DUF3455 - PFAM28P - GREMLIN Contacts

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DUF3455 - Protein of unknown function (DUF3455)

PFAM:	PF11937	Sequences: PAGNEKLFLVGHAVGTQNYVCLPSAAGAAEWTFKAPEATLFDDSCGAGKQPDILTHLPSIALNPPLPAPSALLPPANLNVIGTHFFSPAGPTWQSSDGSKVWGKVVASADAPSDAASVAPGAIPWLLLQAVGHQGGGTLSKVTFIQRVNTVGGVAPAGCDAATVGAEARVPYTADYYFYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	180 (138)
Sequences:	3352 (2125)
Seq/√Len:	180.9
META:	0.854

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
149_N	175_D	3.160	1.00
11_G	81_I	2.820	1.00
21_C	159_C	2.695	1.00
103_G	128_L	2.629	1.00
148_V	177_Y	2.606	1.00
7_L	177_Y	2.602	1.00
106_V	129_Q	2.371	1.00
111_A	114_D	2.099	1.00
101_V	145_I	2.022	1.00
160_D	163_T	1.999	1.00
105_V	108_S	1.995	1.00
130_A	133_H	1.968	1.00
39_T	50_Q	1.956	1.00
112_P	115_A	1.934	1.00
151_V	173_T	1.923	1.00
94_Q	100_K	1.922	1.00
16_T	169_R	1.919	1.00
84_H	91_P	1.911	1.00
4_N	144_F	1.894	1.00
104_K	129_Q	1.893	1.00
10_V	177_Y	1.871	1.00
8_F	142_V	1.829	1.00
85_F	94_Q	1.812	1.00
81_I	84_H	1.797	1.00
121_G	154_V	1.755	1.00
104_K	131_V	1.741	1.00
111_A	115_A	1.717	1.00
37_E	169_R	1.673	1.00
25_A	28_A	1.661	1.00
108_S	124_P	1.638	1.00
20_V	34_K	1.624	1.00
12_H	175_D	1.621	1.00
163_T	166_A	1.568	1.00
105_V	126_L	1.557	1.00
106_V	127_L	1.531	1.00
125_W	148_V	1.530	1.00
129_Q	144_F	1.521	1.00
172_Y	176_Y	1.496	1.00
109_A	114_D	1.468	1.00
95_S	138_T	1.442	1.00
42_D	49_K	1.433	1.00
4_N	143_T	1.391	1.00
22_L	32_T	1.355	1.00
7_L	10_V	1.348	1.00
18_N	35_A	1.341	1.00
110_D	114_D	1.334	1.00
158_G	163_T	1.299	1.00
41_F	50_Q	1.294	1.00
109_A	112_P	1.279	1.00
110_D	113_S	1.276	1.00
125_W	150_T	1.258	1.00
85_F	100_K	1.239	1.00
100_K	134_Q	1.235	1.00
109_A	113_S	1.227	1.00
17_Q	126_L	1.220	1.00
14_V	41_F	1.201	1.00
139_L	142_V	1.160	1.00
34_K	167_E	1.146	1.00
110_D	115_A	1.145	1.00
101_V	130_A	1.140	1.00
109_A	115_A	1.136	1.00
7_L	179_Y	1.123	1.00
88_P	91_P	1.122	1.00
20_V	167_E	1.116	1.00
31_W	161_A	1.095	1.00
11_G	82_G	1.094	1.00
85_F	91_P	1.094	1.00
7_L	148_V	1.088	1.00
82_G	88_P	1.087	1.00
83_T	94_Q	1.079	1.00
81_I	95_S	1.046	1.00
18_N	169_R	1.031	1.00
9_L	81_I	1.030	1.00
14_V	171_P	1.009	0.99
102_W	132_G	0.979	0.99
82_G	85_F	0.972	0.99
17_Q	84_H	0.971	0.99
92_T	100_K	0.968	0.99
1_P	4_N	0.959	0.99
84_H	88_P	0.959	0.99
85_F	88_P	0.954	0.99
94_Q	98_G	0.950	0.99
82_G	95_S	0.950	0.99
37_E	83_T	0.947	0.99
17_Q	128_L	0.929	0.99
133_H	142_V	0.918	0.99
110_D	124_P	0.903	0.99
16_T	37_E	0.897	0.99
95_S	139_L	0.879	0.98
13_A	123_I	0.874	0.98
127_L	144_F	0.872	0.98
98_G	102_W	0.867	0.98
146_Q	177_Y	0.865	0.98
10_V	43_D	0.857	0.98
133_H	140_S	0.843	0.98
122_A	151_V	0.833	0.98
42_D	47_A	0.825	0.98
99_S	102_W	0.820	0.98
82_G	91_P	0.810	0.97
3_G	144_F	0.803	0.97
10_V	175_D	0.782	0.97
154_V	157_A	0.780	0.97
24_S	27_G	0.771	0.96
9_L	138_T	0.770	0.96
28_A	164_V	0.763	0.96
85_F	92_T	0.762	0.96
113_S	121_G	0.745	0.96
108_S	114_D	0.741	0.96
84_H	126_L	0.732	0.95
25_A	29_A	0.724	0.95
24_S	28_A	0.718	0.95
31_W	35_A	0.717	0.95
83_T	91_P	0.714	0.95
18_N	33_F	0.713	0.95
21_C	160_D	0.711	0.94
11_G	177_Y	0.711	0.94
84_H	128_L	0.704	0.94
122_A	125_W	0.703	0.94
83_T	96_S	0.701	0.94
23_P	27_G	0.699	0.94
108_S	112_P	0.696	0.94
103_G	130_A	0.695	0.94
107_A	127_L	0.690	0.94
127_L	146_Q	0.688	0.93
9_L	178_F	0.686	0.93
156_P	168_A	0.686	0.93
11_G	178_F	0.686	0.93
108_S	113_S	0.683	0.93
129_Q	143_T	0.679	0.93
17_Q	172_Y	0.674	0.93
123_I	150_T	0.671	0.93
47_A	50_Q	0.671	0.93
105_V	131_V	0.670	0.93
158_G	166_A	0.670	0.93
99_S	103_G	0.669	0.92
153_G	156_P	0.665	0.92
40_L	82_G	0.665	0.92
161_A	164_V	0.665	0.92
29_A	32_T	0.664	0.92
124_P	154_V	0.656	0.92
130_A	142_V	0.649	0.91
42_D	137_G	0.636	0.90
81_I	88_P	0.634	0.90
10_V	173_T	0.633	0.90
97_D	103_G	0.628	0.90
35_A	169_R	0.621	0.89
43_D	47_A	0.617	0.89
123_I	126_L	0.617	0.89
82_G	90_G	0.615	0.89
148_V	175_D	0.614	0.89
23_P	26_A	0.610	0.89
47_A	138_T	0.610	0.89
85_F	89_A	0.606	0.88
49_K	137_G	0.605	0.88
158_G	168_A	0.602	0.88
6_K	114_D	0.594	0.87
155_A	158_G	0.591	0.87
82_G	139_L	0.589	0.87
114_D	122_A	0.588	0.87
138_T	141_K	0.583	0.86
29_A	164_V	0.583	0.86
17_Q	36_P	0.583	0.86
23_P	28_A	0.582	0.86
95_S	99_S	0.581	0.86
121_G	151_V	0.580	0.86
136_G	140_S	0.579	0.86
162_A	165_G	0.577	0.86
30_E	33_F	0.576	0.86
34_K	135_G	0.575	0.86
22_L	34_K	0.572	0.85
82_G	137_G	0.572	0.85
33_F	36_P	0.571	0.85
98_G	103_G	0.569	0.85
7_L	11_G	0.569	0.85
137_G	140_S	0.565	0.85
26_A	151_V	0.559	0.84
156_P	170_V	0.559	0.84
16_T	39_T	0.555	0.83
29_A	162_A	0.551	0.83
26_A	29_A	0.550	0.83
101_V	105_V	0.548	0.83
22_L	121_G	0.545	0.82
126_L	147_R	0.545	0.82
14_V	173_T	0.545	0.82
42_D	138_T	0.541	0.82
104_K	107_A	0.539	0.82
106_V	144_F	0.539	0.82
97_D	139_L	0.538	0.82
123_I	169_R	0.533	0.81
83_T	89_A	0.532	0.81
146_Q	179_Y	0.523	0.80
144_F	179_Y	0.522	0.80
33_F	152_G	0.522	0.80
22_L	164_V	0.519	0.79
18_N	37_E	0.519	0.79
133_H	136_G	0.517	0.79
17_Q	38_A	0.514	0.79
17_Q	123_I	0.514	0.79
24_S	29_A	0.513	0.78
88_P	92_T	0.510	0.78
42_D	48_G	0.509	0.78
26_A	161_A	0.509	0.78
97_D	102_W	0.508	0.78
128_L	147_R	0.506	0.78
23_P	143_T	0.505	0.77
93_W	156_P	0.502	0.77
81_I	91_P	0.500	0.77

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
2y8tB	1	0.1944	6.9	0.95	Contact Map
4f2fA	1	0.1889	1.6	0.963	Contact Map
2y5pA	3	0.2056	1.6	0.963	Contact Map
2mryA	1	0.1833	1.6	0.963	Contact Map
1ibyA	3	0.2111	1.5	0.964	Contact Map
2ltlA	1	0.4833	1.4	0.965	Contact Map
1cjaA	1	0.5	1.2	0.966	Contact Map
4kunA	2	0.2278	1.2	0.966	Contact Map
2xfgB	1	0.4222	1.1	0.967	Contact Map
2l1tA	1	0.2833	0.9	0.969	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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