Q9HPL3 - HALSA - GREMLIN Contacts

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Q9HPL3 - Probable cobalamin biosynthesis protein CobD

UniProt:	Q9HPL3	Sequences: MTAAAVGAVAVGVALDAAIAEPPAGCHPVAWFGRAVGVVDRPWTRPLAVGALAAIALPLAAAATVWAAVTVATWGSALAGAVVAGLVVFVTTSRRMLLAEASGVIAATRTENSLDAARRRLRALAGRDPDALSAGELRSAAVESTAENLADGLVAPLAAFAVGAAVVSLPVGAAAAAWVKAVNTLDSMLGYRSKRVGTASARLDDAVMWVPARLAAVLIAATARAPAAVSRAAADAGAPPSPNSGWPMATLAAVLDCRLVKPGVYELREAAALPGLAESRRGVRVVSTAGGLAYALTAAVVYAGGGGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (285)
Sequences:	2622 (2066)
Seq/√Len:	122.4

ECOLI - AMPE
HALSA - Q9HPL3
SULSO - Q97TZ5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
182_V	207_V	5.221	1.00
47_L	198_T	4.691	1.00
54_A	203_L	3.733	1.00
101_A	145_T	3.455	1.00
65_V	177_A	3.300	1.00
216_A	232_A	3.225	1.00
133_S	136_E	3.159	1.00
189_L	200_S	3.002	1.00
32_F	57_L	2.991	1.00
53_A	189_L	2.946	1.00
51_A	198_T	2.902	1.00
113_S	116_A	2.849	1.00
54_A	58_P	2.743	1.00
114_L	137_L	2.638	1.00
91_T	176_A	2.605	1.00
38_V	42_P	2.480	1.00
88_V	160_F	2.479	1.00
62_A	178_W	2.422	1.00
113_S	117_A	2.314	1.00
51_A	199_A	2.295	1.00
95_R	99_A	2.233	1.00
11_V	85_G	2.151	1.00
223_A	254_V	2.080	1.00
132_L	136_E	2.073	1.00
120_R	123_A	2.052	1.00
281_R	287_S	2.038	1.00
262_P	272_A	2.038	1.00
101_A	141_A	2.002	1.00
258_R	275_G	1.958	1.00
149_L	215_A	1.942	1.00
121_L	140_A	1.938	1.00
264_V	270_A	1.918	1.00
154_V	215_A	1.918	1.00
224_R	227_A	1.908	1.00
206_A	209_W	1.886	1.00
58_P	178_W	1.873	1.00
156_P	179_V	1.848	1.00
40_D	195_R	1.821	1.00
35_A	57_L	1.805	1.00
228_A	253_A	1.788	1.00
155_A	179_V	1.767	1.00
262_P	270_A	1.732	1.00
54_A	200_S	1.730	1.00
160_F	176_A	1.707	1.00
178_W	207_V	1.668	1.00
232_A	246_W	1.660	1.00
43_W	196_V	1.645	1.00
198_T	202_R	1.632	1.00
158_A	214_L	1.621	1.00
54_A	185_L	1.619	1.00
236_A	246_W	1.608	1.00
91_T	177_A	1.605	1.00
179_V	208_M	1.595	1.00
203_L	207_V	1.561	1.00
152_G	187_S	1.554	1.00
61_A	65_V	1.537	1.00
227_A	230_S	1.534	1.00
12_G	85_G	1.529	1.00
121_L	137_L	1.529	1.00
220_A	229_V	1.521	1.00
150_A	155_A	1.521	1.00
107_A	116_A	1.511	1.00
219_I	251_L	1.507	1.00
88_V	176_A	1.506	1.00
182_V	203_L	1.492	1.00
46_P	49_V	1.491	1.00
16_D	21_E	1.488	1.00
287_S	290_G	1.485	1.00
34_R	38_V	1.474	1.00
185_L	200_S	1.451	1.00
180_K	187_S	1.436	1.00
231_R	234_A	1.429	1.00
154_V	218_L	1.417	1.00
126_G	191_Y	1.415	1.00
162_V	175_A	1.414	1.00
54_A	199_A	1.409	1.00
44_T	49_V	1.407	1.00
236_A	245_G	1.401	1.00
58_P	203_L	1.388	1.00
116_A	119_R	1.378	1.00
149_L	219_I	1.369	1.00
8_A	12_G	1.358	1.00
72_A	83_V	1.344	1.00
17_A	94_R	1.339	1.00
142_V	259_L	1.334	1.00
21_E	30_A	1.322	1.00
116_A	120_R	1.314	1.00
266_E	269_E	1.311	1.00
273_L	276_L	1.298	1.00
39_V	53_A	1.272	1.00
231_R	235_D	1.268	1.00
232_A	236_A	1.267	1.00
104_V	137_L	1.264	1.00
231_R	253_A	1.262	1.00
32_F	181_A	1.259	1.00
146_A	251_L	1.243	0.99
8_A	85_G	1.243	0.99
272_A	275_G	1.232	0.99
12_G	88_V	1.231	0.99
98_L	102_S	1.227	0.99
228_A	254_V	1.218	0.99
105_I	110_T	1.211	0.99
30_A	34_R	1.209	0.99
25_G	31_W	1.207	0.99
13_V	299_A	1.206	0.99
149_L	154_V	1.203	0.99
179_V	183_N	1.176	0.99
36_V	189_L	1.166	0.99
57_L	60_A	1.160	0.99
100_E	103_G	1.155	0.99
15_L	89_F	1.152	0.99
43_W	53_A	1.148	0.99
9_V	160_F	1.143	0.99
219_I	298_A	1.138	0.99
13_V	94_R	1.135	0.99
80_G	84_A	1.127	0.99
128_D	267_L	1.122	0.99
39_V	56_A	1.118	0.99
152_G	180_K	1.117	0.99
220_A	225_A	1.116	0.99
35_A	60_A	1.104	0.99
44_T	196_V	1.099	0.99
81_A	85_G	1.095	0.99
47_L	199_A	1.092	0.99
240_P	271_A	1.090	0.99
239_P	248_M	1.087	0.99
103_G	120_R	1.080	0.99
36_V	185_L	1.078	0.98
139_S	263_G	1.077	0.98
54_A	182_V	1.073	0.98
33_G	188_M	1.069	0.98
276_L	279_S	1.066	0.98
108_T	138_R	1.059	0.98
159_A	175_A	1.058	0.98
199_A	203_L	1.040	0.98
271_A	276_L	1.035	0.98
100_E	120_R	1.035	0.98
220_A	228_A	1.031	0.98
271_A	279_S	1.026	0.98
251_L	291_G	1.008	0.98
11_V	81_A	1.004	0.98
126_G	248_M	0.999	0.98
150_A	247_P	0.998	0.97
19_I	89_F	0.997	0.97
104_V	107_A	0.982	0.97
108_T	134_A	0.981	0.97
56_A	60_A	0.981	0.97
125_A	129_P	0.980	0.97
126_G	187_S	0.979	0.97
126_G	140_A	0.970	0.97
251_L	294_Y	0.970	0.97
220_A	254_V	0.957	0.97
100_E	144_S	0.955	0.97
119_R	123_A	0.954	0.97
192_R	198_T	0.952	0.97
216_A	246_W	0.950	0.97
48_A	52_L	0.945	0.97
229_V	233_A	0.938	0.96
261_K	267_L	0.931	0.96
47_L	51_A	0.927	0.96
122_R	129_P	0.925	0.96
40_D	44_T	0.923	0.96
186_D	201_A	0.921	0.96
9_V	157_L	0.920	0.96
102_S	105_I	0.920	0.96
43_W	52_L	0.918	0.96
69_V	84_A	0.917	0.96
275_G	278_E	0.911	0.96
43_W	49_V	0.909	0.96
257_C	283_V	0.897	0.95
129_P	132_L	0.890	0.95
284_R	287_S	0.885	0.95
98_L	292_L	0.880	0.95
235_D	253_A	0.880	0.95
72_A	80_G	0.876	0.95
226_P	230_S	0.874	0.95
235_D	238_A	0.873	0.95
134_A	138_R	0.867	0.94
14_A	18_A	0.863	0.94
147_E	183_N	0.860	0.94
273_L	277_A	0.859	0.94
69_V	72_A	0.858	0.94
115_D	130_D	0.856	0.94
183_N	187_S	0.851	0.94
223_A	228_A	0.845	0.94
100_E	123_A	0.844	0.94
87_V	169_L	0.844	0.94
240_P	263_G	0.841	0.93
61_A	181_A	0.839	0.93
150_A	208_M	0.835	0.93
76_S	80_G	0.835	0.93
219_I	250_T	0.831	0.93
216_A	220_A	0.830	0.93
107_A	120_R	0.828	0.93
112_N	117_A	0.825	0.93
178_W	182_V	0.817	0.92
36_V	53_A	0.810	0.92
27_H	33_G	0.809	0.92
69_V	169_L	0.809	0.92
86_L	90_V	0.806	0.92
136_E	263_G	0.802	0.92
69_V	80_G	0.802	0.92
227_A	256_D	0.801	0.92
57_L	181_A	0.799	0.92
132_L	140_A	0.790	0.91
121_L	136_E	0.784	0.91
138_R	142_V	0.780	0.91
215_A	247_P	0.780	0.91
256_D	280_R	0.774	0.90
33_G	148_N	0.773	0.90
236_A	249_A	0.772	0.90
203_L	206_A	0.766	0.90
60_A	63_A	0.762	0.90
8_A	84_A	0.760	0.89
108_T	117_A	0.759	0.89
190_G	197_G	0.757	0.89
150_A	179_V	0.755	0.89
71_V	75_G	0.753	0.89
262_P	275_G	0.749	0.89
67_A	71_V	0.749	0.89
279_S	285_V	0.745	0.88
231_R	278_E	0.739	0.88
232_A	249_A	0.736	0.88
285_V	288_T	0.731	0.88
227_A	231_R	0.731	0.88
216_A	250_T	0.728	0.87
183_N	208_M	0.727	0.87
151_D	186_D	0.726	0.87
193_S	266_E	0.724	0.87
38_V	41_R	0.722	0.87
60_A	64_T	0.722	0.87
158_A	162_V	0.722	0.87
192_R	240_P	0.721	0.87
105_I	289_A	0.721	0.87
284_R	288_T	0.720	0.87
283_V	287_S	0.720	0.87
288_T	291_G	0.719	0.87
154_V	302_Y	0.719	0.87
147_E	151_D	0.719	0.87
102_S	106_A	0.718	0.87
279_S	282_G	0.717	0.87
151_D	204_D	0.715	0.86
97_L	148_N	0.714	0.86
240_P	244_S	0.714	0.86
66_W	70_T	0.714	0.86
126_G	205_D	0.710	0.86
13_V	17_A	0.710	0.86
148_N	188_M	0.709	0.86
147_E	186_D	0.708	0.86
64_T	67_A	0.708	0.86
69_V	83_V	0.705	0.86
214_L	218_L	0.702	0.85
13_V	303_A	0.694	0.85
178_W	181_A	0.694	0.85
228_A	232_A	0.691	0.84
170_P	175_A	0.687	0.84
186_D	190_G	0.684	0.84
45_R	49_V	0.683	0.84
33_G	147_E	0.681	0.84
136_E	139_S	0.681	0.84
12_G	176_A	0.680	0.83
9_V	161_A	0.680	0.83
142_V	251_L	0.679	0.83
95_R	98_L	0.677	0.83
131_A	264_V	0.677	0.83
127_R	265_Y	0.677	0.83
62_A	66_W	0.676	0.83
112_N	134_A	0.675	0.83
186_D	205_D	0.672	0.83
118_R	132_L	0.672	0.83
147_E	204_D	0.667	0.82
142_V	291_G	0.667	0.82
20_A	95_R	0.665	0.82
186_D	241_S	0.663	0.82
6_V	10_A	0.662	0.82
278_E	281_R	0.660	0.82
146_A	239_P	0.659	0.82
147_E	184_T	0.658	0.81
98_L	296_L	0.658	0.81
30_A	89_F	0.657	0.81
139_S	261_K	0.657	0.81
103_G	107_A	0.656	0.81
48_A	51_A	0.650	0.81
218_L	302_Y	0.650	0.81
33_G	184_T	0.649	0.81
90_V	177_A	0.649	0.81
260_V	263_G	0.648	0.80
199_A	206_A	0.646	0.80
142_V	257_C	0.646	0.80
27_H	184_T	0.642	0.80
39_V	57_L	0.641	0.80
75_G	79_A	0.641	0.80
148_N	205_D	0.641	0.80
23_P	30_A	0.640	0.80
145_T	295_A	0.638	0.79
112_N	116_A	0.637	0.79
292_L	295_A	0.637	0.79
100_E	107_A	0.636	0.79
65_V	87_V	0.636	0.79
55_I	59_L	0.634	0.79
131_A	136_E	0.632	0.79
110_T	286_V	0.631	0.79
54_A	207_V	0.628	0.78
106_A	111_E	0.628	0.78
146_A	248_M	0.625	0.78
51_A	55_I	0.623	0.78
63_A	66_W	0.621	0.78
230_S	233_A	0.621	0.78
148_N	191_Y	0.619	0.77
196_V	200_S	0.617	0.77
272_A	279_S	0.616	0.77
98_L	283_V	0.614	0.77
37_G	40_D	0.613	0.77
224_R	228_A	0.613	0.77
148_N	151_D	0.613	0.77
220_A	232_A	0.612	0.77
197_G	201_A	0.611	0.76
153_L	295_A	0.611	0.76
83_V	87_V	0.610	0.76
299_A	302_Y	0.610	0.76
222_T	301_V	0.609	0.76
62_A	175_A	0.609	0.76
218_L	289_A	0.608	0.76
119_R	122_R	0.606	0.76
186_D	204_D	0.604	0.76
96_M	100_E	0.604	0.76
233_A	237_G	0.603	0.76
150_A	215_A	0.603	0.76
33_G	191_Y	0.602	0.75
201_A	205_D	0.600	0.75
30_A	33_G	0.599	0.75
35_A	38_V	0.598	0.75
246_W	253_A	0.597	0.75
33_G	151_D	0.593	0.74
100_E	121_L	0.590	0.74
263_G	267_L	0.589	0.74
231_R	236_A	0.588	0.74
110_T	289_A	0.585	0.73
157_L	161_A	0.584	0.73
97_L	147_E	0.582	0.73
31_W	35_A	0.582	0.73
184_T	188_M	0.579	0.73
58_P	185_L	0.577	0.72
21_E	248_M	0.577	0.72
287_S	291_G	0.571	0.72
291_G	295_A	0.570	0.71
115_D	119_R	0.567	0.71
128_D	264_V	0.567	0.71
254_V	294_Y	0.565	0.71
135_G	282_G	0.564	0.71
250_T	254_V	0.563	0.70
192_R	202_R	0.563	0.70
147_E	201_A	0.563	0.70
190_G	205_D	0.562	0.70
258_R	279_S	0.562	0.70
205_D	241_S	0.562	0.70
102_S	289_A	0.561	0.70
282_G	285_V	0.560	0.70
104_V	125_A	0.559	0.70
224_R	256_D	0.558	0.70
127_R	143_E	0.557	0.70
138_R	196_V	0.554	0.69
32_F	177_A	0.554	0.69
93_S	152_G	0.554	0.69
205_D	242_P	0.553	0.69
136_E	140_A	0.553	0.69
190_G	201_A	0.552	0.69
39_V	43_W	0.551	0.69
91_T	160_F	0.551	0.69
27_H	125_A	0.547	0.68
94_R	299_A	0.547	0.68
151_D	205_D	0.546	0.68
284_R	290_G	0.545	0.68
204_D	241_S	0.544	0.68
183_N	204_D	0.543	0.68
79_A	111_E	0.541	0.67
147_E	205_D	0.541	0.67
184_T	191_Y	0.540	0.67
184_T	187_S	0.539	0.67
84_A	169_L	0.539	0.67
193_S	196_V	0.539	0.67
277_A	280_R	0.538	0.67
201_A	204_D	0.536	0.67
100_E	124_L	0.535	0.67
128_D	131_A	0.534	0.66
239_P	261_K	0.532	0.66
65_V	69_V	0.532	0.66
224_R	253_A	0.532	0.66
117_A	137_L	0.530	0.66
78_L	82_V	0.530	0.66
33_G	205_D	0.528	0.66
10_A	298_A	0.528	0.66
154_V	247_P	0.526	0.65
221_A	225_A	0.525	0.65
39_V	44_T	0.522	0.65
53_A	196_V	0.522	0.65
94_R	153_L	0.522	0.65
276_L	288_T	0.521	0.65
210_V	214_L	0.521	0.65
58_P	182_V	0.519	0.64
92_T	180_K	0.519	0.64
201_A	241_S	0.517	0.64
63_A	67_A	0.517	0.64
151_D	184_T	0.516	0.64
22_P	28_P	0.515	0.64
151_D	190_G	0.514	0.64
222_T	297_T	0.514	0.64
15_L	19_I	0.514	0.64
107_A	117_A	0.513	0.63
155_A	159_A	0.513	0.63
272_A	278_E	0.513	0.63
217_V	229_V	0.512	0.63
58_P	181_A	0.512	0.63
180_K	183_N	0.511	0.63
219_I	254_V	0.511	0.63
111_E	115_D	0.510	0.63
143_E	260_V	0.509	0.63
183_N	186_D	0.508	0.63
72_A	76_S	0.506	0.62
286_V	289_A	0.505	0.62
149_L	298_A	0.504	0.62
101_A	107_A	0.503	0.62
33_G	187_S	0.503	0.62
151_D	183_N	0.501	0.62
212_A	247_P	0.501	0.62
150_A	216_A	0.500	0.61
104_V	121_L	0.500	0.61
155_A	208_M	0.500	0.61

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
2ksdA	1	0.2175	3.2	0.974	Contact Map
4h33A	3	0.2208	2.4	0.976	Contact Map
3j00Z	1	0.3019	2.3	0.976	Contact Map
3j01B	1	0.3766	2.3	0.976	Contact Map
2ls2A	1	0.0617	1.9	0.977	Contact Map
4av3A	2	0.211	1.8	0.977	Contact Map
4pl0A	2	0.7857	1.7	0.978	Contact Map
2qdqA	2	0.1039	1.5	0.978	Contact Map
3rvyA	3	0.2597	1.3	0.979	Contact Map
2kncA	1	0.0909	1.2	0.979	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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