YOBH - BACSU - GREMLIN Contacts

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YOBH - DNA repair protein homolog YobH

UniProt:	C0SPA8	Sequences: MAKAIQSSMWREFGLMCTVGIGDNMLLSKLALDLESKKTKSGIARWRYEDVPNRLWKVRPLSKMWGIGGRMERNLNRMGISTVGQLAKFPLELLEKKFGIMGNQLYYHAHGIDLSEIGAPLMQGQISFGKSQILFRDYTKREEIKAVLLEICEEVARRARTYNKVGRTISLGIGYSKDELGGGFHRSKTIDFPTNITMDIYKCCLMFFNKFYSGKKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (201)
Sequences:	7820 (5639)
Seq/√Len:	397.8

ECOLI - UMUC DPO4
BACSU - YOBH DPO41 DPO42 UVRX
HALSA - DPO4
SULSO - DPO4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_S	72_E	3.243	1.00
145_K	205_L	2.962	1.00
8_S	12_E	2.946	1.00
140_K	143_E	2.658	1.00
76_N	81_S	2.601	1.00
9_M	17_C	2.375	1.00
84_G	88_K	2.290	1.00
145_K	209_N	2.275	1.00
4_A	8_S	2.252	1.00
81_S	85_Q	2.247	1.00
106_Y	110_H	2.206	1.00
10_W	41_S	2.116	1.00
78_M	97_K	2.088	1.00
141_R	209_N	2.073	1.00
95_E	103_N	2.060	1.00
6_Q	41_S	2.050	1.00
7_S	11_R	2.027	1.00
56_W	87_A	2.010	1.00
91_L	103_N	1.988	1.00
107_Y	112_I	1.961	1.00
47_R	50_D	1.931	1.00
62_S	76_N	1.922	1.00
149_L	201_Y	1.860	1.00
72_E	76_N	1.829	1.00
80_I	89_F	1.826	1.00
56_W	84_G	1.821	1.00
52_P	56_W	1.819	1.00
6_Q	43_I	1.796	1.00
188_K	206_M	1.782	1.00
80_I	86_L	1.778	1.00
196_I	199_D	1.692	1.00
131_S	172_G	1.666	1.00
104_Q	108_H	1.660	1.00
156_A	200_I	1.658	1.00
156_A	197_T	1.632	1.00
89_F	93_L	1.594	1.00
27_L	46_W	1.592	1.00
130_K	155_V	1.562	1.00
73_R	77_R	1.543	1.00
188_K	210_K	1.535	1.00
21_I	43_I	1.514	1.00
91_L	106_Y	1.512	1.00
103_N	107_Y	1.503	1.00
153_E	197_T	1.474	1.00
78_M	98_F	1.464	1.00
134_L	147_V	1.459	1.00
130_K	158_R	1.444	1.00
138_Y	144_I	1.440	1.00
94_L	106_Y	1.413	1.00
130_K	154_E	1.410	1.00
141_R	145_K	1.393	1.00
34_L	44_A	1.379	1.00
70_R	73_R	1.374	1.00
82_T	85_Q	1.358	1.00
138_Y	143_E	1.343	1.00
31_A	46_W	1.338	1.00
89_F	94_L	1.332	1.00
190_I	203_C	1.330	1.00
201_Y	205_L	1.320	1.00
35_E	44_A	1.318	1.00
188_K	203_C	1.318	1.00
52_P	87_A	1.309	1.00
3_K	6_Q	1.308	1.00
3_K	7_S	1.305	1.00
102_G	106_Y	1.300	1.00
159_A	166_G	1.287	1.00
3_K	43_I	1.287	1.00
2_A	19_V	1.287	1.00
22_G	27_L	1.283	1.00
152_C	156_A	1.283	1.00
23_D	51_V	1.282	1.00
203_C	206_M	1.275	1.00
156_A	160_R	1.255	1.00
93_L	97_K	1.250	1.00
174_G	183_G	1.230	1.00
74_N	97_K	1.226	1.00
152_C	200_I	1.225	1.00
168_T	187_S	1.216	1.00
199_D	203_C	1.215	1.00
91_L	95_E	1.205	1.00
147_V	150_E	1.197	1.00
152_C	204_C	1.185	1.00
128_F	162_Y	1.179	1.00
168_T	189_T	1.156	1.00
25_M	117_I	1.152	1.00
136_R	143_E	1.148	1.00
90_P	93_L	1.146	1.00
64_M	83_V	1.142	1.00
205_L	209_N	1.135	1.00
171_L	207_F	1.131	1.00
137_D	176_S	1.126	1.00
30_L	58_V	1.124	1.00
50_D	53_N	1.121	1.00
170_S	187_S	1.121	1.00
10_W	16_M	1.108	1.00
67_I	102_G	1.095	1.00
19_V	43_I	1.093	1.00
160_R	197_T	1.090	1.00
99_G	102_G	1.076	1.00
148_L	204_C	1.070	1.00
190_I	194_T	1.070	1.00
134_L	138_Y	1.069	1.00
194_T	199_D	1.067	1.00
165_V	195_N	1.066	1.00
152_C	201_Y	1.063	1.00
144_I	208_F	1.059	1.00
206_M	210_K	1.035	1.00
160_R	195_N	1.029	1.00
148_L	171_L	1.023	1.00
33_D	63_K	1.016	1.00
26_L	108_H	1.015	1.00
2_A	21_I	1.010	1.00
202_K	206_M	1.007	1.00
101_M	104_Q	1.006	1.00
186_R	211_F	1.005	1.00
167_R	193_P	1.004	1.00
21_I	45_R	0.998	1.00
148_L	208_F	0.984	1.00
61_L	80_I	0.984	1.00
198_M	202_K	0.980	1.00
91_L	107_Y	0.961	1.00
197_T	201_Y	0.945	1.00
10_W	14_G	0.943	1.00
16_M	35_E	0.942	1.00
22_G	28_S	0.935	1.00
93_L	96_K	0.929	1.00
146_A	150_E	0.926	1.00
73_R	76_N	0.921	1.00
35_E	42_G	0.918	1.00
175_Y	184_F	0.918	1.00
87_A	110_H	0.915	1.00
87_A	109_A	0.914	1.00
132_Q	147_V	0.909	1.00
61_L	76_N	0.908	1.00
167_R	189_T	0.906	1.00
149_L	205_L	0.901	1.00
57_K	84_G	0.896	1.00
107_Y	114_L	0.887	1.00
30_L	65_W	0.877	1.00
100_I	104_Q	0.873	1.00
98_F	102_G	0.860	1.00
94_L	98_F	0.852	1.00
71_M	98_F	0.849	1.00
188_K	207_F	0.846	1.00
120_P	123_Q	0.842	1.00
113_D	116_E	0.841	1.00
170_S	185_H	0.838	1.00
65_W	108_H	0.837	1.00
152_C	197_T	0.837	1.00
34_L	54_R	0.837	1.00
46_W	54_R	0.836	1.00
184_F	211_F	0.828	1.00
32_L	35_E	0.821	1.00
74_N	98_F	0.819	1.00
53_N	56_W	0.812	1.00
192_F	199_D	0.811	1.00
154_E	157_R	0.806	1.00
148_L	205_L	0.803	1.00
60_P	76_N	0.802	1.00
138_Y	147_V	0.797	1.00
85_Q	88_K	0.796	1.00
71_M	74_N	0.794	1.00
141_R	208_F	0.789	1.00
172_G	183_G	0.784	1.00
24_N	27_L	0.782	1.00
86_L	94_L	0.781	1.00
58_V	63_K	0.776	1.00
61_L	72_E	0.769	1.00
92_E	96_K	0.769	1.00
145_K	149_L	0.763	1.00
153_E	157_R	0.760	1.00
133_I	137_D	0.757	1.00
158_R	162_Y	0.757	1.00
50_D	54_R	0.756	1.00
90_P	110_H	0.753	1.00
67_I	72_E	0.752	1.00
74_N	77_R	0.752	1.00
23_D	27_L	0.745	1.00
60_P	63_K	0.743	1.00
86_L	106_Y	0.743	1.00
142_E	145_K	0.741	1.00
46_W	51_V	0.739	1.00
125_Q	162_Y	0.738	1.00
54_R	58_V	0.736	1.00
98_F	105_L	0.735	1.00
27_L	51_V	0.735	1.00
78_M	93_L	0.734	1.00
84_G	87_A	0.733	1.00
130_K	151_I	0.732	1.00
186_R	210_K	0.729	1.00
4_A	7_S	0.729	1.00
8_S	11_R	0.723	1.00
175_Y	179_E	0.721	1.00
169_I	200_I	0.717	1.00
16_M	41_S	0.715	1.00
51_V	55_L	0.714	1.00
172_G	185_H	0.714	1.00
2_A	43_I	0.713	1.00
9_M	13_F	0.712	1.00
7_S	10_W	0.704	1.00
26_L	64_M	0.704	1.00
6_Q	19_V	0.703	1.00
67_I	105_L	0.701	1.00
148_L	201_Y	0.699	1.00
200_I	204_C	0.695	1.00
173_I	208_F	0.693	1.00
169_I	203_C	0.689	1.00
48_Y	51_V	0.688	1.00
80_I	85_Q	0.686	0.99
25_M	116_E	0.683	0.99
186_R	207_F	0.680	0.99
157_R	161_T	0.675	0.99
78_M	89_F	0.674	0.99
57_K	82_T	0.671	0.99
142_E	146_A	0.666	0.99
10_W	13_F	0.664	0.99
143_E	146_A	0.660	0.99
137_D	179_E	0.660	0.99
199_D	202_K	0.659	0.99
48_Y	52_P	0.657	0.99
146_A	149_L	0.650	0.99
128_F	164_K	0.646	0.99
23_D	47_R	0.638	0.99
132_Q	154_E	0.635	0.99
171_L	208_F	0.634	0.99
52_P	88_K	0.634	0.99
107_Y	110_H	0.629	0.99
18_T	44_A	0.624	0.99
131_S	174_G	0.621	0.99
128_F	159_A	0.620	0.99
198_M	201_Y	0.614	0.99
51_V	56_W	0.612	0.99
61_L	86_L	0.610	0.99
26_L	105_L	0.605	0.99
149_L	153_E	0.605	0.99
124_G	164_K	0.603	0.99
153_E	201_Y	0.602	0.99
26_L	30_L	0.600	0.99
18_T	32_L	0.597	0.99
6_Q	35_E	0.597	0.99
118_G	123_Q	0.595	0.99
69_G	73_R	0.593	0.99
40_K	44_A	0.590	0.98
155_V	166_G	0.587	0.98
86_L	98_F	0.586	0.98
128_F	158_R	0.584	0.98
86_L	109_A	0.583	0.98
125_Q	164_K	0.582	0.98
77_R	97_K	0.579	0.98
71_M	101_M	0.578	0.98
35_E	43_I	0.576	0.98
18_T	35_E	0.576	0.98
55_L	83_V	0.572	0.98
61_L	75_L	0.572	0.98
173_I	211_F	0.571	0.98
156_A	194_T	0.568	0.98
160_R	196_I	0.566	0.98
102_G	105_L	0.566	0.98
67_I	86_L	0.566	0.98
174_G	177_K	0.565	0.98
75_L	105_L	0.563	0.98
91_L	110_H	0.562	0.98
188_K	191_D	0.559	0.98
95_E	102_G	0.559	0.98
119_A	123_Q	0.558	0.98
103_N	106_Y	0.558	0.98
100_I	103_N	0.557	0.98
155_V	169_I	0.553	0.98
133_I	178_D	0.551	0.98
129_G	155_V	0.549	0.98
143_E	147_V	0.549	0.98
171_L	204_C	0.547	0.98
52_P	110_H	0.544	0.97
61_L	82_T	0.543	0.97
94_L	102_G	0.542	0.97
5_I	8_S	0.538	0.97
155_V	159_A	0.535	0.97
149_L	197_T	0.534	0.97
194_T	203_C	0.532	0.97
57_K	83_V	0.531	0.97
191_D	203_C	0.529	0.97
30_L	70_R	0.525	0.97
34_L	63_K	0.525	0.97
203_C	207_F	0.522	0.97
82_T	86_L	0.522	0.97
108_H	113_D	0.520	0.97
101_M	105_L	0.520	0.97
169_I	190_I	0.517	0.97
75_L	80_I	0.517	0.97
53_N	57_K	0.515	0.96
132_Q	151_I	0.515	0.96
206_M	209_N	0.514	0.96
64_M	108_H	0.512	0.96
30_L	63_K	0.507	0.96
51_V	54_R	0.507	0.96
15_L	42_G	0.506	0.96
75_L	89_F	0.506	0.96
166_G	200_I	0.503	0.96
56_W	88_K	0.502	0.96
175_Y	178_D	0.502	0.96
5_I	12_E	0.501	0.96
89_F	106_Y	0.500	0.96

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
4dezA	2	0.53	100	0.18	Contact Map
3osnA	1	0.9677	100	0.183	Contact Map
3gqcA	3	0.9724	100	0.187	Contact Map
4f50A	1	0.9401	100	0.193	Contact Map
4tqrA	1	0.9401	100	0.194	Contact Map
4ecqA	1	0.9631	100	0.2	Contact Map
3pzpA	1	0.9493	100	0.2	Contact Map
2aq4A	1	0.9816	100	0.2	Contact Map
3mfiA	1	0.9585	100	0.204	Contact Map
1t94A	1	0.9355	100	0.205	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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