GREMLIN Database
YPIB - UPF0302 protein YpiB
UniProt: P54390 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 179 (174)
Sequences: 219 (169)
Seq/√Len: 12.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_H57_G3.7720.99
31_I38_H3.3320.98
79_T84_K3.1360.97
167_A170_Q2.8750.95
26_R30_W2.7330.94
158_D162_R2.7230.94
54_C100_Q2.6320.93
70_F85_S2.6140.92
5_V130_K2.6030.92
17_F23_L2.3270.87
61_S101_L2.2460.85
164_D167_A2.1660.83
108_S152_L2.1530.82
87_H91_L1.9750.76
9_E37_S1.9530.75
165_K169_E1.8970.73
44_K99_I1.8960.73
47_F157_D1.8520.71
158_D167_A1.8480.71
50_Q127_F1.8400.71
92_N157_D1.8090.70
152_L174_Q1.7900.69
57_G93_K1.7630.67
86_F90_R1.7430.67
87_H90_R1.7200.65
23_L101_L1.7000.65
23_L70_F1.6980.64
14_I109_S1.6840.64
173_R177_Q1.6610.63
18_L101_L1.6160.60
162_R174_Q1.5990.60
17_F73_Y1.5970.60
74_K90_R1.5870.59
169_E172_S1.5780.59
93_K97_L1.5690.58
107_Y113_A1.5430.57
35_L90_R1.5310.56
33_N140_L1.5210.56
84_K88_D1.5140.55
18_L136_A1.4860.54
11_K26_R1.4810.54
9_E61_S1.4780.53
39_D147_F1.4770.53
42_M65_V1.4380.51
70_F101_L1.4310.51
149_R166_E1.4080.50
23_L85_S1.4060.50
49_E116_L1.4000.49
39_D96_D1.3980.49
30_W90_R1.3870.49
14_I77_V1.3710.48
149_R153_L1.3700.48
80_T89_I1.3700.48
37_S41_L1.3560.47
142_H146_T1.3390.46
128_E165_K1.3390.46
141_E170_Q1.2960.44
153_L175_L1.2950.44
93_K100_Q1.2940.44
30_W83_E1.2820.43
161_D175_L1.2630.42
134_G167_A1.2590.42
93_K139_I1.2580.42
158_D166_E1.2580.42
149_R177_Q1.2070.40
63_H76_N1.2030.39
21_Y102_N1.2000.39
72_F103_F1.1730.38
55_P119_N1.1650.37
58_I95_Q1.1630.37
64_C80_T1.1540.37
59_I130_K1.1440.36
27_E86_F1.1420.36
17_F103_F1.1410.36
17_F59_I1.1350.36
41_L44_K1.1180.35
36_M65_V1.1180.35
148_Q151_K1.1160.35
9_E65_V1.1020.34
27_E90_R1.0960.34
29_V56_R1.0890.34
143_A147_F1.0710.33
15_R19_N1.0680.33
51_A58_I1.0540.32
45_V72_F1.0520.32
79_T161_D1.0500.32
23_L41_L1.0490.32
131_K173_R1.0430.32
108_S155_D1.0400.32
142_H145_S1.0390.32
30_W33_N1.0060.30
47_F61_S0.9960.30
111_E148_Q0.9800.29
7_V65_V0.9760.29
60_M149_R0.9750.29
26_R84_K0.9690.28
55_P121_H0.9640.28
64_C104_R0.9620.28
90_R120_P0.9590.28
166_E169_E0.9540.28
33_N37_S0.9330.27
29_V82_A0.9320.27
5_V174_Q0.9270.27
110_P113_A0.9240.27
29_V73_Y0.9120.26
27_E117_E0.9120.26
23_L83_E0.9010.26
31_I157_D0.8950.25
155_D171_L0.8950.25
151_K173_R0.8880.25
150_E177_Q0.8880.25
71_R127_F0.8800.25
162_R173_R0.8760.25
35_L116_L0.8760.25
37_S96_D0.8740.25
100_Q132_D0.8630.24
46_H98_F0.8620.24
51_A100_Q0.8600.24
11_K71_R0.8560.24
9_E98_F0.8360.23
87_H119_N0.8350.23
18_L61_S0.8330.23
85_S102_N0.8310.23
146_T154_K0.8250.23
11_K34_Y0.8130.22
27_E69_P0.8110.22
56_R71_R0.8090.22
34_Y119_N0.8020.22
151_K155_D0.7910.22
5_V141_E0.7900.22
44_K60_M0.7880.21
110_P158_D0.7870.21
49_E67_E0.7820.21
72_F88_D0.7800.21
7_V150_E0.7770.21
54_C87_H0.7770.21
72_F101_L0.7700.21
5_V107_Y0.7650.21
30_W81_D0.7610.21
21_Y64_C0.7570.20
135_L139_I0.7510.20
24_K28_C0.7490.20
76_N126_L0.7480.20
15_R25_R0.7470.20
25_R72_F0.7460.20
44_K96_D0.7460.20
20_H31_I0.7440.20
96_D108_S0.7400.20
26_R81_D0.7390.20
162_R170_Q0.7380.20
5_V76_N0.7370.20
61_S99_I0.7370.20
25_R31_I0.7340.20
35_L51_A0.7340.20
63_H151_K0.7330.20
97_L177_Q0.7330.20
165_K168_F0.7310.20
33_N46_H0.7290.19
9_E12_D0.7230.19
82_A123_P0.7170.19
71_R136_A0.7080.19
11_K92_N0.7060.19
76_N161_D0.6950.18
25_R59_I0.6950.18
31_I82_A0.6940.18
61_S70_F0.6920.18
112_Y115_V0.6900.18
163_H174_Q0.6860.18
46_H119_N0.6850.18
56_R77_V0.6850.18
52_E125_N0.6820.18
154_K158_D0.6810.18
60_M164_D0.6800.18
27_E30_W0.6730.18
84_K161_D0.6720.18
49_E124_K0.6690.18
172_S175_L0.6690.18
68_V82_A0.6670.18
118_S153_L0.6650.17
149_R158_D0.6650.17
58_I92_N0.6630.17
102_N132_D0.6610.17
65_V105_S0.6610.17
48_V168_F0.6560.17
57_G75_E0.6500.17
8_N93_K0.6440.17
41_L124_K0.6360.17
52_E77_V0.6350.17
17_F175_L0.6330.17
140_L166_E0.6300.16
83_E101_L0.6290.16
52_E104_R0.6280.16
108_S176_N0.6240.16
21_Y73_Y0.6190.16
87_H121_H0.6130.16
58_I121_H0.6090.16
66_E91_L0.6050.16
30_W87_H0.6050.16
56_R112_Y0.6050.16
11_K30_W0.6050.16
46_H92_N0.6050.16
31_I60_M0.6020.16
75_E78_M0.6000.16
7_V164_D0.5980.16
54_C82_A0.5970.16
40_S147_F0.5970.16
44_K56_R0.5960.16
15_R148_Q0.5950.15
134_G137_E0.5920.15
122_I133_Q0.5880.15
148_Q174_Q0.5860.15
57_G107_Y0.5850.15
155_D167_A0.5830.15
101_L136_A0.5810.15
83_E136_A0.5780.15
126_L132_D0.5780.15
77_V169_E0.5770.15
59_I161_D0.5770.15
30_W119_N0.5750.15
26_R86_F0.5740.15
41_L97_L0.5740.15
55_P123_P0.5710.15
77_V93_K0.5710.15
107_Y161_D0.5660.15
138_Q141_E0.5640.15
151_K154_K0.5620.15
12_D142_H0.5590.15
22_Q63_H0.5560.14
156_I168_F0.5560.14
19_N141_E0.5540.14
60_M150_E0.5500.14
4_P118_S0.5480.14
79_T136_A0.5480.14
31_I51_A0.5430.14
146_T162_R0.5420.14
24_K101_L0.5410.14
67_E175_L0.5400.14
79_T88_D0.5380.14
57_G92_N0.5350.14
87_H120_P0.5340.14
54_C84_K0.5340.14
47_F160_L0.5340.14
158_D163_H0.5330.14
40_S176_N0.5300.14
73_Y175_L0.5300.14
54_C79_T0.5290.14
139_I151_K0.5280.14
39_D92_N0.5270.14
26_R33_N0.5270.14
90_R119_N0.5250.14
17_F45_V0.5250.14
19_N92_N0.5180.14
99_I163_H0.5150.13
8_N43_E0.5070.13
74_K83_E0.5060.13
30_W89_I0.5060.13
20_H97_L0.5030.13
96_D126_L0.5010.13
46_H55_P0.5010.13
20_H105_S0.5000.13
32_L103_F0.5000.13
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  
3do9A 1 0.9888 100 0.098 Contact Map
1gp8A 1 0.2235 54 0.943 Contact Map
2fztA 2 0.1899 27.6 0.952 Contact Map
3pehA 2 0.3296 13.3 0.958 Contact Map
2jk1A 2 0.7039 12.1 0.959 Contact Map
2r6aC 1 0.7318 9.1 0.961 Contact Map
1t5qA 1 0.1173 8.2 0.962 Contact Map
2kjgA 1 0.3743 7.7 0.962 Contact Map
1wjtA 1 0.2458 7.6 0.962 Contact Map
1u2zA 1 0.6927 7.4 0.962 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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