GREMLIN Database
YBBJ - Inner membrane protein YbbJ
UniProt: P0AAS3 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13257
Length: 152 (135)
Sequences: 2097 (1595)
Seq/√Len: 137.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
136_E148_R3.8691.00
23_A32_L2.9911.00
130_G133_T2.8781.00
106_P130_G2.8131.00
41_I63_L2.4801.00
138_I148_R2.4161.00
133_T149_A2.3571.00
100_R134_H2.3041.00
99_R117_G2.1881.00
113_H120_S2.1431.00
101_F135_V2.1021.00
106_P131_A2.0511.00
17_G43_G1.9511.00
114_M145_L1.9351.00
17_G40_V1.9161.00
45_V59_M1.8941.00
21_L36_G1.8701.00
38_A63_L1.8311.00
100_R136_E1.8201.00
37_V67_A1.7921.00
114_M123_V1.7801.00
17_G21_L1.7751.00
139_A146_H1.7411.00
106_P128_D1.6811.00
16_L20_L1.6791.00
38_A42_T1.6571.00
103_L123_V1.5951.00
43_G47_W1.5661.00
52_G55_W1.5201.00
127_E149_A1.5071.00
38_A64_T1.5061.00
141_E146_H1.4971.00
17_G36_G1.4881.00
105_S113_H1.4781.00
140_I145_L1.4561.00
42_T59_M1.4511.00
13_W56_Q1.4471.00
124_S146_H1.4331.00
125_A129_L1.4151.00
42_T60_F1.4111.00
111_R122_P1.4081.00
14_L43_G1.3561.00
74_W78_R1.3551.00
35_S64_T1.3201.00
108_V128_D1.2901.00
101_F137_V1.2831.00
65_L69_W1.2621.00
73_K77_R1.2561.00
64_T68_A1.2521.00
90_N94_Q1.2391.00
135_V147_I1.2241.00
45_V51_L1.2231.00
35_S68_A1.1831.00
129_L133_T1.1810.99
36_G40_V1.1790.99
51_L55_W1.1790.99
42_T45_V1.1590.99
12_F16_L1.1300.99
49_V52_G1.1220.99
107_L112_G1.1050.99
34_W71_W1.1010.99
75_L78_R1.0830.99
103_L129_L1.0810.99
103_L107_L1.0580.99
102_V134_H1.0480.99
31_Y68_A1.0460.99
91_Q94_Q1.0350.99
53_W57_G1.0260.99
124_S141_E1.0240.99
111_R124_S1.0170.98
104_E120_S1.0100.98
116_V137_V1.0040.98
101_F123_V0.9910.98
101_F104_E0.9790.98
68_A72_W0.9660.98
39_A60_F0.9630.98
42_T46_V0.9600.98
9_P12_F0.9360.97
103_L131_A0.9280.97
115_R120_S0.9190.97
101_F116_V0.9130.97
42_T63_L0.9030.97
30_G33_L0.9010.97
103_L114_M0.8950.97
40_V44_L0.8950.97
96_L116_V0.8910.97
48_L51_L0.8790.96
92_R95_Q0.8750.96
22_A25_M0.8690.96
28_G31_Y0.8660.96
60_F64_T0.8650.96
61_A65_L0.8640.96
122_P144_T0.8590.96
72_W76_S0.8500.95
72_W75_L0.8470.95
58_V62_I0.8420.95
103_L106_P0.8350.95
105_S131_A0.8330.95
28_G32_L0.8220.95
116_V143_I0.8220.95
18_G22_A0.8190.94
45_V49_V0.8160.94
67_A71_W0.8130.94
18_G21_L0.8100.94
101_F147_I0.8030.94
129_L149_A0.8030.94
38_A41_I0.8020.94
93_G140_I0.8000.94
101_F113_H0.7850.93
102_V115_R0.7830.93
103_L135_V0.7800.93
95_Q99_R0.7750.93
71_W74_W0.7560.92
30_G68_A0.7510.91
113_H122_P0.7460.91
57_G61_A0.7340.91
41_I59_M0.7290.90
122_P143_I0.7250.90
10_H43_G0.7210.90
13_W39_A0.7020.88
21_L33_L0.7010.88
22_A26_L0.6990.88
124_S144_T0.6970.88
10_H46_V0.6940.88
112_G147_I0.6830.87
38_A67_A0.6820.87
63_L67_A0.6790.87
89_L117_G0.6790.87
107_L123_V0.6770.87
104_E115_R0.6760.87
35_S60_F0.6750.86
104_E147_I0.6670.86
27_G30_G0.6660.86
108_V122_P0.6570.85
107_L147_I0.6530.85
102_V132_G0.6410.84
89_L119_S0.6380.83
115_R118_D0.6300.82
90_N118_D0.6300.82
91_Q95_Q0.6260.82
34_W67_A0.6260.82
10_H119_S0.6160.81
95_Q117_G0.6160.81
112_G123_V0.6100.80
112_G135_V0.6100.80
107_L110_G0.6080.80
107_L135_V0.6060.80
101_F112_G0.6040.80
116_V145_L0.6030.80
103_L133_T0.6010.79
71_W75_L0.6000.79
107_L129_L0.5990.79
87_S90_N0.5960.79
29_N72_W0.5940.79
29_N33_L0.5870.78
32_L96_L0.5860.78
20_L32_L0.5860.78
102_V109_N0.5820.77
90_N97_I0.5790.77
29_N34_W0.5740.76
74_W79_V0.5730.76
31_Y66_L0.5720.76
76_S79_V0.5680.76
18_G25_M0.5650.75
107_L125_A0.5590.74
70_L86_D0.5590.74
15_S69_W0.5530.74
124_S143_I0.5520.73
17_G20_L0.5510.73
44_L48_L0.5500.73
34_W38_A0.5500.73
107_L124_S0.5460.73
97_I129_L0.5460.73
97_I139_A0.5440.72
96_L101_F0.5420.72
93_G96_L0.5420.72
13_W60_F0.5370.71
28_G85_S0.5340.71
137_V145_L0.5330.71
116_V119_S0.5310.71
20_L24_E0.5290.70
27_G76_S0.5270.70
142_G145_L0.5250.70
86_D137_V0.5250.70
137_V143_I0.5210.69
66_L70_L0.5200.69
20_L43_G0.5200.69
97_I140_I0.5200.69
15_S128_D0.5190.69
79_V85_S0.5180.69
96_L137_V0.5170.69
41_I51_L0.5120.68
46_V49_V0.5110.68
15_S117_G0.5110.68
75_L143_I0.5110.68
17_G37_V0.5100.68
66_L86_D0.5090.67
28_G56_Q0.5040.67
14_L96_L0.5030.66
24_E28_G0.5020.66
12_F19_L0.5010.66
129_L135_V0.5000.66
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  
2k5hA 1 0.6316 99.6 0.601 Contact Map
3cp0A 1 0.3947 99.6 0.601 Contact Map
2exdA 1 0.4671 99.4 0.642 Contact Map
3wwvA 2 0.4079 99.4 0.642 Contact Map
2k14A 1 0.5 99.4 0.657 Contact Map
4tseA 2 0.6513 33.9 0.92 Contact Map
4ql5A 4 0.375 17.9 0.93 Contact Map
2fhdA 5 0.4605 15.1 0.932 Contact Map
2m20A 2 0.3947 11.5 0.936 Contact Map
2w1tA 2 0.3224 9.9 0.937 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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