YHXD - BACSU - GREMLIN Contacts

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YHXD - Uncharacterized oxidoreductase YhxD

UniProt:	P40398	Sequences: MSDSNLTNPIKAFFHDEFPEQYQEPPGLQKNMKPVPDCGEKSYKGSGKLTGRKALVTGGDSGIGRAAAIAYAREGADVAINYLPEEQPDAEEVKELIEAEGRKAVLIPGDLSDESFCQDLVKQSHHELGGLDVLALVAGKQQAVENIEDLPTEQIYKTFEVNVFSLYWVVKAALPYLPEGASIITTTSVEGYNPSPMLLDYAATKNAIIGFTVGLGKQLASKGIRVNSVAPGPIWTPLQISGGQPTENIPKFGQGTPPAPLNRAGQPVELADVYVFLASENSSYVTSQVYGITGGIPTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	299 (242)
Sequences:	89289 (59493)
Seq/√Len:	3824.3

ECOLI - YGHA IDNO YGCW HDHA SRLD YOHF KDUD FABI UCPA HCAB FABG YBBO YGFF ENTA BDCA YCIK YDFG FOLM
BACSU - YHXD YHDF GS39 YHXC UXUB YWFH YXJF DHBA YXBG DHG2 YVAG YKVO DHG YJDA FABI FABL YVRD FABG FADH YTKK BACC KDUD YXNA YOXD YMFI YUSZ YUXG DLTE BZRD YQJQ
HALSA - Q9HNC5 Q9HQ41 Q9HRV8 Q9HSR4 Q9HMA5 Q9HPP2 Q9HRZ2 Q9HS80 Q9HP93
SULSO - Q97WF0 Q97UK6 Q97ZE4 Q97VV6 Q97UA4 Q97WD7 Q97Y09 Q97WL1 Q97VG2 Q97ZA0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
156_Y	164_F	3.408	1.00
182_S	225_R	2.889	1.00
206_N	210_G	2.801	1.00
156_Y	160_E	2.764	1.00
113_D	116_F	2.687	1.00
54_A	133_V	2.533	1.00
185_T	212_T	2.517	1.00
125_H	176_Y	2.495	1.00
230_A	289_V	2.453	1.00
178_P	222_K	2.410	1.00
118_Q	172_A	2.335	1.00
170_V	215_L	2.305	1.00
133_V	278_A	2.263	1.00
136_L	185_T	2.235	1.00
65_R	69_I	2.217	1.00
187_T	209_I	2.154	1.00
235_W	266_Q	2.146	1.00
81_N	109_G	2.118	1.00
114_E	152_T	2.106	1.00
77_D	103_K	2.099	1.00
121_V	173_A	2.079	1.00
90_A	106_L	2.053	1.00
288_Q	291_G	2.033	1.00
160_E	164_F	1.981	1.00
85_E	91_E	1.972	1.00
70_A	272_D	1.971	1.00
272_D	281_N	1.963	1.00
174_L	219_L	1.945	1.00
65_R	93_V	1.928	1.00
69_I	96_L	1.910	1.00
60_D	82_Y	1.888	1.00
65_R	96_L	1.870	1.00
273_V	290_Y	1.833	1.00
81_N	120_L	1.787	1.00
67_A	274_Y	1.770	1.00
70_A	74_E	1.765	1.00
53_K	77_D	1.752	1.00
105_V	127_E	1.748	1.00
70_A	275_V	1.745	1.00
265_G	284_Y	1.744	1.00
212_T	228_S	1.740	1.00
71_Y	278_A	1.688	1.00
59_G	80_I	1.672	1.00
109_G	116_F	1.649	1.00
79_A	124_S	1.645	1.00
162_N	204_T	1.642	1.00
123_Q	127_E	1.620	1.00
85_E	108_P	1.556	1.00
79_A	128_L	1.543	1.00
74_E	275_V	1.543	1.00
63_I	234_I	1.538	1.00
152_T	168_W	1.523	1.00
48_K	281_N	1.483	1.00
94_K	98_E	1.482	1.00
134_L	169_V	1.480	1.00
151_P	154_Q	1.474	1.00
122_K	126_H	1.463	1.00
166_L	208_I	1.462	1.00
53_K	130_G	1.425	1.00
70_A	73_R	1.422	1.00
94_K	106_L	1.417	1.00
119_D	123_Q	1.415	1.00
159_F	163_V	1.414	1.00
84_P	89_D	1.412	1.00
77_D	102_R	1.407	1.00
135_A	186_T	1.403	1.00
107_I	123_Q	1.401	1.00
61_S	89_D	1.393	1.00
142_Q	157_K	1.370	1.00
192_Y	291_G	1.367	1.00
68_A	80_I	1.349	1.00
123_Q	126_H	1.348	1.00
109_G	120_L	1.348	1.00
48_K	74_E	1.346	1.00
164_F	168_W	1.343	1.00
95_E	99_A	1.322	1.00
235_W	240_I	1.316	1.00
76_A	133_V	1.313	1.00
118_Q	122_K	1.313	1.00
54_A	71_Y	1.310	1.00
117_C	169_V	1.292	1.00
145_E	154_Q	1.289	1.00
114_E	168_W	1.283	1.00
163_V	207_A	1.280	1.00
273_V	292_I	1.277	1.00
229_V	274_Y	1.269	1.00
91_E	95_E	1.267	1.00
69_I	100_E	1.235	1.00
134_L	173_A	1.224	1.00
105_V	128_L	1.224	1.00
215_L	226_V	1.218	1.00
114_E	118_Q	1.211	1.00
61_S	237_P	1.204	1.00
148_E	178_P	1.201	1.00
187_T	228_S	1.195	1.00
71_Y	76_A	1.193	1.00
73_R	100_E	1.192	1.00
53_K	79_A	1.191	1.00
116_F	119_D	1.190	1.00
95_E	98_E	1.167	1.00
79_A	105_V	1.167	1.00
152_T	164_F	1.165	1.00
82_Y	90_A	1.151	1.00
51_G	76_A	1.151	1.00
49_L	76_A	1.148	1.00
136_L	170_V	1.147	1.00
170_V	183_I	1.144	1.00
155_I	164_F	1.142	1.00
107_I	120_L	1.137	1.00
209_I	289_V	1.129	1.00
140_K	161_V	1.129	1.00
131_L	173_A	1.116	1.00
55_L	120_L	1.102	1.00
182_S	227_N	1.099	1.00
228_S	289_V	1.090	1.00
54_A	76_A	1.077	1.00
137_V	186_T	1.072	1.00
70_A	271_A	1.066	1.00
234_I	265_G	1.058	1.00
69_I	73_R	1.053	1.00
159_F	164_F	1.049	1.00
146_N	149_D	1.045	1.00
92_E	96_L	1.040	1.00
212_T	226_V	1.037	1.00
112_S	157_K	1.031	1.00
52_R	280_E	1.028	1.00
79_A	107_I	1.021	1.00
142_Q	154_Q	1.012	1.00
66_A	268_V	1.011	1.00
150_L	200_D	1.005	1.00
67_A	135_A	1.003	1.00
80_I	104_A	0.999	1.00
66_A	69_I	0.998	1.00
91_E	94_K	0.996	1.00
114_E	171_K	0.993	1.00
186_T	274_Y	0.993	1.00
53_K	128_L	0.984	1.00
263_R	269_E	0.982	1.00
276_F	285_V	0.979	1.00
98_E	103_K	0.977	1.00
276_F	282_S	0.974	1.00
111_L	165_S	0.966	1.00
77_D	105_V	0.953	1.00
253_G	257_P	0.937	1.00
107_I	127_E	0.937	1.00
153_E	157_K	0.929	1.00
52_R	132_D	0.928	1.00
182_S	283_S	0.925	1.00
86_E	91_E	0.922	1.00
115_S	119_D	0.922	1.00
140_K	157_K	0.922	1.00
112_S	160_E	0.919	1.00
70_A	268_V	0.915	1.00
97_I	104_A	0.911	1.00
170_V	211_F	0.906	1.00
92_E	95_E	0.901	1.00
176_Y	179_E	0.900	1.00
63_I	67_A	0.897	1.00
85_E	106_L	0.897	1.00
166_L	185_T	0.896	1.00
135_A	274_Y	0.892	1.00
119_D	122_K	0.892	1.00
89_D	92_E	0.891	1.00
167_Y	211_F	0.886	1.00
72_A	102_R	0.881	1.00
124_S	128_L	0.863	1.00
202_A	210_G	0.861	1.00
94_K	104_A	0.856	1.00
72_A	97_I	0.849	1.00
285_V	290_Y	0.845	1.00
201_Y	205_K	0.838	1.00
268_V	272_D	0.837	1.00
191_G	209_I	0.834	1.00
93_V	96_L	0.826	1.00
108_P	116_F	0.822	1.00
162_N	205_K	0.820	1.00
237_P	240_I	0.819	1.00
67_A	271_A	0.815	1.00
105_V	123_Q	0.812	1.00
66_A	267_P	0.809	1.00
61_S	84_P	0.807	1.00
115_S	118_Q	0.807	1.00
152_T	171_K	0.806	1.00
96_L	100_E	0.802	1.00
209_I	228_S	0.800	1.00
147_I	219_L	0.798	1.00
97_I	102_R	0.797	1.00
254_Q	257_P	0.795	1.00
72_A	104_A	0.793	1.00
192_Y	230_A	0.793	1.00
170_V	185_T	0.789	1.00
71_Y	275_V	0.789	1.00
66_A	271_A	0.788	1.00
109_G	117_C	0.782	1.00
172_A	175_P	0.781	1.00
159_F	204_T	0.780	1.00
59_G	81_N	0.779	1.00
199_L	218_Q	0.776	1.00
152_T	156_Y	0.776	1.00
188_S	201_Y	0.773	1.00
61_S	65_R	0.773	1.00
65_R	92_E	0.769	1.00
77_D	128_L	0.763	1.00
194_P	210_G	0.757	1.00
148_E	219_L	0.753	1.00
55_L	131_L	0.753	1.00
55_L	81_N	0.752	1.00
184_I	278_A	0.752	1.00
159_F	203_A	0.750	1.00
114_E	172_A	0.749	1.00
155_I	167_Y	0.747	1.00
131_L	176_Y	0.745	1.00
154_Q	157_K	0.742	1.00
183_I	226_V	0.740	1.00
261_L	286_T	0.738	1.00
273_V	276_F	0.733	1.00
125_H	179_E	0.728	1.00
136_L	169_V	0.723	1.00
57_T	169_V	0.716	1.00
177_L	180_G	0.716	1.00
259_A	284_Y	0.714	1.00
147_I	215_L	0.712	1.00
69_I	97_I	0.712	1.00
202_A	206_N	0.704	1.00
166_L	170_V	0.702	1.00
253_G	256_T	0.699	1.00
180_G	225_R	0.698	1.00
184_I	274_Y	0.696	1.00
158_T	204_T	0.696	1.00
244_Q	248_N	0.692	1.00
125_H	130_G	0.690	1.00
134_L	183_I	0.688	1.00
74_E	281_N	0.681	1.00
192_Y	209_I	0.677	1.00
286_T	295_G	0.677	1.00
130_G	176_Y	0.673	1.00
199_L	211_F	0.673	1.00
122_K	176_Y	0.667	1.00
90_A	108_P	0.667	1.00
121_V	172_A	0.664	1.00
197_M	218_Q	0.664	1.00
244_Q	247_E	0.661	1.00
117_C	168_W	0.659	1.00
60_D	90_A	0.658	1.00
163_V	203_A	0.657	1.00
71_Y	274_Y	0.655	1.00
173_A	177_L	0.655	1.00
178_P	219_L	0.654	1.00
71_Y	133_V	0.651	1.00
245_P	248_N	0.646	1.00
140_K	238_L	0.646	1.00
82_Y	85_E	0.645	1.00
219_L	222_K	0.643	1.00
53_K	124_S	0.640	1.00
121_V	169_V	0.640	1.00
96_L	99_A	0.640	1.00
284_Y	294_G	0.639	1.00
66_A	70_A	0.632	1.00
145_E	149_D	0.632	1.00
117_C	172_A	0.631	1.00
82_Y	108_P	0.630	1.00
243_G	247_E	0.627	1.00
103_K	127_E	0.625	1.00
209_I	230_A	0.624	1.00
271_A	275_V	0.623	1.00
185_T	226_V	0.623	1.00
206_N	213_V	0.622	1.00
57_T	137_V	0.621	1.00
177_L	181_A	0.620	1.00
227_N	277_L	0.620	1.00
139_G	162_N	0.619	1.00
51_G	77_D	0.619	1.00
114_E	153_E	0.618	1.00
164_F	167_Y	0.617	1.00
140_K	204_T	0.614	1.00
243_G	246_T	0.613	1.00
62_G	236_T	0.611	1.00
285_V	292_I	0.611	1.00
98_E	101_G	0.606	1.00
190_E	202_A	0.606	1.00
234_I	270_L	0.606	1.00
70_A	281_N	0.605	1.00
269_E	283_S	0.602	1.00
83_L	110_D	0.600	1.00
263_R	283_S	0.600	1.00
214_G	218_Q	0.597	1.00
280_E	283_S	0.593	1.00
233_P	239_Q	0.592	1.00
91_E	106_L	0.592	1.00
74_E	279_S	0.590	1.00
174_L	178_P	0.588	1.00
167_Y	171_K	0.586	1.00
56_V	68_A	0.586	1.00
166_L	169_V	0.585	1.00
187_T	230_A	0.585	1.00
86_E	89_D	0.583	1.00
82_Y	106_L	0.583	1.00
155_I	200_D	0.582	1.00
209_I	213_V	0.582	1.00
157_K	160_E	0.582	1.00
265_G	294_G	0.581	1.00
221_S	262_N	0.580	1.00
122_K	172_A	0.578	1.00
81_N	111_L	0.577	1.00
80_I	93_V	0.576	1.00
59_G	68_A	0.576	1.00
174_L	222_K	0.574	1.00
72_A	103_K	0.574	1.00
272_D	283_S	0.569	1.00
120_L	169_V	0.567	1.00
80_I	106_L	0.565	1.00
69_I	93_V	0.564	1.00
122_K	125_H	0.560	1.00
69_I	268_V	0.559	1.00
220_A	286_T	0.556	1.00
168_W	172_A	0.555	1.00
54_A	278_A	0.555	1.00
142_Q	145_E	0.554	1.00
256_T	264_A	0.547	1.00
112_S	161_V	0.547	1.00
90_A	94_K	0.546	1.00
279_S	282_S	0.545	1.00
82_Y	89_D	0.545	1.00
118_Q	175_P	0.545	1.00
124_S	127_E	0.544	1.00
61_S	82_Y	0.544	1.00
101_G	104_A	0.543	1.00
206_N	209_I	0.541	1.00
270_L	292_I	0.540	1.00
193_N	296_I	0.539	1.00
202_A	214_G	0.536	1.00
199_L	214_G	0.535	1.00
220_A	261_L	0.534	1.00
52_R	76_A	0.532	1.00
124_S	129_G	0.531	1.00
121_V	125_H	0.530	1.00
52_R	180_G	0.529	1.00
86_E	92_E	0.529	1.00
73_R	268_V	0.527	1.00
81_N	124_S	0.524	1.00
136_L	166_L	0.524	1.00
240_I	244_Q	0.523	1.00
64_G	137_V	0.520	1.00
216_G	287_S	0.519	1.00
68_A	97_I	0.518	1.00
91_E	98_E	0.517	1.00
93_V	97_I	0.516	1.00
161_V	165_S	0.516	1.00
155_I	203_A	0.513	1.00
162_N	201_Y	0.512	1.00
141_Q	238_L	0.512	1.00
266_Q	269_E	0.510	1.00
203_A	211_F	0.509	1.00
155_I	159_F	0.508	1.00
155_I	163_V	0.507	1.00
210_G	213_V	0.506	1.00
179_E	222_K	0.505	1.00
285_V	288_Q	0.505	1.00
55_L	124_S	0.504	1.00
111_L	138_A	0.502	1.00
118_Q	171_K	0.502	1.00
273_V	285_V	0.502	1.00
216_G	286_T	0.500	1.00

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
1vl8A	4	0.8294	100	0.225	Contact Map
3wtcA	4	0.8361	100	0.237	Contact Map
2ae2A	4	0.8462	100	0.24	Contact Map
3r3sA	4	0.9766	100	0.24	Contact Map
4is2A	3	0.7057	100	0.24	Contact Map
1iy8A	4	0.8361	100	0.24	Contact Map
4nbvA	4	0.8161	100	0.241	Contact Map
1zemA	4	0.8261	100	0.242	Contact Map
4bmnA	4	0.806	100	0.242	Contact Map
4nimA	4	0.7525	100	0.242	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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