DUF2938 - PFAM28P - GREMLIN Contacts

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DUF2938 - Protein of unknown function (DUF2938)

PFAM:	PF11158	Sequences: VLIGIGATLVMDLWALLLKRLFGIPSLNYALVGRWLGHMPRGRFRHASIAAAPPVRGELALGWIAHYAIGIAFAALLVALAGLDWLRRPTLLPALLFGIATVVAPFFIMQPAMGAGIAASRTPNPAQARLRSLVTHTVFGLGLYLAALLM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	150 (148)
Sequences:	3046 (2114)
Seq/√Len:	173.8
META:	0.838

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_L	65_A	4.017	1.00
37_G	61_L	3.452	1.00
37_G	55_V	3.109	1.00
77_L	97_F	3.102	1.00
6_G	146_A	2.978	1.00
103_V	107_F	2.857	1.00
39_M	44_F	2.762	1.00
48_S	51_A	2.746	1.00
119_A	128_A	2.656	1.00
78_V	86_L	2.606	1.00
38_H	52_A	2.479	1.00
30_A	59_L	2.471	1.00
126_A	129_R	2.439	1.00
124_N	127_Q	2.089	1.00
81_A	97_F	2.058	1.00
122_T	125_P	1.975	1.00
46_H	49_I	1.934	1.00
65_A	69_I	1.893	1.00
48_S	52_A	1.871	1.00
106_F	132_S	1.790	1.00
107_F	118_A	1.756	1.00
99_I	137_T	1.718	1.00
11_M	29_Y	1.713	1.00
11_M	15_A	1.677	1.00
19_K	26_S	1.650	1.00
98_G	102_V	1.586	1.00
39_M	109_M	1.581	1.00
17_L	21_L	1.580	1.00
128_A	132_S	1.569	1.00
11_M	135_T	1.565	1.00
135_T	138_V	1.544	1.00
3_I	86_L	1.543	1.00
7_A	143_L	1.541	1.00
131_R	135_T	1.521	1.00
106_F	129_R	1.499	1.00
107_F	117_I	1.489	1.00
98_G	101_T	1.474	1.00
27_L	73_F	1.471	1.00
10_V	14_W	1.453	1.00
18_L	21_L	1.442	1.00
83_L	86_L	1.435	1.00
18_L	131_R	1.420	1.00
28_N	59_L	1.347	1.00
9_L	13_L	1.328	1.00
8_T	70_G	1.325	1.00
15_A	26_S	1.314	1.00
126_A	130_L	1.310	1.00
41_R	55_V	1.286	1.00
76_L	104_A	1.261	1.00
109_M	113_M	1.243	1.00
74_A	143_L	1.238	1.00
18_L	22_F	1.221	1.00
60_A	64_I	1.219	1.00
115_A	122_T	1.214	1.00
83_L	87_R	1.202	1.00
104_A	109_M	1.202	1.00
64_I	68_A	1.199	1.00
73_F	104_A	1.162	1.00
100_A	103_V	1.136	1.00
11_M	27_L	1.135	1.00
72_A	139_F	1.128	1.00
76_L	97_F	1.102	1.00
14_W	138_V	1.101	1.00
25_P	28_N	1.095	1.00
77_L	93_P	1.083	1.00
45_R	112_A	1.075	1.00
15_A	32_V	1.067	1.00
13_L	17_L	1.066	1.00
81_A	93_P	1.053	1.00
84_D	87_R	1.034	0.99
124_N	131_R	1.017	0.99
73_F	135_T	1.014	0.99
73_F	97_F	1.007	0.99
124_N	128_A	1.002	0.99
102_V	133_L	1.000	0.99
77_L	85_W	0.987	0.99
32_V	68_A	0.979	0.99
37_G	40_P	0.975	0.99
34_R	58_E	0.966	0.99
50_A	115_A	0.944	0.99
49_I	52_A	0.930	0.99
73_F	98_G	0.920	0.99
97_F	100_A	0.912	0.99
38_H	53_P	0.906	0.99
102_V	132_S	0.900	0.98
4_G	8_T	0.897	0.98
18_L	24_I	0.894	0.98
139_F	143_L	0.887	0.98
29_Y	135_T	0.879	0.98
127_Q	131_R	0.872	0.98
36_L	39_M	0.864	0.98
106_F	128_A	0.856	0.98
85_W	93_P	0.850	0.98
5_I	71_I	0.842	0.98
122_T	128_A	0.837	0.98
3_I	78_V	0.827	0.97
82_G	85_W	0.822	0.97
91_L	95_L	0.814	0.97
81_A	96_L	0.807	0.97
78_V	81_A	0.805	0.97
85_W	89_P	0.799	0.97
28_N	48_S	0.791	0.97
71_I	74_A	0.790	0.97
46_H	52_A	0.781	0.96
40_P	43_R	0.780	0.96
36_L	40_P	0.779	0.96
91_L	141_L	0.776	0.96
102_V	106_F	0.775	0.96
38_H	55_V	0.773	0.96
27_L	32_V	0.771	0.96
140_G	145_L	0.771	0.96
20_R	23_G	0.767	0.96
57_G	60_A	0.766	0.96
110_Q	119_A	0.764	0.96
94_A	143_L	0.762	0.96
38_H	46_H	0.749	0.95
69_I	104_A	0.746	0.95
131_R	134_V	0.738	0.95
15_A	27_L	0.736	0.95
47_A	51_A	0.735	0.95
125_P	128_A	0.732	0.95
10_V	145_L	0.723	0.94
97_F	104_A	0.723	0.94
102_V	139_F	0.719	0.94
13_L	16_L	0.718	0.94
75_A	92_L	0.717	0.94
29_Y	73_F	0.711	0.94
105_P	109_M	0.708	0.94
18_L	134_V	0.704	0.94
63_W	73_F	0.704	0.94
41_R	61_L	0.699	0.93
85_W	118_A	0.693	0.93
75_A	86_L	0.691	0.93
48_S	115_A	0.686	0.93
31_L	50_A	0.674	0.92
18_L	138_V	0.670	0.92
27_L	101_T	0.658	0.91
80_L	97_F	0.656	0.91
22_F	25_P	0.653	0.91
10_V	138_V	0.653	0.91
40_P	61_L	0.648	0.90
14_W	18_L	0.647	0.90
31_L	37_G	0.645	0.90
4_G	7_A	0.645	0.90
19_K	27_L	0.644	0.90
125_P	129_R	0.641	0.90
8_T	15_A	0.639	0.90
132_S	135_T	0.635	0.89
113_M	134_V	0.635	0.89
144_Y	148_L	0.632	0.89
56_R	59_L	0.632	0.89
120_S	129_R	0.630	0.89
130_L	134_V	0.624	0.89
118_A	129_R	0.621	0.88
141_L	145_L	0.620	0.88
28_N	31_L	0.620	0.88
41_R	121_R	0.618	0.88
11_M	142_G	0.617	0.88
15_A	134_V	0.617	0.88
99_I	133_L	0.616	0.88
11_M	138_V	0.615	0.88
62_G	89_P	0.615	0.88
19_K	24_I	0.609	0.87
32_V	105_P	0.607	0.87
13_L	56_R	0.605	0.87
145_L	148_L	0.603	0.87
105_P	132_S	0.603	0.87
43_R	47_A	0.601	0.87
7_A	10_V	0.601	0.87
82_G	147_A	0.590	0.86
32_V	73_F	0.586	0.85
119_A	132_S	0.585	0.85
22_F	106_F	0.585	0.85
77_L	147_A	0.583	0.85
104_A	108_I	0.583	0.85
3_I	146_A	0.582	0.85
18_L	135_T	0.576	0.84
19_K	28_N	0.574	0.84
95_L	137_T	0.571	0.84
8_T	67_Y	0.571	0.84
77_L	83_L	0.569	0.84
19_K	22_F	0.569	0.84
143_L	146_A	0.567	0.84
135_T	139_F	0.562	0.83
46_H	110_Q	0.561	0.83
44_F	50_A	0.560	0.83
29_Y	32_V	0.558	0.83
127_Q	134_V	0.558	0.83
15_A	113_M	0.557	0.82
84_D	96_L	0.557	0.82
85_W	147_A	0.555	0.82
71_I	75_A	0.555	0.82
16_L	20_R	0.554	0.82
93_P	147_A	0.554	0.82
3_I	77_L	0.552	0.82
18_L	26_S	0.545	0.81
77_L	81_A	0.545	0.81
77_L	82_G	0.543	0.81
15_A	107_F	0.541	0.81
65_A	106_F	0.540	0.80
91_L	140_G	0.539	0.80
140_G	143_L	0.539	0.80
41_R	96_L	0.534	0.80
24_I	131_R	0.528	0.79
117_I	120_S	0.526	0.79
26_S	117_I	0.522	0.78
134_V	143_L	0.522	0.78
27_L	131_R	0.518	0.78
10_V	72_A	0.514	0.77
15_A	135_T	0.513	0.77
108_I	112_A	0.509	0.76
9_L	14_W	0.509	0.76
138_V	141_L	0.509	0.76
90_T	93_P	0.507	0.76
54_P	83_L	0.506	0.76
35_W	49_I	0.505	0.76
77_L	146_A	0.505	0.76
17_L	22_F	0.504	0.76
113_M	131_R	0.504	0.76
13_L	141_L	0.503	0.76
56_R	60_A	0.503	0.76
37_G	57_G	0.500	0.75

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
2kncB	1	0.2333	1.9	0.96	Contact Map
4o6yA	2	0.9333	1.8	0.961	Contact Map
2iizA	2	0.36	1.6	0.962	Contact Map
2mawA	1	0.6067	1.5	0.963	Contact Map
1my6A	2	0.3267	1.1	0.966	Contact Map
5a63D	1	0.48	1	0.966	Contact Map
2kluA	1	0.1933	1	0.966	Contact Map
4us3A	1	0.9267	1	0.967	Contact Map
1ma1A	4	0.3333	1	0.967	Contact Map
2rcvA	2	0.3267	1	0.967	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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