Prok_Ub - PFAM28P - GREMLIN Contacts

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Prok_Ub - Prokaryotic Ubiquitin

PFAM:	PF14454	Sequences: QVTTLKRVFKYNGIELPDPDPSLSPEEVRDFYAAQYPELTTATIEGPEIVGDKLVYTFVRAIGT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (63)
Sequences:	1687 (1122)
Seq/√Len:	141.4
META:	0.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_L	32_Y	3.386	1.00
20_D	23_L	2.365	1.00
8_V	15_E	2.325	1.00
19_P	28_V	2.315	1.00
24_S	27_E	2.228	1.00
27_E	30_D	1.973	1.00
25_P	44_I	1.843	1.00
8_V	53_K	1.761	1.00
45_E	59_V	1.723	1.00
6_K	53_K	1.593	1.00
31_F	35_Q	1.577	1.00
10_K	15_E	1.550	1.00
29_R	58_F	1.508	1.00
14_I	36_Y	1.489	1.00
49_I	54_L	1.489	1.00
11_Y	38_E	1.448	1.00
46_G	56_Y	1.413	1.00
26_E	29_R	1.413	1.00
47_P	56_Y	1.382	1.00
7_R	18_D	1.372	1.00
15_E	53_K	1.357	1.00
25_P	56_Y	1.301	1.00
9_F	18_D	1.291	1.00
10_K	55_V	1.239	1.00
32_Y	36_Y	1.238	1.00
10_K	50_V	1.173	1.00
59_V	62_I	1.148	0.99
4_T	22_S	1.117	0.99
23_L	27_E	1.095	0.99
59_V	64_T	1.089	0.99
8_V	55_V	1.076	0.99
18_D	21_P	1.043	0.99
48_E	54_L	1.029	0.99
23_L	31_F	1.028	0.99
33_A	40_T	1.026	0.99
19_P	31_F	1.003	0.99
44_I	58_F	0.994	0.98
50_V	55_V	0.990	0.98
29_R	43_T	0.989	0.98
9_F	19_P	0.965	0.98
38_E	60_R	0.921	0.97
10_K	57_T	0.884	0.97
23_L	28_V	0.860	0.96
11_Y	60_R	0.845	0.96
45_E	57_T	0.844	0.96
3_T	52_D	0.841	0.96
43_T	59_V	0.813	0.95
29_R	42_A	0.790	0.94
30_D	34_A	0.777	0.93
5_L	49_I	0.763	0.93
43_T	64_T	0.761	0.93
43_T	61_A	0.755	0.92
33_A	36_Y	0.751	0.92
31_F	34_A	0.747	0.92
20_D	28_V	0.741	0.92
44_I	47_P	0.739	0.91
32_Y	58_F	0.735	0.91
17_P	21_P	0.695	0.89
26_E	41_T	0.689	0.88
31_F	40_T	0.685	0.88
61_A	64_T	0.682	0.88
45_E	62_I	0.679	0.88
42_A	58_F	0.668	0.87
10_K	14_I	0.666	0.87
26_E	44_I	0.649	0.85
26_E	30_D	0.644	0.85
6_K	50_V	0.642	0.85
6_K	33_A	0.631	0.84
25_P	39_L	0.629	0.83
29_R	61_A	0.627	0.83
12_N	60_R	0.626	0.83
16_L	36_Y	0.616	0.82
20_D	34_A	0.612	0.82
16_L	39_L	0.610	0.81
9_F	58_F	0.607	0.81
28_V	39_L	0.604	0.81
44_I	56_Y	0.601	0.80
39_L	58_F	0.584	0.79
29_R	60_R	0.576	0.78
28_V	44_I	0.569	0.77
50_V	53_K	0.566	0.76
22_S	50_V	0.560	0.76
48_E	61_A	0.560	0.76
29_R	44_I	0.552	0.75
14_I	34_A	0.551	0.74
48_E	57_T	0.549	0.74
23_L	38_E	0.541	0.73
18_D	28_V	0.531	0.72
33_A	39_L	0.527	0.71
46_G	54_L	0.524	0.71
29_R	39_L	0.517	0.70
49_I	52_D	0.512	0.69
28_V	58_F	0.509	0.69
29_R	38_E	0.500	0.67

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
3l7uA	5	0.9375	18.9	0.869	Contact Map
1w7wA	5	1	16.6	0.872	Contact Map
3evoA	5	1	16.1	0.873	Contact Map
2az3A	6	0.9375	15.8	0.873	Contact Map
1iedA	2	0.9219	14.6	0.875	Contact Map
1ehwA	4	0.9375	14	0.876	Contact Map
2dxeA	5	0.9375	13.9	0.876	Contact Map
3ztpA	3	0.9375	12.6	0.879	Contact Map
4dz6A	5	0.9375	12.3	0.879	Contact Map
3q8uA	3	0.9375	11.3	0.881	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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