CobS - PFAM28P - GREMLIN Contacts

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CobS - Cobalamin-5-phosphate synthase

PFAM:	PF02654	Sequences: ALQFLTRLPVPDLARAARFFPLVGLLIGLLLALVAWLLSLLLPLLAAALAVAALVLLTGALHLDGLADTADGLGGGRDRERRLEIMKDSRIGAFGVLALVLVLLLKFAALAALPLLAAPVLSRAAMVLLMALLPYAPDGLGAAFAGAVPRAVAAALAVLALLLAALLAALLAALLLRRLARRRLGGVTGDVLGATQELAELAVLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	205 (197)
Sequences:	17130 (12859)
Seq/√Len:	916.2
META:	0.785

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_R	84_E	4.368	1.00
70_A	98_A	3.729	1.00
126_M	196_Q	3.398	1.00
31_L	54_L	3.312	1.00
82_R	183_R	3.166	1.00
67_A	99_L	2.847	1.00
122_S	196_Q	2.712	1.00
34_V	53_A	2.565	1.00
118_A	203_V	2.475	1.00
52_A	101_L	2.424	1.00
66_L	102_V	2.313	1.00
129_L	195_T	2.256	1.00
51_V	107_F	2.234	1.00
102_V	201_L	2.234	1.00
91_I	96_V	2.219	1.00
48_A	105_L	2.213	1.00
180_A	191_V	2.123	1.00
77_R	81_R	2.095	1.00
5_L	20_F	2.076	1.00
48_A	104_L	2.029	1.00
78_D	81_R	2.016	1.00
60_A	97_L	1.959	1.00
75_G	85_I	1.927	1.00
69_T	191_V	1.898	1.00
44_L	107_F	1.855	1.00
177_R	181_R	1.835	1.00
48_A	107_F	1.831	1.00
55_V	101_L	1.809	1.00
2_L	26_L	1.771	1.00
106_K	200_E	1.725	1.00
176_L	180_A	1.624	1.00
67_A	95_G	1.597	1.00
106_K	197_E	1.596	1.00
100_V	104_L	1.572	1.00
80_E	84_E	1.566	1.00
175_L	179_L	1.541	1.00
133_L	177_R	1.532	1.00
142_A	146_G	1.529	1.00
130_M	192_L	1.528	1.00
105_L	201_L	1.495	1.00
100_V	103_L	1.474	1.00
72_G	86_M	1.428	1.00
79_R	82_R	1.424	1.00
35_A	50_A	1.417	1.00
27_I	57_L	1.417	1.00
35_A	114_P	1.413	1.00
31_L	50_A	1.412	1.00
104_L	107_F	1.398	1.00
178_R	181_R	1.388	1.00
3_Q	10_V	1.382	1.00
187_V	192_L	1.347	1.00
34_V	38_L	1.334	1.00
79_R	83_L	1.329	1.00
17_A	130_M	1.321	1.00
30_L	53_A	1.301	1.00
63_L	99_L	1.285	1.00
69_T	73_L	1.284	1.00
125_A	199_A	1.280	1.00
102_V	106_K	1.272	1.00
172_A	202_A	1.266	1.00
36_W	40_L	1.265	1.00
55_V	63_L	1.244	1.00
174_L	178_R	1.235	1.00
74_G	94_F	1.234	1.00
73_L	82_R	1.232	1.00
27_I	58_T	1.228	1.00
67_A	91_I	1.228	1.00
44_L	111_A	1.215	1.00
55_V	60_A	1.214	1.00
46_A	50_A	1.206	1.00
138_D	142_A	1.201	1.00
63_L	197_E	1.178	1.00
173_A	177_R	1.174	1.00
54_L	119_P	1.166	1.00
179_L	183_R	1.161	1.00
121_L	203_V	1.157	1.00
107_F	111_A	1.145	1.00
187_V	191_V	1.137	1.00
73_L	184_L	1.124	1.00
178_R	182_R	1.124	1.00
48_A	108_A	1.120	1.00
119_P	200_E	1.106	1.00
184_L	191_V	1.101	1.00
25_L	120_V	1.091	1.00
67_A	93_A	1.087	1.00
116_L	120_V	1.085	1.00
47_A	51_V	1.077	1.00
32_A	116_L	1.076	1.00
44_L	108_A	1.075	1.00
109_A	201_L	1.074	1.00
12_D	15_R	1.073	1.00
35_A	39_S	1.070	1.00
82_R	184_L	1.055	1.00
96_V	100_V	1.052	1.00
97_L	103_L	1.047	1.00
55_V	97_L	1.042	1.00
130_M	145_A	1.035	1.00
2_L	23_V	1.034	1.00
66_L	70_A	1.031	1.00
134_P	181_R	1.025	1.00
96_V	99_L	1.020	1.00
66_L	198_L	1.009	1.00
6_T	27_I	1.007	1.00
75_G	82_R	1.006	1.00
68_D	189_G	1.003	1.00
91_I	95_G	1.000	1.00
64_D	68_D	0.998	1.00
79_R	185_G	0.992	1.00
195_T	199_A	0.991	1.00
4_F	140_L	0.988	1.00
3_Q	11_P	0.986	1.00
27_I	119_P	0.982	1.00
176_L	195_T	0.981	1.00
38_L	46_A	0.981	1.00
128_L	132_L	0.977	1.00
55_V	103_L	0.971	1.00
32_A	36_W	0.946	1.00
102_V	197_E	0.942	1.00
135_Y	142_A	0.932	1.00
77_R	85_I	0.927	1.00
37_L	40_L	0.924	1.00
47_A	111_A	0.919	1.00
108_A	112_A	0.916	1.00
136_A	188_T	0.910	1.00
133_L	181_R	0.900	1.00
90_R	93_A	0.899	1.00
116_L	119_P	0.892	1.00
199_A	203_V	0.886	1.00
106_K	201_L	0.880	1.00
133_L	187_V	0.877	1.00
2_L	10_V	0.876	1.00
176_L	183_R	0.872	1.00
25_L	116_L	0.871	1.00
38_L	42_L	0.870	1.00
77_R	82_R	0.853	1.00
31_L	35_A	0.849	1.00
63_L	97_L	0.848	1.00
123_R	196_Q	0.846	1.00
78_D	84_E	0.826	1.00
27_I	31_L	0.825	1.00
30_L	57_L	0.823	1.00
129_L	133_L	0.823	1.00
118_A	204_L	0.821	1.00
7_R	56_L	0.817	1.00
136_A	186_G	0.816	1.00
54_L	118_A	0.814	1.00
47_A	107_F	0.808	1.00
129_L	177_R	0.807	1.00
109_A	112_A	0.800	1.00
63_L	106_K	0.796	1.00
23_V	26_L	0.795	1.00
7_R	59_G	0.794	1.00
45_L	109_A	0.793	1.00
135_Y	140_L	0.790	1.00
37_L	41_L	0.787	1.00
67_A	96_V	0.784	1.00
66_L	98_A	0.782	1.00
169_A	173_A	0.776	1.00
119_P	122_S	0.775	1.00
8_L	57_L	0.775	1.00
83_L	188_T	0.773	1.00
118_A	122_S	0.773	1.00
93_A	97_L	0.769	1.00
196_Q	199_A	0.769	1.00
75_G	78_D	0.766	1.00
17_A	127_V	0.763	1.00
179_L	191_V	0.762	1.00
47_A	110_L	0.760	1.00
110_L	115_L	0.750	1.00
35_A	46_A	0.749	1.00
105_L	109_A	0.748	1.00
36_W	39_S	0.742	1.00
122_S	200_E	0.740	1.00
39_S	46_A	0.736	1.00
68_D	190_D	0.724	1.00
17_A	148_V	0.722	1.00
140_L	143_A	0.719	1.00
49_L	105_L	0.716	1.00
63_L	103_L	0.710	1.00
180_A	183_R	0.708	1.00
109_A	204_L	0.707	1.00
8_L	30_L	0.707	1.00
72_G	76_G	0.707	1.00
43_P	112_A	0.706	1.00
51_V	103_L	0.701	1.00
38_L	41_L	0.701	1.00
135_Y	141_G	0.700	1.00
54_L	200_E	0.700	1.00
197_E	200_E	0.695	1.00
84_E	90_R	0.688	1.00
151_A	156_L	0.688	1.00
19_F	22_L	0.680	1.00
5_L	23_V	0.675	1.00
119_P	197_E	0.674	1.00
132_L	177_R	0.672	1.00
50_A	54_L	0.671	1.00
28_G	32_A	0.671	1.00
105_L	108_A	0.668	1.00
20_F	144_F	0.664	1.00
137_P	142_A	0.659	1.00
117_A	203_V	0.658	1.00
31_L	119_P	0.651	1.00
124_A	128_L	0.649	1.00
89_S	94_F	0.647	1.00
198_L	202_A	0.646	1.00
52_A	56_L	0.644	1.00
35_A	47_A	0.642	1.00
60_A	94_F	0.638	1.00
78_D	82_R	0.635	1.00
42_L	46_A	0.635	1.00
115_L	119_P	0.635	1.00
160_A	164_A	0.633	1.00
74_G	82_R	0.631	1.00
83_L	86_M	0.630	1.00
5_L	126_M	0.629	1.00
31_L	53_A	0.628	1.00
16_A	20_F	0.627	1.00
34_V	37_L	0.619	1.00
4_F	13_L	0.618	1.00
82_R	94_F	0.618	1.00
32_A	119_P	0.617	1.00
44_L	47_A	0.613	1.00
172_A	176_L	0.613	1.00
125_A	173_A	0.612	1.00
168_A	172_A	0.609	1.00
122_S	203_V	0.606	1.00
85_I	94_F	0.603	1.00
70_A	94_F	0.603	1.00
176_L	179_L	0.603	1.00
108_A	111_A	0.603	1.00
51_V	101_L	0.602	1.00
59_G	76_G	0.598	1.00
135_Y	145_A	0.597	1.00
28_G	119_P	0.594	1.00
73_L	191_V	0.589	1.00
87_K	138_D	0.587	1.00
187_V	195_T	0.585	1.00
64_D	190_D	0.584	1.00
126_M	192_L	0.583	1.00
29_L	33_L	0.583	1.00
28_G	120_V	0.577	1.00
170_L	174_L	0.573	1.00
133_L	192_L	0.573	1.00
32_A	35_A	0.573	1.00
131_A	148_V	0.573	1.00
3_Q	7_R	0.572	1.00
33_L	37_L	0.571	1.00
88_D	93_A	0.569	1.00
175_L	178_R	0.568	1.00
70_A	194_A	0.565	1.00
145_A	192_L	0.564	1.00
71_D	88_D	0.563	1.00
192_L	195_T	0.563	1.00
51_V	110_L	0.558	1.00
43_P	46_A	0.557	1.00
38_L	49_L	0.556	1.00
27_I	54_L	0.552	1.00
66_L	194_A	0.552	1.00
53_A	57_L	0.551	1.00
60_A	74_G	0.549	1.00
25_L	29_L	0.549	1.00
69_T	74_G	0.549	1.00
172_A	198_L	0.549	1.00
69_T	184_L	0.545	1.00
69_T	194_A	0.544	1.00
33_L	36_W	0.540	1.00
157_A	160_A	0.539	1.00
125_A	195_T	0.538	1.00
72_G	82_R	0.533	1.00
44_L	48_A	0.532	1.00
117_A	120_V	0.531	1.00
59_G	94_F	0.530	1.00
76_G	81_R	0.527	1.00
129_L	187_V	0.527	1.00
124_A	127_V	0.527	1.00
7_R	76_G	0.525	1.00
131_A	150_R	0.525	1.00
126_M	195_T	0.523	1.00
128_L	173_A	0.522	1.00
17_A	144_F	0.522	1.00
98_A	102_V	0.522	1.00
38_L	43_P	0.520	1.00
18_R	21_P	0.520	1.00
74_G	77_R	0.520	1.00
62_H	68_D	0.518	1.00
130_M	133_L	0.512	1.00
24_G	28_G	0.509	1.00
145_A	187_V	0.508	1.00
181_R	185_G	0.507	1.00
52_A	105_L	0.506	1.00
179_L	182_R	0.505	1.00
72_G	85_I	0.505	1.00
4_F	61_L	0.504	1.00
68_D	71_D	0.503	1.00
93_A	96_V	0.501	1.00
91_I	99_L	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
3j45G	1	0.2927	2.2	0.961	Contact Map
4o6mA	2	0.8341	1.8	0.963	Contact Map
4bpmA	3	0.278	1.8	0.963	Contact Map
2jttC	1	0.1512	1.7	0.963	Contact Map
2wjnL	1	0.5707	1.6	0.964	Contact Map
2zydA	2	0.2878	1.6	0.964	Contact Map
3ic9A	2	0.2537	1.4	0.965	Contact Map
1afoA	2	0.1951	1.3	0.966	Contact Map
3d9sA	3	0.2829	1.2	0.966	Contact Map
2kogA	1	0.1854	1.1	0.967	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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