GREMLIN Database
YPIF - Uncharacterized protein YpiF
UniProt: P54391 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 148 (146)
Sequences: 163 (131)
Seq/√Len: 10.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
102_R110_M3.1760.96
21_A62_L3.0380.94
93_V141_L2.6900.90
18_I40_K2.6620.89
38_A41_G2.5680.88
38_A93_V2.5450.87
18_I69_D2.1600.76
107_L110_M2.0380.72
21_A85_L1.9800.70
43_F115_S1.9030.66
104_E110_M1.8710.65
53_R130_L1.8530.64
15_K69_D1.8430.64
27_N40_K1.7670.60
92_V134_T1.7560.60
10_D56_K1.7470.59
18_I129_I1.7410.59
11_Y133_R1.6930.57
69_D113_T1.6840.56
11_Y96_T1.6820.56
51_L111_I1.6640.56
93_V133_R1.6330.54
39_E119_E1.6280.54
72_E78_L1.6060.53
81_L104_E1.6030.53
44_T97_S1.6010.53
6_T11_Y1.5880.52
76_Q129_I1.5730.51
35_K56_K1.5480.50
3_W108_G1.5360.49
16_D116_V1.4570.46
25_L98_D1.4510.45
55_L137_I1.4490.45
47_L130_L1.4470.45
3_W81_L1.4320.45
121_L127_R1.4160.44
125_L142_L1.4010.43
26_I49_E1.3990.43
46_L53_R1.3850.42
67_Y114_S1.3710.42
71_N111_I1.3700.42
65_Y101_W1.3680.42
54_Q117_P1.3680.42
47_L115_S1.3550.41
2_R45_Q1.3540.41
77_G81_L1.3320.40
81_L114_S1.3230.39
44_T135_A1.3130.39
17_Y138_L1.2990.38
27_N98_D1.2860.38
48_S74_T1.2800.38
8_A60_Y1.2740.37
54_Q139_N1.2710.37
81_L133_R1.2680.37
125_L137_I1.2390.36
10_D14_A1.2290.35
113_T140_V1.2210.35
134_T139_N1.2160.35
117_P126_K1.1810.33
11_Y94_L1.1750.33
5_I26_I1.1750.33
83_E106_A1.1620.32
66_T121_L1.1550.32
9_K35_K1.1390.31
94_L132_E1.1370.31
82_R94_L1.1360.31
50_E53_R1.1290.31
51_L113_T1.1260.31
92_V138_L1.1260.31
55_L139_N1.1100.30
114_S133_R1.1060.30
18_I140_V1.0940.30
60_Y70_R1.0850.29
21_A54_Q1.0740.29
27_N112_V1.0710.29
14_A56_K1.0610.28
5_I120_H1.0550.28
36_M82_R1.0430.28
44_T137_I1.0370.27
22_V80_D1.0330.27
18_I68_V1.0290.27
87_T141_L1.0240.27
12_L17_Y1.0170.27
59_V125_L1.0020.26
9_K62_L0.9940.26
50_E131_D0.9560.24
102_R122_N0.9530.24
67_Y133_R0.9520.24
18_I45_Q0.9470.24
133_R136_E0.9430.24
98_D101_W0.9380.24
22_V113_T0.9300.24
122_N128_K0.9240.23
6_T55_L0.9190.23
112_V144_L0.9180.23
109_K123_D0.9160.23
90_P121_L0.9150.23
35_K119_E0.9120.23
55_L119_E0.9120.23
25_L67_Y0.9030.23
74_T121_L0.9020.23
27_N81_L0.9000.23
29_R62_L0.8940.22
11_Y69_D0.8850.22
70_R137_I0.8850.22
21_A89_F0.8720.22
29_R48_S0.8660.21
139_N143_Q0.8550.21
79_K106_A0.8420.21
22_V59_V0.8350.20
55_L135_A0.8340.20
28_I64_P0.8310.20
92_V118_L0.8200.20
3_W16_D0.8110.20
9_K38_A0.8090.20
2_R14_A0.8070.20
28_I144_L0.8070.20
75_V100_S0.8060.20
31_N71_N0.8060.20
17_Y50_E0.8050.20
42_E114_S0.8040.20
33_H127_R0.7990.19
21_A135_A0.7890.19
17_Y38_A0.7800.19
41_G64_P0.7700.19
11_Y77_G0.7690.18
40_K141_L0.7650.18
47_L140_V0.7640.18
50_E128_K0.7640.18
28_I115_S0.7600.18
126_K129_I0.7490.18
67_Y91_H0.7480.18
123_D126_K0.7480.18
15_K118_L0.7470.18
32_N121_L0.7470.18
126_K142_L0.7460.18
21_A126_K0.7430.18
29_R78_L0.7400.18
13_Q37_A0.7340.18
112_V133_R0.7310.17
59_V70_R0.7310.17
112_V136_E0.7270.17
51_L140_V0.7160.17
103_A141_L0.7100.17
35_K62_L0.7090.17
31_N92_V0.7000.17
29_R111_I0.6980.17
34_F68_V0.6960.16
21_A33_H0.6910.16
28_I79_K0.6900.16
14_A18_I0.6840.16
76_Q87_T0.6820.16
54_Q121_L0.6800.16
104_E133_R0.6720.16
6_T60_Y0.6640.16
33_H78_L0.6640.16
60_Y89_F0.6630.16
68_V112_V0.6620.16
109_K121_L0.6590.16
33_H126_K0.6550.15
43_F144_L0.6510.15
93_V115_S0.6470.15
65_Y77_G0.6410.15
22_V95_L0.6380.15
4_R141_L0.6370.15
51_L66_T0.6310.15
56_K129_I0.6290.15
33_H87_T0.6280.15
28_I73_I0.6220.15
46_L124_S0.6210.15
9_K53_R0.6210.15
39_E118_L0.6180.15
4_R13_Q0.6180.15
48_S103_A0.6170.15
31_N45_Q0.6160.14
4_R39_E0.6150.14
23_I78_L0.6150.14
47_L66_T0.6140.14
40_K65_Y0.6140.14
35_K47_L0.6090.14
91_H141_L0.6060.14
74_T139_N0.6000.14
22_V131_D0.5970.14
51_L64_P0.5970.14
11_Y115_S0.5950.14
54_Q74_T0.5900.14
89_F115_S0.5790.14
50_E98_D0.5790.14
92_V102_R0.5730.14
3_W27_N0.5720.13
48_S106_A0.5720.13
123_D141_L0.5690.13
17_Y110_M0.5570.13
137_I146_S0.5560.13
43_F139_N0.5550.13
21_A41_G0.5510.13
137_I142_L0.5510.13
51_L124_S0.5510.13
37_A41_G0.5500.13
21_A117_P0.5500.13
4_R84_E0.5400.13
18_I109_K0.5380.13
47_L64_P0.5360.13
119_E138_L0.5350.13
62_L85_L0.5330.13
46_L140_V0.5290.13
84_E127_R0.5270.13
46_L59_V0.5260.12
43_F65_Y0.5230.12
11_Y67_Y0.5180.12
80_D113_T0.5150.12
108_G129_I0.5130.12
55_L127_R0.5080.12
2_R135_A0.5050.12
54_Q88_E0.5050.12
15_K68_V0.5050.12
46_L116_V0.5020.12
6_T93_V0.5010.12
46_L139_N0.5000.12
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  
3lubA 4 0.7703 47.1 0.941 Contact Map
3no4A 5 0.8176 40.1 0.943 Contact Map
1yyaA 2 0.8446 14.7 0.954 Contact Map
1v7zA 5 0.8243 14.1 0.954 Contact Map
1neyA 2 0.8378 13.2 0.955 Contact Map
4y90A 3 0.8243 12.9 0.955 Contact Map
2j27A 2 0.8514 12 0.956 Contact Map
1o5xA 2 0.7973 11.7 0.956 Contact Map
3krsA 2 0.8311 9.9 0.957 Contact Map
3th6A 2 0.7973 9.6 0.958 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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