Hypoth_Ymh - PFAM28P - GREMLIN Contacts

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Hypoth_Ymh - Protein of unknown function (Hypoth_ymh)

PFAM:	PF09509	Sequences: RNLHPEILKACRALFLDGHYDHAVFEAFKAVEDRVREKSGLTDDGADLMRKAFSPKNPLLALNDLTTESEKSEQEGFMNLFAGAFGAIRNPTAHRPVIDPIDPEEALEILSLASLLLRRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (117)
Sequences:	6214 (4713)
Seq/√Len:	435.7
META:	0.927

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_R	82_A	3.710	1.00
22_H	26_E	3.114	1.00
25_F	29_K	2.590	1.00
35_V	49_M	2.385	1.00
32_E	85_F	2.153	1.00
75_E	79_N	2.076	1.00
108_E	118_R	2.064	1.00
14_L	22_H	1.890	1.00
89_R	93_A	1.886	1.00
50_R	79_N	1.769	1.00
79_N	82_A	1.767	1.00
25_F	93_A	1.762	1.00
34_R	38_K	1.736	1.00
12_R	16_L	1.731	1.00
6_E	9_K	1.728	1.00
68_E	72_S	1.699	1.00
46_A	50_R	1.660	1.00
76_G	86_G	1.651	1.00
28_F	84_A	1.607	1.00
50_R	78_M	1.583	1.00
49_M	85_F	1.559	1.00
31_V	113_A	1.535	1.00
75_E	78_M	1.518	1.00
28_F	113_A	1.502	1.00
33_D	37_E	1.482	1.00
78_M	82_A	1.480	1.00
32_E	44_D	1.477	1.00
46_A	86_G	1.465	1.00
34_R	117_L	1.465	1.00
47_D	50_R	1.464	1.00
63_N	70_E	1.449	1.00
6_E	34_R	1.440	1.00
55_P	75_E	1.438	1.00
41_L	51_K	1.432	1.00
13_A	17_D	1.424	1.00
77_F	87_A	1.420	1.00
31_V	81_F	1.408	1.00
47_D	51_K	1.380	1.00
81_F	116_L	1.373	1.00
14_L	19_H	1.361	1.00
46_A	75_E	1.352	1.00
109_I	115_L	1.338	1.00
33_D	36_R	1.318	1.00
21_D	29_K	1.285	1.00
84_A	112_L	1.277	1.00
41_L	52_A	1.265	1.00
8_L	12_R	1.228	1.00
39_S	52_A	1.221	1.00
43_D	51_K	1.216	1.00
55_P	78_M	1.202	1.00
14_L	26_E	1.193	1.00
34_R	37_E	1.190	1.00
75_E	86_G	1.179	1.00
55_P	71_K	1.126	1.00
6_E	30_A	1.120	1.00
102_D	105_E	1.111	1.00
84_A	113_A	1.108	1.00
67_T	70_E	1.069	1.00
71_K	75_E	1.066	1.00
54_S	74_Q	1.053	1.00
35_V	52_A	1.051	1.00
33_D	96_P	1.033	1.00
54_S	78_M	1.029	1.00
7_I	117_L	1.029	1.00
54_S	57_N	1.027	1.00
19_H	22_H	1.002	1.00
30_A	34_R	1.000	1.00
108_E	111_S	0.979	1.00
33_D	95_R	0.975	1.00
85_F	89_R	0.968	1.00
32_E	36_R	0.965	1.00
30_A	96_P	0.965	1.00
51_K	54_S	0.962	1.00
7_I	11_C	0.962	1.00
80_L	112_L	0.952	1.00
56_K	71_K	0.948	1.00
4_H	114_S	0.936	1.00
8_L	11_C	0.933	1.00
90_N	94_H	0.920	1.00
24_V	106_A	0.905	1.00
88_I	115_L	0.904	1.00
63_N	66_T	0.890	1.00
79_N	86_G	0.886	1.00
64_D	70_E	0.883	1.00
49_M	81_F	0.872	1.00
46_A	82_A	0.871	1.00
61_A	65_L	0.860	1.00
88_I	109_I	0.852	1.00
108_E	114_S	0.845	1.00
26_E	29_K	0.843	1.00
35_V	53_F	0.836	1.00
38_K	60_L	0.835	1.00
105_E	108_E	0.834	1.00
27_A	113_A	0.826	1.00
32_E	45_G	0.799	1.00
13_A	19_H	0.792	1.00
45_G	48_L	0.792	1.00
14_L	17_D	0.780	1.00
67_T	74_Q	0.761	1.00
107_L	111_S	0.751	1.00
68_E	71_K	0.751	1.00
51_K	59_L	0.751	1.00
50_R	75_E	0.747	1.00
30_A	117_L	0.738	1.00
28_F	109_I	0.726	1.00
115_L	119_R	0.724	1.00
62_L	77_F	0.717	1.00
9_K	12_R	0.717	1.00
89_R	94_H	0.715	1.00
66_T	70_E	0.711	1.00
24_V	109_I	0.710	1.00
25_F	92_T	0.707	1.00
112_L	116_L	0.706	1.00
56_K	75_E	0.702	1.00
10_A	19_H	0.696	1.00
111_S	114_S	0.693	1.00
4_H	7_I	0.693	1.00
29_K	96_P	0.692	1.00
81_F	84_A	0.688	1.00
92_T	101_I	0.687	1.00
108_E	115_L	0.686	1.00
75_E	82_A	0.680	1.00
3_L	8_L	0.676	1.00
63_N	73_E	0.674	1.00
13_A	16_L	0.666	1.00
101_I	109_I	0.639	0.99
43_D	47_D	0.637	0.99
11_C	30_A	0.631	0.99
77_F	119_R	0.628	0.99
29_K	93_A	0.612	0.99
67_T	71_K	0.611	0.99
29_K	33_D	0.609	0.99
10_A	26_E	0.607	0.99
22_H	25_F	0.607	0.99
92_T	99_D	0.598	0.99
10_A	30_A	0.596	0.99
20_Y	103_P	0.595	0.99
51_K	57_N	0.593	0.99
62_L	65_L	0.586	0.99
45_G	90_N	0.584	0.99
111_S	115_L	0.580	0.99
104_E	118_R	0.579	0.99
31_V	117_L	0.577	0.99
103_P	107_L	0.577	0.99
88_I	119_R	0.576	0.99
15_F	20_Y	0.568	0.99
46_A	79_N	0.566	0.99
6_E	37_E	0.566	0.99
105_E	109_I	0.557	0.98
36_R	44_D	0.557	0.98
6_E	10_A	0.556	0.98
27_A	110_L	0.553	0.98
23_A	110_L	0.552	0.98
12_R	15_F	0.550	0.98
101_I	106_A	0.548	0.98
21_D	92_T	0.547	0.98
51_K	56_K	0.546	0.98
39_S	59_L	0.539	0.98
69_S	87_A	0.536	0.98
98_I	101_I	0.532	0.98
110_L	114_S	0.529	0.98
21_D	25_F	0.527	0.98
53_F	78_M	0.526	0.98
28_F	85_F	0.525	0.98
69_S	91_P	0.521	0.98
21_D	26_E	0.521	0.98
35_V	39_S	0.520	0.97
72_S	86_G	0.517	0.97
41_L	48_L	0.515	0.97
105_E	118_R	0.514	0.97
92_T	109_I	0.510	0.97
4_H	34_R	0.510	0.97
108_E	112_L	0.507	0.97
112_L	115_L	0.505	0.97
61_A	64_D	0.501	0.97
3_L	110_L	0.500	0.97

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
1wolA	1	0.875	54.1	0.873	Contact Map
2hsbA	2	0.8917	32.5	0.889	Contact Map
1o3uA	2	0.85	32.2	0.889	Contact Map
3pvhA	1	0.3667	28.2	0.892	Contact Map
4i8oA	2	0.9583	26.1	0.894	Contact Map
4oa3A	1	0.4583	25.3	0.895	Contact Map
1ufbA	3	0.9167	17.8	0.902	Contact Map
4uxvA	1	0.375	17	0.902	Contact Map
3o10A	2	0.9083	15.2	0.905	Contact Map
2kw7A	1	0.3833	14.5	0.905	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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