GREMLIN Database
YDBP - Thioredoxin-like protein YdbP
UniProt: P96611 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 106 (97)
Sequences: 8346 (5419)
Seq/√Len: 550.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_K63_A2.8771.00
11_N65_K2.3581.00
41_D94_P2.2411.00
93_T96_E2.1301.00
45_E94_P1.9971.00
75_L87_H1.9421.00
7_N61_D1.8431.00
23_K53_E1.8331.00
29_C32_C1.8131.00
5_T52_Y1.8061.00
20_I50_D1.7891.00
7_N62_L1.7341.00
66_Y77_F1.7071.00
45_E98_T1.6971.00
75_L82_K1.6951.00
38_F41_D1.6801.00
91_A96_E1.6521.00
39_I51_W1.6451.00
46_Y98_T1.6221.00
55_N58_E1.5861.00
38_F94_P1.5741.00
11_N15_Q1.5591.00
7_N59_L1.5571.00
19_E76_I1.5471.00
49_N102_S1.5141.00
21_I39_I1.4891.00
82_K87_H1.4841.00
18_K50_D1.4711.00
42_I51_W1.4551.00
21_I74_L1.4461.00
96_E99_E1.4181.00
13_L50_D1.4131.00
46_Y102_S1.3951.00
88_S92_K1.3631.00
98_T102_S1.3471.00
9_Q13_L1.3301.00
27_D55_N1.3241.00
42_I98_T1.3221.00
20_I52_Y1.2421.00
6_T9_Q1.2241.00
23_K36_N1.2201.00
35_M38_F1.1921.00
42_I94_P1.1781.00
54_L62_L1.1641.00
36_N40_G1.1321.00
13_L20_I1.1231.00
56_K71_I1.1221.00
5_T13_L1.1191.00
35_M74_L1.0931.00
22_V77_F1.0691.00
81_E84_A1.0351.00
6_T59_L1.0331.00
60_P64_E1.0151.00
39_I74_L0.9881.00
76_I100_F0.9851.00
76_I101_L0.9791.00
46_Y49_N0.9411.00
84_A88_S0.9061.00
35_M97_V0.9051.00
88_S100_F0.9001.00
40_G53_E0.8941.00
42_I97_V0.8931.00
36_N53_E0.8911.00
95_E99_E0.8861.00
44_E47_N0.8841.00
42_I46_Y0.8811.00
78_K83_T0.8761.00
14_I20_I0.8591.00
30_P33_T0.8541.00
84_A100_F0.8481.00
19_E78_K0.8451.00
17_D79_N0.8401.00
21_I51_W0.8391.00
60_P63_A0.8331.00
10_F24_F0.8211.00
54_L63_A0.8181.00
25_Y53_E0.8091.00
92_K96_E0.8091.00
17_D20_I0.8021.00
62_L65_K0.7991.00
94_P98_T0.7991.00
5_T9_Q0.7971.00
23_K35_M0.7881.00
27_D57_D0.7871.00
74_L97_V0.7871.00
9_Q52_Y0.7801.00
12_E15_Q0.7641.00
38_F93_T0.7301.00
59_L62_L0.7161.00
84_A87_H0.7131.00
23_K31_D0.7041.00
35_M92_K0.7021.00
25_Y71_I0.6971.00
61_D65_K0.6971.00
38_F42_I0.6901.00
87_H90_N0.6871.00
31_D34_R0.6851.00
99_E102_S0.6841.00
5_T22_V0.6841.00
25_Y55_N0.6821.00
34_R91_A0.6821.00
10_F14_I0.6801.00
10_F62_L0.6711.00
35_M39_I0.6651.00
24_F66_Y0.6641.00
21_I97_V0.6581.00
19_E79_N0.6561.00
54_L59_L0.6541.00
31_D70_G0.6481.00
78_K81_E0.6451.00
43_L51_W0.6341.00
28_W33_T0.6291.00
21_I101_L0.6291.00
16_S19_E0.6271.00
92_K100_F0.6181.00
18_K79_N0.6181.00
18_K48_Q0.6161.00
27_D33_T0.6081.00
45_E102_S0.6051.00
41_D44_E0.6041.00
10_F66_Y0.6021.00
9_Q12_E0.6001.00
10_F22_V0.5971.00
24_F75_L0.5961.00
80_G84_A0.5931.00
61_D64_E0.5851.00
34_R38_F0.5841.00
13_L17_D0.5831.00
21_I76_I0.5810.99
12_E16_S0.5810.99
28_W57_D0.5740.99
77_F82_K0.5740.99
26_A57_D0.5690.99
27_D56_K0.5370.99
24_F56_K0.5370.99
39_I101_L0.5340.99
68_V73_S0.5330.99
69_M87_H0.5310.99
30_P34_R0.5250.99
38_F91_A0.5240.99
46_Y51_W0.5220.99
26_A32_C0.5200.99
39_I42_I0.5180.99
31_D92_K0.5080.99
26_A68_V0.5040.99
16_S50_D0.5000.98
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  
2r2jA 2 0.9717 99.8 0.199 Contact Map
2b5eA 1 1 99.8 0.209 Contact Map
3f8uA 2 0.9811 99.8 0.213 Contact Map
3apoA 1 0.9057 99.8 0.213 Contact Map
4ekzA 1 1 99.8 0.23 Contact Map
4i6xA 1 0.9717 99.7 0.241 Contact Map
3us3A 2 0.9717 99.7 0.243 Contact Map
1sjiA 2 0.9717 99.7 0.247 Contact Map
3ed3A 1 1 99.7 0.259 Contact Map
3uemA 1 0.9811 99.7 0.276 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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