DUF2924 - PFAM28P - GREMLIN Contacts

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DUF2924 - Protein of unknown function (DUF2924)

PFAM:	PF11149	Sequences: AEIAALRDLSLAELRARWRELFGRPPPPLSRDLLRRRLAYRLQELAYGGLSPATRRRLDRLARDAAARGARARRPRRRLKPGTRLVREWQGRTHRVTVLEDGFEYNGRTYRSLSAIARAITGTRWNGPRFFGLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (132)
Sequences:	9601 (6276)
Seq/√Len:	546.3
META:	0.968

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_R	35_R	3.831	1.00
118_R	124_R	3.184	1.00
84_R	95_R	3.071	1.00
11_L	15_R	2.920	1.00
10_S	13_E	2.880	1.00
17_R	20_E	2.879	1.00
92_R	106_N	2.657	1.00
94_H	120_I	2.560	1.00
2_E	17_R	2.406	1.00
41_R	44_E	2.391	1.00
97_T	104_E	2.251	1.00
99_L	104_E	2.246	1.00
103_F	116_I	2.193	1.00
108_R	119_A	2.157	1.00
94_H	105_Y	2.125	1.00
51_S	54_T	2.031	1.00
19_R	25_P	2.019	1.00
88_E	93_T	1.925	1.00
40_Y	44_E	1.900	1.00
44_E	49_G	1.846	1.00
99_L	109_T	1.754	1.00
104_E	107_G	1.667	1.00
84_R	97_T	1.596	1.00
3_I	39_A	1.523	1.00
86_V	93_T	1.507	1.00
99_L	102_G	1.505	1.00
2_E	5_A	1.488	1.00
110_Y	119_A	1.488	1.00
115_A	119_A	1.455	1.00
98_V	103_F	1.448	1.00
65_A	68_R	1.436	1.00
105_Y	119_A	1.429	1.00
57_R	60_R	1.422	1.00
111_R	115_A	1.417	1.00
104_E	109_T	1.398	1.00
7_R	35_R	1.384	1.00
41_R	45_L	1.380	1.00
85_L	98_V	1.363	1.00
105_Y	116_I	1.314	1.00
17_R	21_L	1.298	1.00
5_A	17_R	1.295	1.00
9_L	13_E	1.271	1.00
101_D	109_T	1.251	1.00
22_F	41_R	1.250	1.00
96_V	131_F	1.223	1.00
32_D	36_R	1.208	1.00
29_L	33_L	1.202	1.00
118_R	121_T	1.201	1.00
79_L	98_V	1.170	1.00
114_S	117_A	1.163	1.00
116_I	119_A	1.141	1.00
13_E	16_A	1.137	1.00
21_L	45_L	1.130	1.00
66_A	69_G	1.129	1.00
38_L	42_L	1.127	1.00
50_L	54_T	1.122	1.00
18_W	38_L	1.118	1.00
22_F	38_L	1.113	1.00
86_V	95_R	1.092	1.00
52_P	56_R	1.076	1.00
68_R	71_R	1.074	1.00
88_E	91_G	1.056	1.00
121_T	125_W	1.051	1.00
57_R	61_L	1.034	1.00
58_L	62_A	1.032	1.00
6_L	35_R	1.028	1.00
16_A	20_E	1.015	1.00
115_A	124_R	1.007	1.00
42_L	46_A	1.004	1.00
79_L	85_L	1.001	1.00
65_A	69_G	0.992	1.00
6_L	42_L	0.992	1.00
9_L	17_R	0.972	1.00
21_L	38_L	0.971	1.00
114_S	124_R	0.936	1.00
52_P	55_R	0.927	1.00
125_W	129_R	0.921	1.00
123_T	129_R	0.906	1.00
32_D	35_R	0.902	1.00
116_I	131_F	0.883	1.00
22_F	37_R	0.883	1.00
125_W	132_G	0.877	1.00
115_A	128_P	0.876	1.00
40_Y	50_L	0.869	1.00
128_P	132_G	0.869	1.00
39_A	42_L	0.853	1.00
67_A	70_A	0.841	1.00
66_A	70_A	0.840	1.00
94_H	106_N	0.833	1.00
26_P	34_L	0.818	1.00
4_A	7_R	0.811	1.00
21_L	41_R	0.809	1.00
54_T	57_R	0.805	1.00
29_L	37_R	0.801	1.00
79_L	103_F	0.801	1.00
128_P	133_L	0.800	1.00
89_W	94_H	0.777	1.00
96_V	103_F	0.770	1.00
55_R	59_D	0.769	1.00
56_R	60_R	0.767	1.00
65_A	70_A	0.760	1.00
6_L	39_A	0.746	1.00
69_G	72_A	0.740	1.00
15_R	29_L	0.734	1.00
81_P	100_E	0.731	1.00
89_W	121_T	0.731	1.00
66_A	73_R	0.730	1.00
12_A	16_A	0.729	1.00
67_A	71_R	0.728	1.00
34_L	37_R	0.727	1.00
56_R	59_D	0.727	1.00
68_R	73_R	0.721	1.00
33_L	37_R	0.716	1.00
74_R	78_R	0.714	1.00
66_A	71_R	0.708	1.00
30_S	35_R	0.707	1.00
65_A	71_R	0.706	1.00
44_E	47_Y	0.699	1.00
66_A	72_A	0.696	1.00
15_R	26_P	0.694	1.00
30_S	33_L	0.692	1.00
18_W	24_R	0.692	1.00
84_R	89_W	0.687	1.00
11_L	31_R	0.682	1.00
60_R	64_D	0.676	1.00
114_S	118_R	0.672	1.00
69_G	73_R	0.671	1.00
39_A	43_Q	0.670	1.00
19_R	26_P	0.666	1.00
72_A	76_R	0.663	1.00
65_A	72_A	0.661	1.00
3_I	35_R	0.660	1.00
86_V	97_T	0.658	1.00
43_Q	48_G	0.656	1.00
6_L	14_L	0.654	1.00
68_R	74_R	0.652	1.00
67_A	72_A	0.651	1.00
21_L	42_L	0.630	1.00
124_R	129_R	0.628	1.00
11_L	28_P	0.626	1.00
38_L	41_R	0.626	1.00
110_Y	116_I	0.620	1.00
18_W	27_P	0.619	1.00
5_A	9_L	0.610	1.00
77_R	80_K	0.605	1.00
3_I	7_R	0.601	1.00
50_L	58_L	0.601	1.00
116_I	120_I	0.600	1.00
69_G	75_P	0.596	1.00
10_S	31_R	0.596	1.00
35_R	38_L	0.596	1.00
30_S	129_R	0.589	1.00
75_P	78_R	0.589	1.00
67_A	75_P	0.586	1.00
3_I	9_L	0.581	0.99
15_R	19_R	0.581	0.99
18_W	33_L	0.581	0.99
5_A	8_D	0.576	0.99
96_V	120_I	0.575	0.99
71_R	75_P	0.573	0.99
19_R	23_G	0.572	0.99
61_L	64_D	0.570	0.99
27_P	33_L	0.568	0.99
5_A	13_E	0.566	0.99
51_S	55_R	0.555	0.99
70_A	77_R	0.550	0.99
118_R	129_R	0.549	0.99
60_R	110_Y	0.547	0.99
4_A	8_D	0.543	0.99
65_A	73_R	0.542	0.99
29_L	126_N	0.540	0.99
54_T	60_R	0.539	0.99
71_R	74_R	0.536	0.99
114_S	129_R	0.529	0.99
6_L	38_L	0.528	0.99
67_A	74_R	0.526	0.99
64_D	69_G	0.526	0.99
105_Y	115_A	0.524	0.99
71_R	76_R	0.524	0.99
73_R	76_R	0.524	0.99
35_R	42_L	0.521	0.99
115_A	118_R	0.521	0.99
89_W	92_R	0.520	0.99
102_G	109_T	0.519	0.99
24_R	27_P	0.519	0.99
68_R	72_A	0.519	0.99
20_E	23_G	0.517	0.99
89_W	125_W	0.516	0.99
30_S	37_R	0.512	0.99
125_W	128_P	0.510	0.99
72_A	75_P	0.509	0.99
73_R	77_R	0.507	0.99
26_P	29_L	0.507	0.99
96_V	116_I	0.507	0.99
18_W	21_L	0.504	0.99
48_G	54_T	0.503	0.99
70_A	76_R	0.500	0.98
94_H	116_I	0.500	0.98

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
3gwbA	2	0.8433	15.9	0.934	Contact Map
3hdiA	2	0.8731	14.9	0.935	Contact Map
1t3wA	4	0.5075	13.3	0.936	Contact Map
3plxA	3	0.1866	12.7	0.937	Contact Map
1grjA	1	0.9104	12.6	0.937	Contact Map
3c9pA	1	0.6119	12.2	0.937	Contact Map
2f23A	1	0.9254	9	0.941	Contact Map
1uheB	2	0.1791	8.5	0.942	Contact Map
1vc3A	1	0.1791	8.5	0.942	Contact Map
3bg3A	4	0.8433	7.8	0.943	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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