YPHA - BACSU - GREMLIN Contacts

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YPHA - Uncharacterized protein YphA

UniProt:	P50741	Sequences: MEQFYYYWSMWFLWVLTTFIFEKTKRRIAVSVFILTNIILSIHDIALYFSLNAAYLMFFVCGCVYAGYLGMYRFRYIMVYLTLVAAYAFVYLFALYDPVWFIIKPEWAAVILIVLLTASVERNFEKQLVLFVLGMCQGELVYSFVIQKLAGAMAVGGFQWLNACSAGMILLFGISKYEHLASQIGQKSKRSNKGATKMS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	199 (190)
Sequences:	114 (98)
Seq/√Len:	7.1

BACSU - YPHA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_Q	162_N	5.451	1.00
94_A	105_P	4.998	0.99
51_L	74_F	3.397	0.91
14_W	35_L	3.229	0.88
141_V	145_V	2.906	0.82
81_L	84_V	2.826	0.80
96_Y	174_I	2.676	0.76
15_V	88_A	2.582	0.73
11_W	19_F	2.282	0.63
139_E	156_G	2.217	0.61
59_F	63_C	2.184	0.60
87_Y	97_D	2.174	0.59
20_I	164_C	2.140	0.58
31_S	81_L	2.121	0.57
3_Q	6_Y	2.071	0.56
63_C	137_Q	2.025	0.54
6_Y	58_F	1.986	0.52
122_R	139_E	1.978	0.52
38_I	47_L	1.951	0.51
99_V	174_I	1.891	0.49
116_L	129_V	1.882	0.48
100_W	142_Y	1.873	0.48
133_L	184_I	1.818	0.46
31_S	92_L	1.812	0.46
82_T	115_L	1.708	0.42
3_Q	134_G	1.696	0.41
1_M	11_W	1.657	0.40
21_F	58_F	1.635	0.39
93_F	149_L	1.629	0.39
32_V	56_L	1.602	0.38
26_R	161_L	1.576	0.37
82_T	94_A	1.571	0.37
4_F	180_L	1.551	0.36
6_Y	10_M	1.530	0.35
34_I	139_E	1.504	0.34
90_V	109_A	1.502	0.34
5_Y	122_R	1.453	0.32
51_L	66_A	1.451	0.32
13_L	82_T	1.434	0.32
18_T	96_Y	1.433	0.32
122_R	145_V	1.401	0.31
20_I	167_G	1.390	0.30
39_I	166_A	1.382	0.30
115_L	120_V	1.378	0.30
14_W	18_T	1.377	0.30
23_K	35_L	1.370	0.30
59_F	140_L	1.369	0.30
84_V	167_G	1.367	0.30
5_Y	16_L	1.361	0.29
134_G	162_N	1.350	0.29
6_Y	174_I	1.341	0.29
11_W	98_P	1.339	0.29
1_M	19_F	1.325	0.28
70_G	135_M	1.320	0.28
108_A	120_V	1.314	0.28
97_D	104_K	1.286	0.27
86_A	142_Y	1.274	0.27
50_S	78_M	1.269	0.27
45_I	56_L	1.265	0.26
93_F	97_D	1.265	0.26
52_N	133_L	1.264	0.26
17_T	31_S	1.257	0.26
60_V	114_V	1.250	0.26
83_L	169_I	1.249	0.26
15_V	170_L	1.240	0.26
142_Y	146_I	1.236	0.26
10_M	38_I	1.236	0.26
9_S	160_W	1.230	0.25
59_F	139_E	1.227	0.25
2_E	95_L	1.215	0.25
55_Y	96_Y	1.194	0.24
18_T	156_G	1.185	0.24
89_F	128_L	1.179	0.24
135_M	164_C	1.171	0.24
103_I	185_G	1.169	0.24
41_S	161_L	1.149	0.23
18_T	31_S	1.143	0.23
85_A	101_F	1.130	0.23
29_A	123_N	1.121	0.22
18_T	41_S	1.120	0.22
6_Y	162_N	1.119	0.22
7_Y	127_Q	1.107	0.22
96_Y	110_V	1.104	0.22
19_F	98_P	1.098	0.22
54_A	165_S	1.098	0.22
21_F	28_I	1.098	0.22
84_V	91_Y	1.096	0.22
91_Y	151_G	1.087	0.21
101_F	110_V	1.075	0.21
2_E	93_F	1.061	0.21
21_F	112_L	1.047	0.20
55_Y	136_C	1.043	0.20
11_W	14_W	1.042	0.20
66_A	152_A	1.030	0.20
51_L	165_S	1.021	0.20
82_T	90_V	1.020	0.20
93_F	146_I	1.017	0.20
61_C	169_I	1.009	0.19
50_S	159_Q	0.987	0.19
16_L	20_I	0.979	0.19
73_R	83_L	0.978	0.19
35_L	38_I	0.977	0.19
109_A	173_G	0.974	0.19
53_A	158_F	0.974	0.19
66_A	130_L	0.972	0.19
100_W	143_S	0.960	0.18
31_S	166_A	0.959	0.18
84_V	104_K	0.959	0.18
116_L	184_I	0.947	0.18
36_T	44_D	0.946	0.18
12_F	15_V	0.946	0.18
53_A	106_E	0.946	0.18
15_V	20_I	0.933	0.18
88_A	128_L	0.931	0.18
170_L	178_E	0.926	0.18
95_L	142_Y	0.922	0.17
12_F	180_L	0.915	0.17
155_V	160_W	0.902	0.17
118_A	127_Q	0.897	0.17
24_T	55_Y	0.893	0.17
162_N	166_A	0.889	0.17
16_L	93_F	0.889	0.17
107_W	110_V	0.881	0.17
17_T	45_I	0.879	0.16
58_F	119_S	0.877	0.16
117_T	149_L	0.871	0.16
28_I	136_C	0.866	0.16
82_T	184_I	0.863	0.16
113_I	164_C	0.861	0.16
103_I	189_K	0.857	0.16
86_A	106_E	0.853	0.16
56_L	78_M	0.852	0.16
8_W	102_I	0.849	0.16
70_G	171_L	0.846	0.16
73_R	107_W	0.846	0.16
137_Q	165_S	0.843	0.16
108_A	119_S	0.838	0.16
81_L	92_L	0.837	0.16
64_V	74_F	0.829	0.15
55_Y	69_L	0.829	0.15
161_L	173_G	0.828	0.15
83_L	133_L	0.826	0.15
53_A	60_V	0.816	0.15
69_L	84_V	0.815	0.15
45_I	115_L	0.812	0.15
54_A	119_S	0.810	0.15
50_S	70_G	0.808	0.15
42_I	100_W	0.802	0.15
31_S	77_I	0.791	0.15
90_V	97_D	0.791	0.15
45_I	127_Q	0.790	0.15
110_V	159_Q	0.776	0.14
8_W	80_Y	0.775	0.14
110_V	174_I	0.771	0.14
101_F	107_W	0.766	0.14
53_A	135_M	0.765	0.14
27_R	98_P	0.759	0.14
45_I	112_L	0.759	0.14
8_W	24_T	0.758	0.14
89_F	99_V	0.758	0.14
29_A	118_A	0.758	0.14
86_A	90_V	0.753	0.14
45_I	128_L	0.752	0.14
37_N	176_K	0.752	0.14
160_W	166_A	0.749	0.14
96_Y	156_G	0.739	0.14
131_F	157_G	0.737	0.14
119_S	131_F	0.734	0.14
7_Y	41_S	0.733	0.14
30_V	59_F	0.730	0.14
93_F	173_G	0.729	0.14
86_A	97_D	0.726	0.13
86_A	92_L	0.723	0.13
36_T	112_L	0.720	0.13
125_E	181_A	0.719	0.13
158_F	171_L	0.713	0.13
30_V	96_Y	0.711	0.13
31_S	102_I	0.707	0.13
61_C	126_K	0.698	0.13
104_K	136_C	0.698	0.13
61_C	144_F	0.697	0.13
96_Y	178_E	0.694	0.13
27_R	138_G	0.690	0.13
51_L	174_I	0.687	0.13
7_Y	55_Y	0.685	0.13
160_W	185_G	0.684	0.13
2_E	5_Y	0.679	0.13
7_Y	171_L	0.673	0.13
45_I	78_M	0.671	0.13
1_M	98_P	0.670	0.12
66_A	113_I	0.662	0.12
72_Y	169_I	0.661	0.12
4_F	10_M	0.660	0.12
104_K	149_L	0.656	0.12
68_Y	84_V	0.656	0.12
20_I	110_V	0.655	0.12
107_W	140_L	0.654	0.12
98_P	138_G	0.650	0.12
7_Y	11_W	0.643	0.12
58_F	165_S	0.636	0.12
127_Q	165_S	0.635	0.12
117_T	120_V	0.635	0.12
83_L	89_F	0.630	0.12
53_A	161_L	0.629	0.12
23_K	37_N	0.628	0.12
121_E	161_L	0.621	0.12
2_E	128_L	0.620	0.12
20_I	90_V	0.620	0.12
1_M	92_L	0.619	0.12
14_W	19_F	0.619	0.12
34_I	115_L	0.615	0.12
167_G	172_F	0.610	0.12
118_A	185_G	0.608	0.11
13_L	36_T	0.606	0.11
158_F	161_L	0.602	0.11
6_Y	112_L	0.602	0.11
78_M	122_R	0.600	0.11
90_V	108_A	0.598	0.11
149_L	155_V	0.598	0.11
153_M	183_Q	0.596	0.11
37_N	54_A	0.595	0.11
70_G	77_I	0.593	0.11
48_Y	112_L	0.592	0.11
8_W	11_W	0.592	0.11
101_F	130_L	0.592	0.11
95_L	146_I	0.590	0.11
28_I	96_Y	0.590	0.11
14_W	161_L	0.589	0.11
23_K	87_Y	0.588	0.11
31_S	160_W	0.588	0.11
76_Y	107_W	0.588	0.11
99_V	138_G	0.587	0.11
135_M	160_W	0.587	0.11
111_I	158_F	0.586	0.11
83_L	170_L	0.582	0.11
23_K	97_D	0.579	0.11
49_F	112_L	0.578	0.11
58_F	171_L	0.575	0.11
59_F	95_L	0.566	0.11
45_I	176_K	0.564	0.11
13_L	63_C	0.564	0.11
12_F	20_I	0.563	0.11
97_D	137_Q	0.560	0.11
118_A	175_S	0.559	0.11
34_I	164_C	0.559	0.11
14_W	23_K	0.556	0.11
96_Y	149_L	0.555	0.11
96_Y	139_E	0.555	0.11
49_F	62_G	0.553	0.11
115_L	153_M	0.552	0.11
32_V	158_F	0.552	0.11
57_M	75_R	0.549	0.11
116_L	122_R	0.546	0.11
31_S	131_F	0.546	0.11
90_V	96_Y	0.545	0.11
81_L	132_V	0.544	0.11
48_Y	51_L	0.544	0.11
20_I	70_G	0.541	0.10
55_Y	124_F	0.540	0.10
62_G	65_Y	0.540	0.10
85_A	130_L	0.534	0.10
22_E	153_M	0.533	0.10
107_W	158_F	0.533	0.10
20_I	168_M	0.532	0.10
61_C	90_V	0.532	0.10
164_C	173_G	0.532	0.10
143_S	146_I	0.531	0.10
68_Y	165_S	0.529	0.10
43_H	160_W	0.528	0.10
117_T	140_L	0.527	0.10
20_I	53_A	0.524	0.10
80_Y	120_V	0.523	0.10
100_W	153_M	0.520	0.10
75_R	162_N	0.520	0.10
49_F	154_A	0.520	0.10
11_W	27_R	0.519	0.10
97_D	149_L	0.517	0.10
40_L	57_M	0.516	0.10
116_L	176_K	0.511	0.10
37_N	73_R	0.509	0.10
47_L	168_M	0.503	0.10
12_F	124_F	0.503	0.10
66_A	133_L	0.503	0.10
89_F	162_N	0.502	0.10
67_G	177_Y	0.500	0.10

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
4rfsS	1	0.7638	23.5	0.95	Contact Map
4hzuS	1	0.7538	23.5	0.95	Contact Map
4huqS	1	0.799	21.7	0.951	Contact Map
3p5nA	2	0.7538	13.8	0.955	Contact Map
2kncB	1	0.2764	5	0.964	Contact Map
3rkoN	1	0.5176	3.3	0.967	Contact Map
1r48A	2	0.1407	2.9	0.968	Contact Map
4he8A	1	0.1508	2.7	0.968	Contact Map
2yufA	1	0.2412	2.7	0.968	Contact Map
3dinC	1	0.4221	2.3	0.969	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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