DUF1275 - PFAM28P - GREMLIN Contacts

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DUF1275 - Protein of unknown function (DUF1275)

PFAM:	PF06912	Sequences: LALLLAFVAGFVDAVGFLGLGGVFTAHMTGNVVLLGAALAGGDWLSALASLLALLAFVLGAALGGLLARRLRRRRRLALLLEALLLLAAALLGAAGGAAPLLIALLAFAMGLQNAAVRRLSGADVRTTVLTGTLTDLGIDLARLLRGRPRRLRRRLLLILAFLAGAVLGALLFRHAWALLLPAALLLLLALM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	192 (189)
Sequences:	12880 (9578)
Seq/√Len:	696.7
META:	0.738

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_V	138_G	3.627	1.00
75_R	82_E	3.482	1.00
32_V	163_L	3.046	1.00
3_L	161_A	2.834	1.00
63_L	108_F	2.760	1.00
56_A	104_A	2.628	1.00
113_Q	127_T	2.591	1.00
78_A	82_E	2.588	1.00
114_N	128_T	2.391	1.00
129_V	132_G	2.385	1.00
7_F	168_L	2.212	1.00
62_A	142_A	2.196	1.00
152_L	155_R	2.175	1.00
177_W	180_L	2.092	1.00
32_V	159_I	2.032	1.00
26_A	110_M	1.952	1.00
65_G	143_R	1.927	1.00
28_M	31_N	1.891	1.00
19_G	173_F	1.882	1.00
16_G	25_T	1.868	1.00
62_A	138_G	1.854	1.00
35_L	47_A	1.778	1.00
83_A	190_A	1.777	1.00
79_L	82_E	1.738	1.00
64_G	115_A	1.723	1.00
126_R	129_V	1.684	1.00
38_A	43_D	1.669	1.00
43_D	46_S	1.668	1.00
8_V	186_L	1.638	1.00
60_G	108_F	1.619	1.00
58_V	134_L	1.615	1.00
64_G	112_L	1.606	1.00
32_V	130_L	1.595	1.00
130_L	133_T	1.583	1.00
74_R	82_E	1.559	1.00
56_A	60_G	1.555	1.00
14_A	169_G	1.546	1.00
56_A	107_A	1.545	1.00
83_A	187_L	1.535	1.00
90_A	180_L	1.530	1.00
62_A	145_L	1.502	1.00
65_G	139_I	1.471	1.00
76_R	82_E	1.451	1.00
46_S	49_A	1.418	1.00
11_F	169_G	1.411	1.00
84_L	88_A	1.388	1.00
171_L	175_H	1.384	1.00
150_R	154_R	1.377	1.00
83_A	87_L	1.360	1.00
77_L	82_E	1.319	1.00
15_V	178_A	1.312	1.00
7_F	161_A	1.311	1.00
36_G	166_A	1.301	1.00
11_F	181_L	1.292	1.00
93_G	96_G	1.290	1.00
152_L	156_L	1.281	1.00
89_A	93_G	1.278	1.00
17_F	22_G	1.272	1.00
118_R	136_D	1.235	1.00
114_N	129_V	1.224	1.00
28_M	53_A	1.196	1.00
87_L	183_A	1.188	1.00
134_L	159_I	1.167	1.00
141_L	144_L	1.164	1.00
137_L	156_L	1.163	1.00
76_R	79_L	1.158	1.00
140_D	155_R	1.157	1.00
128_T	132_G	1.154	1.00
84_L	87_L	1.153	1.00
54_L	134_L	1.144	1.00
87_L	91_L	1.138	1.00
6_A	158_L	1.118	1.00
151_R	155_R	1.114	1.00
62_A	141_L	1.112	1.00
137_L	159_I	1.103	1.00
75_R	79_L	1.102	1.00
32_V	134_L	1.094	1.00
72_R	76_R	1.089	1.00
94_A	97_G	1.087	1.00
153_R	157_L	1.085	1.00
56_A	108_F	1.083	1.00
72_R	75_R	1.080	1.00
16_G	106_L	1.080	1.00
74_R	77_L	1.060	1.00
135_T	139_I	1.043	1.00
91_L	95_A	1.036	1.00
52_L	104_A	1.036	1.00
90_A	94_A	1.036	1.00
83_A	86_L	1.030	1.00
177_W	182_P	1.027	1.00
73_R	78_A	1.016	1.00
17_F	24_F	1.005	1.00
82_E	113_Q	1.003	1.00
11_F	15_V	1.000	1.00
25_T	106_L	0.999	1.00
114_N	135_T	0.997	1.00
163_L	167_V	0.996	1.00
24_F	34_L	0.992	1.00
50_S	53_A	0.989	1.00
45_L	49_A	0.980	1.00
17_F	34_L	0.980	1.00
31_N	54_L	0.978	1.00
73_R	76_R	0.965	1.00
184_A	188_L	0.962	1.00
61_A	138_G	0.952	1.00
37_A	170_A	0.949	1.00
78_A	112_L	0.946	1.00
179_L	182_P	0.946	1.00
38_A	47_A	0.939	1.00
85_L	90_A	0.937	1.00
58_V	62_A	0.934	1.00
46_S	50_S	0.934	1.00
120_L	123_A	0.932	1.00
90_A	183_A	0.927	1.00
66_L	142_A	0.920	1.00
141_L	145_L	0.919	1.00
89_A	106_L	0.918	1.00
138_G	142_A	0.917	1.00
133_T	159_I	0.914	1.00
172_L	178_A	0.913	1.00
137_L	152_L	0.909	1.00
92_L	95_A	0.904	1.00
126_R	136_D	0.903	1.00
39_L	47_A	0.900	1.00
27_H	33_V	0.896	1.00
160_L	164_A	0.894	1.00
93_G	97_G	0.891	1.00
4_L	8_V	0.891	1.00
38_A	41_G	0.889	1.00
83_A	93_G	0.889	1.00
73_R	81_L	0.889	1.00
178_A	182_P	0.886	1.00
28_M	134_L	0.883	1.00
88_A	92_L	0.880	1.00
77_L	81_L	0.880	1.00
182_P	185_L	0.879	1.00
11_F	172_L	0.879	1.00
66_L	70_R	0.871	1.00
97_G	100_P	0.866	1.00
8_V	12_V	0.864	1.00
75_R	78_A	0.862	1.00
4_L	185_L	0.860	1.00
35_L	50_S	0.860	1.00
35_L	51_L	0.844	1.00
40_A	170_A	0.840	1.00
61_A	65_G	0.839	1.00
74_R	78_A	0.839	1.00
13_D	33_V	0.838	1.00
14_A	37_A	0.838	1.00
27_H	126_R	0.833	1.00
60_G	64_G	0.830	1.00
36_G	40_A	0.825	1.00
64_G	116_A	0.821	1.00
60_G	111_G	0.818	1.00
28_M	130_L	0.816	1.00
34_L	38_A	0.815	1.00
23_V	103_I	0.812	1.00
78_A	116_A	0.806	1.00
178_A	183_A	0.801	1.00
154_R	157_L	0.799	1.00
36_G	163_L	0.798	1.00
44_W	48_L	0.795	1.00
34_L	50_S	0.794	1.00
150_R	153_R	0.791	1.00
38_A	46_S	0.789	1.00
142_A	145_L	0.776	1.00
176_A	181_L	0.776	1.00
177_W	181_L	0.776	1.00
58_V	137_L	0.774	1.00
37_A	41_G	0.772	1.00
35_L	54_L	0.771	1.00
18_L	37_A	0.768	1.00
8_V	11_F	0.768	1.00
91_L	94_A	0.765	1.00
7_F	165_G	0.757	1.00
130_L	159_I	0.750	1.00
3_L	157_L	0.746	1.00
129_V	135_T	0.743	1.00
60_G	107_A	0.742	1.00
77_L	80_L	0.741	1.00
61_A	115_A	0.732	1.00
96_G	100_P	0.731	1.00
8_V	113_Q	0.728	1.00
35_L	38_A	0.728	1.00
11_F	182_P	0.727	1.00
172_L	181_L	0.727	1.00
83_A	183_A	0.726	1.00
74_R	79_L	0.725	1.00
162_F	166_A	0.725	1.00
137_L	141_L	0.715	1.00
89_A	92_L	0.714	1.00
59_L	108_F	0.714	1.00
168_L	172_L	0.710	1.00
12_V	86_L	0.708	1.00
90_A	93_G	0.707	1.00
27_H	135_T	0.703	1.00
179_L	183_A	0.702	1.00
170_A	174_R	0.701	1.00
34_L	37_A	0.700	1.00
101_L	104_A	0.699	1.00
114_N	126_R	0.698	1.00
11_F	178_A	0.694	1.00
31_N	53_A	0.691	1.00
51_L	55_L	0.688	1.00
178_A	181_L	0.688	1.00
8_V	182_P	0.687	1.00
36_G	167_V	0.686	1.00
179_L	186_L	0.685	1.00
95_A	98_A	0.675	1.00
118_R	139_I	0.674	1.00
35_L	39_L	0.671	1.00
110_M	128_T	0.671	1.00
32_V	54_L	0.662	1.00
52_L	55_L	0.655	1.00
21_G	103_I	0.653	1.00
9_A	27_H	0.652	1.00
118_R	121_S	0.652	1.00
126_R	135_T	0.650	1.00
180_L	183_A	0.645	1.00
94_A	177_W	0.644	1.00
132_G	136_D	0.644	1.00
41_G	174_R	0.639	1.00
164_A	168_L	0.638	1.00
161_A	165_G	0.632	1.00
140_D	144_L	0.630	1.00
93_G	102_L	0.629	1.00
47_A	50_S	0.626	1.00
95_A	100_P	0.625	1.00
45_L	48_L	0.625	1.00
146_R	149_P	0.618	1.00
133_T	155_R	0.616	1.00
48_L	51_L	0.614	1.00
85_L	105_L	0.610	1.00
12_V	109_A	0.609	1.00
87_L	95_A	0.604	1.00
73_R	77_L	0.600	1.00
65_G	69_R	0.600	1.00
67_L	71_L	0.595	1.00
113_Q	186_L	0.589	1.00
126_R	132_G	0.588	1.00
87_L	90_A	0.588	1.00
61_A	135_T	0.586	1.00
120_L	125_V	0.583	1.00
7_F	164_A	0.579	1.00
25_T	113_Q	0.579	1.00
9_A	126_R	0.578	1.00
64_G	129_V	0.578	1.00
28_M	32_V	0.577	1.00
78_A	81_L	0.575	1.00
15_V	169_G	0.572	1.00
4_L	189_L	0.572	1.00
169_G	174_R	0.571	1.00
86_L	106_L	0.569	1.00
2_A	161_A	0.567	1.00
49_A	52_L	0.564	1.00
13_D	26_A	0.559	1.00
176_A	179_L	0.557	1.00
134_L	138_G	0.557	1.00
69_R	146_R	0.555	1.00
164_A	167_V	0.554	1.00
49_A	107_A	0.551	1.00
68_A	115_A	0.545	1.00
23_V	31_N	0.543	1.00
177_W	183_A	0.542	1.00
169_G	172_L	0.541	1.00
171_L	174_R	0.540	1.00
55_L	59_L	0.535	1.00
44_W	47_A	0.533	1.00
6_A	24_F	0.533	1.00
94_A	180_L	0.527	1.00
64_G	68_A	0.526	1.00
34_L	53_A	0.524	1.00
183_A	186_L	0.524	1.00
136_D	140_D	0.523	1.00
12_V	110_M	0.519	1.00
18_L	173_F	0.516	1.00
126_R	133_T	0.515	0.99
27_H	162_F	0.514	0.99
13_D	24_F	0.507	0.99
127_T	135_T	0.507	0.99
66_L	145_L	0.502	0.99
47_A	51_L	0.502	0.99
184_A	187_L	0.501	0.99
35_L	163_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
4pypA	1	0.8958	41.4	0.905	Contact Map
4zw9A	1	0.8958	36.5	0.908	Contact Map
4j05A	3	0.875	33.1	0.91	Contact Map
4ldsA	2	0.8594	32.1	0.91	Contact Map
4gc0A	1	0.8906	19.3	0.919	Contact Map
4tphA	2	0.875	14.9	0.923	Contact Map
3o7qA	1	0.8646	13.9	0.924	Contact Map
1pw4A	1	0.8594	13.5	0.925	Contact Map
2gfpA	2	0.8542	13.1	0.925	Contact Map
4ikvA	1	0.8906	9.9	0.929	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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