GREMLIN Database
YGGS - UPF0001 protein YggS
UniProt: P67080 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12979
Length: 234 (222)
Sequences: 4727 (3392)
Seq/√Len: 227.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_Q78_E3.7341.00
124_N159_R3.5491.00
14_K209_E2.9751.00
113_N157_R2.9271.00
177_F180_A2.8341.00
38_K42_A2.7191.00
87_S107_R2.6791.00
84_P138_S2.6701.00
140_I148_L2.4781.00
19_A29_I2.3701.00
124_N161_R2.3441.00
44_A48_D2.3241.00
62_G97_F2.2251.00
21_R213_A2.1661.00
106_L151_A2.1481.00
110_T151_A2.1471.00
199_T217_T1.9981.00
34_V82_I1.9951.00
32_L218_M1.9821.00
15_I31_L1.9761.00
111_R115_Q1.9361.00
111_R114_D1.9331.00
14_K208_M1.8631.00
103_I112_L1.7731.00
47_I52_R1.7591.00
163_L200_L1.7441.00
181_R214_A1.7441.00
15_I212_I1.7331.00
47_I77_L1.7271.00
52_R76_G1.7121.00
115_Q118_A1.7111.00
30_T53_Q1.7061.00
12_R26_P1.6981.00
19_A27_E1.6971.00
30_T199_T1.6861.00
39_P42_A1.6851.00
106_L110_T1.6811.00
184_A188_A1.6591.00
221_I224_A1.6431.00
35_S54_F1.6401.00
13_D17_A1.6261.00
161_R198_D1.6191.00
113_N156_P1.6161.00
99_W126_L1.6141.00
177_F214_A1.6061.00
205_S224_A1.6031.00
101_H218_M1.5781.00
117_P157_R1.5731.00
122_P159_R1.5561.00
113_N155_L1.5001.00
116_R123_L1.4941.00
181_R185_V1.4701.00
109_A155_L1.4561.00
25_S28_E1.4551.00
85_L93_V1.4361.00
126_L199_T1.4341.00
177_F186_A1.4201.00
33_A51_Q1.4181.00
127_I148_L1.3831.00
103_I125_V1.3751.00
151_A154_E1.3621.00
127_I149_A1.3581.00
59_V81_F1.3461.00
78_E98_D1.3271.00
144_E147_E1.3181.00
133_D141_Q1.3041.00
147_E150_A1.2911.00
109_A152_V1.2751.00
199_T218_M1.2741.00
129_I145_L1.2671.00
180_A186_A1.2671.00
47_I54_F1.2491.00
8_L12_R1.2481.00
64_D68_H1.2441.00
90_S108_I1.2381.00
17_A20_T1.2371.00
177_F187_F1.2281.00
149_A160_L1.2171.00
133_D143_A1.2131.00
42_A45_E1.2051.00
11_V221_I1.2031.00
113_N117_P1.2021.00
32_L53_Q1.1941.00
44_A69_F1.1801.00
40_A68_H1.1791.00
16_S20_T1.1751.00
94_A123_L1.1521.00
66_I96_H1.1441.00
87_S105_R1.1271.00
21_R209_E1.1271.00
19_A25_S1.1251.00
46_A49_A1.1191.00
60_Q88_N1.1131.00
33_A225_I1.1121.00
105_R108_I1.1041.00
47_I76_G1.0821.00
9_A13_D1.0791.00
95_E119_E1.0781.00
181_R184_A1.0721.00
81_F93_V1.0691.00
29_I212_I1.0661.00
66_I97_F1.0661.00
59_V85_L1.0651.00
180_A187_F1.0611.00
63_V92_L1.0471.00
206_D223_T1.0421.00
176_Q179_V1.0401.00
172_E175_R1.0381.00
59_V63_V1.0331.00
173_Y210_A1.0331.00
32_L101_H1.0311.00
5_A9_A1.0291.00
140_I145_L1.0241.00
8_L51_Q1.0221.00
93_V97_F1.0221.00
179_V182_Q1.0071.00
62_G66_I1.0051.00
126_L218_M1.0011.00
141_Q144_E1.0001.00
19_A26_P0.9971.00
98_D124_N0.9961.00
46_A225_I0.9941.00
110_T155_L0.9911.00
126_L161_R0.9891.00
110_T114_D0.9871.00
43_I54_F0.9841.00
178_E214_A0.9721.00
146_D150_A0.9641.00
127_I140_I0.9601.00
12_R16_S0.9511.00
30_T218_M0.9441.00
87_S111_R0.9421.00
131_I176_Q0.9411.00
87_S108_I0.9371.00
29_I219_V0.9361.00
40_A69_F0.9301.00
84_P104_D0.9251.00
100_C112_L0.9251.00
178_E182_Q0.9191.00
180_A184_A0.9181.00
19_A28_E0.9100.99
210_A214_A0.9100.99
63_V96_H0.9090.99
18_A22_C0.9080.99
37_T57_N0.9060.99
37_T58_Y0.9050.99
100_C103_I0.9040.99
130_N133_D0.9040.99
44_A75_T0.9010.99
13_D16_S0.9010.99
109_A158_L0.9010.99
95_E121_P0.8940.99
16_S19_A0.8850.99
24_R28_E0.8780.99
17_A21_R0.8740.99
210_A213_A0.8740.99
10_Q14_K0.8730.99
19_A24_R0.8730.99
8_L46_A0.8650.99
194_Y197_I0.8620.99
99_W218_M0.8590.99
38_K228_A0.8540.99
99_W124_N0.8470.99
187_F191_K0.8450.99
152_V160_L0.8420.99
176_Q180_A0.8360.99
142_L186_A0.8360.99
59_V93_V0.8340.99
90_S111_R0.8300.99
58_Y102_T0.8260.99
177_F213_A0.8230.99
90_S112_L0.8220.99
67_R96_H0.8170.99
104_D108_I0.8110.99
103_I148_L0.8070.99
30_T78_E0.8070.99
40_A43_I0.7990.99
99_W161_R0.7910.99
131_I165_A0.7910.99
132_S168_A0.7890.99
134_E137_K0.7890.99
110_T154_E0.7840.98
91_R115_Q0.7830.98
69_F77_L0.7820.98
125_V158_L0.7820.98
31_L221_I0.7750.98
90_S94_A0.7720.98
131_I180_A0.7670.98
80_H99_W0.7650.98
81_F85_L0.7630.98
35_S226_F0.7620.98
103_I108_I0.7610.98
114_D118_A0.7590.98
128_Q166_I0.7560.98
59_V92_L0.7550.98
70_Q76_G0.7540.98
176_Q210_A0.7500.98
179_V183_M0.7500.98
208_M212_I0.7470.98
93_V96_H0.7470.98
145_L163_L0.7460.98
212_I219_V0.7460.98
32_L216_S0.7420.98
187_F197_I0.7370.98
84_P105_R0.7370.98
175_R179_V0.7350.98
35_S51_Q0.7210.97
185_V189_G0.7190.97
16_S26_P0.7140.97
165_A180_A0.7130.97
24_R27_E0.7120.97
159_R196_H0.7110.97
100_C123_L0.7080.97
115_Q119_E0.7080.97
85_L108_I0.7070.97
43_I69_F0.7050.97
20_T26_P0.7040.97
116_R121_P0.7040.97
185_V188_A0.6980.97
70_Q75_T0.6900.97
53_Q101_H0.6860.96
106_L155_L0.6830.96
47_I75_T0.6820.96
161_R199_T0.6760.96
6_H9_A0.6750.96
45_E48_D0.6750.96
46_A226_F0.6740.96
37_T61_E0.6690.96
147_E151_A0.6690.96
182_Q186_A0.6640.96
15_I29_I0.6610.96
175_R178_E0.6600.96
37_T230_D0.6570.96
90_S115_Q0.6560.95
46_A51_Q0.6550.95
151_A155_L0.6530.95
55_G82_I0.6520.95
44_A70_Q0.6510.95
59_V62_G0.6500.95
47_I69_F0.6500.95
51_Q54_F0.6460.95
138_S166_I0.6460.95
94_A121_P0.6410.95
117_P156_P0.6390.95
99_W199_T0.6370.95
163_L183_M0.6360.95
44_A68_H0.6350.95
186_A190_L0.6330.95
62_G93_V0.6330.95
116_R122_P0.6310.94
120_L157_R0.6290.94
132_S167_P0.6280.94
149_A197_I0.6250.94
95_E123_L0.6250.94
7_N10_Q0.6240.94
165_A202_L0.6200.94
54_F77_L0.6170.94
103_I109_A0.6170.94
9_A12_R0.6150.94
26_P29_I0.6150.94
174_V178_E0.6140.94
56_E65_K0.6130.94
40_A65_K0.6120.93
35_S65_K0.6070.93
10_Q13_D0.6050.93
40_A44_A0.6050.93
61_E229_R0.6000.93
184_A187_F0.5980.93
150_A153_A0.5960.93
177_F184_A0.5950.93
186_A189_G0.5920.92
66_I70_Q0.5910.92
142_L179_V0.5910.92
179_V186_A0.5900.92
59_V97_F0.5890.92
41_S44_A0.5870.92
85_L100_C0.5840.92
80_H101_H0.5800.92
61_E65_K0.5800.92
14_K224_A0.5800.92
107_R110_T0.5780.91
132_S165_A0.5750.91
150_A193_R0.5740.91
146_D190_L0.5730.91
112_L158_L0.5700.91
5_A46_A0.5690.91
58_Y166_I0.5660.91
8_L225_I0.5650.90
166_I204_M0.5600.90
169_P206_D0.5570.90
11_V208_M0.5540.90
142_L146_D0.5530.90
92_L95_E0.5530.90
66_I79_W0.5510.89
127_I145_L0.5490.89
33_A226_F0.5480.89
37_T43_I0.5460.89
18_A209_E0.5450.89
41_S68_H0.5440.89
133_D142_L0.5410.89
146_D149_A0.5410.89
11_V18_A0.5340.88
187_F190_L0.5300.88
170_E175_R0.5300.88
183_M187_F0.5280.87
190_L193_R0.5270.87
140_I144_E0.5250.87
5_A49_A0.5240.87
18_A212_I0.5220.87
149_A190_L0.5210.87
182_Q185_V0.5210.87
177_F185_V0.5200.87
106_L148_L0.5200.87
129_I183_M0.5190.86
22_C25_S0.5190.86
208_M224_A0.5170.86
24_R29_I0.5150.86
131_I142_L0.5140.86
148_L155_L0.5120.86
14_K18_A0.5110.86
38_K223_T0.5110.86
188_A191_K0.5100.85
177_F181_R0.5100.85
180_A202_L0.5090.85
189_G193_R0.5080.85
88_N92_L0.5060.85
91_R118_A0.5040.85
78_E99_W0.5030.85
170_E173_Y0.5020.85
54_F79_W0.5010.84
125_V161_R0.5010.84
37_T223_T0.5000.84
205_S223_T0.5000.84
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  
3sy1A 1 0.9744 100 0.509 Contact Map
1ct5A 1 0.8846 100 0.516 Contact Map
3cpgA 1 0.9658 100 0.518 Contact Map
3r79A 2 0.953 100 0.522 Contact Map
3e5pA 2 0.9274 100 0.627 Contact Map
4beuA 2 0.9487 100 0.627 Contact Map
4a3qA 2 0.9017 100 0.629 Contact Map
4bf5A 2 0.953 100 0.631 Contact Map
1bd0A 2 0.9188 100 0.634 Contact Map
3kw3A 2 0.9188 100 0.637 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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