YVAE - BACSU - GREMLIN Contacts

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YVAE - Uncharacterized membrane protein YvaE

UniProt:	O32227	Sequences: MNWVFLCLAILFEVAGTVSMKLSSGFTKLIPSLLLIFFYGGSLFFLTLTLKSIDVSVAYAVWSGMGIVLITVVGFLFFQEHVSVMKVISIGLIIAGVVSLNLIEHVAVSEPVHKSGQYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (103)
Sequences:	4697 (3238)
Seq/√Len:	319.0

ECOLI - MDTJ SUGE MDTI EMRE
BACSU - YVAE EBRB YVDR YKKC YKKD YVDS EBRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_S	99_S	2.848	1.00
12_F	41_G	2.614	1.00
48_L	51_K	2.544	1.00
75_F	82_V	2.313	1.00
5_F	48_L	2.286	1.00
19_S	34_L	2.259	1.00
2_N	52_S	2.190	1.00
15_A	38_F	2.073	1.00
73_V	77_F	1.975	1.00
10_I	65_M	1.917	1.00
71_T	90_I	1.897	1.00
92_L	96_G	1.702	1.00
50_L	58_A	1.700	1.00
53_I	58_A	1.692	1.00
44_F	48_L	1.606	1.00
16_G	38_F	1.591	1.00
91_G	95_A	1.549	1.00
26_F	32_S	1.500	1.00
39_Y	43_L	1.498	1.00
30_I	34_L	1.495	1.00
84_V	88_I	1.486	1.00
18_V	22_L	1.478	1.00
36_I	40_G	1.455	1.00
50_L	55_V	1.450	1.00
18_V	73_V	1.430	1.00
15_A	34_L	1.422	1.00
92_L	95_A	1.420	1.00
28_K	31_P	1.400	1.00
20_M	35_L	1.396	1.00
16_G	39_Y	1.357	1.00
23_S	32_S	1.353	1.00
5_F	45_F	1.344	1.00
14_V	69_L	1.336	1.00
23_S	26_F	1.333	1.00
49_T	58_A	1.327	1.00
89_S	103_I	1.319	1.00
12_F	38_F	1.316	1.00
22_L	78_F	1.283	1.00
89_S	96_G	1.265	1.00
98_V	102_L	1.252	1.00
93_I	96_G	1.236	1.00
87_V	91_G	1.230	1.00
83_S	86_K	1.216	1.00
85_M	103_I	1.192	1.00
29_L	32_S	1.177	1.00
86_K	100_L	1.174	1.00
93_I	97_V	1.166	1.00
15_A	19_S	1.122	1.00
90_I	100_L	1.118	1.00
67_I	71_T	1.095	1.00
40_G	44_F	1.090	1.00
81_H	86_K	1.075	1.00
46_L	58_A	1.069	1.00
30_I	33_L	1.039	1.00
24_S	28_K	1.037	1.00
82_V	87_V	1.027	1.00
89_S	93_I	1.024	1.00
85_M	88_I	1.022	1.00
74_G	80_E	1.009	1.00
80_E	86_K	0.992	1.00
67_I	94_I	0.974	1.00
3_W	61_V	0.943	1.00
4_V	8_L	0.934	1.00
72_V	76_L	0.930	1.00
19_S	22_L	0.928	1.00
68_V	90_I	0.908	1.00
56_S	60_A	0.897	1.00
21_K	25_G	0.895	1.00
7_C	65_M	0.889	1.00
84_V	87_V	0.886	1.00
82_V	86_K	0.883	1.00
29_L	33_L	0.873	1.00
33_L	37_F	0.865	1.00
8_L	45_F	0.856	1.00
27_T	32_S	0.854	1.00
55_V	70_I	0.854	1.00
24_S	27_T	0.852	1.00
57_V	86_K	0.846	1.00
7_C	10_I	0.845	1.00
73_V	78_F	0.838	1.00
95_A	99_S	0.837	1.00
10_I	42_S	0.826	1.00
60_A	63_S	0.820	1.00
89_S	92_L	0.816	1.00
61_V	65_M	0.813	1.00
19_S	38_F	0.812	1.00
2_N	53_I	0.783	1.00
54_D	57_V	0.763	0.99
14_V	73_V	0.760	0.99
9_A	45_F	0.751	0.99
81_H	84_V	0.745	0.99
27_T	51_K	0.743	0.99
64_G	97_V	0.736	0.99
19_S	35_L	0.735	0.99
85_M	89_S	0.727	0.99
32_S	35_L	0.723	0.99
76_L	79_Q	0.712	0.99
74_G	78_F	0.707	0.99
6_L	49_T	0.706	0.99
17_T	70_I	0.705	0.99
13_E	42_S	0.703	0.99
75_F	87_V	0.699	0.99
2_N	5_F	0.690	0.99
99_S	103_I	0.686	0.99
101_N	104_E	0.684	0.99
94_I	98_V	0.681	0.99
37_F	41_G	0.675	0.99
19_S	23_S	0.671	0.99
27_T	31_P	0.670	0.99
68_V	94_I	0.670	0.99
34_L	38_F	0.668	0.99
20_M	62_W	0.664	0.99
39_Y	63_S	0.663	0.99
26_F	31_P	0.663	0.99
63_S	70_I	0.661	0.98
18_V	78_F	0.658	0.98
11_L	69_L	0.653	0.98
5_F	49_T	0.653	0.98
88_I	92_L	0.649	0.98
18_V	74_G	0.635	0.98
55_V	78_F	0.631	0.98
23_S	27_T	0.624	0.98
80_E	83_S	0.620	0.98
92_L	99_S	0.617	0.98
65_M	69_L	0.607	0.97
39_Y	55_V	0.607	0.97
48_L	52_S	0.600	0.97
17_T	39_Y	0.598	0.97
9_A	46_L	0.579	0.97
64_G	67_I	0.574	0.96
23_S	28_K	0.574	0.96
57_V	60_A	0.573	0.96
33_L	36_I	0.568	0.96
20_M	43_L	0.566	0.96
16_G	35_L	0.561	0.96
60_A	90_I	0.558	0.96
11_L	15_A	0.553	0.96
54_D	104_E	0.551	0.95
63_S	74_G	0.550	0.95
18_V	21_K	0.531	0.94
19_S	36_I	0.530	0.94
60_A	100_L	0.525	0.94
23_S	35_L	0.524	0.94
43_L	50_L	0.523	0.94
10_I	97_V	0.523	0.94
75_F	81_H	0.522	0.94
2_N	49_T	0.516	0.94
74_G	86_K	0.514	0.93
6_L	58_A	0.513	0.93
69_L	73_V	0.509	0.93
26_F	29_L	0.509	0.93
75_F	80_E	0.506	0.93
20_M	42_S	0.501	0.93
18_V	55_V	0.500	0.93

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
3b5dA	2	0.8571	99.9	0.371	Contact Map
2i68A	2	0.6555	99.9	0.388	Contact Map
4ikvA	1	0.916	12.7	0.929	Contact Map
1pw4A	1	0.9832	8.6	0.934	Contact Map
4bgnA	3	0.7395	8.2	0.934	Contact Map
4tphA	2	0.8487	8	0.935	Contact Map
2cfqA	1	0.9664	7.5	0.935	Contact Map
2r9rB	3	0.7059	7.4	0.936	Contact Map
4xnjA	1	0.8908	6.5	0.937	Contact Map
4nv5A	1	0.9496	6.2	0.938	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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