DUF695 - PFAM28P - GREMLIN Contacts

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DUF695 - Family of unknown function (DUF695)

PFAM:	PF05117	Sequences: DDWDVYEAEVDGKPASIRVNLGLREFAPKASYPWLLSVTIKYKGPDENGLPSEEEAELLNEIEDALEAALEKDGGALLVGRITGNGRREFYFYTKDPEEFEKALNEALAKFPGYPIEIGIEEDPEWETYLEFLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (129)
Sequences:	4102 (3432)
Seq/√Len:	302.2
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_T	88_R	3.470	1.00
13_K	85_N	2.661	1.00
52_S	55_E	2.618	1.00
18_R	81_R	2.569	1.00
67_E	92_F	2.513	1.00
34_W	97_P	2.399	1.00
56_A	60_N	2.291	1.00
36_L	94_T	2.285	1.00
78_L	81_R	2.275	1.00
42_Y	51_P	2.175	1.00
39_T	89_E	2.115	1.00
60_N	64_D	2.106	1.00
39_T	87_R	2.078	1.00
34_W	122_E	2.021	1.00
32_Y	77_L	2.018	1.00
76_A	94_T	1.995	1.00
35_L	91_Y	1.940	1.00
23_L	79_V	1.910	1.00
65_A	111_F	1.669	1.00
101_E	105_N	1.652	1.00
35_L	121_E	1.574	1.00
65_A	110_K	1.571	1.00
10_V	15_A	1.560	1.00
43_K	55_E	1.559	1.00
127_E	131_E	1.556	1.00
9_E	12_G	1.536	1.00
37_S	89_E	1.504	1.00
79_V	93_Y	1.485	1.00
55_E	114_Y	1.437	1.00
15_A	82_I	1.431	1.00
37_S	119_G	1.419	1.00
40_I	90_F	1.408	1.00
99_E	103_A	1.387	1.00
44_G	86_G	1.386	1.00
8_A	17_I	1.344	1.00
59_L	88_R	1.323	1.00
40_I	59_L	1.322	1.00
40_I	62_I	1.302	1.00
15_A	84_G	1.292	1.00
58_L	61_E	1.260	1.00
7_E	16_S	1.251	1.00
23_L	77_L	1.238	1.00
33_P	122_E	1.236	1.00
8_A	15_A	1.212	1.00
41_K	115_P	1.210	1.00
44_G	52_S	1.209	1.00
61_E	65_A	1.189	1.00
57_E	61_E	1.179	1.00
42_Y	45_P	1.177	1.00
101_E	118_I	1.162	1.00
67_E	71_E	1.158	1.00
99_E	102_K	1.148	1.00
5_V	18_R	1.143	1.00
46_D	52_S	1.134	1.00
56_A	88_R	1.125	1.00
102_K	106_E	1.109	1.00
29_K	32_Y	1.108	1.00
123_D	128_T	1.105	1.00
26_F	29_K	1.104	1.00
108_L	116_I	1.099	1.00
39_T	119_G	1.086	1.00
27_A	130_L	1.046	1.00
34_W	120_I	1.045	1.00
4_D	19_V	1.042	1.00
35_L	93_Y	1.035	1.00
58_L	114_Y	1.034	1.00
100_F	104_L	1.032	1.00
73_D	103_A	1.030	1.00
105_N	108_L	1.004	1.00
41_K	117_E	1.002	1.00
111_F	114_Y	1.001	1.00
57_E	60_N	0.998	1.00
5_V	16_S	0.996	1.00
24_R	130_L	0.985	1.00
63_E	67_E	0.983	1.00
20_N	24_R	0.982	1.00
4_D	21_L	0.969	1.00
81_R	88_R	0.966	1.00
51_P	83_T	0.957	1.00
23_L	27_A	0.955	1.00
66_L	90_F	0.948	1.00
91_Y	128_T	0.946	1.00
45_P	86_G	0.944	1.00
55_E	58_L	0.943	1.00
10_V	13_K	0.931	1.00
63_E	90_F	0.930	1.00
63_E	81_R	0.921	1.00
97_P	120_I	0.912	1.00
122_E	127_E	0.900	1.00
36_L	100_F	0.899	1.00
42_Y	59_L	0.897	1.00
41_K	87_R	0.897	1.00
40_I	116_I	0.887	1.00
75_G	103_A	0.877	1.00
19_V	80_G	0.849	1.00
98_E	101_E	0.843	1.00
42_Y	50_L	0.841	1.00
78_L	90_F	0.833	1.00
62_I	111_F	0.830	1.00
69_A	106_E	0.828	1.00
37_S	91_Y	0.825	1.00
31_S	95_K	0.824	1.00
6_Y	80_G	0.819	1.00
67_E	78_L	0.810	1.00
63_E	88_R	0.807	1.00
75_G	95_K	0.800	1.00
62_I	66_L	0.792	1.00
44_G	54_E	0.789	0.99
23_L	28_P	0.779	0.99
74_G	77_L	0.771	0.99
4_D	8_A	0.758	0.99
96_D	99_E	0.753	0.99
43_K	47_E	0.746	0.99
105_N	118_I	0.745	0.99
28_P	31_S	0.743	0.99
53_E	57_E	0.735	0.99
69_A	103_A	0.718	0.99
53_E	56_A	0.718	0.99
35_L	128_T	0.714	0.99
38_V	66_L	0.711	0.99
106_E	109_A	0.709	0.99
107_A	111_F	0.707	0.99
109_A	112_P	0.704	0.99
24_R	29_K	0.703	0.99
59_L	90_F	0.693	0.99
39_T	117_E	0.692	0.99
82_I	87_R	0.690	0.99
58_L	62_I	0.687	0.99
16_S	50_L	0.682	0.99
97_P	101_E	0.681	0.99
81_R	90_F	0.676	0.98
4_D	7_E	0.672	0.98
37_S	128_T	0.666	0.98
56_A	81_R	0.665	0.98
34_W	118_I	0.659	0.98
66_L	92_F	0.654	0.98
80_G	91_Y	0.651	0.98
72_K	95_K	0.642	0.98
103_A	106_E	0.641	0.98
94_T	100_F	0.640	0.98
102_K	105_N	0.637	0.98
30_A	33_P	0.635	0.98
38_V	90_F	0.633	0.98
32_Y	94_T	0.621	0.97
60_N	63_E	0.620	0.97
20_N	40_I	0.619	0.97
78_L	92_F	0.617	0.97
36_L	104_L	0.616	0.97
87_R	91_Y	0.616	0.97
126_W	130_L	0.613	0.97
73_D	106_E	0.612	0.97
22_G	80_G	0.611	0.97
82_I	91_Y	0.611	0.97
100_F	103_A	0.599	0.97
26_F	31_S	0.594	0.97
42_Y	55_E	0.591	0.96
6_Y	17_I	0.590	0.96
121_E	128_T	0.587	0.96
6_Y	15_A	0.583	0.96
22_G	28_P	0.582	0.96
58_L	113_G	0.579	0.96
70_L	92_F	0.578	0.96
128_T	131_E	0.574	0.96
104_L	118_I	0.569	0.96
23_L	126_W	0.568	0.96
5_V	12_G	0.565	0.95
92_F	100_F	0.560	0.95
70_L	76_A	0.558	0.95
123_D	126_W	0.555	0.95
18_R	60_N	0.554	0.95
64_D	68_A	0.554	0.95
89_E	119_G	0.554	0.95
20_N	23_L	0.552	0.95
74_G	95_K	0.547	0.95
17_I	21_L	0.534	0.94
104_L	116_I	0.532	0.94
3_W	6_Y	0.530	0.94
38_V	108_L	0.528	0.93
6_Y	19_V	0.526	0.93
69_A	73_D	0.525	0.93
38_V	104_L	0.523	0.93
69_A	107_A	0.521	0.93
45_P	55_E	0.519	0.93
34_W	96_D	0.519	0.93
16_S	56_A	0.517	0.93
122_E	125_E	0.517	0.93
20_N	80_G	0.514	0.93
84_G	87_R	0.512	0.92
23_L	26_F	0.512	0.92
42_Y	52_S	0.510	0.92
110_K	113_G	0.508	0.92
76_A	92_F	0.505	0.92
20_N	81_R	0.504	0.92
6_Y	20_N	0.500	0.91

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
4j37A	1	0.7164	13.3	0.904	Contact Map
1ghhA	1	0.6045	7.9	0.913	Contact Map
3b3jA	1	0.0075	6.6	0.916	Contact Map
3uoaB	2	0.4403	5.8	0.919	Contact Map
1v02A	2	0.291	5.8	0.919	Contact Map
4dweA	1	0.8134	5.4	0.92	Contact Map
3dnxA	2	0.5448	4.7	0.922	Contact Map
1mliA	5	0.6567	4.3	0.923	Contact Map
2pbeA	1	0.5373	4.1	0.924	Contact Map
3kspA	2	0.6119	4.1	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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