YQCA - BACSU - GREMLIN Contacts

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YQCA - Uncharacterized protein YqcA

UniProt:	P45936	Sequences: MSKLDEMTAYLPPFLTKLKEMAELLKAEAPEFEKQNNSIFDLTDQLFVTTATWGLERWEKILNVPRESGDTDEIRRLRLISKMSNIPPATYRAIEHALNRFLKNPSAQVRLLPGEYRFKVDIDIDDMQHMSELIETLENMKPAHLAYTLRAALNEPLQIKDTVILNNRRYRKASELKVGYSVTLNNNEVVLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (170)
Sequences:	393 (347)
Seq/√Len:	26.6

BACSU - YQCA XKDU

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_Q	52_T	4.943	1.00
156_P	173_A	4.486	1.00
165_L	173_A	4.326	1.00
156_P	165_L	4.114	1.00
49_T	80_I	3.708	1.00
112_L	115_E	3.680	1.00
118_F	141_K	3.643	1.00
15_L	21_M	2.742	1.00
70_D	78_R	2.718	0.99
55_L	79_L	2.642	0.99
41_D	52_T	2.634	0.99
51_A	55_L	2.584	0.99
45_Q	53_W	2.430	0.99
62_L	83_M	2.210	0.98
41_D	45_Q	2.130	0.97
67_E	70_D	2.036	0.96
160_K	177_K	1.981	0.96
164_I	167_N	1.957	0.95
11_L	25_L	1.873	0.94
59_E	75_R	1.861	0.94
173_A	177_K	1.858	0.94
171_R	175_E	1.846	0.93
55_L	76_R	1.842	0.93
118_F	145_L	1.833	0.93
23_E	26_K	1.813	0.93
55_L	72_D	1.741	0.91
160_K	169_R	1.665	0.89
48_V	79_L	1.647	0.89
138_E	141_K	1.604	0.87
14_F	17_K	1.585	0.87
48_V	83_M	1.569	0.86
141_K	147_Y	1.563	0.86
163_V	168_R	1.549	0.85
95_E	99_N	1.540	0.85
137_L	147_Y	1.534	0.85
9_A	79_L	1.521	0.84
7_M	25_L	1.466	0.82
58_W	83_M	1.445	0.81
25_L	28_E	1.435	0.81
157_L	166_N	1.391	0.78
160_K	171_R	1.360	0.77
173_A	176_L	1.347	0.76
171_R	177_K	1.342	0.76
169_R	176_L	1.333	0.75
41_D	53_W	1.326	0.75
165_L	171_R	1.307	0.74
165_L	175_E	1.281	0.72
15_L	24_L	1.249	0.70
142_P	145_L	1.212	0.68
170_Y	174_S	1.211	0.68
91_Y	111_L	1.194	0.67
126_D	149_L	1.193	0.67
168_R	173_A	1.188	0.66
48_V	62_L	1.183	0.66
6_E	33_E	1.168	0.65
46_L	144_H	1.166	0.65
165_L	172_K	1.159	0.64
10_Y	31_E	1.154	0.64
7_M	29_A	1.150	0.64
27_A	40_F	1.147	0.64
101_F	133_L	1.135	0.63
74_I	78_R	1.130	0.62
170_Y	177_K	1.113	0.61
51_A	76_R	1.104	0.61
168_R	171_R	1.096	0.60
165_L	169_R	1.088	0.59
169_R	177_K	1.082	0.59
163_V	171_R	1.073	0.58
171_R	174_S	1.050	0.57
160_K	174_S	1.030	0.55
71_T	81_S	1.027	0.55
82_K	139_N	1.026	0.55
170_Y	176_L	1.022	0.55
165_L	176_L	1.014	0.54
50_T	76_R	1.010	0.54
8_T	22_A	1.010	0.54
95_E	108_Q	0.995	0.53
118_F	147_Y	0.993	0.53
111_L	145_L	0.991	0.52
53_W	82_K	0.987	0.52
169_R	175_E	0.985	0.52
157_L	160_K	0.981	0.52
28_E	32_F	0.975	0.51
29_A	33_E	0.974	0.51
119_K	150_R	0.973	0.51
6_E	79_L	0.966	0.50
171_R	176_L	0.961	0.50
170_Y	175_E	0.952	0.49
133_L	149_L	0.949	0.49
45_Q	58_W	0.948	0.49
15_L	18_L	0.947	0.49
127_M	151_A	0.947	0.49
160_K	173_A	0.940	0.49
159_I	176_L	0.925	0.47
88_P	111_L	0.913	0.47
53_W	144_H	0.905	0.46
158_Q	174_S	0.900	0.46
165_L	168_R	0.880	0.44
169_R	174_S	0.878	0.44
137_L	141_K	0.876	0.44
8_T	25_L	0.866	0.43
90_T	116_Y	0.865	0.43
156_P	177_K	0.853	0.42
165_L	177_K	0.853	0.42
160_K	166_N	0.847	0.42
156_P	175_E	0.838	0.41
62_L	79_L	0.835	0.41
84_S	97_A	0.831	0.41
54_G	66_R	0.827	0.40
167_N	175_E	0.820	0.40
118_F	138_E	0.818	0.40
85_N	139_N	0.818	0.40
99_N	119_K	0.817	0.40
70_D	132_E	0.809	0.39
167_N	171_R	0.803	0.39
102_L	124_I	0.802	0.38
110_R	120_V	0.798	0.38
163_V	173_A	0.797	0.38
160_K	168_R	0.795	0.38
27_A	38_S	0.795	0.38
112_L	117_R	0.794	0.38
169_R	173_A	0.791	0.38
89_A	92_R	0.783	0.37
167_N	170_Y	0.770	0.36
134_I	149_L	0.770	0.36
45_Q	54_G	0.769	0.36
6_E	29_A	0.767	0.36
126_D	130_M	0.758	0.35
77_L	100_R	0.756	0.35
64_V	111_L	0.755	0.35
155_E	158_Q	0.739	0.34
70_D	74_I	0.736	0.34
162_T	166_N	0.735	0.34
45_Q	144_H	0.734	0.34
156_P	168_R	0.731	0.34
166_N	175_E	0.730	0.33
56_E	66_R	0.728	0.33
89_A	98_L	0.726	0.33
162_T	177_K	0.721	0.33
163_V	170_Y	0.720	0.33
159_I	168_R	0.714	0.32
155_E	175_E	0.712	0.32
151_A	156_P	0.712	0.32
120_V	155_E	0.711	0.32
73_E	120_V	0.709	0.32
17_K	30_P	0.705	0.32
116_Y	145_L	0.704	0.32
121_D	150_R	0.703	0.32
54_G	58_W	0.702	0.32
103_K	120_V	0.699	0.31
159_I	163_V	0.694	0.31
156_P	160_K	0.687	0.31
165_L	170_Y	0.686	0.31
138_E	147_Y	0.686	0.31
48_V	107_A	0.685	0.31
98_L	124_I	0.681	0.30
131_S	134_I	0.681	0.30
17_K	22_A	0.678	0.30
112_L	119_K	0.671	0.30
31_E	47_F	0.665	0.29
107_A	126_D	0.663	0.29
157_L	174_S	0.662	0.29
166_N	176_L	0.661	0.29
94_I	109_V	0.660	0.29
41_D	58_W	0.658	0.29
151_A	173_A	0.658	0.29
47_F	59_E	0.647	0.28
8_T	15_L	0.645	0.28
101_F	130_M	0.644	0.28
109_V	120_V	0.643	0.28
102_L	123_D	0.642	0.28
6_E	9_A	0.636	0.28
163_V	167_N	0.635	0.27
7_M	18_L	0.634	0.27
174_S	177_K	0.634	0.27
45_Q	82_K	0.630	0.27
26_K	32_F	0.629	0.27
88_P	144_H	0.627	0.27
119_K	148_T	0.622	0.27
31_E	54_G	0.622	0.27
94_I	106_S	0.621	0.27
97_A	118_F	0.616	0.26
20_E	28_E	0.616	0.26
9_A	29_A	0.605	0.26
46_L	94_I	0.603	0.26
159_I	177_K	0.598	0.25
167_N	177_K	0.596	0.25
21_M	92_R	0.596	0.25
162_T	170_Y	0.591	0.25
154_N	176_L	0.591	0.25
91_Y	109_V	0.589	0.25
77_L	130_M	0.587	0.25
98_L	127_M	0.582	0.24
64_V	95_E	0.577	0.24
51_A	54_G	0.575	0.24
73_E	76_R	0.575	0.24
160_K	176_L	0.574	0.24
89_A	93_A	0.574	0.24
121_D	154_N	0.573	0.24
99_N	112_L	0.572	0.24
81_S	154_N	0.570	0.24
162_T	168_R	0.566	0.24
27_A	159_I	0.565	0.24
114_G	162_T	0.564	0.23
49_T	78_R	0.564	0.23
48_V	80_I	0.562	0.23
156_P	176_L	0.562	0.23
56_E	79_L	0.562	0.23
135_E	140_M	0.562	0.23
18_L	21_M	0.560	0.23
54_G	137_L	0.558	0.23
22_A	26_K	0.556	0.23
155_E	160_K	0.556	0.23
20_E	144_H	0.556	0.23
158_Q	167_N	0.551	0.23
133_L	140_M	0.549	0.23
11_L	57_R	0.545	0.22
108_Q	124_I	0.545	0.22
14_F	36_N	0.544	0.22
126_D	131_S	0.544	0.22
30_P	36_N	0.543	0.22
24_L	60_K	0.543	0.22
169_R	172_K	0.540	0.22
94_I	130_M	0.540	0.22
163_V	169_R	0.540	0.22
98_L	102_L	0.538	0.22
166_N	172_K	0.537	0.22
163_V	175_E	0.537	0.22
8_T	16_T	0.536	0.22
50_T	90_T	0.535	0.22
32_F	158_Q	0.535	0.22
102_L	106_S	0.533	0.22
89_A	113_P	0.531	0.22
47_F	75_R	0.530	0.22
98_L	137_L	0.530	0.22
7_M	20_E	0.529	0.22
156_P	171_R	0.520	0.21
10_Y	20_E	0.518	0.21
84_S	100_R	0.518	0.21
8_T	14_F	0.518	0.21
98_L	103_K	0.516	0.21
156_P	163_V	0.515	0.21
17_K	137_L	0.514	0.21
66_R	69_G	0.512	0.21
89_A	94_I	0.511	0.21
44_D	57_R	0.508	0.21
157_L	171_R	0.507	0.21
27_A	73_E	0.505	0.20
68_S	137_L	0.503	0.20
164_I	170_Y	0.502	0.20
115_E	145_L	0.502	0.20
22_A	33_E	0.501	0.20
88_P	98_L	0.501	0.20
85_N	98_L	0.500	0.20
87_P	98_L	0.500	0.20

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
3vlfB	1	0.3646	33.4	0.938	Contact Map
3kw6A	1	0.3698	14.9	0.947	Contact Map
4jpoC	1	0.375	14.3	0.948	Contact Map
3ajiB	1	0.3646	12	0.95	Contact Map
3n4sA	2	0.2031	10.6	0.951	Contact Map
5afrA	2	0	9.6	0.952	Contact Map
3chbD	3	0.4375	7.4	0.954	Contact Map
4q86A	3	0.4844	6.7	0.955	Contact Map
3smaA	2	0.5208	6.5	0.955	Contact Map
1oksA	1	0.276	5.9	0.956	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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