DUF1326 - PFAM28P - GREMLIN Contacts

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DUF1326 - Protein of unknown function (DUF1326)

PFAM:	PF07040	Sequences: ENCNCDVGCPCQFNAPPTHGYCEAVLAWHIDEGHYGGVDLDGLNVALVADWPGAMHEGNWTVGLYVDERASDEQREALLAIFSGQAGGPFAVLAPLIGEVLGVERAPIEFEVDGDRGRVRIGGVVEAEIEPIRGPVTGEPVRVRNTGHPAGELTVAEAGRGSRVSAFGIDWDLSGRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	177 (172)
Sequences:	13645 (7581)
Seq/√Len:	578.0
META:	0.969

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_R	105_R	4.586	1.00
29_H	44_N	4.092	1.00
61_T	99_E	3.228	1.00
68_E	107_P	3.054	1.00
59_N	98_G	2.993	1.00
24_A	49_A	2.809	1.00
80_A	85_Q	2.759	1.00
109_E	120_R	2.734	1.00
120_R	126_E	2.559	1.00
76_E	80_A	2.519	1.00
61_T	101_L	2.504	1.00
34_H	37_G	2.428	1.00
165_S	170_D	2.424	1.00
35_Y	86_A	2.384	1.00
111_E	118_R	2.277	1.00
27_A	119_V	2.246	1.00
80_A	86_A	2.245	1.00
23_E	50_D	2.239	1.00
45_V	82_F	2.204	1.00
65_Y	106_A	2.073	1.00
148_H	151_G	1.966	1.00
72_D	76_E	1.962	1.00
43_L	70_A	1.828	1.00
43_L	69_R	1.814	1.00
6_D	19_H	1.792	1.00
76_E	79_L	1.789	1.00
43_L	78_L	1.752	1.00
73_E	76_E	1.732	1.00
147_G	155_V	1.719	1.00
46_A	121_I	1.674	1.00
72_D	105_R	1.669	1.00
32_E	41_D	1.659	1.00
21_Y	50_D	1.626	1.00
79_L	103_V	1.605	1.00
35_Y	40_L	1.559	1.00
66_V	105_R	1.503	1.00
75_R	79_L	1.470	1.00
2_N	127_A	1.402	1.00
147_G	150_A	1.401	1.00
27_A	46_A	1.387	1.00
118_R	128_E	1.379	1.00
37_G	73_E	1.341	1.00
34_H	39_D	1.339	1.00
50_D	61_T	1.324	1.00
28_W	45_V	1.320	1.00
44_N	69_R	1.298	1.00
4_N	19_H	1.292	1.00
72_D	75_R	1.284	1.00
136_V	139_E	1.280	1.00
25_V	125_V	1.276	1.00
116_R	130_E	1.272	1.00
141_V	145_N	1.254	1.00
62_V	97_I	1.246	1.00
53_G	57_E	1.244	1.00
104_E	124_V	1.222	1.00
63_G	104_E	1.222	1.00
44_N	108_I	1.166	1.00
35_Y	81_I	1.158	1.00
144_R	147_G	1.151	1.00
91_A	94_A	1.145	1.00
10_P	18_T	1.140	1.00
35_Y	80_A	1.132	1.00
130_E	159_G	1.129	1.00
126_E	160_R	1.116	1.00
134_G	137_T	1.101	1.00
4_N	21_Y	1.099	1.00
66_V	70_A	1.098	1.00
155_V	158_A	1.097	1.00
29_H	110_F	1.094	1.00
92_V	95_P	1.090	1.00
121_I	125_V	1.088	1.00
51_W	60_W	1.073	1.00
16_P	54_A	1.055	1.00
79_L	83_S	1.017	1.00
65_Y	124_V	1.016	1.00
144_R	155_V	1.015	1.00
32_E	39_D	1.004	1.00
17_P	20_G	1.003	1.00
40_L	81_I	1.000	1.00
144_R	152_E	1.000	1.00
64_L	82_F	0.998	1.00
130_E	133_R	0.993	1.00
8_G	13_F	0.983	1.00
71_S	74_Q	0.974	1.00
35_Y	77_A	0.972	1.00
147_G	151_G	0.972	1.00
45_V	78_L	0.967	1.00
113_D	116_R	0.966	1.00
44_N	67_D	0.955	1.00
162_S	165_S	0.952	1.00
81_I	90_F	0.949	1.00
63_G	102_G	0.945	1.00
16_P	57_E	0.941	1.00
142_R	145_N	0.940	1.00
116_R	140_P	0.938	1.00
46_A	108_I	0.930	1.00
7_V	15_A	0.929	1.00
6_D	18_T	0.922	1.00
104_E	166_A	0.921	1.00
163_R	172_D	0.916	1.00
38_V	73_E	0.912	1.00
65_Y	104_E	0.910	1.00
6_D	15_A	0.908	1.00
51_W	96_L	0.900	1.00
64_L	79_L	0.896	1.00
66_V	75_R	0.888	1.00
65_Y	121_I	0.880	1.00
70_A	105_R	0.877	1.00
51_W	55_M	0.872	1.00
164_V	167_F	0.872	1.00
54_A	57_E	0.869	1.00
64_L	100_V	0.867	1.00
66_V	103_V	0.865	1.00
64_L	83_S	0.862	1.00
62_V	100_V	0.859	1.00
145_N	158_A	0.859	1.00
108_I	121_I	0.855	1.00
107_P	122_G	0.855	1.00
141_V	144_R	0.844	1.00
109_E	118_R	0.835	1.00
43_L	67_D	0.835	1.00
70_A	75_R	0.833	1.00
133_R	140_P	0.831	1.00
143_V	146_T	0.822	1.00
8_G	12_Q	0.819	1.00
162_S	173_L	0.819	1.00
142_R	152_E	0.818	1.00
47_L	62_V	0.807	1.00
26_L	47_L	0.805	1.00
137_T	140_P	0.799	1.00
141_V	146_T	0.797	1.00
43_L	71_S	0.792	1.00
47_L	64_L	0.785	1.00
120_R	123_G	0.783	1.00
25_V	48_V	0.778	1.00
112_V	117_G	0.776	1.00
30_I	82_F	0.772	1.00
79_L	85_Q	0.769	1.00
129_I	159_G	0.764	1.00
29_H	112_V	0.762	1.00
100_V	103_V	0.758	1.00
116_R	128_E	0.744	1.00
134_G	138_G	0.742	1.00
154_T	158_A	0.742	1.00
84_G	87_G	0.740	1.00
27_A	110_F	0.737	1.00
79_L	105_R	0.735	1.00
20_G	53_G	0.735	1.00
83_S	100_V	0.734	1.00
36_G	86_A	0.729	1.00
164_V	172_D	0.728	1.00
110_F	119_V	0.723	1.00
29_H	42_G	0.719	1.00
38_V	74_Q	0.715	1.00
163_R	166_A	0.711	1.00
48_V	63_G	0.710	1.00
52_P	58_G	0.706	1.00
68_E	105_R	0.705	1.00
106_A	121_I	0.702	1.00
118_R	126_E	0.700	1.00
164_V	171_W	0.695	1.00
140_P	145_N	0.691	1.00
167_F	171_W	0.688	1.00
115_D	133_R	0.686	1.00
44_N	110_F	0.685	1.00
164_V	169_I	0.683	1.00
97_I	100_V	0.679	1.00
163_R	170_D	0.666	1.00
36_G	80_A	0.656	1.00
38_V	77_A	0.655	1.00
117_G	129_I	0.654	1.00
128_E	159_G	0.652	1.00
5_C	11_C	0.652	1.00
94_A	97_I	0.651	1.00
148_H	153_L	0.650	1.00
8_G	15_A	0.650	1.00
102_G	167_F	0.647	1.00
162_S	166_A	0.647	1.00
143_V	148_H	0.640	1.00
154_T	157_E	0.638	1.00
153_L	157_E	0.628	1.00
165_S	169_I	0.626	1.00
6_D	16_P	0.620	1.00
155_V	159_G	0.619	1.00
78_L	82_F	0.618	1.00
159_G	162_S	0.613	1.00
133_R	139_E	0.613	1.00
7_V	132_I	0.611	1.00
106_A	122_G	0.609	1.00
165_S	171_W	0.608	1.00
133_R	136_V	0.607	1.00
153_L	158_A	0.607	1.00
79_L	100_V	0.607	1.00
91_A	95_P	0.605	1.00
162_S	170_D	0.604	1.00
15_A	18_T	0.603	1.00
132_I	141_V	0.603	1.00
133_R	138_G	0.598	1.00
115_D	140_P	0.596	1.00
7_V	13_F	0.595	1.00
90_F	93_L	0.595	1.00
68_E	106_A	0.589	1.00
92_V	97_I	0.587	1.00
12_Q	24_A	0.583	1.00
115_D	142_R	0.579	1.00
25_V	127_A	0.573	1.00
60_W	98_G	0.570	1.00
7_V	14_N	0.570	1.00
35_Y	38_V	0.568	1.00
119_V	127_A	0.567	0.99
7_V	12_Q	0.565	0.99
88_G	91_A	0.564	0.99
30_I	78_L	0.562	0.99
94_A	98_G	0.560	0.99
140_P	143_V	0.560	0.99
19_H	23_E	0.557	0.99
81_I	86_A	0.557	0.99
42_G	69_R	0.556	0.99
7_V	160_R	0.556	0.99
119_V	125_V	0.553	0.99
87_G	91_A	0.552	0.99
46_A	125_V	0.551	0.99
66_V	79_L	0.551	0.99
48_V	65_Y	0.550	0.99
47_L	90_F	0.549	0.99
122_G	125_V	0.546	0.99
14_N	56_H	0.545	0.99
4_N	23_E	0.544	0.99
30_I	33_G	0.544	0.99
49_A	62_V	0.532	0.99
13_F	18_T	0.530	0.99
63_G	167_F	0.530	0.99
12_Q	15_A	0.527	0.99
95_P	98_G	0.527	0.99
162_S	167_F	0.526	0.99
90_F	95_P	0.524	0.99
136_V	145_N	0.523	0.99
163_R	174_S	0.523	0.99
101_L	104_E	0.522	0.99
17_P	53_G	0.520	0.99
55_M	93_L	0.519	0.99
128_E	160_R	0.517	0.99
63_G	168_G	0.516	0.99
134_G	141_V	0.516	0.99
8_G	14_N	0.516	0.99
61_T	98_G	0.516	0.99
65_Y	166_A	0.516	0.99
25_V	119_V	0.513	0.99
123_G	126_E	0.513	0.99
63_G	124_V	0.512	0.99
63_G	101_L	0.508	0.99
2_N	25_V	0.508	0.99
170_D	173_L	0.506	0.99
162_S	169_I	0.503	0.99
133_R	137_T	0.502	0.99
64_L	103_V	0.501	0.99
24_A	51_W	0.500	0.99
153_L	156_A	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
2eplX	2	0.5254	14	0.943	Contact Map
4ftfA	1	0.5085	13.1	0.944	Contact Map
3b64A	3	0.5932	10.1	0.947	Contact Map
3u52A	2	0.3616	10.1	0.947	Contact Map
1c7kA	1	0.4972	9.2	0.948	Contact Map
2co3A	2	0.3785	7.5	0.95	Contact Map
2incA	2	0.3672	6.6	0.951	Contact Map
2x4kA	4	0.339	5.9	0.952	Contact Map
2db3A	1	0.5198	5.8	0.952	Contact Map
2l61A	1	0.1186	5.7	0.952	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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