RPAP1_C - PFAM28P - GREMLIN Contacts

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RPAP1_C - RPAP1-like, C-terminal

PFAM:	PF08620	Sequences: ELRFDFNGNLIPSADIPTHLGLHHHGDEPEAAGYTLPELLHLSRSTVPAQRCIALQTLGRILYRLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (64)
Sequences:	544 (374)
Seq/√Len:	46.8
META:	0.362

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_L	23_H	3.124	1.00
39_L	57_T	2.966	1.00
28_E	31_A	2.779	1.00
5_D	9_N	2.715	1.00
26_G	29_P	2.342	1.00
39_L	54_A	2.280	1.00
44_R	51_R	2.263	1.00
5_D	11_I	2.159	1.00
16_I	20_L	1.940	0.99
9_N	64_R	1.939	0.99
6_F	57_T	1.826	0.99
2_L	10_L	1.796	0.99
17_P	20_L	1.654	0.98
47_V	51_R	1.587	0.97
17_P	23_H	1.483	0.96
23_H	32_A	1.431	0.95
21_G	24_H	1.385	0.94
4_F	36_L	1.308	0.91
6_F	24_H	1.284	0.91
51_R	62_L	1.266	0.90
36_L	40_L	1.222	0.88
53_I	56_Q	1.182	0.87
21_G	25_H	1.119	0.83
2_L	31_A	1.095	0.82
8_G	35_T	1.094	0.82
14_A	59_G	1.085	0.82
6_F	60_R	1.073	0.81
51_R	65_L	1.006	0.76
46_T	52_C	0.980	0.74
48_P	52_C	0.970	0.74
5_D	63_Y	0.965	0.73
2_L	28_E	0.965	0.73
59_G	63_Y	0.960	0.73
22_L	34_Y	0.950	0.72
13_S	64_R	0.922	0.70
29_P	38_E	0.914	0.69
33_G	38_E	0.907	0.69
29_P	62_L	0.887	0.67
7_N	55_L	0.882	0.66
3_R	8_G	0.882	0.66
25_H	39_L	0.874	0.66
15_D	35_T	0.874	0.66
32_A	42_L	0.869	0.65
6_F	10_L	0.860	0.64
56_Q	60_R	0.859	0.64
26_G	38_E	0.845	0.63
22_L	29_P	0.845	0.63
37_P	49_A	0.812	0.60
36_L	43_S	0.804	0.59
21_G	32_A	0.797	0.58
13_S	16_I	0.768	0.56
43_S	56_Q	0.748	0.54
40_L	46_T	0.735	0.52
48_P	60_R	0.729	0.52
53_I	58_L	0.725	0.51
58_L	61_I	0.724	0.51
42_L	45_S	0.718	0.51
30_E	58_L	0.713	0.50
37_P	53_I	0.699	0.49
39_L	43_S	0.697	0.49
27_D	41_H	0.694	0.48
35_T	38_E	0.676	0.47
18_T	32_A	0.660	0.45
10_L	13_S	0.651	0.44
12_P	61_I	0.648	0.44
2_L	46_T	0.648	0.44
5_D	25_H	0.635	0.43
10_L	18_T	0.628	0.42
4_F	8_G	0.621	0.41
38_E	41_H	0.617	0.41
19_H	40_L	0.613	0.40
22_L	33_G	0.608	0.40
54_A	57_T	0.595	0.39
36_L	61_I	0.588	0.38
7_N	56_Q	0.586	0.38
14_A	18_T	0.579	0.37
4_F	10_L	0.575	0.37
41_H	47_V	0.568	0.36
55_L	59_G	0.565	0.36
28_E	40_L	0.560	0.35
6_F	22_L	0.558	0.35
13_S	27_D	0.554	0.35
7_N	12_P	0.547	0.34
27_D	37_P	0.537	0.33
14_A	27_D	0.533	0.33
19_H	46_T	0.532	0.33
60_R	64_R	0.528	0.33
13_S	44_R	0.526	0.32
31_A	56_Q	0.525	0.32
40_L	55_L	0.522	0.32
25_H	32_A	0.517	0.32
43_S	58_L	0.512	0.31
19_H	62_L	0.505	0.31
5_D	24_H	0.503	0.30
25_H	50_Q	0.503	0.30
31_A	49_A	0.500	0.30

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
4f7gB	1	0.303	45.3	0.858	Contact Map
4rxhB	1	0.4848	35.7	0.866	Contact Map
4kkiA	1	0	33.6	0.868	Contact Map
4anrA	1	0.4242	33.5	0.868	Contact Map
3qxfA	1	0.2121	28.6	0.873	Contact Map
3npgA	4	1	24.2	0.877	Contact Map
1b3uA	1	0.6364	22.6	0.878	Contact Map
4adyA	1	0.5	18	0.884	Contact Map
2uzxB	1	0	16.7	0.886	Contact Map
4plqA	1	0.5455	14.7	0.888	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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