UPF0093 - PFAM28P - GREMLIN Contacts

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UPF0093 - Uncharacterised protein family (UPF0093)

PFAM:	PF03653	Sequences: MANLYLWIKALHIIFVISWFAGLFYLPRLFVYHAEAEDGSEESERFKVMERRLLRGIMTPAMILTWIFGLLLLALNPGLVWLSQGWLHAKLALVLLLSGYHGYCGRLLKDFAADRNTRSHRFYRIFNEVPTLLLIAIVILVVVKPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (143)
Sequences:	17721 (10190)
Seq/√Len:	852.1
META:	0.891

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_W	98_S	4.414	1.00
35_E	120_H	3.183	1.00
106_R	110_D	2.917	1.00
103_Y	107_L	2.744	1.00
54_L	105_G	2.561	1.00
33_H	50_E	2.372	1.00
42_E	45_R	2.271	1.00
22_G	58_M	2.255	1.00
16_V	65_T	2.035	1.00
139_I	143_V	1.941	1.00
88_H	92_A	1.859	1.00
110_D	115_R	1.818	1.00
93_L	136_A	1.808	1.00
51_R	56_G	1.774	1.00
70_L	74_A	1.768	1.00
43_S	47_K	1.752	1.00
100_Y	104_C	1.746	1.00
64_L	68_F	1.732	1.00
118_R	122_F	1.709	1.00
15_F	64_L	1.673	1.00
47_K	114_D	1.664	1.00
6_L	9_K	1.660	1.00
103_Y	126_F	1.648	1.00
108_L	112_A	1.626	1.00
18_S	61_A	1.587	1.00
32_Y	48_V	1.575	1.00
89_A	140_L	1.547	1.00
10_A	139_I	1.518	1.00
107_L	126_F	1.510	1.00
54_L	108_L	1.506	1.00
41_E	44_E	1.496	1.00
98_S	102_G	1.478	1.00
48_V	52_R	1.458	1.00
85_G	89_A	1.458	1.00
86_W	141_V	1.443	1.00
85_G	88_H	1.422	1.00
121_R	125_I	1.419	1.00
133_L	137_I	1.411	1.00
43_S	114_D	1.368	1.00
104_C	126_F	1.368	1.00
36_A	42_E	1.342	1.00
107_L	122_F	1.341	1.00
51_R	112_A	1.340	1.00
14_I	135_I	1.302	1.00
109_K	113_A	1.299	1.00
105_G	108_L	1.276	1.00
8_I	71_L	1.275	1.00
102_G	106_R	1.274	1.00
17_I	134_L	1.272	1.00
107_L	110_D	1.262	1.00
30_F	108_L	1.256	1.00
72_L	76_N	1.230	1.00
62_M	98_S	1.213	1.00
59_T	102_G	1.211	1.00
87_L	91_L	1.208	1.00
13_I	142_V	1.198	1.00
93_L	137_I	1.187	1.00
99_G	102_G	1.180	1.00
36_A	45_R	1.179	1.00
110_D	117_T	1.175	1.00
52_R	56_G	1.157	1.00
93_L	133_L	1.154	1.00
34_A	120_H	1.142	1.00
77_P	80_V	1.138	1.00
111_F	116_N	1.118	1.00
14_I	138_V	1.112	1.00
93_L	140_L	1.107	1.00
122_F	126_F	1.104	1.00
103_Y	122_F	1.095	1.00
59_T	101_H	1.081	1.00
37_E	41_E	1.070	1.00
107_L	123_Y	1.070	1.00
81_W	84_Q	1.066	1.00
39_G	42_E	1.059	1.00
44_E	47_K	1.053	1.00
71_L	75_L	1.048	1.00
74_A	77_P	1.048	1.00
4_L	8_I	1.040	1.00
77_P	81_W	1.038	1.00
63_I	67_I	1.030	1.00
59_T	63_I	1.000	1.00
109_K	112_A	0.995	1.00
66_W	70_L	0.994	1.00
110_D	113_A	0.994	1.00
129_V	133_L	0.977	1.00
7_W	143_V	0.973	1.00
84_Q	88_H	0.966	1.00
36_A	43_S	0.959	1.00
11_L	68_F	0.955	1.00
76_N	79_L	0.945	1.00
51_R	55_R	0.943	1.00
42_E	46_F	0.930	1.00
78_G	81_W	0.927	1.00
99_G	103_Y	0.926	1.00
27_P	104_C	0.890	1.00
73_L	87_L	0.888	1.00
15_F	68_F	0.872	1.00
103_Y	106_R	0.871	1.00
116_N	123_Y	0.863	1.00
54_L	59_T	0.863	1.00
19_W	62_M	0.857	1.00
107_L	118_R	0.853	1.00
136_A	140_L	0.846	1.00
10_A	14_I	0.846	1.00
95_L	99_G	0.840	1.00
10_A	143_V	0.833	1.00
55_R	108_L	0.816	1.00
24_F	131_T	0.806	1.00
79_L	82_L	0.804	1.00
59_T	62_M	0.803	1.00
62_M	102_G	0.801	1.00
72_L	75_L	0.798	1.00
96_L	133_L	0.786	1.00
39_G	44_E	0.786	1.00
31_V	34_A	0.783	1.00
61_A	65_T	0.775	1.00
119_S	122_F	0.772	1.00
41_E	45_R	0.770	1.00
102_G	105_G	0.770	1.00
23_L	58_M	0.765	1.00
26_L	30_F	0.765	1.00
65_T	68_F	0.762	1.00
80_V	84_Q	0.760	1.00
55_R	59_T	0.760	1.00
77_P	82_L	0.756	1.00
37_E	43_S	0.748	1.00
60_P	64_L	0.747	1.00
7_W	139_I	0.744	1.00
36_A	41_E	0.741	1.00
31_V	123_Y	0.739	1.00
37_E	47_K	0.738	1.00
46_F	49_M	0.736	1.00
110_D	116_N	0.735	1.00
59_T	105_G	0.719	1.00
55_R	60_P	0.718	1.00
94_V	98_S	0.717	1.00
38_D	41_E	0.708	1.00
105_G	109_K	0.704	1.00
25_Y	49_M	0.703	1.00
13_I	17_I	0.692	1.00
7_W	11_L	0.690	1.00
100_Y	126_F	0.690	1.00
14_I	134_L	0.689	1.00
34_A	111_F	0.688	1.00
92_A	96_L	0.680	1.00
13_I	16_V	0.674	1.00
125_I	129_V	0.670	1.00
33_H	111_F	0.670	1.00
76_N	80_V	0.669	1.00
110_D	118_R	0.669	1.00
33_H	47_K	0.666	1.00
118_R	123_Y	0.662	1.00
63_I	102_G	0.657	1.00
40_S	43_S	0.652	1.00
83_S	88_H	0.647	1.00
62_M	66_W	0.647	1.00
39_G	43_S	0.644	1.00
8_I	72_L	0.635	1.00
76_N	84_Q	0.630	1.00
47_K	108_L	0.628	1.00
56_G	61_A	0.627	1.00
38_D	42_E	0.626	1.00
132_L	136_A	0.618	1.00
76_N	82_L	0.614	1.00
126_F	129_V	0.614	1.00
20_F	24_F	0.612	1.00
36_A	40_S	0.611	1.00
73_L	77_P	0.611	1.00
4_L	7_W	0.610	1.00
140_L	145_P	0.610	1.00
106_R	109_K	0.608	1.00
7_W	10_A	0.608	1.00
100_Y	129_V	0.605	1.00
57_I	60_P	0.593	1.00
102_G	109_K	0.593	1.00
81_W	87_L	0.593	1.00
96_L	129_V	0.575	1.00
37_E	42_E	0.575	1.00
130_P	134_L	0.575	1.00
71_L	74_A	0.573	1.00
20_F	134_L	0.571	1.00
62_M	65_T	0.570	1.00
120_H	124_R	0.559	1.00
15_F	18_S	0.557	1.00
18_S	131_T	0.555	1.00
14_I	24_F	0.551	1.00
31_V	124_R	0.546	1.00
84_Q	87_L	0.546	1.00
82_L	91_L	0.540	1.00
131_T	135_I	0.538	1.00
80_V	83_S	0.537	1.00
47_K	112_A	0.531	1.00
34_A	116_N	0.531	1.00
82_L	87_L	0.529	1.00
8_I	68_F	0.526	1.00
66_W	95_L	0.526	1.00
77_P	84_Q	0.524	1.00
50_E	111_F	0.523	1.00
76_N	81_W	0.519	1.00
131_T	134_L	0.516	1.00
103_Y	118_R	0.515	1.00
14_I	139_I	0.514	1.00
58_M	101_H	0.514	1.00
141_V	144_K	0.512	1.00
94_V	137_I	0.511	1.00
29_L	50_E	0.509	1.00
4_L	75_L	0.509	1.00
17_I	20_F	0.509	1.00
104_C	107_L	0.508	1.00
18_S	24_F	0.507	1.00
37_E	40_S	0.506	1.00
79_L	84_Q	0.502	1.00
11_L	64_L	0.500	1.00
25_Y	29_L	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
2xq2A	2	0.7877	17.7	0.904	Contact Map
3dh4A	3	0.6575	9.7	0.914	Contact Map
1eysL	1	0.589	4.2	0.928	Contact Map
2wdqD	2	0.6849	3	0.933	Contact Map
2wswA	3	0.7123	3	0.933	Contact Map
4c7rA	3	0.6438	2.8	0.934	Contact Map
2wjnL	1	0.5959	2.2	0.938	Contact Map
4lz6A	1	0.7466	2	0.939	Contact Map
4b4aA	1	0.5753	1.8	0.94	Contact Map
4o6yA	2	0.9178	1.8	0.941	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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