1.00
19_L	22_L	0.598	1.00
32_L	51_L	0.597	1.00
11_L	74_V	0.597	1.00
83_L	115_G	0.593	1.00
61_R	64_E	0.592	1.00
50_E	53_A	0.590	1.00
30_R	34_E	0.586	1.00
17_P	21_D	0.583	1.00
70_E	76_V	0.574	1.00
9_N	12_L	0.572	1.00
38_A	42_R	0.572	1.00
27_R	30_R	0.571	1.00
48_G	56_E	0.571	1.00
3_F	11_L	0.564	1.00
72_L	84_V	0.563	1.00
98_C	103_E	0.560	1.00
20_E	23_V	0.558	1.00
12_L	16_R	0.557	1.00
94_E	112_L	0.555	1.00
3_F	86_F	0.553	1.00
11_L	86_F	0.549	1.00
3_F	74_V	0.546	1.00
42_R	47_G	0.544	1.00
18_L	72_L	0.543	1.00
96_Y	113_D	0.542	1.00
8_A	106_I	0.531	1.00
12_L	19_L	0.528	1.00
19_L	84_V	0.523	1.00
90_R	109_W	0.522	1.00
88_A	94_E	0.519	1.00
42_R	46_N	0.515	1.00
34_E	38_A	0.515	1.00
23_V	27_R	0.514	1.00
83_L	116_F	0.513	1.00
24_E	27_R	0.512	1.00
77_K	96_Y	0.509	1.00
22_L	76_V	0.508	1.00
44_R	47_G	0.505	1.00
54_E	57_R	0.503	1.00
33_E	43_I	0.503	1.00
58_L	61_R	0.502	1.00
76_V	79_L	0.501	1.00
53_A	57_R	0.500	1.00
2_L	88_A	0.500	1.00

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
1ccwB	2	0.877	30.7	0.897	Contact Map
4rsiA	1	0.3197	23.2	0.902	Contact Map
4jrbA	1	0.6393	14.7	0.911	Contact Map
3pmrA	2	0.4508	12.3	0.914	Contact Map
3mq9A	4	0.5902	10.8	0.916	Contact Map
4bwnA	2	0.5574	9.3	0.919	Contact Map
3umhA	1	0.4262	8.7	0.92	Contact Map
4fdgB	1	0.1639	7.4	0.922	Contact Map
3ja85	1	0.1885	6.9	0.923	Contact Map
3kbtA	1	0.4672	6.5	0.924	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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