URE2 - BACSU - GREMLIN Contacts

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URE2 - Urease subunit beta

UniProt:	P71035	Sequences: MKPGAFQIAEGTITINEGREIREVTVKNTGSRSIQVGSHFHFAEANGALLFDRELAIGMRLDVPSGTSVRFEPGEQKTVSLVEIRGRKTIRGLNGMADTFIDERGKEKTLANLKQAGWMEGVIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	124 (101)
Sequences:	1542 (774)
Seq/√Len:	77.0

BACSU - URE2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_D	80_S	3.689	1.00
47_G	96_M	3.261	1.00
14_T	17_E	3.065	1.00
20_E	59_M	2.921	1.00
59_M	83_E	2.790	1.00
84_I	90_I	2.639	1.00
20_E	83_E	2.546	1.00
19_R	85_R	2.478	1.00
25_T	76_Q	2.331	1.00
23_E	78_T	2.273	1.00
21_I	62_D	2.231	1.00
29_T	50_L	2.224	1.00
47_G	94_N	2.206	1.00
24_V	56_A	2.204	1.00
22_R	59_M	2.030	1.00
57_I	97_A	2.024	1.00
25_T	78_T	2.006	1.00
42_F	81_L	1.959	1.00
89_T	100_F	1.954	1.00
83_E	88_K	1.924	1.00
84_I	93_L	1.838	1.00
60_R	84_I	1.827	1.00
93_L	97_A	1.765	1.00
63_V	67_T	1.631	1.00
21_I	80_S	1.607	1.00
27_K	76_Q	1.601	1.00
26_V	42_F	1.591	1.00
88_K	102_D	1.527	0.99
52_D	55_L	1.478	0.99
2_K	5_A	1.465	0.99
16_N	62_D	1.440	0.99
23_E	80_S	1.331	0.98
95_G	98_D	1.319	0.98
40_F	94_N	1.309	0.98
35_Q	72_E	1.268	0.98
75_E	98_D	1.261	0.97
30_G	48_A	1.242	0.97
8_I	11_G	1.218	0.97
91_R	98_D	1.217	0.97
43_A	57_I	1.138	0.95
44_E	95_G	1.123	0.95
21_I	82_V	0.963	0.89
26_V	81_L	0.962	0.89
32_R	35_Q	0.944	0.88
43_A	56_A	0.941	0.88
21_I	59_M	0.937	0.88
28_N	34_I	0.921	0.87
45_A	49_L	0.916	0.87
21_I	83_E	0.908	0.86
44_E	97_A	0.907	0.86
43_A	93_L	0.894	0.85
43_A	96_M	0.891	0.85
34_I	45_A	0.866	0.84
33_S	37_G	0.860	0.83
24_V	55_L	0.842	0.82
57_I	101_I	0.824	0.80
31_S	35_Q	0.819	0.80
88_K	101_I	0.815	0.80
22_R	80_S	0.812	0.79
40_F	44_E	0.812	0.79
32_R	37_G	0.810	0.79
24_V	78_T	0.800	0.78
75_E	95_G	0.799	0.78
29_T	48_A	0.781	0.77
43_A	90_I	0.766	0.75
42_F	51_F	0.758	0.75
19_R	83_E	0.756	0.74
34_I	48_A	0.751	0.74
41_H	93_L	0.748	0.74
50_L	55_L	0.747	0.74
36_V	56_A	0.746	0.73
31_S	72_E	0.742	0.73
32_R	72_E	0.734	0.72
27_K	50_L	0.729	0.72
40_F	93_L	0.719	0.71
80_S	83_E	0.715	0.70
57_I	102_D	0.715	0.70
93_L	98_D	0.710	0.70
49_L	71_F	0.702	0.69
22_R	56_A	0.701	0.69
33_S	68_S	0.699	0.69
51_F	81_L	0.683	0.67
68_S	72_E	0.681	0.67
31_S	40_F	0.681	0.67
59_M	82_V	0.677	0.66
14_T	18_G	0.668	0.65
7_Q	63_V	0.666	0.65
60_R	87_R	0.663	0.64
25_T	89_T	0.662	0.64
2_K	7_Q	0.656	0.64
35_Q	68_S	0.652	0.63
54_E	57_I	0.646	0.62
15_I	64_P	0.643	0.62
15_I	66_G	0.632	0.61
44_E	98_D	0.630	0.60
33_S	60_R	0.626	0.60
43_A	47_G	0.625	0.60
60_R	82_V	0.617	0.59
24_V	87_R	0.617	0.59
37_G	63_V	0.614	0.59
22_R	55_L	0.596	0.56
35_Q	70_R	0.593	0.56
42_F	61_L	0.584	0.55
16_N	60_R	0.582	0.55
64_P	75_E	0.581	0.54
28_N	68_S	0.581	0.54
90_I	93_L	0.581	0.54
63_V	68_S	0.581	0.54
85_R	95_G	0.580	0.54
36_V	49_L	0.580	0.54
36_V	45_A	0.577	0.54
44_E	93_L	0.568	0.53
43_A	54_E	0.567	0.53
12_T	25_T	0.565	0.52
40_F	52_D	0.564	0.52
26_V	79_V	0.564	0.52
44_E	96_M	0.562	0.52
22_R	81_L	0.560	0.52
40_F	45_A	0.557	0.51
15_I	62_D	0.554	0.51
8_I	15_I	0.553	0.51
44_E	91_R	0.550	0.50
15_I	95_G	0.549	0.50
37_G	68_S	0.547	0.50
31_S	37_G	0.546	0.50
26_V	49_L	0.546	0.50
66_G	102_D	0.545	0.50
16_N	37_G	0.544	0.50
65_S	68_S	0.542	0.49
59_M	68_S	0.536	0.49
29_T	45_A	0.535	0.49
64_P	77_K	0.532	0.48
16_N	21_I	0.532	0.48
8_I	52_D	0.529	0.48
50_L	76_Q	0.529	0.48
87_R	100_F	0.528	0.48
33_S	71_F	0.525	0.47
90_I	97_A	0.524	0.47
7_Q	50_L	0.515	0.46
9_A	52_D	0.514	0.46
23_E	54_E	0.510	0.45
37_G	40_F	0.508	0.45
6_F	78_T	0.507	0.45
15_I	49_L	0.506	0.45
26_V	61_L	0.504	0.45
20_E	56_A	0.504	0.45
57_I	94_N	0.504	0.45
57_I	96_M	0.502	0.44
43_A	91_R	0.502	0.44
14_T	34_I	0.502	0.44
15_I	77_K	0.501	0.44
89_T	98_D	0.500	0.44

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
4gy7A	3	1	100	0.05	Contact Map
1e9yA	5	1	100	0.051	Contact Map
3qgaA	3	0.9677	100	0.057	Contact Map
4ac7B	1	0.9677	100	0.07	Contact Map
4ep8B	1	0.8145	100	0.121	Contact Map
4phzA	3	0.8871	79.3	0.922	Contact Map
1yewA	3	0.8952	73.3	0.926	Contact Map
3ay2A	1	0.8306	64.5	0.931	Contact Map
1cuoA	1	0.8306	53.5	0.935	Contact Map
2x41A	1	0.879	50.8	0.936	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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