DUF563 - PFAM28P - GREMLIN Contacts

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DUF563 - Protein of unknown function (DUF563)

PFAM:	PF04577	Sequences: NNYGHWLLDVLPRLLLLEELGPDPDDPLLVPSSWDLPPFQRESLELLGISPEDRIVVDPDEPVRVERLIVPSPPFPSGGYSPPLLRWLRDRLRERLGPPPPSKPERKIYISRRDAGRRRILNEDELEELLEKYGFEIVDPEDLSFAEQIALFSNAEVIVGPHGAGLTNLLFCPPGTKVIELFPPGYVNPCYWNLASALGLDYYYLVGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	208 (201)
Sequences:	11163 (10000)
Seq/√Len:	705.4
META:	0.796

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
160_G	166_L	3.529	1.00
172_C	176_T	2.693	1.00
177_K	201_D	2.682	1.00
144_S	147_E	2.672	1.00
127_E	137_I	2.556	1.00
106_R	156_E	2.459	1.00
111_S	139_D	2.448	1.00
135_F	157_V	2.418	1.00
129_L	133_Y	2.390	1.00
130_L	159_V	2.291	1.00
140_P	152_F	2.273	1.00
114_D	141_E	2.242	1.00
162_H	180_E	2.238	1.00
106_R	136_E	2.194	1.00
2_N	164_A	2.148	1.00
42_E	146_A	2.139	1.00
157_V	177_K	2.136	1.00
89_R	93_R	2.104	1.00
6_W	43_S	2.074	1.00
155_A	158_I	2.024	1.00
139_D	142_D	1.995	1.00
105_E	156_E	1.983	1.00
107_K	135_F	1.982	1.00
109_Y	123_E	1.959	1.00
43_S	145_F	1.910	1.00
138_V	151_L	1.895	1.00
143_L	151_L	1.857	1.00
107_K	156_E	1.845	1.00
108_I	155_A	1.828	1.00
65_V	68_L	1.826	1.00
3_Y	168_N	1.819	1.00
4_G	167_T	1.776	1.00
150_A	154_N	1.700	1.00
111_S	123_E	1.675	1.00
123_E	127_E	1.668	1.00
7_L	171_F	1.641	1.00
5_H	9_D	1.621	1.00
106_R	154_N	1.614	1.00
145_F	149_I	1.594	1.00
180_E	202_Y	1.591	1.00
192_W	196_S	1.581	1.00
51_P	54_R	1.565	1.00
110_I	165_G	1.562	1.00
157_V	179_I	1.523	1.00
147_E	150_A	1.515	1.00
176_T	200_L	1.510	1.00
68_L	71_P	1.506	1.00
114_D	139_D	1.505	1.00
38_P	42_E	1.494	1.00
122_N	125_E	1.491	1.00
166_L	178_V	1.473	1.00
127_E	131_E	1.467	1.00
110_I	152_F	1.426	1.00
152_F	158_I	1.421	1.00
172_C	200_L	1.410	1.00
138_V	143_L	1.401	1.00
123_E	161_P	1.398	1.00
37_P	40_Q	1.393	1.00
152_F	172_C	1.377	1.00
111_S	137_I	1.364	1.00
107_K	157_V	1.337	1.00
177_K	203_Y	1.335	1.00
114_D	142_D	1.294	1.00
149_I	171_F	1.293	1.00
160_G	165_G	1.287	1.00
42_E	45_E	1.277	1.00
46_L	146_A	1.257	1.00
4_G	164_A	1.253	1.00
195_A	200_L	1.252	1.00
158_I	172_C	1.241	1.00
18_E	91_R	1.233	1.00
4_G	8_L	1.227	1.00
178_V	200_L	1.222	1.00
54_R	58_D	1.219	1.00
146_A	150_A	1.209	1.00
169_L	178_V	1.197	1.00
15_L	19_E	1.182	1.00
195_A	202_Y	1.178	1.00
68_L	72_S	1.176	1.00
113_R	139_D	1.174	1.00
28_L	31_P	1.148	1.00
91_R	95_R	1.139	1.00
143_L	147_E	1.125	1.00
32_S	58_D	1.121	1.00
21_G	24_P	1.099	1.00
135_F	159_V	1.092	1.00
7_L	167_T	1.086	1.00
153_S	173_P	1.085	1.00
129_L	132_K	1.076	1.00
128_E	131_E	1.074	1.00
140_P	143_L	1.074	1.00
27_P	30_V	1.057	1.00
111_S	127_E	1.054	1.00
122_N	126_L	1.046	1.00
186_Y	190_C	1.045	1.00
7_L	145_F	1.042	1.00
120_I	161_P	1.027	1.00
143_L	148_Q	1.025	1.00
109_Y	159_V	1.018	1.00
88_L	91_R	1.017	1.00
131_E	134_G	0.998	1.00
192_W	202_Y	0.997	1.00
63_V	66_E	0.991	1.00
110_I	140_P	0.991	1.00
89_R	92_L	0.982	1.00
15_L	18_E	0.979	1.00
169_L	195_A	0.977	1.00
42_E	144_S	0.970	1.00
86_R	90_D	0.968	1.00
113_R	137_I	0.967	1.00
112_R	163_G	0.958	1.00
85_L	89_R	0.958	1.00
20_L	23_D	0.935	1.00
20_L	24_P	0.923	1.00
90_D	94_E	0.923	1.00
93_R	153_S	0.923	1.00
179_I	205_L	0.922	1.00
36_L	41_R	0.920	1.00
26_D	29_L	0.918	1.00
17_L	20_L	0.917	1.00
182_F	204_Y	0.915	1.00
36_L	40_Q	0.914	1.00
136_E	151_L	0.913	1.00
169_L	172_C	0.911	1.00
8_L	167_T	0.908	1.00
164_A	167_T	0.905	1.00
174_P	199_G	0.903	1.00
148_Q	168_N	0.893	1.00
128_E	132_K	0.887	1.00
109_Y	120_I	0.879	1.00
152_F	168_N	0.876	1.00
32_S	35_D	0.869	1.00
167_T	191_Y	0.869	1.00
126_L	129_L	0.868	1.00
112_R	118_R	0.867	1.00
159_V	179_I	0.866	1.00
69_I	72_S	0.865	1.00
11_L	43_S	0.862	1.00
173_P	176_T	0.859	1.00
145_F	148_Q	0.857	1.00
140_P	165_G	0.850	1.00
76_P	79_G	0.847	1.00
130_L	135_F	0.847	1.00
87_W	91_R	0.847	1.00
166_L	180_E	0.844	1.00
104_P	156_E	0.843	1.00
16_L	20_L	0.833	1.00
82_P	86_R	0.830	1.00
6_W	39_F	0.829	1.00
192_W	204_Y	0.824	1.00
110_I	158_I	0.823	1.00
81_S	84_L	0.820	1.00
152_F	155_A	0.819	1.00
137_I	140_P	0.818	1.00
123_E	137_I	0.801	1.00
109_Y	130_L	0.798	1.00
93_R	97_G	0.798	1.00
8_L	170_L	0.795	1.00
7_L	11_L	0.794	1.00
21_G	25_D	0.794	1.00
173_P	200_L	0.792	1.00
109_Y	127_E	0.792	1.00
79_G	82_P	0.789	1.00
108_I	151_L	0.786	1.00
77_S	80_Y	0.786	1.00
105_E	154_N	0.784	1.00
140_P	148_Q	0.783	1.00
105_E	136_E	0.782	1.00
87_W	90_D	0.780	1.00
91_R	94_E	0.779	1.00
156_E	173_P	0.771	1.00
89_R	198_L	0.770	1.00
80_Y	84_L	0.769	1.00
113_R	127_E	0.769	1.00
83_P	86_R	0.769	1.00
81_S	85_L	0.768	1.00
193_N	197_A	0.763	1.00
8_L	194_L	0.762	1.00
82_P	85_L	0.760	1.00
125_E	128_E	0.748	1.00
158_I	169_L	0.746	1.00
189_P	192_W	0.743	1.00
17_L	21_G	0.740	1.00
22_P	25_D	0.740	1.00
49_I	52_E	0.739	1.00
46_L	95_R	0.738	1.00
148_Q	152_F	0.735	1.00
149_I	153_S	0.723	1.00
169_L	200_L	0.722	1.00
175_G	200_L	0.718	1.00
159_V	181_L	0.714	1.00
131_E	137_I	0.704	1.00
107_K	136_E	0.702	1.00
110_I	160_G	0.699	1.00
182_F	187_V	0.696	1.00
41_R	45_E	0.692	1.00
62_P	65_V	0.690	1.00
182_F	186_Y	0.689	1.00
72_S	75_F	0.679	1.00
53_D	56_V	0.679	1.00
168_N	171_F	0.677	1.00
107_K	133_Y	0.675	1.00
97_G	153_S	0.673	1.00
130_L	134_G	0.671	1.00
124_D	128_E	0.671	1.00
115_A	119_R	0.669	1.00
58_D	61_E	0.667	1.00
105_E	108_I	0.663	1.00
166_L	191_Y	0.662	1.00
187_V	190_C	0.659	1.00
65_V	69_I	0.657	1.00
42_E	46_L	0.647	1.00
113_R	123_E	0.647	1.00
186_Y	189_P	0.646	1.00
126_L	130_L	0.639	1.00
81_S	86_R	0.638	1.00
4_G	190_C	0.637	1.00
194_L	198_L	0.637	1.00
108_I	138_V	0.636	1.00
6_W	40_Q	0.636	1.00
130_L	133_Y	0.635	1.00
127_E	132_K	0.632	1.00
7_L	43_S	0.632	1.00
185_G	188_N	0.631	1.00
27_P	53_D	0.627	1.00
38_P	41_R	0.627	1.00
15_L	21_G	0.623	1.00
88_L	92_L	0.622	1.00
67_R	71_P	0.622	1.00
93_R	96_L	0.619	1.00
157_V	161_P	0.615	1.00
193_N	196_S	0.614	1.00
80_Y	85_L	0.613	1.00
15_L	20_L	0.611	1.00
19_E	87_W	0.610	1.00
124_D	127_E	0.608	1.00
120_I	181_L	0.607	1.00
41_R	52_E	0.601	1.00
92_L	96_L	0.601	1.00
45_E	48_G	0.601	1.00
29_L	65_V	0.600	1.00
106_R	135_F	0.598	1.00
13_R	73_P	0.595	1.00
45_E	146_A	0.594	1.00
59_P	62_P	0.592	1.00
162_H	182_F	0.590	1.00
162_H	191_Y	0.590	1.00
179_I	203_Y	0.590	1.00
18_E	21_G	0.587	1.00
78_G	82_P	0.585	1.00
67_R	72_S	0.585	1.00
102_S	154_N	0.585	1.00
20_L	25_D	0.581	1.00
3_Y	167_T	0.581	1.00
4_G	191_Y	0.580	1.00
112_R	164_A	0.578	1.00
90_D	93_R	0.577	1.00
58_D	63_V	0.571	1.00
162_H	202_Y	0.570	1.00
80_Y	83_P	0.569	1.00
93_R	173_P	0.568	1.00
9_D	13_R	0.568	1.00
31_P	35_D	0.566	1.00
59_P	63_V	0.565	1.00
44_L	49_I	0.558	1.00
85_L	88_L	0.558	1.00
172_C	178_V	0.556	1.00
189_P	193_N	0.556	1.00
191_Y	194_L	0.555	1.00
13_R	71_P	0.555	1.00
76_P	83_P	0.554	1.00
63_V	68_L	0.550	1.00
156_E	177_K	0.549	1.00
150_A	153_S	0.549	1.00
182_F	190_C	0.549	1.00
118_R	164_A	0.547	1.00
32_S	56_V	0.547	1.00
136_E	154_N	0.547	1.00
79_G	84_L	0.547	1.00
151_L	155_A	0.546	1.00
90_D	198_L	0.543	1.00
77_S	81_S	0.540	1.00
27_P	31_P	0.538	1.00
76_P	80_Y	0.538	1.00
45_E	52_E	0.537	1.00
49_I	53_D	0.536	1.00
120_I	126_L	0.536	1.00
88_L	93_R	0.533	1.00
53_D	60_D	0.532	1.00
54_R	57_V	0.531	1.00
63_V	67_R	0.526	1.00
107_K	134_G	0.522	1.00
7_L	12_P	0.522	1.00
191_Y	195_A	0.521	1.00
39_F	42_E	0.519	1.00
45_E	51_P	0.516	1.00
161_P	183_P	0.513	1.00
162_H	165_G	0.513	1.00
183_P	186_Y	0.509	0.99
144_S	148_Q	0.508	0.99
110_I	166_L	0.506	0.99
162_H	166_L	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
4pxyA	4	0.5385	13.9	0.927	Contact Map
4jelA	2	0.5096	10	0.932	Contact Map
4mcjA	3	0.6058	8.9	0.933	Contact Map
4jemA	2	0.5096	7.8	0.935	Contact Map
4ohrA	2	0.5048	6.3	0.938	Contact Map
3sozA	3	0.5	6	0.938	Contact Map
1iugA	2	0.476	5.7	0.939	Contact Map
2g76A	2	0.4567	5.4	0.94	Contact Map
1wwkA	2	0.4519	4.9	0.941	Contact Map
4e5vA	1	0.4952	4.8	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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