CobT - PFAM28P - GREMLIN Contacts

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CobT - Cobalamin biosynthesis protein CobT

PFAM:	PF06213	Sequences: ESPLEPFKRALAAAARAIAGDPELEVSFGADPPGLSGKKARLPEPPRDLTPEEVAIARGEADSLALRLRHHDAALHARLAPAGPEARAVFDALEQARVEALGARRMPGVAANLDAMLEDRYRRKGYDRITDREDAPLAEALALLVRERLTGRPPPPAARKVVDLWRPWIEEKAGADLDALADALEDQAAFARLARDLLEDLDLGDELGDDPDEEDDEEEEDEEEEDDEEEDEDEEGEDEDEEESEEAESEESEEEDDDEEEGEVEADDAADDDMSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	276 (268)
Sequences:	5710 (4129)
Seq/√Len:	252.2
META:	0.856

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_D	152_R	3.761	1.00
186_D	189_A	3.755	1.00
148_R	178_D	3.239	1.00
15_A	40_A	3.111	1.00
93_L	145_V	3.098	1.00
21_D	68_L	3.040	1.00
159_R	163_D	2.998	1.00
62_D	112_N	2.972	1.00
147_E	166_R	2.958	1.00
46_P	53_E	2.827	1.00
70_H	105_R	2.677	1.00
89_V	141_L	2.664	1.00
18_I	109_V	2.596	1.00
80_A	87_R	2.580	1.00
35_L	40_A	2.481	1.00
110_A	152_R	2.336	1.00
156_P	159_R	2.258	1.00
170_E	174_G	2.235	1.00
15_A	61_A	2.068	1.00
145_V	149_L	2.062	1.00
11_L	15_A	2.046	1.00
63_S	95_Q	1.992	1.00
242_E	245_E	1.980	1.00
43_P	60_E	1.960	1.00
264_V	267_D	1.856	1.00
176_D	200_D	1.843	1.00
196_D	199_E	1.808	1.00
129_I	135_A	1.805	1.00
248_E	252_S	1.785	1.00
173_A	197_L	1.763	1.00
163_D	167_P	1.761	1.00
265_E	269_A	1.736	1.00
118_E	157_A	1.717	1.00
248_E	251_E	1.715	1.00
223_E	226_D	1.696	1.00
135_A	161_V	1.647	1.00
20_G	69_R	1.647	1.00
199_E	204_G	1.628	1.00
209_D	212_D	1.604	1.00
168_W	171_E	1.602	1.00
239_E	248_E	1.598	1.00
21_D	38_K	1.591	1.00
51_P	55_A	1.588	1.00
58_R	112_N	1.584	1.00
245_E	248_E	1.562	1.00
118_E	122_R	1.560	1.00
244_S	247_A	1.548	1.00
244_S	248_E	1.544	1.00
49_L	54_V	1.530	1.00
147_E	162_V	1.521	1.00
260_E	264_V	1.520	1.00
67_R	98_V	1.516	1.00
252_S	256_D	1.513	1.00
233_D	236_G	1.510	1.00
224_E	228_E	1.506	1.00
63_S	98_V	1.499	1.00
7_F	11_L	1.478	1.00
140_A	165_W	1.471	1.00
80_A	91_D	1.470	1.00
93_L	194_A	1.467	1.00
246_E	249_S	1.463	1.00
187_Q	190_F	1.463	1.00
241_E	244_S	1.434	1.00
58_R	62_D	1.432	1.00
196_D	200_D	1.423	1.00
154_P	162_V	1.421	1.00
244_S	249_S	1.420	1.00
111_A	152_R	1.420	1.00
247_A	250_E	1.420	1.00
259_E	262_G	1.412	1.00
179_A	182_D	1.400	1.00
263_E	266_A	1.385	1.00
224_E	227_D	1.372	1.00
27_S	39_K	1.370	1.00
66_L	102_G	1.367	1.00
153_P	159_R	1.367	1.00
66_L	109_V	1.359	1.00
195_R	204_G	1.345	1.00
266_A	269_A	1.340	1.00
81_P	90_F	1.333	1.00
7_F	54_V	1.332	1.00
267_D	270_A	1.329	1.00
249_S	252_S	1.329	1.00
254_E	257_D	1.312	1.00
88_A	138_A	1.306	1.00
251_E	254_E	1.288	1.00
83_G	198_L	1.288	1.00
147_E	153_P	1.284	1.00
162_V	169_I	1.283	1.00
131_D	134_D	1.278	1.00
121_Y	126_Y	1.263	1.00
12_A	28_F	1.242	1.00
226_D	229_E	1.222	1.00
67_R	95_Q	1.218	1.00
35_L	64_L	1.213	1.00
90_F	191_A	1.205	1.00
76_H	91_D	1.200	1.00
71_H	76_H	1.198	1.00
168_W	172_K	1.193	1.00
261_E	264_V	1.189	1.00
95_Q	99_E	1.182	1.00
119_D	123_R	1.176	1.00
50_T	53_E	1.167	1.00
243_E	246_E	1.160	1.00
27_S	41_R	1.157	1.00
222_E	225_E	1.156	1.00
241_E	249_S	1.152	1.00
262_G	266_A	1.151	1.00
244_S	252_S	1.147	1.00
15_A	24_L	1.142	1.00
166_R	170_E	1.134	1.00
236_G	242_E	1.127	1.00
243_E	248_E	1.119	1.00
262_G	269_A	1.107	1.00
33_P	64_L	1.107	1.00
73_A	77_A	1.106	1.00
141_L	198_L	1.105	1.00
106_M	109_V	1.105	1.00
116_M	120_R	1.104	1.00
252_S	255_E	1.103	1.00
10_A	13_A	1.096	1.00
240_D	245_E	1.084	1.00
247_A	251_E	1.080	1.00
238_D	251_E	1.079	1.00
114_D	118_E	1.078	1.00
259_E	266_A	1.078	1.00
250_E	253_E	1.074	1.00
183_A	193_L	1.074	1.00
246_E	257_D	1.065	1.00
83_G	86_A	1.058	1.00
261_E	267_D	1.054	1.00
252_S	257_D	1.049	1.00
260_E	266_A	1.047	1.00
225_E	228_E	1.034	1.00
79_L	188_A	1.032	1.00
247_A	252_S	1.028	1.00
243_E	247_A	1.026	1.00
183_A	189_A	1.017	1.00
24_L	38_K	1.009	1.00
95_Q	98_V	1.003	1.00
104_R	185_E	0.998	1.00
139_E	142_A	0.994	1.00
124_K	139_E	0.994	1.00
167_P	171_E	0.990	1.00
194_A	197_L	0.988	1.00
126_Y	129_I	0.986	1.00
78_R	188_A	0.984	1.00
245_E	249_S	0.983	1.00
253_E	256_D	0.980	1.00
245_E	250_E	0.980	1.00
250_E	254_E	0.977	1.00
148_R	177_L	0.970	1.00
234_E	247_A	0.966	1.00
110_A	114_D	0.961	1.00
239_E	242_E	0.954	1.00
236_G	239_E	0.954	1.00
92_A	96_A	0.948	1.00
79_L	90_F	0.948	1.00
60_E	64_L	0.934	1.00
259_E	263_E	0.931	1.00
255_E	264_V	0.924	1.00
5_E	9_R	0.924	1.00
245_E	252_S	0.923	1.00
179_A	193_L	0.919	1.00
188_A	192_R	0.914	1.00
179_A	196_D	0.913	1.00
206_E	209_D	0.908	1.00
56_I	119_D	0.906	1.00
236_G	244_S	0.904	1.00
101_L	105_R	0.904	1.00
189_A	192_R	0.900	1.00
237_E	241_E	0.892	1.00
241_E	246_E	0.890	1.00
63_S	99_E	0.877	1.00
103_A	113_L	0.869	1.00
219_E	223_E	0.867	1.00
126_Y	161_V	0.865	0.99
8_K	15_A	0.862	0.99
24_L	68_L	0.861	0.99
36_S	39_K	0.858	0.99
244_S	250_E	0.854	0.99
242_E	248_E	0.854	0.99
263_E	267_D	0.846	0.99
247_A	254_E	0.844	0.99
247_A	257_D	0.842	0.99
240_D	254_E	0.840	0.99
241_E	254_E	0.836	0.99
248_E	253_E	0.835	0.99
129_I	161_V	0.834	0.99
75_L	79_L	0.829	0.99
260_E	263_E	0.829	0.99
125_G	128_R	0.828	0.99
66_L	98_V	0.826	0.99
228_E	231_D	0.825	0.99
249_S	255_E	0.823	0.99
262_G	270_A	0.822	0.99
237_E	240_D	0.818	0.99
258_D	262_G	0.818	0.99
63_S	116_M	0.810	0.99
211_P	214_E	0.807	0.99
100_A	150_T	0.807	0.99
172_K	175_A	0.806	0.99
239_E	247_A	0.804	0.99
132_R	168_W	0.803	0.99
119_D	122_R	0.803	0.99
121_Y	143_L	0.801	0.99
81_P	86_A	0.801	0.99
236_G	248_E	0.799	0.99
261_E	270_A	0.798	0.99
3_P	6_P	0.796	0.99
45_P	49_L	0.795	0.99
19_A	22_P	0.793	0.99
40_A	64_L	0.790	0.99
247_A	256_D	0.788	0.99
251_E	255_E	0.788	0.99
238_D	241_E	0.784	0.99
245_E	257_D	0.783	0.99
246_E	250_E	0.783	0.99
107_P	111_A	0.783	0.99
243_E	249_S	0.779	0.99
138_A	142_A	0.777	0.99
264_V	270_A	0.770	0.99
215_D	218_E	0.770	0.99
240_D	248_E	0.767	0.99
179_A	183_A	0.763	0.99
93_L	197_L	0.755	0.99
97_R	101_L	0.754	0.99
132_R	135_A	0.752	0.99
236_G	243_E	0.751	0.99
253_E	257_D	0.746	0.99
262_G	267_D	0.742	0.98
240_D	244_S	0.742	0.98
6_P	9_R	0.742	0.98
223_E	227_D	0.742	0.98
250_E	256_D	0.741	0.98
235_E	248_E	0.737	0.98
246_E	252_S	0.737	0.98
266_A	270_A	0.736	0.98
204_G	207_L	0.730	0.98
145_V	190_F	0.730	0.98
234_E	238_D	0.727	0.98
251_E	257_D	0.727	0.98
235_E	249_S	0.726	0.98
241_E	245_E	0.724	0.98
136_P	164_L	0.724	0.98
197_L	200_D	0.718	0.98
262_G	265_E	0.716	0.98
107_P	110_A	0.716	0.98
30_A	34_G	0.715	0.98
241_E	250_E	0.714	0.98
237_E	250_E	0.711	0.98
11_L	57_A	0.711	0.98
240_D	269_A	0.707	0.98
263_E	269_A	0.706	0.98
240_D	257_D	0.706	0.98
198_L	204_G	0.701	0.98
222_E	228_E	0.700	0.98
133_E	136_P	0.699	0.98
249_S	256_D	0.699	0.98
250_E	258_D	0.697	0.98
140_A	161_V	0.696	0.98
235_E	245_E	0.695	0.98
167_P	170_E	0.691	0.98
243_E	254_E	0.690	0.98
225_E	229_E	0.687	0.97
90_F	198_L	0.687	0.97
239_E	243_E	0.685	0.97
237_E	251_E	0.682	0.97
241_E	251_E	0.681	0.97
244_S	254_E	0.681	0.97
144_L	166_R	0.680	0.97
79_L	191_A	0.676	0.97
260_E	269_A	0.675	0.97
265_E	268_D	0.671	0.97
247_A	258_D	0.671	0.97
58_R	187_Q	0.670	0.97
241_E	247_A	0.670	0.97
117_L	121_Y	0.666	0.97
8_K	45_P	0.665	0.97
215_D	224_E	0.665	0.97
243_E	259_E	0.664	0.97
15_A	64_L	0.663	0.97
140_A	162_V	0.662	0.97
260_E	270_A	0.659	0.97
24_L	40_A	0.658	0.97
26_V	33_P	0.657	0.97
239_E	244_S	0.657	0.97
252_S	268_D	0.656	0.97
257_D	261_E	0.654	0.97
9_R	29_G	0.653	0.97
132_R	164_L	0.651	0.96
101_L	184_L	0.648	0.96
79_L	192_R	0.647	0.96
248_E	263_E	0.647	0.96
144_L	169_I	0.646	0.96
15_A	28_F	0.634	0.96
240_D	243_E	0.632	0.96
81_P	187_Q	0.632	0.96
234_E	250_E	0.631	0.96
6_P	10_A	0.628	0.96
111_A	115_A	0.624	0.96
261_E	265_E	0.624	0.96
239_E	262_G	0.624	0.96
62_D	108_G	0.622	0.95
34_G	41_R	0.617	0.95
79_L	207_L	0.616	0.95
35_L	68_L	0.616	0.95
121_Y	125_G	0.616	0.95
101_L	185_E	0.615	0.95
233_D	237_E	0.615	0.95
14_A	61_A	0.615	0.95
185_E	188_A	0.615	0.95
252_S	263_E	0.614	0.95
109_V	113_L	0.612	0.95
18_I	66_L	0.612	0.95
220_E	226_D	0.611	0.95
259_E	270_A	0.609	0.95
60_E	63_S	0.608	0.95
254_E	258_D	0.603	0.95
108_G	112_N	0.602	0.95
169_I	173_A	0.602	0.95
80_A	90_F	0.600	0.95
259_E	269_A	0.599	0.94
149_L	184_L	0.599	0.94
249_S	258_D	0.598	0.94
245_E	254_E	0.598	0.94
247_A	253_E	0.597	0.94
182_D	185_E	0.596	0.94
160_K	167_P	0.596	0.94
241_E	248_E	0.593	0.94
150_T	154_P	0.593	0.94
237_E	249_S	0.591	0.94
206_E	212_D	0.590	0.94
194_A	198_L	0.588	0.94
233_D	244_S	0.588	0.94
13_A	17_A	0.588	0.94
132_R	165_W	0.586	0.94
236_G	240_D	0.584	0.94
112_N	187_Q	0.584	0.94
260_E	267_D	0.581	0.94
219_E	229_E	0.579	0.93
238_D	242_E	0.579	0.93
264_V	269_A	0.576	0.93
246_E	254_E	0.575	0.93
121_Y	158_A	0.575	0.93
261_E	266_A	0.574	0.93
254_E	263_E	0.574	0.93
169_I	183_A	0.572	0.93
176_D	180_L	0.572	0.93
243_E	251_E	0.571	0.93
184_L	194_A	0.571	0.93
238_D	246_E	0.569	0.93
253_E	258_D	0.569	0.93
249_S	254_E	0.567	0.93
83_G	204_G	0.561	0.92
125_G	129_I	0.560	0.92
235_E	240_D	0.557	0.92
144_L	162_V	0.557	0.92
121_Y	142_A	0.555	0.92
258_D	267_D	0.555	0.92
252_S	258_D	0.553	0.92
7_F	57_A	0.553	0.92
265_E	270_A	0.553	0.92
5_E	8_K	0.552	0.92
91_D	95_Q	0.551	0.92
260_E	265_E	0.548	0.91
238_D	247_A	0.544	0.91
84_P	88_A	0.544	0.91
242_E	247_A	0.542	0.91
206_E	210_D	0.540	0.91
175_A	178_D	0.539	0.91
259_E	268_D	0.538	0.91
245_E	251_E	0.537	0.91
243_E	256_D	0.534	0.90
121_Y	154_P	0.534	0.90
95_Q	120_R	0.533	0.90
104_R	181_A	0.532	0.90
249_S	261_E	0.530	0.90
33_P	47_R	0.528	0.90
253_E	262_G	0.526	0.90
104_R	184_L	0.525	0.90
163_D	166_R	0.525	0.90
246_E	253_E	0.523	0.89
162_V	166_R	0.521	0.89
113_L	117_L	0.521	0.89
19_A	69_R	0.520	0.89
11_L	61_A	0.520	0.89
220_E	224_E	0.517	0.89
29_G	32_P	0.516	0.89
21_D	24_L	0.516	0.89
30_A	47_R	0.515	0.89
259_E	264_V	0.515	0.89
242_E	246_E	0.514	0.89
106_M	124_K	0.514	0.89
120_R	139_E	0.512	0.88
248_E	256_D	0.511	0.88
89_V	92_A	0.508	0.88
237_E	248_E	0.507	0.88
234_E	240_D	0.506	0.88
252_S	266_A	0.505	0.88
241_E	264_V	0.504	0.88
236_G	247_A	0.500	0.87

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
4u7aA	1	0	91.7	0.903	Contact Map
4qhjA	2	0.337	71.1	0.925	Contact Map
3cqbA	4	0.2826	67.6	0.926	Contact Map
4jixA	2	0.3696	32.2	0.941	Contact Map
4qu4A	1	0	19.2	0.947	Contact Map
4fp9B	2	0.6341	12.2	0.951	Contact Map
4jiuA	1	0.3623	10.3	0.953	Contact Map
4kblA	2	0	9	0.954	Contact Map
2yhsA	1	0.192	7.8	0.956	Contact Map
3mlfA	2	0.3442	7.1	0.956	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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