YWRF - BACSU - GREMLIN Contacts

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YWRF - Uncharacterized protein YwrF

UniProt:	O05220	Sequences: MYIFQADQLSAKDTYKLLSGTVIPRPIAFVTTLSSGGAVNAAPFSFYNVVSSDPPLLSISVNRTEGRQKDTARNAVENGEFVVHVSDEAIIEDINETAASLRPDESELTRTSLHPVESKAVSVPGIKEARVRFECKLERHITFDNDQGITTADLLIGRVVCFHLDEKVYDAEKGYILTDELKPASRLAGNHYAKLGEEFTLIRPS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (169)
Sequences:	3701 (2656)
Seq/√Len:	204.3

ECOLI - YDDH
BACSU - YWRF YDFE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_H	128_E	3.834	1.00
120_A	160_V	3.347	1.00
81_F	157_G	3.334	1.00
136_K	158_R	3.160	1.00
34_S	38_A	3.077	1.00
88_E	182_K	2.984	1.00
35_S	77_E	2.733	1.00
136_K	160_V	2.715	1.00
106_S	109_T	2.436	1.00
138_E	158_R	2.430	1.00
116_V	127_K	2.405	1.00
31_T	82_V	2.288	1.00
39_V	115_P	2.273	1.00
170_D	173_K	2.230	1.00
76_V	140_H	2.143	1.00
101_L	110_R	2.091	1.00
86_S	94_I	2.089	1.00
41_A	126_I	2.056	1.00
33_L	39_V	2.050	1.00
80_E	136_K	1.995	1.00
88_E	194_K	1.902	1.00
114_H	127_K	1.893	1.00
82_V	121_V	1.871	1.00
33_L	122_S	1.796	1.00
108_L	115_P	1.766	1.00
118_S	125_G	1.744	1.00
125_G	132_R	1.691	1.00
80_E	122_S	1.612	1.00
73_R	103_P	1.585	1.00
101_L	105_E	1.583	1.00
58_S	154_L	1.550	1.00
50_V	58_S	1.535	1.00
39_V	124_P	1.528	1.00
170_D	177_L	1.510	1.00
18_L	49_V	1.493	1.00
119_K	161_C	1.489	1.00
118_S	134_E	1.485	1.00
57_L	83_V	1.482	1.00
121_V	134_E	1.440	1.00
140_H	153_D	1.426	1.00
118_S	123_V	1.415	1.00
29_F	41_A	1.410	1.00
185_S	193_A	1.408	1.00
81_F	135_C	1.406	1.00
56_L	156_I	1.382	1.00
31_T	41_A	1.362	1.00
87_D	90_I	1.353	1.00
75_A	137_L	1.352	1.00
106_S	115_P	1.329	1.00
29_F	97_T	1.284	1.00
118_S	121_V	1.284	1.00
75_A	81_F	1.278	1.00
177_L	180_E	1.271	1.00
73_R	77_E	1.262	1.00
133_F	162_F	1.249	1.00
120_A	161_C	1.245	1.00
170_D	180_E	1.240	1.00
86_S	184_A	1.230	1.00
56_L	138_E	1.227	1.00
21_T	131_V	1.219	1.00
68_Q	76_V	1.195	1.00
125_G	163_H	1.192	1.00
50_V	156_I	1.176	1.00
91_I	184_A	1.150	1.00
90_I	128_E	1.148	1.00
86_S	129_A	1.147	1.00
116_V	125_G	1.136	1.00
194_K	197_E	1.133	1.00
42_A	71_T	1.127	1.00
41_A	108_L	1.122	1.00
84_H	132_R	1.115	1.00
80_E	121_V	1.107	1.00
72_A	76_V	1.103	1.00
39_V	106_S	1.066	1.00
89_A	182_K	1.062	1.00
68_Q	72_A	1.045	1.00
135_C	157_G	1.038	1.00
32_T	75_A	1.021	1.00
29_F	90_I	1.019	1.00
93_D	111_T	1.010	1.00
82_V	125_G	1.008	1.00
137_L	140_H	1.007	1.00
168_V	181_L	1.002	1.00
137_L	155_L	0.997	1.00
72_A	153_D	0.986	1.00
28_A	47_Y	0.972	1.00
72_A	155_L	0.971	1.00
97_T	111_T	0.968	1.00
70_D	73_R	0.958	0.99
57_L	133_F	0.954	0.99
32_T	74_N	0.953	0.99
78_N	122_S	0.950	0.99
33_L	123_V	0.944	0.99
51_S	143_F	0.910	0.99
87_D	130_R	0.910	0.99
32_T	71_T	0.906	0.99
93_D	113_L	0.901	0.99
140_H	155_L	0.900	0.99
105_E	110_R	0.897	0.99
82_V	118_S	0.896	0.99
164_L	168_V	0.894	0.99
187_L	193_A	0.892	0.99
142_T	153_D	0.861	0.99
70_D	103_P	0.858	0.99
51_S	152_A	0.855	0.99
133_F	159_V	0.853	0.99
141_I	156_I	0.844	0.99
165_D	168_V	0.837	0.99
96_E	101_L	0.836	0.99
88_E	91_I	0.830	0.98
58_S	156_I	0.829	0.98
116_V	132_R	0.829	0.98
33_L	117_E	0.825	0.98
83_V	135_C	0.823	0.98
33_L	78_N	0.814	0.98
31_T	123_V	0.814	0.98
31_T	126_I	0.813	0.98
44_F	61_V	0.807	0.98
48_N	58_S	0.800	0.98
130_R	165_D	0.797	0.98
191_H	198_E	0.793	0.98
96_E	110_R	0.792	0.98
34_S	77_E	0.787	0.98
168_V	176_I	0.786	0.98
38_A	104_D	0.785	0.98
185_S	195_L	0.784	0.98
94_I	184_A	0.783	0.98
38_A	103_P	0.783	0.98
50_V	56_L	0.782	0.98
182_K	194_K	0.782	0.98
34_S	74_N	0.777	0.98
117_E	122_S	0.769	0.98
67_R	142_T	0.769	0.98
168_V	180_E	0.767	0.97
80_E	123_V	0.764	0.97
85_V	181_L	0.758	0.97
131_V	181_L	0.757	0.97
30_V	59_I	0.749	0.97
178_T	183_P	0.748	0.97
50_V	60_S	0.747	0.97
44_F	59_I	0.745	0.97
143_F	156_I	0.745	0.97
76_V	79_G	0.744	0.97
31_T	84_H	0.742	0.97
94_I	129_A	0.742	0.97
82_V	132_R	0.741	0.97
85_V	183_P	0.739	0.97
70_D	74_N	0.736	0.97
39_V	108_L	0.734	0.97
90_I	129_A	0.728	0.97
170_D	175_Y	0.726	0.97
84_H	126_I	0.724	0.96
79_G	137_L	0.724	0.96
22_V	49_V	0.723	0.96
76_V	142_T	0.721	0.96
31_T	108_L	0.719	0.96
79_G	136_K	0.716	0.96
183_P	195_L	0.709	0.96
50_V	154_L	0.696	0.96
46_F	49_V	0.692	0.95
139_R	142_T	0.690	0.95
29_F	126_I	0.685	0.95
120_A	134_E	0.685	0.95
89_A	130_R	0.684	0.95
176_I	181_L	0.683	0.95
132_R	163_H	0.682	0.95
93_D	128_E	0.677	0.95
57_L	159_V	0.675	0.95
20_G	188_A	0.675	0.95
92_E	96_E	0.674	0.95
29_F	94_I	0.668	0.94
29_F	129_A	0.667	0.94
33_L	37_G	0.664	0.94
23_I	183_P	0.663	0.94
19_S	52_S	0.662	0.94
47_Y	85_V	0.660	0.94
28_A	83_V	0.655	0.94
102_R	105_E	0.654	0.94
80_E	134_E	0.650	0.94
116_V	119_K	0.649	0.94
72_A	140_H	0.648	0.94
70_D	107_E	0.645	0.93
109_T	112_S	0.642	0.93
47_Y	58_S	0.636	0.93
56_L	143_F	0.636	0.93
39_V	123_V	0.635	0.93
21_T	133_F	0.635	0.93
111_T	126_I	0.631	0.93
187_L	191_H	0.628	0.92
71_T	74_N	0.628	0.92
85_V	131_V	0.624	0.92
74_N	78_N	0.624	0.92
27_I	43_P	0.622	0.92
59_I	155_L	0.622	0.92
75_A	157_G	0.622	0.92
191_H	195_L	0.620	0.92
53_D	145_N	0.618	0.92
96_E	99_A	0.617	0.92
115_P	128_E	0.616	0.92
30_V	44_F	0.614	0.92
118_S	132_R	0.614	0.92
167_K	180_E	0.613	0.92
61_V	155_L	0.609	0.91
67_R	153_D	0.608	0.91
68_Q	73_R	0.607	0.91
75_A	155_L	0.606	0.91
96_E	105_E	0.606	0.91
59_I	75_A	0.605	0.91
44_F	71_T	0.604	0.91
138_E	156_I	0.602	0.91
96_E	111_T	0.602	0.91
168_V	178_T	0.600	0.91
90_I	113_L	0.596	0.90
82_V	123_V	0.595	0.90
131_V	164_L	0.592	0.90
113_L	126_I	0.591	0.90
60_S	152_A	0.590	0.90
178_T	187_L	0.584	0.89
43_P	86_S	0.575	0.89
29_F	113_L	0.574	0.89
57_L	157_G	0.571	0.88
23_I	178_T	0.569	0.88
36_G	77_E	0.563	0.88
84_H	123_V	0.560	0.87
27_I	86_S	0.559	0.87
138_E	141_I	0.554	0.87
193_A	196_G	0.552	0.87
109_T	115_P	0.549	0.86
169_Y	176_I	0.548	0.86
33_L	118_S	0.540	0.86
164_L	176_I	0.536	0.85
108_L	126_I	0.529	0.84
93_D	96_E	0.527	0.84
75_A	79_G	0.527	0.84
22_V	57_L	0.526	0.84
29_F	42_A	0.526	0.84
91_I	94_I	0.526	0.84
56_L	60_S	0.525	0.84
48_N	60_S	0.525	0.84
98_A	101_L	0.523	0.84
61_V	72_A	0.519	0.83
79_G	139_R	0.519	0.83
117_E	124_P	0.517	0.83
108_L	111_T	0.517	0.83
61_V	66_G	0.513	0.83
179_D	198_E	0.513	0.83
30_V	81_F	0.512	0.82
115_P	124_P	0.511	0.82
87_D	129_A	0.509	0.82
145_N	161_C	0.507	0.82
66_G	152_A	0.502	0.81
114_H	126_I	0.502	0.81
187_L	195_L	0.501	0.81
120_A	136_K	0.500	0.81

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
3bpkA	2	0.9707	100	0.23	Contact Map
3fgeA	2	0.9317	100	0.266	Contact Map
1ejeA	2	0.9073	100	0.339	Contact Map
3hmzA	2	0.8878	100	0.369	Contact Map
2r6vA	2	0.8878	100	0.378	Contact Map
2d5mA	2	0.8683	100	0.381	Contact Map
3bnkA	2	0.878	100	0.401	Contact Map
3e4vA	2	0.8537	100	0.409	Contact Map
1uscA	2	0.8683	100	0.416	Contact Map
3cb0A	2	0.7805	100	0.491	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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