Yip1 - PFAM28P - GREMLIN Contacts

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Yip1 - Yip1 domain

PFAM:	PF04893	Sequences: VLFSPRETFERIAAEPRVLGLWLLPLLLLALIGAVAGLIGALLIGGSLGGGEQAARLGLGSALGAAIGGYVLALIGVFILALILHLLARLFGGKGSFKQALAVVAYASTPLILAGLLLLLPLLALGGALLLLGLLFGIWSLYLLYIGLPVVHKLSTGKALLAVLLPWVLLIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	172 (166)
Sequences:	27265 (22137)
Seq/√Len:	1718.2
META:	0.889

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_E	150_V	4.330	1.00
4_S	7_E	4.045	1.00
149_P	156_T	3.114	1.00
96_S	99_Q	2.980	1.00
103_V	147_G	2.673	1.00
22_W	25_P	2.620	1.00
142_Y	146_I	2.582	1.00
139_W	143_L	2.243	1.00
95_G	152_H	2.234	1.00
99_Q	102_A	2.176	1.00
155_S	158_K	2.046	1.00
166_P	170_L	2.020	1.00
111_L	140_S	1.976	1.00
145_Y	160_L	1.952	1.00
100_A	152_H	1.933	1.00
25_P	28_L	1.894	1.00
6_R	150_V	1.865	1.00
159_A	163_V	1.851	1.00
103_V	151_V	1.779	1.00
77_V	105_A	1.761	1.00
145_Y	156_T	1.758	1.00
70_Y	74_L	1.753	1.00
81_A	101_L	1.739	1.00
138_I	142_Y	1.681	1.00
23_L	27_L	1.666	1.00
87_L	90_L	1.634	1.00
66_A	70_Y	1.633	1.00
82_L	97_F	1.627	1.00
82_L	85_H	1.593	1.00
24_L	28_L	1.583	1.00
154_L	159_A	1.555	1.00
93_G	154_L	1.516	1.00
95_G	100_A	1.503	1.00
6_R	10_E	1.501	1.00
13_A	153_K	1.487	1.00
107_A	144_L	1.476	1.00
82_L	86_L	1.473	1.00
67_I	70_Y	1.442	1.00
110_P	113_L	1.424	1.00
85_H	89_R	1.418	1.00
114_A	136_F	1.414	1.00
26_L	105_A	1.413	1.00
80_L	84_L	1.410	1.00
145_Y	149_P	1.406	1.00
77_V	101_L	1.400	1.00
21_L	25_P	1.394	1.00
160_L	164_L	1.387	1.00
52_E	56_R	1.382	1.00
97_F	101_L	1.371	1.00
59_L	63_L	1.360	1.00
77_V	81_A	1.316	1.00
100_A	148_L	1.314	1.00
56_R	59_L	1.308	1.00
85_H	97_F	1.305	1.00
101_L	105_A	1.305	1.00
107_A	147_G	1.297	1.00
8_T	12_I	1.297	1.00
110_P	140_S	1.269	1.00
156_T	160_L	1.264	1.00
58_G	62_A	1.221	1.00
45_G	49_G	1.202	1.00
21_L	24_L	1.186	1.00
60_G	64_G	1.186	1.00
86_L	90_L	1.182	1.00
47_S	50_G	1.177	1.00
145_Y	159_A	1.170	1.00
8_T	11_R	1.166	1.00
7_E	10_E	1.158	1.00
85_H	95_G	1.158	1.00
110_P	143_L	1.147	1.00
43_L	46_G	1.146	1.00
85_H	152_H	1.141	1.00
55_A	58_G	1.136	1.00
55_A	59_L	1.131	1.00
47_S	51_G	1.130	1.00
116_L	120_L	1.105	1.00
10_E	13_A	1.101	1.00
166_P	169_L	1.091	1.00
78_F	97_F	1.080	1.00
94_K	153_K	1.079	1.00
158_K	161_L	1.076	1.00
107_A	110_P	1.073	1.00
109_T	112_I	1.068	1.00
11_R	15_E	1.054	1.00
81_A	85_H	1.052	1.00
69_G	73_A	1.050	1.00
59_L	62_A	1.030	1.00
93_G	152_H	1.022	1.00
81_A	100_A	1.003	1.00
53_Q	56_R	0.998	1.00
84_L	148_L	0.993	1.00
99_Q	151_V	0.986	1.00
70_Y	73_A	0.986	1.00
62_A	66_A	0.982	1.00
46_G	50_G	0.977	1.00
6_R	146_I	0.960	1.00
24_L	27_L	0.955	1.00
146_I	150_V	0.954	1.00
98_K	102_A	0.951	1.00
53_Q	57_L	0.951	1.00
78_F	101_L	0.946	1.00
10_E	14_A	0.940	1.00
152_H	162_A	0.931	1.00
88_A	92_G	0.922	1.00
81_A	97_F	0.915	1.00
85_H	100_A	0.913	1.00
160_L	163_V	0.913	1.00
26_L	29_L	0.902	1.00
66_A	69_G	0.894	1.00
9_F	143_L	0.888	1.00
157_G	161_L	0.882	1.00
117_L	120_L	0.869	1.00
87_L	92_G	0.866	1.00
31_L	34_A	0.865	1.00
149_P	159_A	0.859	1.00
21_L	26_L	0.856	1.00
122_L	125_L	0.843	1.00
7_E	11_R	0.841	1.00
26_L	30_A	0.836	1.00
62_A	65_A	0.828	1.00
13_A	99_Q	0.826	1.00
25_P	29_L	0.820	1.00
52_E	55_A	0.806	1.00
27_L	30_A	0.798	1.00
23_L	26_L	0.796	1.00
33_G	37_G	0.790	1.00
35_V	39_I	0.786	1.00
87_L	162_A	0.779	1.00
161_L	165_L	0.775	1.00
56_R	60_G	0.773	1.00
85_H	96_S	0.770	1.00
111_L	115_G	0.769	1.00
83_I	86_L	0.767	1.00
45_G	50_G	0.767	1.00
108_S	111_L	0.762	1.00
22_W	26_L	0.761	1.00
44_I	49_G	0.750	1.00
133_G	136_F	0.750	1.00
42_L	46_G	0.748	1.00
12_I	106_Y	0.744	1.00
36_A	40_G	0.740	1.00
139_W	142_Y	0.739	1.00
44_I	47_S	0.733	1.00
60_G	63_L	0.732	1.00
154_L	158_K	0.727	1.00
114_A	118_L	0.720	1.00
156_T	159_A	0.717	1.00
84_L	104_V	0.716	1.00
104_V	144_L	0.714	1.00
42_L	45_G	0.711	1.00
78_F	81_A	0.709	1.00
43_L	47_S	0.705	1.00
58_G	61_S	0.705	1.00
68_G	72_L	0.701	1.00
109_T	113_L	0.697	1.00
86_L	89_R	0.690	1.00
68_G	71_V	0.687	1.00
46_G	49_G	0.685	1.00
9_F	12_I	0.685	1.00
11_R	14_A	0.683	1.00
146_I	156_T	0.683	1.00
9_F	147_G	0.682	1.00
161_L	164_L	0.674	1.00
134_L	138_I	0.673	1.00
88_A	148_L	0.671	1.00
65_A	69_G	0.663	1.00
21_L	28_L	0.661	1.00
78_F	82_L	0.661	1.00
145_Y	163_V	0.659	1.00
61_S	65_A	0.659	1.00
17_R	98_K	0.658	1.00
103_V	107_A	0.655	1.00
130_L	134_L	0.650	1.00
63_L	67_I	0.650	1.00
100_A	103_V	0.644	1.00
158_K	162_A	0.641	1.00
2_L	109_T	0.640	1.00
89_R	92_G	0.634	1.00
104_V	108_S	0.633	1.00
28_L	32_I	0.631	1.00
60_G	65_A	0.629	1.00
88_A	162_A	0.623	1.00
12_I	102_A	0.621	1.00
149_P	155_S	0.618	1.00
146_I	149_P	0.618	1.00
25_P	33_G	0.617	1.00
28_L	40_G	0.616	1.00
67_I	71_V	0.613	1.00
76_G	80_L	0.612	1.00
28_L	70_Y	0.610	1.00
22_W	40_G	0.610	1.00
57_L	65_A	0.610	1.00
48_L	51_G	0.609	1.00
24_L	38_L	0.609	1.00
57_L	61_S	0.608	1.00
116_L	119_L	0.605	1.00
34_A	38_L	0.605	1.00
32_I	36_A	0.604	1.00
148_L	163_V	0.599	1.00
43_L	50_G	0.595	1.00
45_G	48_L	0.594	1.00
89_R	94_K	0.593	1.00
130_L	133_G	0.592	1.00
9_F	13_A	0.591	1.00
31_L	35_V	0.589	1.00
79_I	82_L	0.586	1.00
87_L	91_F	0.586	1.00
63_L	66_A	0.584	1.00
42_L	51_G	0.581	1.00
56_R	61_S	0.580	1.00
134_L	137_G	0.579	1.00
115_G	118_L	0.573	1.00
17_R	102_A	0.571	1.00
88_A	91_F	0.571	1.00
54_A	59_L	0.570	1.00
84_L	144_L	0.569	1.00
121_P	125_L	0.568	1.00
57_L	62_A	0.568	1.00
131_L	135_L	0.568	1.00
128_A	132_L	0.562	1.00
113_L	117_L	0.561	1.00
2_L	8_T	0.560	1.00
151_V	154_L	0.554	1.00
61_S	64_G	0.551	1.00
54_A	57_L	0.551	1.00
43_L	49_G	0.543	1.00
136_F	140_S	0.539	1.00
121_P	124_A	0.538	1.00
57_L	60_G	0.536	1.00
13_A	151_V	0.532	1.00
119_L	122_L	0.530	1.00
118_L	122_L	0.530	1.00
30_A	34_A	0.524	1.00
140_S	144_L	0.524	1.00
88_A	93_G	0.523	1.00
123_L	126_G	0.522	1.00
23_L	30_A	0.520	1.00
137_G	140_S	0.519	1.00
118_L	121_P	0.518	1.00
89_R	95_G	0.516	1.00
159_A	162_A	0.516	1.00
88_A	152_H	0.515	1.00
22_W	30_A	0.514	1.00
36_A	39_I	0.512	1.00
124_A	127_G	0.510	1.00
75_I	78_F	0.507	1.00
43_L	48_L	0.506	1.00
131_L	134_L	0.501	1.00
167_W	170_L	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
3pjzA	2	0.4535	4.9	0.899	Contact Map
3hi7A	2	0.3372	3.4	0.907	Contact Map
4xp4A	1	0.9186	2.8	0.91	Contact Map
4o6yA	2	0.4651	2.6	0.912	Contact Map
4us3A	1	0.8663	2.1	0.917	Contact Map
3mk7A	1	0.8895	2.1	0.917	Contact Map
2ksfA	1	0.2384	1.8	0.92	Contact Map
4nv5A	1	0.8372	1.4	0.924	Contact Map
3klyA	3	0.8488	1.4	0.924	Contact Map
3kcuA	3	0.8256	1.4	0.924	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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