GREMLIN Database
YSGA - Uncharacterized tRNA/rRNA methyltransferase YsgA
UniProt: P94538 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 248 (221)
Sequences: 8347 (5670)
Seq/√Len: 381.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
203_V235_V3.9311.00
181_G218_T3.3871.00
108_L200_A3.1601.00
212_A216_E2.7981.00
237_V240_A2.7951.00
182_T242_L2.6711.00
121_M239_A2.6431.00
49_K94_H2.6421.00
181_G210_V2.3961.00
203_V239_A2.3801.00
50_E70_Y2.2071.00
170_D217_K2.1971.00
107_L121_M2.0331.00
183_A215_L2.0271.00
38_V91_A1.9321.00
132_A159_P1.9301.00
173_K219_D1.9091.00
110_D211_D1.8941.00
122_I133_V1.8741.00
180_Y222_L1.8361.00
128_A244_Y1.8071.00
77_F90_A1.7951.00
47_I94_H1.7801.00
104_R198_S1.7801.00
126_D158_I1.7411.00
105_K130_L1.6981.00
239_A243_V1.6801.00
151_A155_H1.6701.00
106_V132_A1.6621.00
188_A220_L1.6601.00
107_L243_V1.6351.00
178_K220_L1.6251.00
164_N167_S1.6211.00
126_D228_G1.6131.00
29_T49_K1.5891.00
180_Y199_F1.5641.00
148_L155_H1.5631.00
130_L243_V1.5151.00
201_L242_L1.4971.00
202_I210_V1.4921.00
177_V198_S1.4881.00
56_E74_E1.4851.00
125_A130_L1.4831.00
154_S230_A1.4731.00
127_A226_L1.4581.00
55_D71_M1.4571.00
177_V200_A1.4431.00
180_Y220_L1.4411.00
190_Y242_L1.4391.00
50_E92_V1.4181.00
74_E78_S1.4021.00
107_L125_A1.3861.00
128_A190_Y1.3811.00
32_I41_A1.3771.00
189_P192_E1.3611.00
113_Q207_G1.3551.00
201_L246_L1.3481.00
51_I91_A1.3441.00
126_D154_S1.3381.00
169_V179_V1.3281.00
104_R131_D1.3231.00
128_A241_I1.3161.00
120_T236_A1.3121.00
72_L77_F1.2961.00
107_L130_L1.2951.00
170_D174_A1.2891.00
102_T131_D1.2781.00
172_L200_A1.2781.00
193_I222_L1.2781.00
72_L76_A1.2771.00
126_D157_H1.2771.00
184_L223_Y1.2681.00
112_V235_V1.2571.00
215_L221_N1.2471.00
183_A221_N1.2371.00
205_N208_A1.2341.00
181_G221_N1.2331.00
105_K131_D1.2241.00
178_K219_D1.2211.00
134_V168_Y1.2181.00
106_V177_V1.2171.00
124_T240_A1.2121.00
166_P217_K1.1981.00
202_I214_L1.1971.00
55_D73_S1.1871.00
111_A138_G1.1861.00
126_D230_A1.1761.00
39_E43_K1.1751.00
48_V91_A1.1691.00
76_A79_A1.1661.00
108_L169_V1.1651.00
171_E175_E1.1591.00
203_V238_A1.1441.00
40_E157_H1.1421.00
106_V134_V1.1401.00
48_V93_C1.1341.00
132_A161_V1.1321.00
186_N223_Y1.1191.00
189_P223_Y1.1061.00
108_L165_L1.1021.00
107_L203_V1.0961.00
172_L177_V1.0931.00
188_A192_E1.0921.00
179_V200_A1.0901.00
135_L160_V1.0821.00
54_K74_E1.0781.00
169_V214_L1.0761.00
28_N95_M1.0731.00
125_A133_V1.0691.00
105_K246_L1.0521.00
118_L135_L1.0491.00
46_G96_P1.0391.00
122_I160_V1.0331.00
118_L140_A1.0301.00
75_D78_S1.0271.00
166_P213_A1.0231.00
211_D214_L1.0221.00
124_T237_V1.0221.00
195_Q246_L1.0141.00
38_V89_I1.0091.00
54_K57_T0.9991.00
182_T203_V0.9951.00
218_T221_N0.9911.00
166_P170_D0.9901.00
40_E43_K0.9881.00
171_E174_A0.9851.00
124_T243_V0.9741.00
73_S76_A0.9721.00
191_Q245_H0.9711.00
195_Q199_F0.9661.00
105_K243_V0.9651.00
170_D173_K0.9621.00
116_G150_S0.9591.00
190_Y195_Q0.9571.00
122_I147_T0.9541.00
135_L139_T0.9541.00
157_H229_Q0.9521.00
81_T90_A0.9471.00
129_G227_Y0.9411.00
188_A193_I0.9401.00
202_I218_T0.9381.00
32_I93_C0.9371.00
98_E175_E0.9341.00
165_L214_L0.9291.00
109_I203_V0.9231.00
137_D163_R0.9221.00
46_G156_F0.9191.00
126_D229_Q0.9101.00
128_A191_Q0.9041.00
32_I37_L0.8991.00
30_F93_C0.8961.00
222_L242_L0.8941.00
109_I121_M0.8921.00
124_T128_A0.8921.00
96_P143_F0.8861.00
31_L90_A0.8791.00
53_V71_M0.8781.00
109_I118_L0.8771.00
60_P63_L0.8771.00
105_K199_F0.8751.00
41_A45_P0.8731.00
181_G215_L0.8671.00
52_L80_V0.8641.00
178_K197_E0.8511.00
167_S170_D0.8491.00
103_A131_D0.8491.00
110_D214_L0.8471.00
36_H152_Q0.8411.00
167_S171_E0.8361.00
108_L202_I0.8291.00
213_A216_E0.8281.00
53_V89_I0.8281.00
185_Q221_N0.8271.00
116_G120_T0.8211.00
191_Q225_P0.8161.00
31_L92_V0.8141.00
54_K77_F0.8111.00
104_R177_V0.8091.00
106_V172_L0.8081.00
111_A136_G0.8081.00
110_D210_V0.8071.00
199_F246_L0.8051.00
140_A144_N0.8051.00
59_I62_D0.8031.00
111_A208_A0.7981.00
185_Q215_L0.7951.00
134_V163_R0.7931.00
29_T92_V0.7931.00
213_A217_K0.7921.00
103_A197_E0.7901.00
50_E68_Q0.7881.00
53_V69_C0.7821.00
188_A223_Y0.7821.00
82_E145_G0.7821.00
29_T94_H0.7811.00
163_R167_S0.7781.00
182_T210_V0.7771.00
169_V200_A0.7761.00
193_I220_L0.7731.00
122_I155_H0.7701.00
108_L172_L0.7691.00
127_A230_A0.7681.00
169_V217_K0.7671.00
187_G223_Y0.7671.00
137_D164_N0.7661.00
166_P214_L0.7621.00
72_L90_A0.7611.00
128_A243_V0.7601.00
111_A211_D0.7601.00
41_A93_C0.7601.00
111_A205_N0.7571.00
178_K199_F0.7561.00
44_S157_H0.7551.00
212_A215_L0.7531.00
52_L72_L0.7531.00
112_V118_L0.7521.00
179_V202_I0.7411.00
180_Y193_I0.7401.00
41_A156_F0.7361.00
118_L147_T0.7271.00
98_E101_A0.7261.00
49_K68_Q0.7241.00
61_S64_E0.7211.00
112_V121_M0.7191.00
148_L156_F0.7191.00
168_Y172_L0.7191.00
39_E61_S0.7171.00
183_A186_N0.7171.00
173_K217_K0.7101.00
210_V218_T0.7091.00
49_K92_V0.7081.00
33_E83_T0.7061.00
52_L92_V0.7041.00
52_L70_Y0.7041.00
203_V242_L0.6990.99
184_L231_E0.6850.99
185_Q223_Y0.6810.99
122_I154_S0.6800.99
173_K179_V0.6780.99
113_Q205_N0.6780.99
121_M235_V0.6760.99
127_A231_E0.6740.99
133_V158_I0.6710.99
109_I112_V0.6700.99
181_G202_I0.6700.99
191_Q244_Y0.6690.99
157_H230_A0.6690.99
33_E149_R0.6610.99
51_I62_D0.6590.99
116_G146_K0.6580.99
176_G198_S0.6570.99
78_S84_E0.6570.99
125_A243_V0.6540.99
80_V90_A0.6530.99
183_A223_Y0.6520.99
128_A224_V0.6500.99
135_L142_A0.6480.99
61_S65_T0.6460.99
195_Q245_H0.6440.99
187_G221_N0.6430.99
163_R168_Y0.6410.99
120_T237_V0.6350.99
77_F87_Q0.6350.99
134_V172_L0.6340.99
141_D144_N0.6330.99
108_L134_V0.6330.99
131_D177_V0.6270.99
124_T239_A0.6260.99
35_E39_E0.6190.99
32_I48_V0.6120.99
191_Q195_Q0.6110.99
128_A226_L0.6110.99
224_V244_Y0.6100.99
186_N221_N0.6070.99
108_L136_G0.6040.99
36_H39_E0.6030.98
182_T201_L0.6020.98
53_V58_R0.6000.98
116_G236_A0.5910.98
128_A227_Y0.5900.98
154_S157_H0.5900.98
38_V51_I0.5860.98
77_F86_P0.5800.98
138_G211_D0.5790.98
106_V200_A0.5770.98
183_A210_V0.5760.98
30_F46_G0.5700.98
77_F81_T0.5670.98
78_S86_P0.5660.98
241_I244_Y0.5650.98
168_Y171_E0.5630.98
113_Q208_A0.5590.98
33_E145_G0.5590.98
136_G165_L0.5540.97
178_K196_S0.5540.97
43_K229_Q0.5520.97
142_A162_R0.5480.97
168_Y176_G0.5480.97
37_L148_L0.5460.97
210_V214_L0.5450.97
33_E90_A0.5430.97
127_A244_Y0.5410.97
54_K71_M0.5410.97
32_I148_L0.5390.97
33_E84_E0.5370.97
236_A239_A0.5360.97
64_E67_I0.5360.97
136_G214_L0.5320.97
191_Q194_P0.5310.97
224_V238_A0.5310.97
75_D79_A0.5290.97
148_L151_A0.5270.97
59_I63_L0.5260.96
72_L80_V0.5240.96
87_Q114_D0.5240.96
205_N231_E0.5220.96
45_P65_T0.5180.96
169_V173_K0.5180.96
127_A233_L0.5140.96
224_V241_I0.5140.96
104_R132_A0.5120.96
108_L168_Y0.5120.96
103_A198_S0.5100.96
143_F147_T0.5080.96
37_L152_Q0.5060.96
214_L217_K0.5050.96
151_A156_F0.5020.95
58_R71_M0.5010.95
111_A214_L0.5010.95
37_L156_F0.5010.95
62_D67_I0.5000.95
83_T87_Q0.5000.95
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  
1ipaA 1 0.9758 100 0.128 Contact Map
3nk6A 2 0.9677 100 0.128 Contact Map
1x7oA 2 0.9718 100 0.144 Contact Map
2i6dA 2 0.9637 100 0.175 Contact Map
1gz0A 2 0.9315 100 0.24 Contact Map
4kgnA 2 0.5927 100 0.428 Contact Map
3n4jA 2 0.5887 100 0.437 Contact Map
1zjrA 2 0.6573 100 0.44 Contact Map
3l8uA 2 0.5524 100 0.453 Contact Map
1v2xA 2 0.6613 100 0.454 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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