VanZ - PFAM28P - GREMLIN Contacts

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VanZ - VanZ like family

PFAM:	PF04892	Sequences: FWLYLLLWLALIFFPSSQPGSASSETSGFILRLINLIPFATIRDYLIYREFAAFIIRNIAHFVPLGFLLPLLFRRLFKRALLLGFLYSLLDELHQLFVPGRTADVDDVLLNTLGALLGLLLYRLFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (119)
Sequences:	24414 (20387)
Seq/√Len:	1868.9
META:	0.817

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_G	115_A	6.302	1.00
85_F	112_T	3.440	1.00
96_L	103_A	2.927	1.00
93_L	96_L	2.456	1.00
89_L	108_V	2.419	1.00
58_N	61_H	2.096	1.00
85_F	108_V	2.028	1.00
62_F	117_L	1.995	1.00
90_L	94_H	1.892	1.00
9_L	87_Y	1.871	1.00
59_I	63_V	1.810	1.00
81_L	119_L	1.794	1.00
88_S	111_N	1.776	1.00
81_L	112_T	1.695	1.00
103_A	108_V	1.611	1.00
88_S	115_A	1.576	1.00
95_Q	107_D	1.556	1.00
88_S	112_T	1.528	1.00
40_A	43_R	1.520	1.00
37_I	40_A	1.505	1.00
70_P	122_Y	1.502	1.00
17_S	94_H	1.487	1.00
93_L	97_F	1.448	1.00
105_V	109_L	1.439	1.00
41_T	44_D	1.432	1.00
10_A	14_F	1.401	1.00
94_H	98_V	1.377	1.00
11_L	15_P	1.372	1.00
18_Q	26_T	1.362	1.00
67_F	71_L	1.359	1.00
88_S	108_V	1.348	1.00
81_L	116_L	1.331	1.00
61_H	64_P	1.321	1.00
106_D	110_L	1.310	1.00
4_Y	8_W	1.297	1.00
91_D	94_H	1.273	1.00
80_A	84_G	1.244	1.00
51_F	54_F	1.229	1.00
40_A	44_D	1.189	1.00
106_D	109_L	1.188	1.00
109_L	113_L	1.171	1.00
65_L	71_L	1.166	1.00
12_I	91_D	1.149	1.00
113_L	116_L	1.146	1.00
58_N	110_L	1.144	1.00
65_L	69_L	1.144	1.00
57_R	110_L	1.138	1.00
57_R	61_H	1.122	1.00
118_G	122_Y	1.115	1.00
19_P	22_A	1.112	1.00
60_A	64_P	1.112	1.00
58_N	62_F	1.102	1.00
119_L	123_R	1.101	1.00
86_L	90_L	1.100	1.00
42_I	45_Y	1.099	1.00
59_I	110_L	1.079	1.00
13_F	94_H	1.076	1.00
81_L	85_F	1.055	1.00
26_T	29_F	1.048	1.00
84_G	88_S	1.040	1.00
39_F	43_R	1.034	1.00
29_F	32_R	1.027	1.00
8_W	12_I	1.015	1.00
25_E	28_G	1.013	1.00
89_L	93_L	1.003	1.00
91_D	111_N	0.993	1.00
92_E	95_Q	0.984	1.00
38_P	43_R	0.946	1.00
15_P	18_Q	0.942	1.00
28_G	31_L	0.937	1.00
28_G	32_R	0.925	1.00
73_F	76_L	0.916	1.00
67_F	122_Y	0.909	1.00
58_N	111_N	0.908	1.00
69_L	119_L	0.905	1.00
9_L	13_F	0.904	1.00
15_P	101_R	0.886	1.00
93_L	103_A	0.886	1.00
12_I	15_P	0.877	1.00
85_F	89_L	0.872	1.00
107_D	111_N	0.862	1.00
84_G	112_T	0.850	1.00
69_L	73_F	0.850	1.00
8_W	11_L	0.850	1.00
59_I	62_F	0.845	1.00
58_N	64_P	0.844	1.00
39_F	45_Y	0.844	1.00
17_S	20_G	0.839	1.00
37_I	43_R	0.838	1.00
39_F	44_D	0.826	1.00
22_A	26_T	0.825	1.00
70_P	74_R	0.825	1.00
29_F	33_L	0.817	1.00
39_F	42_I	0.815	1.00
87_Y	91_D	0.796	1.00
98_V	101_R	0.795	1.00
14_F	18_Q	0.794	1.00
23_S	27_S	0.782	1.00
37_I	41_T	0.781	1.00
69_L	76_L	0.781	1.00
41_T	45_Y	0.771	1.00
70_P	76_L	0.766	1.00
57_R	60_A	0.762	1.00
16_S	19_P	0.752	1.00
77_F	116_L	0.752	1.00
24_S	28_G	0.752	1.00
116_L	120_L	0.749	1.00
80_A	115_A	0.748	1.00
68_L	72_L	0.748	1.00
21_S	24_S	0.737	1.00
4_Y	7_L	0.733	1.00
90_L	93_L	0.729	1.00
76_L	79_R	0.724	1.00
5_L	9_L	0.721	1.00
7_L	11_L	0.719	1.00
71_L	76_L	0.713	1.00
89_L	105_V	0.712	1.00
70_P	80_A	0.710	1.00
35_N	38_P	0.709	1.00
92_E	107_D	0.702	1.00
70_P	119_L	0.698	1.00
58_N	63_V	0.696	1.00
83_L	87_Y	0.691	1.00
24_S	27_S	0.690	1.00
120_L	123_R	0.690	1.00
115_A	119_L	0.689	1.00
60_A	63_V	0.683	1.00
8_W	15_P	0.681	1.00
82_L	86_L	0.680	1.00
20_G	23_S	0.676	1.00
35_N	40_A	0.664	1.00
59_I	117_L	0.656	1.00
112_T	115_A	0.652	1.00
72_L	76_L	0.650	1.00
5_L	72_L	0.648	1.00
56_I	59_I	0.646	1.00
52_A	55_I	0.644	1.00
6_L	10_A	0.643	1.00
12_I	16_S	0.642	1.00
34_I	38_P	0.641	1.00
18_Q	21_S	0.641	1.00
11_L	14_F	0.634	1.00
87_Y	90_L	0.631	1.00
8_W	68_L	0.630	1.00
65_L	87_Y	0.629	1.00
40_A	45_Y	0.629	1.00
25_E	29_F	0.627	1.00
66_G	118_G	0.620	1.00
71_L	122_Y	0.606	1.00
88_S	103_A	0.603	1.00
95_Q	101_R	0.599	1.00
13_F	87_Y	0.595	1.00
113_L	117_L	0.594	1.00
15_P	19_P	0.592	1.00
18_Q	22_A	0.588	1.00
87_Y	94_H	0.584	1.00
65_L	84_G	0.579	1.00
15_P	64_P	0.576	1.00
77_F	119_L	0.575	1.00
108_V	112_T	0.571	1.00
58_N	103_A	0.571	1.00
38_P	41_T	0.567	1.00
26_T	32_R	0.562	1.00
2_W	5_L	0.559	1.00
89_L	103_A	0.557	1.00
95_Q	102_T	0.549	1.00
27_S	32_R	0.541	1.00
84_G	119_L	0.539	1.00
109_L	112_T	0.530	1.00
13_F	90_L	0.525	1.00
9_L	72_L	0.520	1.00
105_V	108_V	0.513	1.00
21_S	25_E	0.508	1.00
26_T	31_L	0.507	1.00
80_A	88_S	0.506	1.00
22_A	25_E	0.504	1.00
58_N	107_D	0.502	1.00
66_G	70_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
4wd8A	3	0.4127	4.4	0.895	Contact Map
3bo0B	1	0.3968	1	0.926	Contact Map
2kv5A	1	0.1746	0.8	0.93	Contact Map
4b19A	1	0.1667	0.8	0.931	Contact Map
4njnA	4	0.9286	0.8	0.931	Contact Map
2kluA	1	0.2143	0.7	0.932	Contact Map
2nr9A	2	0.9127	0.7	0.933	Contact Map
1iijA	1	0.2222	0.7	0.933	Contact Map
4px7A	1	0.9921	0.7	0.935	Contact Map
2ksfA	1	0.5873	0.6	0.935	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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