RAMP4 - PFAM28P - GREMLIN Contacts

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RAMP4 - Ribosome associated membrane protein RAMP4

PFAM:	PF06624	Sequences: AQTRRMRLKNEKFAKNITKRGKVPKSLKKKEEKSPVGPWLLGFFLFVVVGSALFQIIRSI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (58)
Sequences:	933 (707)
Seq/√Len:	92.8
META:	0.647

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_L	49_V	2.287	1.00
3_T	6_M	2.154	1.00
10_N	14_A	2.152	1.00
39_W	42_G	2.049	1.00
16_N	23_V	2.007	1.00
17_I	20_R	1.966	1.00
55_Q	59_S	1.947	1.00
36_V	41_L	1.914	1.00
3_T	7_R	1.506	1.00
11_E	15_K	1.500	1.00
5_R	9_K	1.498	1.00
4_R	9_K	1.495	1.00
46_F	54_F	1.450	1.00
8_L	11_E	1.428	0.99
4_R	7_R	1.330	0.99
20_R	23_V	1.317	0.99
37_G	41_L	1.311	0.99
44_F	52_A	1.288	0.99
39_W	43_F	1.269	0.99
36_V	40_L	1.266	0.99
45_L	48_V	1.247	0.99
6_M	10_N	1.243	0.98
53_L	58_R	1.191	0.98
45_L	56_I	1.152	0.98
53_L	59_S	1.127	0.97
35_P	41_L	1.122	0.97
9_K	49_V	1.100	0.97
2_Q	6_M	1.081	0.96
40_L	44_F	1.081	0.96
38_P	42_G	1.076	0.96
4_R	8_L	1.070	0.96
16_N	20_R	1.041	0.95
7_R	10_N	1.039	0.95
5_R	47_V	1.039	0.95
13_F	37_G	1.022	0.95
6_M	9_K	1.017	0.95
3_T	9_K	1.003	0.94
16_N	19_K	0.993	0.94
38_P	51_S	0.978	0.94
42_G	46_F	0.919	0.91
3_T	57_I	0.909	0.91
25_K	28_K	0.909	0.91
2_Q	33_K	0.906	0.91
41_L	46_F	0.904	0.91
54_F	57_I	0.856	0.88
23_V	26_S	0.837	0.87
6_M	13_F	0.837	0.87
2_Q	7_R	0.827	0.86
9_K	12_K	0.819	0.86
38_P	59_S	0.810	0.85
29_K	45_L	0.789	0.84
3_T	8_L	0.788	0.84
10_N	13_F	0.783	0.83
43_F	48_V	0.783	0.83
55_Q	58_R	0.778	0.83
7_R	11_E	0.757	0.81
43_F	52_A	0.742	0.80
36_V	44_F	0.731	0.79
54_F	58_R	0.724	0.78
37_G	40_L	0.697	0.76
26_S	29_K	0.687	0.75
2_Q	5_R	0.685	0.74
19_K	30_K	0.683	0.74
41_L	48_V	0.664	0.72
48_V	52_A	0.661	0.72
48_V	51_S	0.653	0.71
24_P	27_L	0.652	0.71
17_I	21_G	0.635	0.69
18_T	24_P	0.634	0.69
12_K	15_K	0.631	0.68
40_L	43_F	0.628	0.68
5_R	8_L	0.619	0.67
15_K	25_K	0.596	0.64
29_K	32_E	0.594	0.64
22_K	25_K	0.593	0.63
8_L	19_K	0.584	0.62
53_L	57_I	0.567	0.60
11_E	14_A	0.565	0.60
7_R	31_E	0.564	0.60
5_R	43_F	0.563	0.59
2_Q	47_V	0.549	0.58
24_P	30_K	0.543	0.57
27_L	57_I	0.541	0.56
13_F	16_N	0.528	0.55
2_Q	10_N	0.518	0.53
52_A	59_S	0.511	0.52
31_E	56_I	0.500	0.51

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
3ukmA	2	0.5	18.8	0.845	Contact Map
3owqA	1	0	13	0.856	Contact Map
1rz2A	1	0.0833	11	0.86	Contact Map
1pfiA	7	0.7667	10.1	0.863	Contact Map
3pe5A	1	0	8.6	0.867	Contact Map
4p6vC	1	0.45	8.4	0.868	Contact Map
4twkA	2	0.5667	6	0.876	Contact Map
4bw5A	2	0.4833	5.8	0.877	Contact Map
4wfeA	2	0.4833	5.2	0.879	Contact Map
3zhgA	3	0	4.7	0.882	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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