RPT - PFAM28P - GREMLIN Contacts

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RPT - A repeated domain in UCH-protein

PFAM:	PF13446	Sequences: DLEQAYRYLGIDPDVDDDLIITAYQARVEDDPSQKEELREALRVIAEARNSERLRNFLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (56)
Sequences:	896 (713)
Seq/√Len:	95.2
META:	0.358

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_L	6_Y	4.265	1.00
46_A	54_L	4.234	1.00
17_D	51_S	4.013	1.00
17_D	49_R	3.199	1.00
24_Y	39_R	2.565	1.00
8_Y	41_A	2.123	1.00
8_Y	38_L	2.036	1.00
47_E	55_R	1.663	1.00
18_D	53_R	1.387	0.99
3_E	7_R	1.362	0.99
2_L	48_A	1.339	0.99
26_A	30_D	1.299	0.99
23_A	26_A	1.298	0.99
34_Q	37_E	1.297	0.99
43_R	47_E	1.218	0.98
27_R	38_L	1.216	0.98
23_A	27_R	1.187	0.98
24_Y	42_L	1.168	0.98
25_Q	43_R	1.124	0.97
9_L	41_A	1.113	0.97
10_G	27_R	1.100	0.97
31_D	38_L	1.038	0.96
12_D	28_V	1.038	0.96
34_Q	38_L	1.003	0.95
13_P	29_E	0.986	0.94
19_L	23_A	0.954	0.93
28_V	43_R	0.936	0.93
6_Y	45_I	0.904	0.91
44_V	48_A	0.875	0.90
24_Y	32_P	0.870	0.90
15_V	19_L	0.840	0.88
4_Q	7_R	0.821	0.87
52_E	55_R	0.807	0.86
21_I	29_E	0.807	0.86
41_A	54_L	0.802	0.86
7_R	40_E	0.798	0.85
5_A	11_I	0.782	0.84
20_I	45_I	0.780	0.84
18_D	57_F	0.776	0.84
22_T	26_A	0.774	0.83
13_P	48_A	0.759	0.82
50_N	55_R	0.750	0.81
43_R	48_A	0.746	0.81
11_I	15_V	0.745	0.81
10_G	25_Q	0.743	0.81
16_D	19_L	0.738	0.80
52_E	56_N	0.723	0.79
26_A	29_E	0.720	0.79
12_D	22_T	0.716	0.78
42_L	46_A	0.692	0.76
46_A	55_R	0.681	0.75
7_R	15_V	0.681	0.75
31_D	34_Q	0.663	0.73
6_Y	29_E	0.663	0.73
21_I	39_R	0.662	0.73
20_I	39_R	0.661	0.73
11_I	20_I	0.658	0.72
24_Y	38_L	0.657	0.72
18_D	22_T	0.645	0.71
40_E	43_R	0.641	0.70
43_R	56_N	0.631	0.69
17_D	20_I	0.627	0.69
14_D	49_R	0.626	0.69
32_P	35_K	0.615	0.67
42_L	57_F	0.602	0.66
16_D	30_D	0.597	0.65
40_E	48_A	0.584	0.63
40_E	47_E	0.576	0.62
28_V	38_L	0.561	0.60
16_D	52_E	0.560	0.60
6_Y	13_P	0.537	0.57
16_D	27_R	0.533	0.56
7_R	37_E	0.530	0.56
19_L	26_A	0.529	0.56
11_I	56_N	0.527	0.55
27_R	51_S	0.525	0.55
19_L	24_Y	0.521	0.55
33_S	41_A	0.521	0.55
22_T	29_E	0.516	0.54
30_D	35_K	0.515	0.54
14_D	48_A	0.515	0.54
21_I	57_F	0.506	0.53
19_L	22_T	0.504	0.52
9_L	47_E	0.500	0.52

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
2guzB	1	0.9492	90.5	0.651	Contact Map
3apqA	1	0.9831	84	0.687	Contact Map
3lz8A	2	0	82.4	0.692	Contact Map
2ctqA	1	1	77.2	0.707	Contact Map
4rwuA	1	1	76.5	0.709	Contact Map
2guzA	2	0.8814	75.4	0.712	Contact Map
2yuaA	1	1	74.1	0.714	Contact Map
2ctpA	1	1	74	0.715	Contact Map
1gh6A	1	1	72.8	0.718	Contact Map
4j80A	2	1	72.5	0.718	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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