GREMLIN Database
RPAP1_C - RPAP1-like, C-terminal
PFAM: PF08620 Sequences:
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_L23_H3.1241.00
39_L57_T2.9661.00
28_E31_A2.7791.00
5_D9_N2.7151.00
26_G29_P2.3421.00
39_L54_A2.2801.00
44_R51_R2.2631.00
5_D11_I2.1591.00
16_I20_L1.9400.99
9_N64_R1.9390.99
6_F57_T1.8260.99
2_L10_L1.7960.99
17_P20_L1.6540.98
47_V51_R1.5870.97
17_P23_H1.4830.96
23_H32_A1.4310.95
21_G24_H1.3850.94
4_F36_L1.3080.91
6_F24_H1.2840.91
51_R62_L1.2660.90
36_L40_L1.2220.88
53_I56_Q1.1820.87
21_G25_H1.1190.83
2_L31_A1.0950.82
8_G35_T1.0940.82
14_A59_G1.0850.82
6_F60_R1.0730.81
51_R65_L1.0060.76
46_T52_C0.9800.74
48_P52_C0.9700.74
5_D63_Y0.9650.73
2_L28_E0.9650.73
59_G63_Y0.9600.73
22_L34_Y0.9500.72
13_S64_R0.9220.70
29_P38_E0.9140.69
33_G38_E0.9070.69
29_P62_L0.8870.67
7_N55_L0.8820.66
3_R8_G0.8820.66
25_H39_L0.8740.66
15_D35_T0.8740.66
32_A42_L0.8690.65
6_F10_L0.8600.64
56_Q60_R0.8590.64
26_G38_E0.8450.63
22_L29_P0.8450.63
37_P49_A0.8120.60
36_L43_S0.8040.59
21_G32_A0.7970.58
13_S16_I0.7680.56
43_S56_Q0.7480.54
40_L46_T0.7350.52
48_P60_R0.7290.52
53_I58_L0.7250.51
58_L61_I0.7240.51
42_L45_S0.7180.51
30_E58_L0.7130.50
37_P53_I0.6990.49
39_L43_S0.6970.49
27_D41_H0.6940.48
35_T38_E0.6760.47
18_T32_A0.6600.45
10_L13_S0.6510.44
12_P61_I0.6480.44
2_L46_T0.6480.44
5_D25_H0.6350.43
10_L18_T0.6280.42
4_F8_G0.6210.41
38_E41_H0.6170.41
19_H40_L0.6130.40
22_L33_G0.6080.40
54_A57_T0.5950.39
36_L61_I0.5880.38
7_N56_Q0.5860.38
14_A18_T0.5790.37
4_F10_L0.5750.37
41_H47_V0.5680.36
55_L59_G0.5650.36
28_E40_L0.5600.35
6_F22_L0.5580.35
13_S27_D0.5540.35
7_N12_P0.5470.34
27_D37_P0.5370.33
14_A27_D0.5330.33
19_H46_T0.5320.33
60_R64_R0.5280.33
13_S44_R0.5260.32
31_A56_Q0.5250.32
40_L55_L0.5220.32
25_H32_A0.5170.32
43_S58_L0.5120.31
19_H62_L0.5050.31
5_D24_H0.5030.30
25_H50_Q0.5030.30
31_A49_A0.5000.30
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

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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