GREMLIN Database
RAMP4 - Ribosome associated membrane protein RAMP4
PFAM: PF06624 Sequences:
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_L49_V2.2871.00
3_T6_M2.1541.00
10_N14_A2.1521.00
39_W42_G2.0491.00
16_N23_V2.0071.00
17_I20_R1.9661.00
55_Q59_S1.9471.00
36_V41_L1.9141.00
3_T7_R1.5061.00
11_E15_K1.5001.00
5_R9_K1.4981.00
4_R9_K1.4951.00
46_F54_F1.4501.00
8_L11_E1.4280.99
4_R7_R1.3300.99
20_R23_V1.3170.99
37_G41_L1.3110.99
44_F52_A1.2880.99
39_W43_F1.2690.99
36_V40_L1.2660.99
45_L48_V1.2470.99
6_M10_N1.2430.98
53_L58_R1.1910.98
45_L56_I1.1520.98
53_L59_S1.1270.97
35_P41_L1.1220.97
9_K49_V1.1000.97
2_Q6_M1.0810.96
40_L44_F1.0810.96
38_P42_G1.0760.96
4_R8_L1.0700.96
16_N20_R1.0410.95
7_R10_N1.0390.95
5_R47_V1.0390.95
13_F37_G1.0220.95
6_M9_K1.0170.95
3_T9_K1.0030.94
16_N19_K0.9930.94
38_P51_S0.9780.94
42_G46_F0.9190.91
3_T57_I0.9090.91
25_K28_K0.9090.91
2_Q33_K0.9060.91
41_L46_F0.9040.91
54_F57_I0.8560.88
23_V26_S0.8370.87
6_M13_F0.8370.87
2_Q7_R0.8270.86
9_K12_K0.8190.86
38_P59_S0.8100.85
29_K45_L0.7890.84
3_T8_L0.7880.84
10_N13_F0.7830.83
43_F48_V0.7830.83
55_Q58_R0.7780.83
7_R11_E0.7570.81
43_F52_A0.7420.80
36_V44_F0.7310.79
54_F58_R0.7240.78
37_G40_L0.6970.76
26_S29_K0.6870.75
2_Q5_R0.6850.74
19_K30_K0.6830.74
41_L48_V0.6640.72
48_V52_A0.6610.72
48_V51_S0.6530.71
24_P27_L0.6520.71
17_I21_G0.6350.69
18_T24_P0.6340.69
12_K15_K0.6310.68
40_L43_F0.6280.68
5_R8_L0.6190.67
15_K25_K0.5960.64
29_K32_E0.5940.64
22_K25_K0.5930.63
8_L19_K0.5840.62
53_L57_I0.5670.60
11_E14_A0.5650.60
7_R31_E0.5640.60
5_R43_F0.5630.59
2_Q47_V0.5490.58
24_P30_K0.5430.57
27_L57_I0.5410.56
13_F16_N0.5280.55
2_Q10_N0.5180.53
52_A59_S0.5110.52
31_E56_I0.5000.51
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

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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