GREMLIN Database
YKOF - Putative HMP/thiamine-binding protein YkoF
UniProt: O34911 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 200 (185)
Sequences: 102 (84)
Seq/√Len: 6.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
21_T27_V4.7860.98
14_R140_A4.0710.95
18_Y77_V3.5410.89
138_D141_K3.1100.81
17_L78_M2.8240.74
145_T166_T2.8060.74
31_A73_E2.5410.66
30_S142_A2.5330.65
35_T64_A2.4530.63
89_D152_Y2.3640.60
62_A82_F2.3400.59
27_V74_Q2.2930.57
146_F154_S2.2250.55
93_D152_Y2.1670.53
69_A145_T2.1560.52
115_A163_V2.1100.51
60_D104_N2.0300.48
18_Y186_N1.9780.46
14_R48_S1.9410.45
154_S163_V1.8420.41
40_V52_R1.8040.40
146_F163_V1.7710.39
188_S191_S1.7550.38
124_M182_T1.7480.38
110_G182_T1.7470.38
23_D26_S1.6620.35
30_S134_M1.6470.35
11_A55_I1.6470.35
17_L116_P1.6310.34
58_V93_D1.5900.33
16_S116_P1.5750.32
29_K154_S1.5710.32
76_I155_E1.5530.32
166_T181_I1.5430.31
76_I193_S1.5140.31
166_T170_V1.4440.28
93_D129_Y1.4320.28
70_A189_A1.4300.28
10_I89_D1.3950.27
46_H155_E1.3930.27
81_T184_T1.3780.27
87_P180_H1.3540.26
25_I125_N1.3490.26
34_K100_D1.3480.26
66_Y189_A1.3460.26
69_A76_I1.3410.26
15_F182_T1.3400.25
17_L115_A1.3330.25
140_A166_T1.3330.25
18_Y66_Y1.3140.25
119_F189_A1.3080.25
67_L114_E1.2840.24
52_R60_D1.2790.24
63_K149_G1.2740.24
131_G134_M1.2690.24
120_A127_P1.2580.23
15_F65_I1.2550.23
22_D103_V1.2530.23
16_S77_V1.2470.23
59_F119_F1.2460.23
41_W89_D1.2420.23
104_N152_Y1.2260.22
27_V120_A1.2200.22
88_G130_M1.1940.22
86_C130_M1.1940.22
16_S174_A1.1860.22
167_L171_F1.1830.21
101_K183_M1.1820.21
15_F27_V1.1800.21
10_I152_Y1.1710.21
35_T140_A1.1660.21
91_Q115_A1.1610.21
21_T194_R1.1560.21
134_M141_K1.1530.21
110_G124_M1.1440.21
24_F164_F1.1390.20
75_H180_H1.1350.20
26_S115_A1.1260.20
50_V152_Y1.1190.20
19_P40_V1.1190.20
59_F171_F1.1180.20
67_L128_D1.1070.20
23_D169_A1.1020.20
32_L119_F1.0970.19
13_F62_A1.0940.19
22_D44_T1.0930.19
15_F58_V1.0910.19
60_D168_E1.0850.19
51_L111_L1.0850.19
41_W152_Y1.0810.19
49_T133_I1.0790.19
174_A185_V1.0580.19
188_S193_S1.0510.18
126_E137_V1.0310.18
99_G149_G1.0170.18
23_D107_A1.0090.18
82_F183_M1.0010.17
130_M137_V0.9990.17
45_D118_Q0.9870.17
93_D125_N0.9870.17
89_D151_H0.9820.17
89_D93_D0.9820.17
58_V64_A0.9800.17
120_A187_L0.9730.17
35_T62_A0.9720.17
118_Q181_I0.9700.17
64_A129_Y0.9670.17
178_T181_I0.9580.16
45_D48_S0.9560.16
79_N163_V0.9540.16
21_T31_A0.9530.16
25_I29_K0.9520.16
63_K105_E0.9440.16
30_S127_P0.9410.16
29_K114_E0.9410.16
15_F123_P0.9400.16
96_L115_A0.9380.16
88_G180_H0.9350.16
86_C180_H0.9350.16
24_F45_D0.9330.16
41_W52_R0.9220.16
79_N186_N0.9180.16
10_I41_W0.9180.16
58_V110_G0.9080.16
75_H192_P0.9040.15
17_L42_T0.9000.15
13_F82_F0.9000.15
41_W93_D0.8960.15
21_T32_L0.8920.15
131_G137_V0.8900.15
44_T192_P0.8840.15
10_I144_G0.8700.15
106_D169_A0.8640.15
59_F167_L0.8500.14
17_L69_A0.8500.14
132_L169_A0.8470.14
72_S163_V0.8410.14
18_Y65_I0.8410.14
10_I92_G0.8350.14
114_E194_R0.8340.14
113_A145_T0.8320.14
11_A31_A0.8300.14
39_K179_N0.8270.14
57_H60_D0.8260.14
134_M137_V0.8240.14
84_I181_I0.8220.14
27_V160_A0.8190.14
47_I183_M0.8160.14
29_K43_K0.8100.14
24_F59_F0.8090.14
149_G181_I0.8040.14
51_L116_P0.8020.14
107_A112_K0.8000.14
118_Q154_S0.7950.14
51_L166_T0.7840.13
83_S151_H0.7690.13
119_F123_P0.7680.13
24_F28_I0.7660.13
32_L191_S0.7550.13
171_F184_T0.7490.13
136_A189_A0.7480.13
118_Q150_V0.7340.13
143_Q169_A0.7290.12
47_I61_A0.7280.12
145_T163_V0.7280.12
21_T139_I0.7260.12
46_H116_P0.7250.12
46_H121_L0.7210.12
90_T135_E0.7190.12
40_V129_Y0.7180.12
170_V175_E0.7100.12
128_D194_R0.7060.12
52_R58_V0.7020.12
119_F171_F0.6990.12
29_K160_A0.6990.12
117_C163_V0.6970.12
47_I57_H0.6950.12
16_S24_F0.6900.12
60_D111_L0.6890.12
36_D190_N0.6840.12
47_I123_P0.6800.12
140_A170_V0.6760.12
163_V167_L0.6750.12
16_S19_P0.6700.12
52_R89_D0.6680.12
147_V163_V0.6660.11
35_T152_Y0.6590.11
11_A147_V0.6580.11
112_K186_N0.6550.11
35_T104_N0.6510.11
140_A153_A0.6500.11
47_I70_A0.6440.11
124_M172_R0.6410.11
19_P45_D0.6390.11
169_A186_N0.6360.11
69_A109_R0.6350.11
15_F60_D0.6330.11
121_L124_M0.6310.11
34_K50_V0.6300.11
15_F73_E0.6290.11
85_G122_Y0.6280.11
101_K120_A0.6220.11
102_R168_E0.6190.11
108_V111_L0.6170.11
54_S89_D0.6160.11
38_S67_L0.6130.11
138_D142_A0.6120.11
47_I124_M0.6100.11
75_H87_P0.6070.11
56_D102_R0.6050.11
52_R104_N0.6040.11
96_L194_R0.5970.11
83_S88_G0.5930.10
26_S155_E0.5930.10
83_S86_C0.5930.10
43_K160_A0.5920.10
149_G194_R0.5920.10
72_S110_G0.5910.10
75_H85_G0.5900.10
71_N149_G0.5890.10
74_Q190_N0.5860.10
108_V124_M0.5820.10
38_S167_L0.5820.10
10_I104_N0.5810.10
25_I182_T0.5810.10
62_A174_A0.5790.10
54_S94_T0.5740.10
17_L48_S0.5740.10
24_F168_E0.5730.10
112_K161_H0.5730.10
80_G162_D0.5730.10
89_D104_N0.5690.10
73_E121_L0.5670.10
42_T139_I0.5650.10
180_H192_P0.5640.10
87_P130_M0.5640.10
35_T82_F0.5620.10
105_E161_H0.5610.10
51_L61_A0.5580.10
68_H127_P0.5540.10
33_K165_S0.5510.10
63_K161_H0.5490.10
68_H111_L0.5450.10
19_P24_F0.5450.10
120_A150_V0.5440.10
59_F80_G0.5420.10
162_D172_R0.5410.10
130_M180_H0.5410.10
120_A169_A0.5370.10
95_Y153_A0.5360.10
16_S95_Y0.5360.10
22_D74_Q0.5360.10
35_T179_N0.5340.10
22_D30_S0.5340.10
61_A78_M0.5320.10
52_R93_D0.5320.10
39_K104_N0.5310.10
67_L172_R0.5250.10
137_V174_A0.5240.10
28_I188_S0.5240.10
14_R149_G0.5240.10
107_A176_Q0.5200.10
63_K139_I0.5170.09
10_I120_A0.5160.09
113_A137_V0.5150.09
34_K112_K0.5140.09
34_K71_N0.5120.09
59_F168_E0.5090.09
62_A173_M0.5090.09
81_T164_F0.5080.09
10_I94_T0.5060.09
84_I89_D0.5060.09
101_K109_R0.5050.09
118_Q163_V0.5030.09
34_K141_K0.5010.09
56_D106_D0.5010.09
48_S126_E0.5010.09
97_S102_R0.5000.09
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  
1s99A 2 0.93 100 0.344 Contact Map
2epiA 4 0.455 98.6 0.881 Contact Map
1yqhA 3 0.46 98.5 0.885 Contact Map
2iboA 4 0.425 97.5 0.911 Contact Map
1lxnA 4 0.435 97.3 0.913 Contact Map
1lxjA 4 0.455 97.3 0.913 Contact Map
1vk8A 4 0.445 97 0.918 Contact Map
3iixA 1 0.77 40.4 0.961 Contact Map
3t7vA 1 0.755 33.4 0.963 Contact Map
4rtbA 2 0.835 12.6 0.969 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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