GREMLIN Database
YNFD - Uncharacterized protein YnfD
UniProt: P76172 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13842
Length: 101 (88)
Sequences: 106 (70)
Seq/√Len: 7.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
42_V79_R4.4270.98
43_P46_S4.3080.98
38_I42_V2.9310.84
63_Q71_D2.6860.78
62_S76_L2.3640.68
13_A32_D1.9140.51
18_A53_P1.8080.47
62_S73_H1.7930.46
54_N63_Q1.7930.46
64_V71_D1.7890.46
53_P56_Q1.7860.46
23_P73_H1.7160.43
36_R50_S1.6570.41
25_S29_I1.6010.39
51_I71_D1.5780.38
14_L18_A1.5610.38
67_H71_D1.4900.35
63_Q67_H1.4620.34
3_L36_R1.4020.32
29_I69_A1.3850.31
7_C18_A1.3710.31
3_L8_A1.3660.31
28_R69_A1.3230.29
76_L82_S1.3140.29
55_D74_K1.3090.29
5_T8_A1.2640.27
78_T83_G1.2420.27
22_A59_Q1.2380.26
24_G28_R1.2350.26
16_S21_A1.2000.25
32_D38_I1.1920.25
10_L13_A1.1880.25
51_I67_H1.1770.25
28_R36_R1.1750.25
3_L6_C1.1600.24
76_L80_T1.1370.23
52_V74_K1.1190.23
6_C62_S1.0770.22
85_V89_A1.0730.22
21_A35_Q1.0710.22
56_Q71_D1.0690.22
16_S85_V1.0680.22
31_S62_S1.0670.22
58_D64_V1.0500.21
5_T17_P1.0450.21
2_K81_T1.0290.21
45_S81_T1.0260.20
19_V28_R0.9960.20
16_S19_V0.9820.19
22_A43_P0.9680.19
10_L39_N0.9610.19
11_L34_S0.9500.19
29_I78_T0.9430.18
25_S52_V0.9370.18
12_L79_R0.9350.18
23_P69_A0.9280.18
67_H74_K0.9240.18
4_S34_S0.9220.18
28_R76_L0.9140.18
79_R86_S0.9080.18
9_A80_T0.8950.17
2_K5_T0.8830.17
50_S60_P0.8810.17
23_P28_R0.8700.17
55_D63_Q0.8680.17
31_S73_H0.8580.16
29_I61_D0.8510.16
3_L50_S0.8310.16
54_N69_A0.8210.16
60_P82_S0.8080.15
23_P29_I0.8060.15
18_A78_T0.7870.15
7_C73_H0.7750.15
36_R61_D0.7710.15
52_V71_D0.7670.15
25_S67_H0.7620.14
81_T88_P0.7610.14
30_Q46_S0.7610.14
2_K83_G0.7520.14
24_G73_H0.7440.14
11_L38_I0.7440.14
52_V55_D0.7360.14
18_A21_A0.7280.14
34_S45_S0.7140.14
29_I70_N0.7040.13
15_A80_T0.6890.13
6_C14_L0.6880.13
15_A24_G0.6530.12
80_T84_N0.6390.12
20_L45_S0.6390.12
48_T70_N0.6310.12
27_E38_I0.6280.12
52_V58_D0.6260.12
2_K8_A0.6170.12
7_C23_P0.6150.12
82_S86_S0.6150.12
35_Q39_N0.6080.12
54_N67_H0.6070.12
36_R82_S0.5970.12
36_R76_L0.5950.12
15_A57_V0.5890.11
13_A50_S0.5800.11
37_I42_V0.5770.11
38_I48_T0.5770.11
51_I56_Q0.5750.11
50_S82_S0.5740.11
86_S89_A0.5710.11
5_T31_S0.5700.11
31_S84_N0.5680.11
8_A73_H0.5670.11
34_S48_T0.5650.11
16_S35_Q0.5630.11
30_Q35_Q0.5610.11
15_A21_A0.5540.11
52_V65_V0.5490.11
31_S60_P0.5480.11
6_C28_R0.5460.11
80_T83_G0.5390.11
7_C17_P0.5370.11
47_F56_Q0.5300.11
50_S76_L0.5300.11
18_A87_A0.5170.10
10_L89_A0.5150.10
55_D67_H0.5140.10
13_A17_P0.5130.10
13_A88_P0.5110.10
38_I53_P0.5090.10
23_P70_N0.5090.10
10_L27_E0.5060.10
6_C18_A0.5060.10
12_L80_T0.5000.10
19_V62_S0.5000.10
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  
2jnaA 2 0.8812 56 0.92 Contact Map
3tdgA 2 0.6337 20.4 0.937 Contact Map
3nb3A 2 0.396 18.7 0.938 Contact Map
4ivkA 4 0.5446 15.4 0.94 Contact Map
3zbiC 1 0.2673 14.5 0.941 Contact Map
4mxgA 1 0.6535 12.6 0.943 Contact Map
3oa8B 3 0.5842 12.5 0.943 Contact Map
3hunA 1 0.6238 12.4 0.943 Contact Map
2pjhA 1 0.7327 10.2 0.945 Contact Map
3bxwB 2 0.6337 8.6 0.947 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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