DUF21 - PFAM28P - GREMLIN Contacts

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DUF21 - Domain of unknown function DUF21

PFAM:	PF01595	Sequences: WLLLLILLLLLLSAFFSASETALVSLRRSRLEQLAEEGDRGARRALRLLENPDRLLSTILLGNTLANILAGALAEALLARLLGPLTLAVAIATLVITFLILVFGELVPKTLALRNPERIALLVAPPLRLLSRLLYPLVWLLNGSTNLLLRLLGIKPEEEPAVSEEELRALVEEGEEEGVIEEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	184 (181)
Sequences:	72584 (45516)
Seq/√Len:	3383.2
META:	0.864

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_R	132_R	3.785	1.00
139_W	143_G	3.284	1.00
35_A	46_L	2.857	1.00
44_R	128_R	2.812	1.00
115_N	118_R	2.764	1.00
47_R	128_R	2.459	1.00
98_F	144_S	2.318	1.00
122_L	126_P	2.317	1.00
135_Y	139_W	2.261	1.00
143_G	147_L	2.229	1.00
30_R	117_E	2.172	1.00
44_R	125_P	2.095	1.00
46_L	50_E	2.024	1.00
18_A	112_A	2.019	1.00
12_L	66_A	2.009	1.00
51_N	54_R	1.984	1.00
126_P	129_L	1.970	1.00
118_R	122_L	1.953	1.00
34_L	121_L	1.903	1.00
70_A	96_I	1.894	1.00
16_F	62_G	1.888	1.00
19_S	123_V	1.875	1.00
39_D	121_L	1.874	1.00
34_L	39_D	1.853	1.00
32_E	46_L	1.817	1.00
54_R	135_Y	1.804	1.00
147_L	151_L	1.791	1.00
47_R	51_N	1.704	1.00
143_G	146_N	1.667	1.00
33_Q	37_E	1.666	1.00
35_A	43_R	1.664	1.00
132_R	135_Y	1.640	1.00
45_A	120_A	1.640	1.00
54_R	131_S	1.630	1.00
16_F	130_L	1.612	1.00
13_S	67_N	1.607	1.00
15_F	126_P	1.600	1.00
44_R	124_A	1.585	1.00
58_T	131_S	1.554	1.00
45_A	124_A	1.543	1.00
125_P	129_L	1.506	1.00
48_L	124_A	1.489	1.00
74_A	96_I	1.462	1.00
147_L	150_R	1.451	1.00
59_I	127_L	1.443	1.00
15_F	123_V	1.437	1.00
123_V	126_P	1.435	1.00
122_L	125_P	1.421	1.00
131_S	135_Y	1.420	1.00
54_R	139_W	1.363	1.00
40_R	125_P	1.358	1.00
72_A	75_E	1.349	1.00
41_G	121_L	1.345	1.00
42_A	121_L	1.345	1.00
164_E	168_R	1.316	1.00
41_G	125_P	1.310	1.00
78_L	81_L	1.300	1.00
18_A	119_I	1.279	1.00
142_N	146_N	1.278	1.00
32_E	35_A	1.263	1.00
44_R	47_R	1.258	1.00
136_P	140_L	1.250	1.00
86_T	90_A	1.241	1.00
32_E	36_E	1.238	1.00
72_A	76_A	1.237	1.00
21_T	24_V	1.225	1.00
128_R	131_S	1.196	1.00
58_T	130_L	1.189	1.00
54_R	142_N	1.163	1.00
88_A	92_A	1.151	1.00
30_R	33_Q	1.135	1.00
53_D	146_N	1.123	1.00
30_R	34_L	1.122	1.00
43_R	46_L	1.109	1.00
67_N	100_I	1.103	1.00
80_R	83_G	1.098	1.00
48_L	55_L	1.096	1.00
106_L	110_T	1.089	1.00
18_A	123_V	1.065	1.00
9_L	66_A	1.063	1.00
6_I	70_A	1.061	1.00
58_T	138_V	1.058	1.00
118_R	121_L	1.054	1.00
140_L	143_G	1.050	1.00
81_L	84_P	1.049	1.00
68_I	71_G	1.043	1.00
90_A	94_L	1.041	1.00
52_P	55_L	1.034	1.00
5_L	73_L	1.032	1.00
76_A	80_R	1.010	1.00
8_L	12_L	1.009	1.00
149_L	154_I	1.008	1.00
31_L	45_A	1.003	1.00
39_D	42_A	1.000	1.00
133_L	136_P	0.999	1.00
31_L	46_L	0.992	1.00
169_A	173_E	0.983	1.00
3_L	7_L	0.981	1.00
19_S	127_L	0.977	1.00
10_L	104_G	0.976	1.00
129_L	132_R	0.971	1.00
9_L	70_A	0.971	1.00
31_L	49_L	0.964	1.00
174_G	178_G	0.962	1.00
10_L	99_L	0.962	1.00
34_L	117_E	0.958	1.00
53_D	142_N	0.954	1.00
87_L	91_I	0.952	1.00
13_S	63_N	0.945	1.00
75_E	79_A	0.941	1.00
9_L	69_L	0.939	1.00
20_E	109_K	0.938	1.00
112_A	119_I	0.930	1.00
87_L	90_A	0.929	1.00
34_L	37_E	0.929	1.00
43_R	47_R	0.919	1.00
119_I	123_V	0.915	1.00
78_L	82_L	0.914	1.00
28_R	50_E	0.912	1.00
89_V	93_T	0.902	1.00
80_R	84_P	0.881	1.00
26_L	30_R	0.874	1.00
4_L	8_L	0.873	1.00
55_L	131_S	0.866	1.00
104_G	108_P	0.862	1.00
40_R	43_R	0.855	1.00
135_Y	138_V	0.848	1.00
74_A	78_L	0.847	1.00
125_P	128_R	0.845	1.00
78_L	92_A	0.844	1.00
73_L	76_A	0.841	1.00
26_L	117_E	0.838	1.00
26_L	31_L	0.836	1.00
139_W	142_N	0.830	1.00
136_P	139_W	0.829	1.00
45_A	49_L	0.828	1.00
111_L	119_I	0.827	1.00
174_G	179_V	0.826	1.00
140_L	144_S	0.826	1.00
73_L	77_L	0.825	1.00
41_G	44_R	0.817	1.00
146_N	150_R	0.816	1.00
170_L	173_E	0.805	1.00
79_A	83_G	0.804	1.00
14_A	18_A	0.799	1.00
129_L	133_L	0.795	1.00
26_L	45_A	0.789	1.00
47_R	50_E	0.786	1.00
53_D	57_S	0.784	1.00
130_L	134_L	0.783	1.00
175_E	182_E	0.779	1.00
11_L	14_A	0.776	1.00
173_E	177_E	0.767	1.00
5_L	9_L	0.765	1.00
74_A	92_A	0.761	1.00
37_E	42_A	0.761	1.00
82_L	85_L	0.760	1.00
41_G	124_A	0.759	1.00
132_R	136_P	0.757	1.00
68_I	72_A	0.756	1.00
41_G	122_L	0.756	1.00
151_L	155_K	0.754	1.00
26_L	116_P	0.753	1.00
39_D	43_R	0.750	1.00
26_L	120_A	0.746	1.00
162_V	167_L	0.745	1.00
18_A	22_A	0.744	1.00
134_L	138_V	0.743	1.00
51_N	142_N	0.734	1.00
26_L	49_L	0.732	1.00
22_A	119_I	0.729	1.00
6_I	74_A	0.729	1.00
162_V	170_L	0.718	1.00
63_N	67_N	0.715	1.00
149_L	153_G	0.715	1.00
150_R	155_K	0.701	1.00
62_G	134_L	0.700	1.00
4_L	7_L	0.697	1.00
77_L	81_L	0.694	1.00
107_V	148_L	0.693	1.00
78_L	88_A	0.690	1.00
41_G	45_A	0.689	1.00
7_L	11_L	0.689	1.00
77_L	80_R	0.687	1.00
168_R	172_E	0.687	1.00
69_L	93_T	0.686	1.00
22_A	112_A	0.681	1.00
23_L	45_A	0.672	1.00
61_L	64_T	0.669	1.00
94_L	98_F	0.668	1.00
138_V	142_N	0.665	1.00
31_L	42_A	0.662	1.00
27_R	30_R	0.660	1.00
28_R	46_L	0.658	1.00
49_L	52_P	0.652	1.00
65_L	69_L	0.650	1.00
38_G	43_R	0.648	1.00
119_I	122_L	0.644	1.00
83_G	87_L	0.644	1.00
63_N	66_A	0.643	1.00
88_A	91_I	0.638	1.00
28_R	49_L	0.632	1.00
76_A	79_A	0.630	1.00
10_L	14_A	0.628	1.00
15_F	19_S	0.628	1.00
167_L	180_I	0.626	1.00
68_I	93_T	0.625	1.00
10_L	70_A	0.622	1.00
174_G	180_I	0.616	1.00
42_A	46_L	0.613	1.00
5_L	8_L	0.611	1.00
38_G	42_A	0.611	1.00
59_I	63_N	0.609	1.00
83_G	88_A	0.606	1.00
92_A	96_I	0.604	1.00
29_S	33_Q	0.603	1.00
48_L	52_P	0.601	1.00
28_R	32_E	0.599	1.00
95_V	98_F	0.599	1.00
74_A	77_L	0.598	1.00
73_L	78_L	0.598	1.00
58_T	127_L	0.595	1.00
144_S	147_L	0.595	1.00
153_G	156_P	0.593	1.00
30_R	116_P	0.593	1.00
81_L	85_L	0.590	1.00
21_T	112_A	0.589	1.00
161_A	164_E	0.583	1.00
151_L	154_I	0.576	1.00
161_A	177_E	0.576	1.00
110_T	114_R	0.575	1.00
13_S	17_S	0.574	1.00
65_L	97_T	0.569	1.00
68_I	100_I	0.565	1.00
79_A	84_P	0.564	1.00
62_G	130_L	0.562	1.00
59_I	106_L	0.558	1.00
35_A	39_D	0.556	1.00
111_L	115_N	0.553	1.00
34_L	38_G	0.553	1.00
48_L	131_S	0.549	1.00
115_N	122_L	0.548	1.00
117_E	121_L	0.547	1.00
110_T	113_L	0.546	1.00
168_R	171_V	0.542	1.00
110_T	146_N	0.541	1.00
14_A	104_G	0.541	1.00
31_L	35_A	0.539	1.00
23_L	55_L	0.538	1.00
67_N	70_A	0.536	1.00
13_S	100_I	0.533	1.00
23_L	48_L	0.531	1.00
22_A	116_P	0.528	1.00
35_A	42_A	0.528	1.00
48_L	128_R	0.523	1.00
44_R	48_L	0.523	1.00
6_I	77_L	0.521	1.00
82_L	91_I	0.520	1.00
34_L	42_A	0.518	1.00
57_S	142_N	0.517	1.00
69_L	73_L	0.516	1.00
16_F	66_A	0.515	1.00
55_L	59_I	0.514	1.00
63_N	104_G	0.512	1.00
143_G	150_R	0.511	1.00
6_I	96_I	0.510	1.00
67_N	105_E	0.505	1.00
45_A	121_L	0.504	1.00
63_N	100_I	0.501	1.00
171_V	174_G	0.501	1.00
62_G	66_A	0.500	1.00
121_L	125_P	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
4twkA	2	0.7663	34.2	0.892	Contact Map
4wfeA	2	0.7554	29.5	0.895	Contact Map
4h33A	3	0.4891	25.5	0.898	Contact Map
3pjsK	4	0.6685	25	0.899	Contact Map
3vouA	4	0.7337	23.9	0.9	Contact Map
3ukmA	2	0.7337	17.1	0.906	Contact Map
4bw5A	2	0.7772	15.5	0.908	Contact Map
3effK	4	0.7065	11.3	0.914	Contact Map
1rh5A	1	0.5	7.2	0.921	Contact Map
2kvcA	1	0.2772	7.1	0.921	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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