DUF177 - PFAM28P - GREMLIN Contacts

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DUF177 - Uncharacterized ACR, COG1399

PFAM:	PF02620	Sequences: VTGRLSATVELECDRCLEPFELPVDVDFDLLFVPGEEEAEEEEEEEDEEDEEVLPYEGDEIDLAELVREELLLALPMKPLCREDCKGEMLCPVCGANLNEEPCDCEEEEIDPRWAALKKLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (114)
Sequences:	48384 (34407)
Seq/√Len:	3222.5
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_T	23_P	2.782	1.00
6_S	25_D	2.767	1.00
14_D	79_P	2.635	1.00
116_A	119_K	2.524	1.00
8_T	21_E	2.495	1.00
3_G	28_F	2.389	1.00
10_E	21_E	2.387	1.00
16_C	85_C	2.372	1.00
2_T	29_D	2.214	1.00
15_R	80_L	2.096	1.00
4_R	27_D	2.022	1.00
10_E	19_P	2.012	1.00
115_A	118_K	1.989	1.00
26_V	74_A	1.978	1.00
96_A	101_E	1.961	1.00
4_R	25_D	1.861	1.00
85_C	91_C	1.848	1.00
16_C	81_C	1.827	1.00
65_E	69_E	1.823	1.00
52_E	56_Y	1.818	1.00
14_D	78_K	1.772	1.00
20_F	79_P	1.742	1.00
32_F	66_L	1.742	1.00
5_L	26_V	1.700	1.00
30_L	70_E	1.674	1.00
11_L	22_L	1.632	1.00
52_E	55_P	1.619	1.00
18_E	81_C	1.566	1.00
7_A	24_V	1.538	1.00
51_E	55_P	1.489	1.00
6_S	23_P	1.476	1.00
86_K	99_N	1.434	1.00
68_R	72_L	1.420	1.00
18_E	97_N	1.374	1.00
11_L	79_P	1.336	1.00
53_V	56_Y	1.328	1.00
11_L	20_F	1.304	1.00
92_P	95_G	1.292	1.00
12_E	19_P	1.288	1.00
91_C	94_C	1.263	1.00
12_E	20_F	1.225	1.00
28_F	70_E	1.203	1.00
62_D	65_E	1.190	1.00
110_I	115_A	1.170	1.00
16_C	91_C	1.169	1.00
111_D	116_A	1.165	1.00
84_D	87_G	1.160	1.00
90_L	94_C	1.135	1.00
51_E	54_L	1.133	1.00
18_E	100_E	1.127	1.00
13_C	16_C	1.123	1.00
32_F	61_I	1.115	1.00
65_E	68_R	1.110	1.00
11_L	75_L	1.095	1.00
26_V	70_E	1.042	1.00
97_N	100_E	1.033	1.00
7_A	71_L	1.022	1.00
22_L	76_P	1.012	1.00
81_C	85_C	1.011	1.00
26_V	30_L	0.996	1.00
99_N	102_P	0.990	1.00
20_F	81_C	0.990	1.00
91_C	95_G	0.972	1.00
94_C	97_N	0.961	1.00
94_C	98_L	0.956	1.00
98_L	101_E	0.952	1.00
110_I	118_K	0.945	1.00
64_A	68_R	0.945	1.00
85_C	90_L	0.940	1.00
93_V	98_L	0.937	1.00
96_A	102_P	0.935	1.00
35_G	38_E	0.919	1.00
110_I	113_R	0.901	1.00
87_G	91_C	0.896	1.00
70_E	74_A	0.886	1.00
9_V	22_L	0.879	1.00
66_L	69_E	0.866	1.00
96_A	99_N	0.865	1.00
112_P	115_A	0.865	1.00
66_L	70_E	0.863	1.00
104_D	107_E	0.847	1.00
50_D	54_L	0.840	1.00
115_A	119_K	0.828	1.00
30_L	66_L	0.806	1.00
106_E	109_E	0.789	1.00
91_C	98_L	0.783	1.00
114_W	117_L	0.779	1.00
91_C	96_A	0.776	1.00
93_V	96_A	0.773	1.00
11_L	76_P	0.768	1.00
70_E	73_L	0.763	1.00
23_P	26_V	0.758	1.00
93_V	105_C	0.752	1.00
2_T	27_D	0.747	1.00
9_V	24_V	0.735	1.00
95_G	98_L	0.727	1.00
92_P	96_A	0.721	1.00
22_L	79_P	0.716	1.00
114_W	118_K	0.710	1.00
56_Y	59_D	0.701	1.00
81_C	84_D	0.699	1.00
15_R	78_K	0.698	1.00
30_L	69_E	0.694	1.00
12_E	17_L	0.691	1.00
49_E	52_E	0.680	1.00
51_E	56_Y	0.678	1.00
3_G	66_L	0.666	1.00
97_N	103_C	0.663	1.00
87_G	90_L	0.661	1.00
9_V	75_L	0.654	1.00
41_E	44_E	0.646	1.00
24_V	74_A	0.644	1.00
92_P	98_L	0.638	1.00
93_V	107_E	0.636	1.00
96_A	100_E	0.636	1.00
90_L	95_G	0.632	1.00
14_D	17_L	0.626	1.00
95_G	99_N	0.622	1.00
93_V	97_N	0.615	1.00
94_C	99_N	0.614	1.00
91_C	97_N	0.605	1.00
18_E	82_R	0.604	1.00
93_V	104_D	0.604	1.00
98_L	102_P	0.600	1.00
101_E	104_D	0.597	1.00
35_G	39_A	0.595	1.00
34_P	56_Y	0.595	1.00
91_C	99_N	0.592	1.00
99_N	103_C	0.592	1.00
111_D	114_W	0.591	1.00
90_L	93_V	0.588	1.00
98_L	103_C	0.587	1.00
13_C	81_C	0.585	1.00
13_C	85_C	0.585	1.00
107_E	110_I	0.582	1.00
42_E	45_E	0.582	1.00
94_C	103_C	0.576	1.00
34_P	38_E	0.575	1.00
92_P	97_N	0.572	1.00
5_L	70_E	0.565	1.00
82_R	86_K	0.560	1.00
100_E	103_C	0.558	1.00
33_V	53_V	0.557	1.00
97_N	101_E	0.548	1.00
50_D	56_Y	0.546	1.00
103_C	107_E	0.545	1.00
38_E	55_P	0.542	1.00
113_R	116_A	0.541	1.00
93_V	106_E	0.540	1.00
38_E	42_E	0.537	1.00
20_F	78_K	0.532	1.00
69_E	73_L	0.531	1.00
114_W	120_L	0.530	1.00
101_E	105_C	0.527	1.00
50_D	55_P	0.527	1.00
28_F	74_A	0.526	1.00
37_E	41_E	0.524	1.00
41_E	45_E	0.524	1.00
81_C	87_G	0.523	1.00
5_L	67_V	0.522	1.00
72_L	75_L	0.517	1.00
94_C	105_C	0.517	1.00
54_L	66_L	0.514	1.00
96_A	104_D	0.514	1.00
65_E	72_L	0.508	1.00
97_N	102_P	0.507	1.00
95_G	103_C	0.505	1.00
22_L	25_D	0.505	1.00
75_L	79_P	0.503	1.00
83_E	86_K	0.501	1.00
90_L	103_C	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
1ee8A	2	0.3388	4.8	0.906	Contact Map
1ornA	1	0.8099	2.7	0.917	Contact Map
3zmsC	1	0	2.4	0.919	Contact Map
3wupA	3	0.2562	2.4	0.919	Contact Map
1i7fA	2	0	2.2	0.921	Contact Map
2i5oA	1	0.2727	2	0.923	Contact Map
2gviA	3	0.3223	1.5	0.927	Contact Map
1wiiA	1	0.3967	1.5	0.928	Contact Map
4odjA	2	0.8017	1.4	0.93	Contact Map
1fv5A	1	0.2975	1.2	0.932	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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