GREMLIN Database
YKFF - UPF0401 protein YkfF
UniProt: P75677 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14283
Length: 79 (70)
Sequences: 101 (54)
Seq/√Len: 6.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
47_R67_I2.7420.74
31_D38_R2.6160.70
33_Q36_H2.5550.68
52_A56_E2.4880.66
8_P24_Y2.4110.63
41_V48_M2.3200.60
62_G70_S1.9830.48
10_G28_T1.8800.44
19_A23_T1.7320.39
41_V47_R1.6170.35
11_P28_T1.5600.33
17_A29_L1.5500.33
16_Q19_A1.5130.32
9_P61_E1.4890.31
17_A53_W1.4880.31
27_I46_G1.4380.29
6_L57_P1.4300.29
57_P70_S1.3900.28
27_I74_T1.3670.27
15_R25_S1.3460.27
30_E48_M1.3090.26
15_R22_T1.2590.24
5_V19_A1.2510.24
7_L17_A1.2350.24
9_P20_V1.2290.23
30_E39_L1.1890.22
50_W71_G1.1840.22
9_P41_V1.1790.22
44_T65_R1.1770.22
26_N40_V1.1180.21
24_Y64_N1.0860.20
11_P58_D1.0770.20
68_R73_R1.0690.19
18_Q43_D1.0670.19
47_R68_R1.0640.19
8_P53_W1.0550.19
15_R18_Q1.0370.19
8_P30_E0.9910.18
56_E66_Y0.9900.18
13_T55_F0.9830.18
45_E52_A0.9800.17
21_T28_T0.9750.17
8_P64_N0.9680.17
13_T51_R0.9660.17
14_R59_A0.9340.17
15_R62_G0.9320.16
23_T61_E0.9270.16
41_V68_R0.9170.16
32_D36_H0.9090.16
31_D66_Y0.8980.16
41_V67_I0.8810.15
68_R72_I0.8760.15
15_R23_T0.8710.15
11_P72_I0.8450.15
47_R56_E0.8390.15
14_R42_R0.8290.14
9_P27_I0.8260.14
22_T45_E0.8170.14
16_Q40_V0.8090.14
39_L48_M0.7890.14
44_T56_E0.7850.14
12_F32_D0.7710.13
40_V50_W0.7500.13
6_L23_T0.7370.13
26_N50_W0.7320.13
15_R43_D0.7290.13
22_T74_T0.7170.13
15_R46_G0.7150.13
35_S74_T0.6890.12
67_I73_R0.6860.12
30_E53_W0.6650.12
5_V21_T0.6550.12
8_P55_F0.6500.12
32_D64_N0.6460.11
30_E55_F0.6410.11
35_S56_E0.6380.11
28_T71_G0.6310.11
33_Q65_R0.6300.11
11_P52_A0.6260.11
34_G69_T0.6200.11
40_V52_A0.6190.11
6_L25_S0.6170.11
9_P59_A0.6110.11
49_V67_I0.6060.11
15_R19_A0.6050.11
16_Q21_T0.6030.11
42_R54_N0.5850.11
43_D73_R0.5770.10
38_R50_W0.5730.10
38_R66_Y0.5710.10
27_I35_S0.5700.10
27_I61_E0.5690.10
29_L74_T0.5610.10
53_W64_N0.5580.10
33_Q74_T0.5580.10
32_D51_R0.5540.10
25_S73_R0.5480.10
34_G67_I0.5390.10
39_L55_F0.5350.10
12_F55_F0.5260.10
41_V49_V0.5160.10
18_Q53_W0.5160.10
16_Q36_H0.5150.10
9_P25_S0.5020.09
6_L20_V0.5000.09
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  
2hjjA 1 0.8354 100 0.088 Contact Map
5am2A 2 0.481 17.8 0.934 Contact Map
3cnhA 1 0.519 16.2 0.935 Contact Map
2q01A 3 0.8987 15.8 0.935 Contact Map
2hi0A 2 0.5316 13.7 0.937 Contact Map
2hdoA 1 0.519 10.9 0.94 Contact Map
4aq1A 1 0 10.3 0.94 Contact Map
3magA 2 0.8734 10.1 0.941 Contact Map
2zg6A 2 0.519 9 0.942 Contact Map
1vptA 2 0.8481 8.6 0.942 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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