GREMLIN Database
YNJA - Uncharacterized protein YnjA
UniProt: P76222 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14003
Length: 182 (148)
Sequences: 4876 (3152)
Seq/√Len: 259.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
122_A134_L4.0361.00
139_A144_A3.4551.00
88_A94_S3.3141.00
143_D146_A2.7841.00
118_E137_R2.5461.00
122_A131_D2.3841.00
69_R121_E2.3211.00
119_Y151_T2.3071.00
94_S98_L2.2731.00
66_V150_L2.2411.00
112_E142_F2.0941.00
132_D136_T2.0681.00
136_T140_A2.0661.00
62_V116_A1.9421.00
92_G96_K1.9271.00
124_S158_N1.7891.00
70_I120_A1.7651.00
155_G159_L1.7621.00
164_N169_I1.7601.00
73_M125_V1.7591.00
61_V113_E1.7271.00
57_P149_E1.7221.00
64_S83_T1.6861.00
62_V112_E1.6711.00
131_D134_L1.6391.00
123_A166_A1.6381.00
115_L134_L1.6361.00
132_D168_D1.6271.00
112_E146_A1.6261.00
119_Y138_L1.6111.00
40_I152_A1.5981.00
93_S96_K1.5891.00
59_D62_V1.5651.00
137_R140_A1.5641.00
110_S113_E1.5441.00
139_A147_L1.5011.00
63_R153_L1.4921.00
138_L147_L1.4871.00
116_A150_L1.4671.00
119_Y130_V1.4621.00
66_V116_A1.4561.00
116_A142_F1.4001.00
71_A161_A1.3951.00
61_V96_K1.3871.00
112_E141_H1.3721.00
76_C79_C1.3561.00
99_A108_L1.3131.00
65_L117_L1.2941.00
73_M121_E1.2561.00
87_V92_G1.2291.00
145_Q149_E1.2071.00
158_N162_R1.2021.00
142_F150_L1.1741.00
47_F156_L1.1421.00
37_I149_E1.1401.00
88_A98_L1.1331.00
70_I124_S1.1271.00
48_V156_L1.1261.00
134_L137_R1.1261.00
99_A106_S1.1121.00
64_S90_R1.1091.00
129_T168_D1.0931.00
74_C161_A1.0921.00
57_P146_A1.0911.00
67_S157_Q1.0831.00
114_R118_E1.0831.00
50_W149_E1.0701.00
42_Y46_M1.0511.00
44_V159_L1.0461.00
111_D141_H1.0301.00
139_A143_D1.0291.00
69_R73_M1.0241.00
69_R117_L1.0151.00
119_Y166_A1.0061.00
57_P145_Q1.0061.00
120_A154_I1.0021.00
48_V67_S0.9931.00
135_R139_A0.9921.00
115_L137_R0.9711.00
37_I145_Q0.9631.00
62_V113_E0.9521.00
57_P143_D0.9471.00
72_Q80_V0.9361.00
118_E134_L0.9321.00
65_L113_E0.9311.00
36_R144_A0.9301.00
111_D114_R0.9231.00
85_M89_E0.9221.00
111_D137_R0.9031.00
36_R148_T0.8991.00
96_K113_E0.8971.00
104_R118_E0.8971.00
84_S88_A0.8951.00
62_V142_F0.8941.00
71_A157_Q0.8921.00
72_Q121_E0.8841.00
86_K89_E0.8831.00
82_I172_Q0.8771.00
98_L101_A0.8721.00
68_A97_L0.8701.00
136_T139_A0.8591.00
56_S149_E0.8530.99
98_L102_D0.8520.99
105_Q118_E0.8510.99
124_S162_R0.8440.99
120_A124_S0.8330.99
51_L153_L0.8320.99
151_T167_M0.8220.99
76_C161_A0.8200.99
81_D95_D0.8180.99
64_S67_S0.8120.99
115_L141_H0.8120.99
86_K90_R0.8070.99
111_D140_A0.8050.99
148_T163_F0.8040.99
29_S32_R0.8020.99
74_C158_N0.8010.99
60_P63_R0.7980.99
132_D135_R0.7950.99
46_M49_G0.7940.99
133_A140_A0.7890.99
65_L100_V0.7840.99
58_L63_R0.7810.99
87_V91_T0.7720.99
35_G41_F0.7700.99
73_M124_S0.7680.99
82_I160_S0.7580.99
84_S97_L0.7580.99
123_A151_T0.7470.99
67_S79_C0.7450.99
130_V134_L0.7440.99
143_D147_L0.7420.99
99_A109_F0.7290.98
61_V92_G0.7240.98
95_D98_L0.7230.98
68_A84_S0.7210.98
118_E121_E0.7190.98
78_F82_I0.7190.98
49_G55_R0.7130.98
29_S78_F0.7090.98
70_I157_Q0.7070.98
40_I50_W0.7060.98
48_V160_S0.7040.98
74_C124_S0.7030.98
69_R72_Q0.7020.98
43_L46_M0.7000.98
37_I148_T0.6980.98
68_A80_V0.6960.98
46_M50_W0.6870.98
118_E122_A0.6870.98
79_C161_A0.6870.98
79_C164_N0.6820.98
64_S86_K0.6770.97
131_D136_T0.6740.97
74_C162_R0.6740.97
67_S83_T0.6720.97
138_L142_F0.6620.97
87_V97_L0.6540.97
137_R141_H0.6530.97
126_T129_T0.6480.97
119_Y123_A0.6350.96
133_A136_T0.6340.96
60_P90_R0.6330.96
81_D172_Q0.6310.96
71_A79_C0.6240.96
59_D112_E0.6200.96
84_S98_L0.6190.96
81_D171_A0.6150.96
104_R121_E0.6120.95
34_W163_F0.6100.95
109_F117_L0.6080.95
116_A120_A0.6050.95
129_T165_S0.6020.95
76_C164_N0.5970.95
148_T152_A0.5960.95
133_A137_R0.5940.95
24_Y28_L0.5940.95
150_L154_I0.5930.95
148_T167_M0.5890.94
78_F172_Q0.5870.94
99_A107_P0.5860.94
29_S82_I0.5810.94
42_Y45_S0.5750.94
60_P64_S0.5730.94
44_V48_V0.5680.93
119_Y167_M0.5670.93
41_F164_N0.5640.93
96_K109_F0.5620.93
51_L149_E0.5610.93
83_T157_Q0.5590.93
151_T166_A0.5560.92
34_W41_F0.5530.92
71_A76_C0.5500.92
157_Q160_S0.5480.92
114_R117_L0.5450.92
47_F159_L0.5440.92
24_Y27_V0.5420.92
109_F113_E0.5390.91
119_Y150_L0.5350.91
95_D107_P0.5340.91
156_L160_S0.5330.91
128_P134_L0.5330.91
85_M172_Q0.5310.91
36_R145_Q0.5290.91
138_L150_L0.5280.90
121_E125_V0.5270.90
103_W106_S0.5250.90
70_I154_I0.5250.90
43_L47_F0.5240.90
135_R168_D0.5210.90
152_A163_F0.5210.90
152_A155_G0.5130.89
33_W169_I0.5110.89
95_D99_A0.5100.89
153_L157_Q0.5100.89
39_F145_Q0.5090.89
63_R67_S0.5080.89
112_E116_A0.5080.89
79_C157_Q0.5050.88
80_V102_D0.5050.88
44_V47_F0.5010.88
135_R147_L0.5000.88
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  
3c1lA 5 0.978 100 0.226 Contact Map
2pfxA 3 0.978 100 0.229 Contact Map
2oyoA 4 0.978 100 0.231 Contact Map
2prrA 5 0.9835 100 0.236 Contact Map
3lvyA 2 0.967 100 0.25 Contact Map
2o4dA 3 0.7857 100 0.317 Contact Map
2gmyA 3 0.8077 100 0.32 Contact Map
2ouwA 6 0.7033 99.9 0.516 Contact Map
3bjxA 2 0.7473 99.8 0.568 Contact Map
4n2xA 4 0.7473 99.7 0.579 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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