RMLD - ECOLI - GREMLIN Contacts

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RMLD - dTDP-4-dehydrorhamnose reductase

UniProt:	P37760	Sequences: MNILLFGKTGQVGWELQRALAPLGNLIAFDVHSTDYCGDFSNPEGVAETVRSIRPDIIVNAAAHTAVDKAESEPEFAQLINATSVEAIAKAANEVGAWVIHYSTDYVFPGNGDMPWLETDATAPLNVYGETKLAGEKALQEYCAKHLIFRTSWVYAGKGNNFAKTMLRLAKEREELAVINDQFGAPTGAELLADCTAHAIRVALNKPDVAGLYHLVASGTTTWYDYAALVFEEARKAGIPLALNKLNAVPTTAYPTPARRPHNSRLNTEKFQQNFALVLPDWQVGVKRMLNELFTTTAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12411
Length:	299 (271)
Sequences:	56921 (39639)
Seq/√Len:	2407.9

ECOLI - RMLD RMLB1 GALE RMLB2 GM4D YBJS FCL HLDD YFCH YEEZ QOR2 ARNA YBJT YRAR
BACSU - SPSK GALE YFNG YTCB RMLB YFHF YTBQ YHFK YWNB YESF YHEG
HALSA - Q9HSV1 Q9HSU9 Q9HRD1 Q9HML4 Q9HSE7 Q9HS50 Q9HPF1 Q9HSQ3 Q9HNV3 Q9HR86
SULSO - Q97VN5 Q980W1 Q7LXE8 Q7LXG5 Q97UM3 Q97XJ9 Q97XG1 Q7LX44 Q7LXE6 Q97XF9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_K	28_A	3.121	1.00
229_L	283_Q	2.832	1.00
2_N	25_N	2.822	1.00
195_C	215_L	2.740	1.00
213_Y	274_N	2.673	1.00
19_A	194_D	2.660	1.00
211_G	270_K	2.562	1.00
47_A	94_E	2.395	1.00
79_L	83_T	2.390	1.00
281_D	284_V	2.388	1.00
57_I	200_I	2.322	1.00
73_E	76_F	2.275	1.00
232_E	283_Q	2.188	1.00
102_Y	196_T	2.185	1.00
269_E	273_Q	2.173	1.00
19_A	23_L	2.096	1.00
98_W	145_K	2.074	1.00
19_A	197_A	2.050	1.00
29_F	38_G	2.023	1.00
60_N	101_H	2.016	1.00
272_Q	278_V	2.015	1.00
42_N	45_G	2.002	1.00
59_V	200_I	1.991	1.00
6_F	60_N	1.955	1.00
233_E	287_K	1.943	1.00
38_G	45_G	1.935	1.00
23_L	201_R	1.909	1.00
5_L	17_Q	1.880	1.00
4_L	55_P	1.879	1.00
27_I	55_P	1.868	1.00
224_Y	228_A	1.858	1.00
229_L	232_E	1.804	1.00
155_Y	285_G	1.803	1.00
194_D	198_H	1.789	1.00
2_N	27_I	1.776	1.00
151_T	196_T	1.774	1.00
190_E	288_R	1.768	1.00
222_T	225_D	1.753	1.00
117_L	120_D	1.739	1.00
218_S	272_Q	1.720	1.00
149_F	199_A	1.677	1.00
168_R	172_E	1.669	1.00
139_L	146_H	1.639	1.00
16_L	193_A	1.631	1.00
23_L	197_A	1.592	1.00
16_L	59_V	1.590	1.00
86_E	138_A	1.587	1.00
41_S	79_L	1.533	1.00
78_Q	134_A	1.532	1.00
118_E	270_K	1.520	1.00
188_G	288_R	1.518	1.00
86_E	90_K	1.512	1.00
43_P	90_K	1.491	1.00
47_A	91_A	1.490	1.00
19_A	22_P	1.482	1.00
197_A	201_R	1.479	1.00
27_I	36_Y	1.470	1.00
83_T	86_E	1.461	1.00
229_L	233_E	1.461	1.00
287_K	291_N	1.455	1.00
19_A	193_A	1.442	1.00
271_F	275_F	1.441	1.00
149_F	196_T	1.438	1.00
268_T	272_Q	1.437	1.00
12_V	154_V	1.431	1.00
133_L	137_K	1.429	1.00
75_E	79_L	1.425	1.00
17_Q	28_A	1.412	1.00
16_L	61_A	1.411	1.00
58_I	92_A	1.406	1.00
103_S	107_V	1.401	1.00
48_E	52_S	1.387	1.00
225_D	228_A	1.382	1.00
122_T	133_L	1.369	1.00
98_W	147_L	1.368	1.00
60_N	85_V	1.362	1.00
52_S	55_P	1.360	1.00
151_T	192_L	1.353	1.00
280_P	288_R	1.349	1.00
85_V	135_G	1.337	1.00
59_V	196_T	1.328	1.00
128_Y	132_K	1.315	1.00
89_A	142_Y	1.307	1.00
189_A	193_A	1.300	1.00
188_G	285_G	1.294	1.00
61_A	102_Y	1.291	1.00
92_A	97_A	1.281	1.00
47_A	95_V	1.267	1.00
108_F	214_H	1.263	1.00
284_V	287_K	1.263	1.00
81_N	131_T	1.255	1.00
187_T	192_L	1.254	1.00
45_G	48_E	1.253	1.00
137_K	140_Q	1.249	1.00
20_L	197_A	1.249	1.00
18_R	158_K	1.246	1.00
211_G	274_N	1.227	1.00
185_A	218_S	1.224	1.00
90_K	93_N	1.222	1.00
88_I	99_V	1.213	1.00
102_Y	151_T	1.202	1.00
8_K	17_Q	1.199	1.00
169_L	174_E	1.194	1.00
152_S	266_L	1.192	1.00
43_P	87_A	1.189	1.00
48_E	51_R	1.180	1.00
183_F	220_T	1.175	1.00
90_K	94_E	1.173	1.00
284_V	288_R	1.171	1.00
43_P	47_A	1.170	1.00
117_L	267_N	1.154	1.00
50_V	55_P	1.153	1.00
143_C	146_H	1.149	1.00
140_Q	148_I	1.136	1.00
51_R	95_V	1.127	1.00
130_E	134_A	1.126	1.00
140_Q	212_L	1.116	1.00
268_T	279_L	1.110	1.00
92_A	99_V	1.091	1.00
15_E	190_E	1.083	1.00
270_K	274_N	1.083	1.00
4_L	29_F	1.080	1.00
3_I	20_L	1.077	1.00
101_H	135_G	1.077	1.00
113_D	117_L	1.074	1.00
195_C	271_F	1.064	1.00
194_D	277_L	1.060	1.00
40_F	84_S	1.058	1.00
188_G	280_P	1.056	1.00
231_F	237_A	1.053	1.00
150_R	212_L	1.052	1.00
221_T	282_W	1.051	1.00
280_P	284_V	1.044	1.00
140_Q	146_H	1.044	1.00
50_V	58_I	1.039	1.00
19_A	190_E	1.037	1.00
9_T	30_D	1.035	1.00
18_R	22_P	1.033	1.00
40_F	62_A	1.022	1.00
138_A	141_E	1.021	1.00
119_T	270_K	1.014	1.00
15_E	189_A	1.012	1.00
113_D	120_D	1.004	1.00
11_Q	156_A	1.003	1.00
188_G	191_L	0.998	1.00
145_K	209_V	0.990	1.00
101_H	139_L	0.988	1.00
216_V	266_L	0.988	1.00
89_A	99_V	0.988	1.00
91_A	95_V	0.986	1.00
47_A	51_R	0.979	1.00
136_E	150_R	0.978	1.00
283_Q	287_K	0.975	1.00
228_A	231_F	0.973	1.00
233_E	290_L	0.970	1.00
69_K	73_E	0.966	1.00
27_I	52_S	0.962	1.00
61_A	196_T	0.961	1.00
220_T	263_N	0.961	1.00
155_Y	188_G	0.959	1.00
101_H	148_I	0.955	1.00
116_W	120_D	0.953	1.00
150_R	214_H	0.937	1.00
2_N	56_D	0.936	1.00
213_Y	270_K	0.935	1.00
44_E	48_E	0.934	1.00
191_L	217_A	0.933	1.00
14_W	158_K	0.933	1.00
32_H	35_D	0.933	1.00
100_I	149_F	0.932	1.00
234_A	290_L	0.927	1.00
46_V	91_A	0.925	1.00
11_Q	189_A	0.924	1.00
2_N	55_P	0.922	1.00
3_I	57_I	0.919	1.00
270_K	273_Q	0.918	1.00
147_L	199_A	0.916	1.00
183_F	222_T	0.915	1.00
80_I	84_S	0.912	1.00
90_K	142_Y	0.912	1.00
221_T	225_D	0.910	1.00
64_H	80_I	0.909	1.00
83_T	87_A	0.908	1.00
21_A	26_L	0.907	1.00
99_V	139_L	0.905	1.00
154_V	192_L	0.902	1.00
220_T	265_R	0.901	1.00
224_Y	248_A	0.898	1.00
162_F	166_M	0.890	1.00
77_A	131_T	0.888	1.00
78_Q	82_A	0.882	1.00
44_E	47_A	0.882	1.00
6_F	88_I	0.878	1.00
198_H	275_F	0.876	1.00
216_V	268_T	0.871	1.00
148_I	212_L	0.870	1.00
89_A	139_L	0.869	1.00
233_E	286_V	0.868	1.00
6_F	62_A	0.868	1.00
195_C	277_L	0.868	1.00
3_I	59_V	0.863	1.00
134_A	137_K	0.858	1.00
29_F	46_V	0.855	1.00
288_R	291_N	0.852	1.00
50_V	91_A	0.851	1.00
50_V	95_V	0.848	1.00
198_H	201_R	0.843	1.00
87_A	90_K	0.842	1.00
103_S	136_E	0.841	1.00
15_E	18_R	0.835	1.00
190_E	280_P	0.835	1.00
149_F	215_L	0.832	1.00
36_Y	49_T	0.829	1.00
233_E	283_Q	0.828	1.00
199_A	275_F	0.823	1.00
219_G	281_D	0.819	1.00
91_A	94_E	0.817	1.00
154_V	187_T	0.817	1.00
17_Q	26_L	0.812	1.00
45_G	49_T	0.811	1.00
231_F	239_I	0.811	1.00
208_D	211_G	0.810	1.00
29_F	49_T	0.810	1.00
93_N	142_Y	0.806	1.00
16_L	20_L	0.805	1.00
29_F	45_G	0.805	1.00
43_P	94_E	0.804	1.00
87_A	91_A	0.800	1.00
218_S	268_T	0.797	1.00
12_V	192_L	0.794	1.00
82_A	134_A	0.793	1.00
269_E	272_Q	0.787	1.00
3_I	200_I	0.787	1.00
78_Q	83_T	0.784	1.00
32_H	37_C	0.783	1.00
168_R	171_K	0.781	1.00
57_I	98_W	0.780	1.00
280_P	285_G	0.780	1.00
194_D	280_P	0.780	1.00
152_S	216_V	0.777	1.00
89_A	138_A	0.777	1.00
231_F	236_K	0.776	1.00
36_Y	52_S	0.773	1.00
198_H	277_L	0.772	1.00
221_T	226_Y	0.770	1.00
165_T	168_R	0.765	1.00
15_E	193_A	0.761	1.00
183_F	263_N	0.760	1.00
161_N	164_K	0.760	1.00
31_V	39_D	0.755	1.00
140_Q	144_A	0.754	1.00
76_F	79_L	0.752	1.00
15_E	19_A	0.751	1.00
78_Q	131_T	0.751	1.00
21_A	24_G	0.750	1.00
137_K	141_E	0.745	1.00
85_V	89_A	0.744	1.00
199_A	271_F	0.741	1.00
76_F	80_I	0.739	1.00
84_S	87_A	0.737	1.00
41_S	80_I	0.733	1.00
194_D	197_A	0.731	1.00
165_T	169_L	0.729	1.00
85_V	139_L	0.728	1.00
170_A	231_F	0.728	1.00
134_A	138_A	0.726	1.00
16_L	196_T	0.726	1.00
64_H	76_F	0.723	1.00
107_V	122_T	0.721	1.00
114_M	120_D	0.720	1.00
109_P	123_A	0.715	1.00
58_I	88_I	0.713	1.00
124_P	129_G	0.711	1.00
50_V	92_A	0.710	1.00
118_E	271_F	0.704	1.00
111_N	116_W	0.702	1.00
215_L	271_F	0.699	1.00
74_P	130_E	0.697	1.00
198_H	276_A	0.695	1.00
233_E	291_N	0.693	1.00
33_S	37_C	0.692	1.00
228_A	232_E	0.691	1.00
229_L	282_W	0.691	1.00
126_N	129_G	0.688	1.00
149_F	195_C	0.685	1.00
107_V	136_E	0.685	1.00
208_D	274_N	0.681	1.00
58_I	99_V	0.681	1.00
225_D	229_L	0.676	1.00
60_N	88_I	0.676	1.00
14_W	18_R	0.675	1.00
105_D	152_S	0.673	1.00
143_C	210_A	0.671	1.00
157_G	288_R	0.671	1.00
173_R	176_L	0.671	1.00
4_L	58_I	0.666	1.00
4_L	38_G	0.666	1.00
226_Y	282_W	0.665	1.00
20_L	200_I	0.661	1.00
130_E	137_K	0.659	1.00
169_L	172_E	0.657	1.00
167_L	171_K	0.655	1.00
64_H	77_A	0.655	1.00
78_Q	130_E	0.655	1.00
146_H	210_A	0.653	1.00
127_V	130_E	0.652	1.00
157_G	188_G	0.645	1.00
219_G	283_Q	0.644	1.00
105_D	266_L	0.644	1.00
135_G	139_L	0.643	1.00
71_E	127_V	0.643	1.00
23_L	198_H	0.641	1.00
46_V	87_A	0.641	1.00
130_E	141_E	0.640	1.00
193_A	197_A	0.635	1.00
138_A	142_Y	0.631	1.00
49_T	52_S	0.627	1.00
131_T	135_G	0.627	1.00
167_L	290_L	0.625	1.00
42_N	46_V	0.625	1.00
39_D	42_N	0.622	1.00
112_G	120_D	0.621	1.00
9_T	32_H	0.618	1.00
182_Q	223_W	0.618	1.00
49_T	55_P	0.617	1.00
272_Q	279_L	0.616	1.00
118_E	214_H	0.612	1.00
227_A	231_F	0.611	1.00
115_P	267_N	0.610	1.00
60_N	99_V	0.609	1.00
140_Q	143_C	0.607	1.00
191_L	280_P	0.605	1.00
192_L	215_L	0.604	1.00
173_R	236_K	0.604	1.00
4_L	49_T	0.602	1.00
100_I	200_I	0.600	1.00
63_A	81_N	0.598	1.00
57_I	100_I	0.596	1.00
17_Q	21_A	0.595	1.00
122_T	137_K	0.594	1.00
185_A	217_A	0.591	1.00
175_E	240_P	0.589	1.00
124_P	133_L	0.587	1.00
89_A	93_N	0.585	1.00
191_L	194_D	0.583	1.00
167_L	230_V	0.582	1.00
100_I	199_A	0.582	1.00
64_H	81_N	0.582	1.00
163_A	166_M	0.578	1.00
46_V	50_V	0.578	1.00
16_L	197_A	0.577	1.00
23_L	194_D	0.576	1.00
27_I	49_T	0.576	1.00
157_G	190_E	0.573	1.00
70_A	77_A	0.573	1.00
18_R	190_E	0.572	1.00
15_E	158_K	0.570	1.00
151_T	154_V	0.570	1.00
153_W	184_G	0.570	1.00
229_L	286_V	0.567	1.00
106_Y	129_G	0.564	1.00
74_P	127_V	0.563	1.00
5_L	28_A	0.562	1.00
117_L	269_E	0.562	1.00
9_T	28_A	0.561	1.00
177_A	180_N	0.560	1.00
38_G	46_V	0.558	1.00
197_A	200_I	0.557	1.00
86_E	142_Y	0.557	1.00
161_N	165_T	0.557	1.00
213_Y	271_F	0.555	1.00
185_A	220_T	0.552	1.00
85_V	101_H	0.552	1.00
139_L	148_I	0.550	1.00
173_R	177_A	0.548	1.00
36_Y	45_G	0.545	1.00
115_P	265_R	0.543	1.00
183_F	265_R	0.542	1.00
141_E	144_A	0.542	1.00
231_F	234_A	0.540	1.00
155_Y	217_A	0.539	1.00
221_T	229_L	0.539	1.00
38_G	49_T	0.539	1.00
147_L	207_P	0.538	1.00
100_I	196_T	0.538	1.00
92_A	95_V	0.538	1.00
20_L	59_V	0.533	1.00
122_T	212_L	0.533	1.00
5_L	20_L	0.529	1.00
236_K	239_I	0.528	1.00
4_L	50_V	0.527	1.00
81_N	128_Y	0.524	1.00
148_I	210_A	0.521	1.00
104_T	132_K	0.520	1.00
147_L	213_Y	0.520	1.00
127_V	131_T	0.516	1.00
209_V	213_Y	0.515	1.00
50_V	88_I	0.507	1.00
17_Q	24_G	0.507	1.00
261_P	264_S	0.506	1.00
102_Y	149_F	0.505	1.00
8_K	30_D	0.504	1.00
51_R	94_E	0.503	1.00
103_S	148_I	0.502	1.00
257_P	260_R	0.501	1.00
230_V	286_V	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
1n2sA	2	0.9866	100	0.163	Contact Map
3sc6A	3	0.9298	100	0.222	Contact Map
1sb8A	2	0.9599	100	0.226	Contact Map
1vl0A	3	0.9298	100	0.227	Contact Map
3rufA	2	0.9465	100	0.236	Contact Map
1rpnA	4	0.9599	100	0.239	Contact Map
1rkxA	3	0.9498	100	0.241	Contact Map
2pzmA	2	0.9431	100	0.241	Contact Map
1oc2A	2	0.9465	100	0.242	Contact Map
2ydyA	1	0.8462	100	0.247	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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