YPHF - BACSU - GREMLIN Contacts

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YPHF - Uncharacterized protein YphF

UniProt:	P39911	Sequences: MGKLKCAIIFAAVVFLSGCLYPNERKSSVHAIPYQDQLKQVQSAVDEFQKANGGLLPIQTKDMSTPLYQKYPIDFNRLAPRYIAEPPSTAFESGGDYQYVLVDVENDPTVKLIDLKMAEKIRDVKLRIQMYRQEHQYPPYKDVLSRDLFTLDEKKLGDGSSLTVTSPISGNSLPLMIDGDGEIYADYRTELASCLKKSKKTFKPGTEIQDMIWHETPFVPAFSVKYTVNDKQEPVFLENDMKKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	244 (227)
Sequences:	209 (181)
Seq/√Len:	12.0

BACSU - YPHF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_L	104_V	5.448	1.00
48_F	55_L	4.537	1.00
102_V	213_W	3.614	0.99
191_L	208_I	3.595	0.99
174_P	189_T	3.593	0.99
117_M	185_A	3.289	0.97
175_L	183_I	3.116	0.96
151_L	177_I	3.080	0.96
38_L	217_P	3.062	0.96
51_A	82_Y	3.004	0.96
178_D	184_Y	2.810	0.94
61_K	72_P	2.709	0.92
86_P	90_A	2.427	0.87
55_L	185_A	2.243	0.83
171_N	193_S	2.200	0.81
168_I	212_I	2.198	0.81
176_M	224_V	2.187	0.81
121_I	183_I	2.148	0.80
124_V	151_L	2.048	0.76
46_D	107_D	2.031	0.76
48_F	77_R	2.027	0.76
89_T	99_Y	1.988	0.74
135_H	168_I	1.961	0.73
68_Y	74_D	1.829	0.68
46_D	49_Q	1.810	0.67
62_D	72_P	1.807	0.67
164_V	175_L	1.786	0.66
195_L	208_I	1.782	0.65
26_K	30_H	1.770	0.65
127_R	147_D	1.706	0.62
116_K	188_R	1.658	0.60
144_L	176_M	1.632	0.58
62_D	156_L	1.629	0.58
18_G	219_V	1.616	0.58
41_V	89_T	1.599	0.57
51_A	86_P	1.587	0.56
35_Q	217_P	1.570	0.55
208_I	228_V	1.565	0.55
56_L	104_V	1.553	0.54
76_N	128_I	1.541	0.54
184_Y	224_V	1.539	0.54
97_Y	217_P	1.513	0.52
14_V	154_K	1.504	0.52
152_D	155_K	1.460	0.50
38_L	113_I	1.444	0.49
99_Y	167_P	1.444	0.49
65_T	156_L	1.409	0.47
103_D	109_T	1.389	0.46
195_L	200_K	1.378	0.46
214_H	232_Q	1.370	0.45
69_Q	202_F	1.366	0.45
20_L	219_V	1.364	0.45
34_Y	82_Y	1.354	0.44
60_T	66_P	1.347	0.44
47_E	50_K	1.347	0.44
121_I	175_L	1.339	0.44
11_A	15_F	1.332	0.43
85_E	165_T	1.292	0.41
126_L	183_I	1.292	0.41
91_F	123_D	1.284	0.41
205_G	227_T	1.284	0.41
101_L	218_F	1.274	0.41
148_L	224_V	1.271	0.40
112_L	213_W	1.268	0.40
35_Q	112_L	1.266	0.40
84_A	237_L	1.262	0.40
66_P	128_I	1.261	0.40
66_P	69_Q	1.250	0.39
68_Y	210_D	1.243	0.39
131_Y	135_H	1.242	0.39
63_M	112_L	1.238	0.39
185_A	190_E	1.233	0.39
51_A	81_R	1.217	0.38
69_Q	113_I	1.200	0.37
26_K	55_L	1.193	0.37
195_L	199_K	1.165	0.35
226_Y	234_P	1.161	0.35
52_N	55_L	1.159	0.35
167_P	173_L	1.155	0.35
145_S	148_L	1.155	0.35
90_A	229_N	1.153	0.35
124_V	177_I	1.149	0.35
33_P	112_L	1.145	0.35
221_A	235_V	1.141	0.34
98_Q	122_R	1.126	0.34
34_Y	101_L	1.100	0.32
36_D	40_Q	1.097	0.32
83_I	86_P	1.085	0.32
148_L	206_T	1.084	0.32
49_Q	91_F	1.067	0.31
204_P	229_N	1.062	0.31
68_Y	175_L	1.059	0.31
205_G	208_I	1.058	0.31
7_A	32_I	1.044	0.30
145_S	222_F	1.043	0.30
11_A	123_D	1.040	0.30
70_K	73_I	1.037	0.30
180_D	228_V	1.030	0.29
181_G	221_A	1.028	0.29
41_V	83_I	1.026	0.29
120_K	154_K	1.019	0.29
68_Y	104_V	1.008	0.29
176_M	222_F	1.007	0.29
64_S	214_H	1.003	0.28
14_V	235_V	1.003	0.28
36_D	103_D	0.999	0.28
49_Q	104_V	0.996	0.28
198_S	215_E	0.990	0.28
32_I	103_D	0.984	0.28
33_P	90_A	0.982	0.28
31_A	75_F	0.977	0.27
221_A	228_V	0.975	0.27
70_K	123_D	0.973	0.27
185_A	222_F	0.972	0.27
75_F	100_V	0.965	0.27
99_Y	173_L	0.964	0.27
106_N	163_T	0.962	0.27
54_G	58_I	0.953	0.26
64_S	155_K	0.948	0.26
11_A	115_L	0.932	0.26
55_L	170_G	0.932	0.26
116_K	221_A	0.931	0.26
54_G	162_L	0.931	0.26
208_I	227_T	0.927	0.25
127_R	151_L	0.926	0.25
180_D	204_P	0.925	0.25
139_P	181_G	0.923	0.25
37_Q	167_P	0.922	0.25
74_D	180_D	0.922	0.25
44_A	135_H	0.921	0.25
68_Y	177_I	0.911	0.25
7_A	90_A	0.911	0.25
128_I	183_I	0.908	0.25
24_E	51_A	0.903	0.24
30_H	88_S	0.903	0.24
63_M	170_G	0.898	0.24
26_K	31_A	0.896	0.24
101_L	184_Y	0.893	0.24
56_L	183_I	0.883	0.24
79_A	102_V	0.882	0.24
70_K	109_T	0.879	0.24
194_C	215_E	0.876	0.23
55_L	193_S	0.875	0.23
46_D	152_D	0.875	0.23
165_T	221_A	0.871	0.23
33_P	233_E	0.870	0.23
64_S	152_D	0.870	0.23
82_Y	103_D	0.868	0.23
155_K	197_K	0.864	0.23
116_K	224_V	0.863	0.23
102_V	237_L	0.855	0.23
64_S	135_H	0.855	0.23
15_F	159_G	0.855	0.23
18_G	228_V	0.853	0.23
31_A	51_A	0.849	0.23
39_K	43_S	0.848	0.22
112_L	233_E	0.839	0.22
9_I	140_Y	0.835	0.22
62_D	180_D	0.835	0.22
135_H	154_K	0.828	0.22
116_K	176_M	0.826	0.22
128_I	234_P	0.823	0.22
9_I	13_V	0.823	0.22
151_L	183_I	0.822	0.22
222_F	236_F	0.819	0.21
76_N	101_L	0.817	0.21
157_G	226_Y	0.815	0.21
55_L	97_Y	0.811	0.21
8_I	89_T	0.810	0.21
60_T	71_Y	0.807	0.21
22_P	31_A	0.807	0.21
112_L	118_A	0.806	0.21
194_C	200_K	0.805	0.21
45_V	175_L	0.804	0.21
33_P	85_E	0.803	0.21
34_Y	60_T	0.801	0.21
100_V	169_S	0.797	0.21
163_T	188_R	0.794	0.21
122_R	222_F	0.793	0.21
88_S	137_Y	0.790	0.21
38_L	97_Y	0.790	0.21
42_Q	169_S	0.786	0.20
77_R	149_F	0.785	0.20
202_F	206_T	0.785	0.20
20_L	124_V	0.784	0.20
89_T	112_L	0.784	0.20
100_V	222_F	0.780	0.20
77_R	171_N	0.774	0.20
89_T	224_V	0.771	0.20
93_S	235_V	0.771	0.20
128_I	136_Q	0.770	0.20
34_Y	80_P	0.769	0.20
125_K	142_D	0.768	0.20
117_M	219_V	0.767	0.20
55_L	62_D	0.767	0.20
148_L	176_M	0.767	0.20
34_Y	79_A	0.764	0.20
81_R	234_P	0.762	0.20
78_L	83_I	0.760	0.20
71_Y	156_L	0.749	0.19
26_K	65_T	0.743	0.19
207_E	212_I	0.743	0.19
20_L	216_T	0.740	0.19
31_A	232_Q	0.739	0.19
78_L	102_V	0.737	0.19
64_S	134_E	0.737	0.19
49_Q	130_M	0.736	0.19
90_A	139_P	0.735	0.19
56_L	100_V	0.734	0.19
55_L	85_E	0.734	0.19
155_K	199_K	0.733	0.19
6_C	11_A	0.726	0.19
75_F	99_Y	0.722	0.18
12_A	144_L	0.721	0.18
22_P	30_H	0.719	0.18
10_F	180_D	0.714	0.18
21_Y	66_P	0.710	0.18
90_A	198_S	0.708	0.18
30_H	159_G	0.708	0.18
151_L	175_L	0.702	0.18
59_Q	72_P	0.701	0.18
8_I	48_F	0.698	0.18
35_Q	83_I	0.697	0.18
124_V	216_T	0.694	0.18
79_A	141_K	0.691	0.17
146_R	149_F	0.688	0.17
148_L	225_K	0.688	0.17
11_A	24_E	0.687	0.17
200_K	206_T	0.687	0.17
93_S	175_L	0.687	0.17
90_A	168_I	0.686	0.17
176_M	184_Y	0.678	0.17
144_L	161_S	0.675	0.17
169_S	178_D	0.668	0.17
100_V	104_V	0.667	0.17
97_Y	112_L	0.666	0.17
10_F	15_F	0.664	0.17
122_R	140_Y	0.659	0.17
46_D	171_N	0.658	0.17
55_L	125_K	0.657	0.17
113_I	195_L	0.655	0.16
111_K	219_V	0.654	0.16
14_V	201_T	0.654	0.16
90_A	105_E	0.651	0.16
93_S	151_L	0.649	0.16
201_T	204_P	0.647	0.16
101_L	113_I	0.646	0.16
191_L	205_G	0.645	0.16
43_S	149_F	0.644	0.16
90_A	93_S	0.641	0.16
156_L	164_V	0.640	0.16
82_Y	229_N	0.640	0.16
55_L	70_K	0.640	0.16
73_I	185_A	0.638	0.16
41_V	180_D	0.635	0.16
7_A	129_Q	0.634	0.16
142_D	229_N	0.633	0.16
38_L	216_T	0.632	0.16
23_N	152_D	0.626	0.16
23_N	40_Q	0.624	0.16
51_A	80_P	0.624	0.16
172_S	234_P	0.623	0.16
71_Y	100_V	0.621	0.16
34_Y	141_K	0.618	0.15
88_S	206_T	0.615	0.15
10_F	161_S	0.611	0.15
130_M	202_F	0.609	0.15
144_L	155_K	0.608	0.15
59_Q	191_L	0.607	0.15
91_F	138_P	0.605	0.15
144_L	178_D	0.604	0.15
56_L	108_P	0.603	0.15
209_Q	212_I	0.603	0.15
149_F	176_M	0.600	0.15
6_C	214_H	0.600	0.15
192_A	196_K	0.599	0.15
97_Y	113_I	0.598	0.15
89_T	96_D	0.597	0.15
52_N	130_M	0.594	0.15
155_K	203_K	0.591	0.15
67_L	73_I	0.591	0.15
37_Q	236_F	0.590	0.15
56_L	91_F	0.588	0.15
63_M	72_P	0.587	0.15
81_R	154_K	0.584	0.15
86_P	111_K	0.584	0.15
121_I	125_K	0.578	0.14
73_I	111_K	0.577	0.14
79_A	82_Y	0.576	0.14
49_Q	60_T	0.575	0.14
97_Y	151_L	0.573	0.14
72_P	100_V	0.573	0.14
9_I	73_I	0.568	0.14
131_Y	149_F	0.568	0.14
154_K	204_P	0.565	0.14
52_N	124_V	0.565	0.14
50_K	142_D	0.564	0.14
50_K	217_P	0.560	0.14
66_P	181_G	0.560	0.14
8_I	13_V	0.560	0.14
45_V	197_K	0.556	0.14
66_P	188_R	0.555	0.14
149_F	199_K	0.552	0.14
173_L	187_Y	0.551	0.14
15_F	18_G	0.551	0.14
66_P	113_I	0.550	0.14
126_L	130_M	0.550	0.14
95_G	166_S	0.546	0.14
40_Q	97_Y	0.544	0.14
189_T	192_A	0.543	0.14
111_K	205_G	0.542	0.14
17_S	20_L	0.540	0.14
67_L	213_W	0.539	0.14
11_A	46_D	0.539	0.14
98_Q	236_F	0.537	0.13
136_Q	177_I	0.533	0.13
90_A	144_L	0.533	0.13
21_Y	100_V	0.531	0.13
125_K	214_H	0.530	0.13
24_E	40_Q	0.529	0.13
59_Q	153_E	0.529	0.13
127_R	130_M	0.528	0.13
132_R	175_L	0.527	0.13
48_F	59_Q	0.527	0.13
6_C	9_I	0.525	0.13
91_F	125_K	0.524	0.13
84_A	147_D	0.523	0.13
128_I	202_F	0.519	0.13
77_R	226_Y	0.519	0.13
98_Q	167_P	0.519	0.13
79_A	149_F	0.517	0.13
12_A	38_L	0.514	0.13
222_F	229_N	0.512	0.13
69_Q	188_R	0.511	0.13
158_D	175_L	0.508	0.13
36_D	158_D	0.508	0.13
82_Y	216_T	0.506	0.13
54_G	121_I	0.505	0.13
113_I	218_F	0.504	0.13
20_L	78_L	0.500	0.13

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
3gn9A	1	0.3648	64.8	0.962	Contact Map
4pj0U	1	0.3566	60.9	0.963	Contact Map
1t92A	2	0.3607	60.6	0.963	Contact Map
2kepA	1	0.373	58.2	0.963	Contact Map
3pmqA	1	0.5082	54.9	0.964	Contact Map
3zbiC	1	0.0984	44.1	0.966	Contact Map
4ba6A	1	0.3648	39.8	0.967	Contact Map
2zo4A	1	0.3648	36	0.968	Contact Map
4n4rB	1	0.541	34.6	0.968	Contact Map
4fybB	1	0.5574	27.8	0.97	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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