YhhN - PFAM28P - GREMLIN Contacts

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YhhN - YhhN-like protein

PFAM:	PF07947	Sequences: WLRYVTKPLLMLLLILLALLAGAGASRYRRLLLAALLFSLLGDVLLMGLPERFFLAGLAAFLLAHLAYIAAFLRRGGLLPLRLLLLLPLLLAAAALLALLWPGLGALRIPVLVYALVISAMAAAALARLLALSATGALLVAAGALLFVLSDSLLALNRFVRPFPLARLLIMLTYYLAQLLIALGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	185 (182)
Sequences:	12434 (9999)
Seq/√Len:	741.2
META:	0.833

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_S	64_A	5.179	1.00
122_A	148_V	4.136	1.00
62_L	117_V	3.611	1.00
68_Y	178_Q	3.258	1.00
153_L	169_L	2.844	1.00
41_L	60_A	2.642	1.00
69_I	124_A	2.372	1.00
45_L	60_A	2.345	1.00
8_P	47_M	2.279	1.00
32_L	71_A	2.253	1.00
8_P	44_V	2.197	1.00
97_L	101_W	2.197	1.00
163_F	166_A	2.115	1.00
126_L	141_A	2.084	1.00
73_L	124_A	2.053	1.00
119_S	148_V	2.011	1.00
92_A	152_S	1.992	1.00
4_Y	47_M	1.950	1.00
38_F	63_L	1.943	1.00
101_W	108_R	1.937	1.00
11_M	14_L	1.917	1.00
63_L	67_A	1.897	1.00
126_L	145_L	1.893	1.00
45_L	56_A	1.888	1.00
121_M	144_A	1.879	1.00
66_L	70_A	1.865	1.00
34_A	67_A	1.771	1.00
140_V	184_G	1.758	1.00
39_S	178_Q	1.754	1.00
46_L	57_G	1.750	1.00
143_G	181_I	1.736	1.00
146_L	176_L	1.709	1.00
12_L	40_L	1.673	1.00
171_M	175_Y	1.659	1.00
69_I	120_A	1.645	1.00
93_A	119_S	1.575	1.00
36_L	182_A	1.570	1.00
10_L	175_Y	1.551	1.00
95_A	99_L	1.498	1.00
31_L	70_A	1.497	1.00
156_L	160_V	1.489	1.00
42_G	60_A	1.452	1.00
38_F	67_A	1.446	1.00
103_G	160_V	1.425	1.00
157_N	166_A	1.415	1.00
58_L	62_L	1.408	1.00
122_A	145_L	1.396	1.00
37_L	41_L	1.385	1.00
101_W	104_L	1.370	1.00
179_L	183_L	1.306	1.00
35_A	68_Y	1.305	1.00
125_A	144_A	1.288	1.00
78_L	82_R	1.284	1.00
154_L	170_I	1.279	1.00
89_L	122_A	1.269	1.00
72_F	121_M	1.256	1.00
15_I	33_L	1.235	1.00
128_R	140_V	1.235	1.00
168_L	172_L	1.213	1.00
40_L	44_V	1.197	1.00
35_A	71_A	1.191	1.00
41_L	45_L	1.187	1.00
11_M	175_Y	1.168	1.00
149_L	173_T	1.163	1.00
170_I	173_T	1.156	1.00
6_T	10_L	1.153	1.00
84_L	88_P	1.148	1.00
31_L	67_A	1.139	1.00
15_I	37_L	1.136	1.00
165_L	168_L	1.125	1.00
52_R	56_A	1.123	1.00
3_R	6_T	1.120	1.00
122_A	144_A	1.112	1.00
128_R	137_A	1.112	1.00
16_L	20_L	1.112	1.00
79_L	83_L	1.102	1.00
19_L	33_L	1.100	1.00
146_L	173_T	1.099	1.00
50_P	53_F	1.086	1.00
176_L	180_L	1.084	1.00
28_Y	184_G	1.084	1.00
65_H	147_F	1.082	1.00
15_I	36_L	1.081	1.00
173_T	177_A	1.069	1.00
54_F	158_R	1.068	1.00
65_H	69_I	1.056	1.00
28_Y	71_A	1.045	1.00
128_R	136_G	1.040	1.00
139_L	183_L	1.027	1.00
88_P	91_L	1.026	1.00
96_L	152_S	1.009	1.00
97_L	115_A	1.006	1.00
28_Y	32_L	0.996	1.00
166_A	170_I	0.992	1.00
58_L	110_P	0.984	1.00
14_L	18_A	0.984	1.00
10_L	13_L	0.970	1.00
92_A	96_L	0.966	1.00
157_N	162_P	0.963	1.00
97_L	112_L	0.963	1.00
15_I	40_L	0.961	1.00
55_L	59_A	0.957	1.00
72_F	140_V	0.944	1.00
39_S	68_Y	0.943	1.00
114_Y	151_D	0.939	1.00
163_F	169_L	0.939	1.00
58_L	111_V	0.939	1.00
143_G	180_L	0.933	1.00
65_H	117_V	0.916	1.00
165_L	169_L	0.915	1.00
30_R	34_A	0.901	1.00
101_W	112_L	0.898	1.00
58_L	155_A	0.880	1.00
109_I	113_V	0.874	1.00
149_L	153_L	0.863	1.00
55_L	107_L	0.862	1.00
143_G	177_A	0.855	1.00
118_I	121_M	0.853	1.00
82_R	86_L	0.851	1.00
38_F	60_A	0.849	1.00
45_L	53_F	0.844	1.00
11_M	178_Q	0.843	1.00
4_Y	8_P	0.839	1.00
55_L	110_P	0.836	1.00
31_L	71_A	0.833	1.00
107_L	110_P	0.832	1.00
118_I	144_A	0.831	1.00
53_F	56_A	0.824	1.00
157_N	170_I	0.816	1.00
150_S	173_T	0.812	1.00
139_L	180_L	0.811	1.00
14_L	182_A	0.810	1.00
32_L	181_I	0.805	1.00
153_L	170_I	0.802	1.00
17_L	183_L	0.799	1.00
62_L	113_V	0.797	1.00
25_A	29_R	0.794	1.00
94_A	98_A	0.789	1.00
138_L	142_A	0.785	1.00
91_L	95_A	0.781	1.00
54_F	58_L	0.771	1.00
99_L	160_V	0.765	1.00
26_S	30_R	0.761	1.00
40_L	175_Y	0.753	1.00
157_N	167_R	0.748	1.00
172_L	175_Y	0.746	1.00
11_M	18_A	0.745	1.00
80_P	83_L	0.743	1.00
93_A	115_A	0.738	1.00
100_L	103_G	0.737	1.00
11_M	40_L	0.736	1.00
14_L	17_L	0.736	1.00
109_I	112_L	0.733	1.00
125_A	140_V	0.731	1.00
77_G	82_R	0.730	1.00
11_M	15_I	0.728	1.00
155_A	159_F	0.728	1.00
59_A	63_L	0.724	1.00
30_R	33_L	0.723	1.00
65_H	177_A	0.722	1.00
10_L	171_M	0.721	1.00
18_A	33_L	0.720	1.00
157_N	163_F	0.718	1.00
70_A	73_L	0.714	1.00
8_P	12_L	0.713	1.00
35_A	67_A	0.711	1.00
115_A	118_I	0.699	1.00
10_L	40_L	0.695	1.00
156_L	166_A	0.694	1.00
56_A	60_A	0.693	1.00
71_A	140_V	0.692	1.00
22_G	25_A	0.691	1.00
167_R	170_I	0.691	1.00
77_G	81_L	0.689	1.00
153_L	172_L	0.689	1.00
49_L	52_R	0.682	1.00
18_A	32_L	0.682	1.00
61_F	174_Y	0.681	1.00
105_G	108_R	0.680	1.00
12_L	16_L	0.680	1.00
83_L	87_L	0.679	1.00
26_S	29_R	0.672	1.00
43_D	46_L	0.671	1.00
169_L	172_L	0.670	1.00
10_L	14_L	0.670	1.00
149_L	154_L	0.669	1.00
145_L	149_L	0.662	1.00
17_L	20_L	0.662	1.00
89_L	92_A	0.661	1.00
86_L	123_A	0.658	1.00
148_V	152_S	0.657	1.00
100_L	104_L	0.656	1.00
156_L	163_F	0.650	1.00
79_L	82_R	0.641	1.00
10_L	18_A	0.639	1.00
172_L	176_L	0.634	1.00
43_D	174_Y	0.632	1.00
85_L	89_L	0.632	1.00
46_L	54_F	0.629	1.00
155_A	158_R	0.629	1.00
144_A	181_I	0.628	1.00
77_G	80_P	0.624	1.00
95_A	98_A	0.624	1.00
129_L	141_A	0.623	1.00
93_A	97_L	0.622	1.00
65_H	151_D	0.622	1.00
76_G	80_P	0.621	1.00
75_R	79_L	0.620	1.00
129_L	138_L	0.617	1.00
69_I	73_L	0.614	1.00
99_L	102_P	0.610	1.00
136_G	140_V	0.607	1.00
156_L	161_R	0.606	1.00
133_S	137_A	0.605	1.00
116_L	120_A	0.602	1.00
120_A	124_A	0.602	1.00
11_M	36_L	0.601	1.00
38_F	41_L	0.600	1.00
153_L	173_T	0.600	1.00
134_A	138_L	0.598	1.00
153_L	163_F	0.597	1.00
15_I	19_L	0.597	1.00
56_A	59_A	0.596	1.00
133_S	136_G	0.596	1.00
177_A	180_L	0.593	1.00
129_L	137_A	0.590	1.00
147_F	151_D	0.588	1.00
38_F	42_G	0.584	1.00
108_R	112_L	0.583	1.00
7_K	14_L	0.580	1.00
49_L	53_F	0.578	1.00
18_A	29_R	0.570	1.00
125_A	141_A	0.568	1.00
33_L	37_L	0.568	1.00
128_R	132_L	0.568	1.00
106_A	110_P	0.567	1.00
96_L	115_A	0.565	1.00
27_R	31_L	0.562	1.00
162_P	166_A	0.562	1.00
89_L	93_A	0.561	1.00
107_L	159_F	0.560	1.00
64_A	68_Y	0.560	1.00
96_L	99_L	0.558	1.00
27_R	30_R	0.551	1.00
42_G	61_F	0.549	1.00
177_A	181_I	0.549	1.00
96_L	100_L	0.548	1.00
7_K	46_L	0.547	1.00
85_L	88_P	0.544	1.00
83_L	86_L	0.537	1.00
92_A	95_A	0.536	1.00
147_F	177_A	0.535	1.00
84_L	87_L	0.533	1.00
98_A	102_P	0.533	1.00
78_L	85_L	0.531	1.00
69_I	117_V	0.527	1.00
99_L	156_L	0.526	1.00
78_L	81_L	0.524	1.00
118_I	122_A	0.524	1.00
18_A	36_L	0.523	1.00
75_R	78_L	0.523	1.00
144_A	177_A	0.522	1.00
153_L	166_A	0.519	1.00
175_Y	179_L	0.518	1.00
134_A	137_A	0.517	1.00
130_L	133_S	0.515	1.00
28_Y	31_L	0.514	1.00
97_L	104_L	0.513	1.00
137_A	141_A	0.511	1.00
74_R	78_L	0.507	1.00
88_P	92_A	0.505	1.00
58_L	159_F	0.505	1.00
124_A	127_A	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
4qtnA	3	0.8649	7.5	0.918	Contact Map
3l1lA	2	0.4486	2.7	0.934	Contact Map
3b5dA	2	0.5297	2.3	0.937	Contact Map
4njnA	4	0.6757	1.4	0.943	Contact Map
3m73A	3	0.5676	1.4	0.943	Contact Map
2i68A	2	0.4216	1.4	0.944	Contact Map
1wazA	1	0.1514	1.4	0.944	Contact Map
4xtrG	1	0.1189	1	0.949	Contact Map
2h3oA	1	0.1568	0.8	0.952	Contact Map
1vkoA	4	0.3027	0.7	0.953	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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