GREMLIN Database
YCBR - Uncharacterized protein YcbR
UniProt: P42250 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 243 (188)
Sequences: 3921 (2420)
Seq/√Len: 176.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
51_E95_L3.9361.00
55_A91_D2.8761.00
112_M150_S2.8031.00
31_L50_V2.7071.00
86_F89_Y2.6961.00
33_I70_V2.6391.00
36_S136_D2.4791.00
29_L50_V2.4581.00
106_N136_D2.3301.00
175_T179_R2.3291.00
148_E152_D2.2581.00
70_V78_L2.1971.00
36_S106_N2.1211.00
115_V131_I2.0771.00
123_E129_A2.0651.00
67_D81_V2.0391.00
113_K117_R2.0321.00
51_E91_D2.0261.00
67_D119_Y1.9911.00
109_P141_K1.9441.00
30_V115_V1.9311.00
144_K172_K1.8781.00
28_G67_D1.8541.00
139_C169_F1.7821.00
151_S175_T1.7701.00
68_V79_K1.7081.00
54_L94_I1.6961.00
77_R114_D1.6731.00
185_N188_H1.6581.00
124_P127_Y1.6571.00
30_V131_I1.6501.00
75_F114_D1.6371.00
84_K93_E1.6271.00
38_R42_K1.6051.00
107_D110_P1.6011.00
116_L150_S1.5871.00
26_R65_L1.5741.00
44_G47_Q1.5611.00
150_S155_V1.5451.00
116_L153_K1.5431.00
167_F171_N1.5161.00
68_V97_N1.4981.00
26_R129_A1.4981.00
42_K99_R1.4731.00
79_K90_V1.4711.00
143_I147_I1.4681.00
116_L146_I1.4611.00
54_L66_L1.4571.00
106_N137_G1.4541.00
131_I157_W1.4361.00
114_D118_K1.4221.00
35_G104_G1.4001.00
159_F174_D1.3951.00
79_K84_K1.3861.00
133_F159_F1.3821.00
138_G166_N1.3671.00
149_A152_D1.3521.00
161_G170_L1.3441.00
38_R99_R1.3381.00
159_F170_L1.3151.00
33_I100_L1.3051.00
28_G81_V1.2841.00
36_S137_G1.2811.00
133_F173_L1.2711.00
77_R80_P1.2711.00
71_Y108_E1.2691.00
84_K89_Y1.2501.00
80_P83_E1.2391.00
33_I43_N1.2371.00
92_R96_N1.2321.00
108_E135_N1.2231.00
28_G119_Y1.2201.00
45_T187_L1.2181.00
46_V186_F1.2031.00
54_L90_V1.2021.00
145_P149_A1.1951.00
158_Q179_R1.1771.00
144_K148_E1.1721.00
131_I150_S1.1571.00
69_W115_V1.1461.00
58_D63_N1.1401.00
32_D137_G1.1361.00
116_L149_A1.1321.00
29_L53_I1.1181.00
113_K146_I1.1031.00
112_M131_I1.0841.00
171_N177_E1.0791.00
55_A87_S1.0751.00
31_L46_V1.0731.00
147_I151_S1.0721.00
108_E133_F1.0681.00
131_I155_V1.0641.00
139_C143_I1.0641.00
109_P146_I1.0300.99
30_V69_W1.0130.99
47_Q94_I1.0070.99
73_N105_R0.9980.99
35_G136_D0.9970.99
82_S122_E0.9960.99
59_Q66_L0.9950.99
146_I149_A0.9900.99
142_S145_P0.9850.99
134_I162_I0.9840.99
48_N52_R0.9770.99
37_M106_N0.9710.99
50_V94_I0.9710.99
28_G115_V0.9550.99
174_D180_V0.9410.99
70_V97_N0.9390.99
75_F110_P0.9370.99
143_I146_I0.9300.99
42_K45_T0.9290.99
156_F179_R0.9250.99
151_S157_W0.9210.99
36_S71_Y0.9150.99
168_D171_N0.9130.99
69_W111_V0.9090.99
108_E169_F0.9070.99
29_L132_V0.8940.98
109_P139_C0.8880.98
128_P156_F0.8820.98
147_I154_P0.8810.98
44_G48_N0.8780.98
171_N175_T0.8780.98
79_K93_E0.8780.98
77_R119_Y0.8760.98
21_T201_Y0.8720.98
48_N51_E0.8710.98
84_K90_V0.8610.98
37_M42_K0.8580.98
150_S157_W0.8580.98
74_E110_P0.8500.98
120_V153_K0.8440.98
26_R124_P0.8440.98
139_C147_I0.8430.98
87_S91_D0.8390.98
147_I157_W0.8370.98
72_D107_D0.8360.98
74_E100_L0.8240.97
49_V189_I0.8230.97
47_Q97_N0.8230.97
35_G105_R0.8200.97
162_I186_F0.8140.97
54_L57_A0.8080.97
54_L87_S0.8060.97
130_F196_S0.8050.97
105_R136_D0.8050.97
69_W119_Y0.7990.97
25_A130_F0.7970.97
132_V200_L0.7950.97
115_V150_S0.7900.97
106_N135_N0.7860.97
121_T124_P0.7830.97
97_N100_L0.7820.96
115_V119_Y0.7740.96
94_I97_N0.7730.96
28_G69_W0.7730.96
27_V66_L0.7680.96
69_W75_F0.7640.96
43_N47_Q0.7620.96
91_D95_L0.7620.96
183_N192_I0.7600.96
70_V143_I0.7590.96
33_I131_I0.7470.95
137_G170_L0.7430.95
171_N176_L0.7410.95
166_N169_F0.7380.95
69_W114_D0.7360.95
27_V130_F0.7280.95
160_V192_I0.7210.94
34_T106_N0.7190.94
36_S135_N0.7180.94
135_N170_L0.7180.94
203_A206_A0.7130.94
105_R140_K0.7110.94
112_M157_W0.7090.94
68_V111_V0.7060.94
113_K149_A0.7040.94
20_L201_Y0.6960.93
71_Y106_N0.6930.93
25_A64_G0.6920.93
161_G165_G0.6900.93
88_G95_L0.6900.93
138_G169_F0.6880.93
24_T127_Y0.6840.93
86_F90_V0.6770.92
167_F182_D0.6750.92
108_E139_C0.6660.92
186_F189_I0.6640.92
70_V100_L0.6640.92
47_Q51_E0.6620.92
33_I72_D0.6600.91
18_K21_T0.6570.91
80_P119_Y0.6570.91
60_F65_L0.6550.91
92_R95_L0.6500.91
32_D36_S0.6470.91
109_P143_I0.6470.91
165_G182_D0.6460.91
69_W77_R0.6420.90
113_K125_S0.6420.90
140_K143_I0.6360.90
110_P113_K0.6350.90
186_F201_Y0.6280.89
78_L97_N0.6280.89
37_M136_D0.6260.89
49_V111_V0.6250.89
148_E151_S0.6240.89
61_D85_D0.6230.89
33_I99_R0.6200.89
28_G111_V0.6190.89
90_V94_I0.6160.88
34_T137_G0.6150.88
151_S179_R0.6130.88
141_K146_I0.6080.88
53_I197_D0.6050.88
73_N104_G0.6020.87
25_A128_P0.6010.87
30_V71_Y0.6010.87
56_V194_R0.5980.87
30_V146_I0.5970.87
69_W174_D0.5950.87
188_H191_E0.5950.87
64_G201_Y0.5930.87
68_V93_E0.5910.86
135_N162_I0.5910.86
76_S100_L0.5900.86
57_A107_D0.5890.86
78_L93_E0.5880.86
181_I196_S0.5860.86
122_E129_A0.5820.85
190_E193_D0.5820.85
143_I169_F0.5800.85
160_V189_I0.5780.85
57_A64_G0.5760.85
67_D155_V0.5760.85
35_G100_L0.5740.85
49_V134_I0.5730.85
132_V160_V0.5720.84
46_V52_R0.5720.84
42_K186_F0.5710.84
25_A127_Y0.5710.84
133_F157_W0.5690.84
45_T190_E0.5670.84
65_L81_V0.5640.84
109_P169_F0.5640.84
113_K116_L0.5610.83
66_L87_S0.5600.83
37_M186_F0.5580.83
147_I173_L0.5580.83
130_F158_Q0.5560.83
17_K20_L0.5510.82
39_P99_R0.5510.82
168_D172_K0.5480.82
116_L155_V0.5470.82
145_P148_E0.5450.82
158_Q196_S0.5450.82
200_L204_L0.5430.81
170_L180_V0.5410.81
112_M133_F0.5410.81
61_D65_L0.5400.81
36_S162_I0.5400.81
26_R127_Y0.5390.81
117_R120_V0.5390.81
59_Q63_N0.5360.81
158_Q199_E0.5350.80
81_V155_V0.5330.80
154_P157_W0.5310.80
71_Y135_N0.5300.80
89_Y92_R0.5280.80
65_L82_S0.5270.79
24_T62_D0.5210.79
108_E173_L0.5200.79
56_V193_D0.5180.78
56_V198_D0.5140.78
143_I172_K0.5120.77
50_V146_I0.5120.77
32_D136_D0.5110.77
125_S129_A0.5060.77
25_A46_V0.5060.77
120_V123_E0.5040.76
167_F180_V0.5000.76
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  
4nehA 1 0.9547 100 0.429 Contact Map
4igiA 1 0.786 100 0.435 Contact Map
4cn9A 1 0.9012 100 0.437 Contact Map
4f1jA 1 0.7695 100 0.439 Contact Map
3n2nF 5 0.7325 100 0.441 Contact Map
4okuA 2 0.8601 100 0.442 Contact Map
1ijbA 1 0.7942 100 0.442 Contact Map
4okrA 1 0.8519 100 0.443 Contact Map
3zqkA 1 0.7243 100 0.456 Contact Map
1shuX 1 0.7243 100 0.458 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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