GREMLIN Database
YGAJ - Uncharacterized peptidase YgaJ
UniProt: P71089 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 230 (206)
Sequences: 1990 (1475)
Seq/√Len: 102.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
113_A118_V4.3801.00
37_C84_M3.6861.00
79_S83_E3.3831.00
81_V106_L2.8661.00
91_G124_S2.7761.00
34_P85_D2.7651.00
87_I118_V2.6471.00
42_A97_L2.6271.00
187_G203_S2.6201.00
35_R63_V2.6021.00
24_Y199_Q2.5491.00
82_M112_E2.4801.00
114_W150_F2.4311.00
24_Y27_N2.4241.00
98_L147_S2.3061.00
182_Y209_A2.2351.00
25_I86_V2.1951.00
24_Y28_Q2.1271.00
78_V112_E2.0621.00
113_A116_N2.0071.00
38_F49_Y1.9901.00
37_C80_F1.9721.00
142_L145_L1.9431.00
37_C67_L1.8951.00
51_Q55_H1.8921.00
35_R85_D1.8871.00
111_R115_K1.8711.00
30_K34_P1.8651.00
78_V109_I1.7831.00
169_Y181_G1.7281.00
87_I110_L1.7281.00
89_V120_V1.7071.00
98_L134_G1.6991.00
65_S80_F1.6911.00
50_I66_H1.6751.00
6_A191_H1.6721.00
35_R65_S1.6631.00
25_I121_A1.6261.00
182_Y190_L1.6241.00
37_C81_V1.6071.00
141_P144_S1.6011.00
132_E153_G1.5851.00
36_I86_V1.5791.00
87_I113_A1.5611.00
112_E116_N1.5601.00
127_A155_F1.5471.00
40_P66_H1.5451.00
161_G185_D1.5191.00
109_I112_E1.5101.00
193_I199_Q1.4651.00
92_G124_S1.4641.00
36_I62_C1.4561.00
173_I181_G1.4451.00
105_G108_H1.4411.00
75_S79_S1.4221.00
91_G125_A1.4191.00
31_R34_P1.4011.00
191_H201_V1.3941.00
21_L29_S1.3741.00
99_V103_E1.3701.00
45_D48_N1.3680.99
53_F57_F1.3540.99
4_I8_G1.3430.99
35_R83_E1.3150.99
65_S84_M1.3120.99
78_V82_M1.2910.99
134_G147_S1.2790.99
33_Q63_V1.2610.99
141_P145_L1.2610.99
88_Y123_I1.2490.99
110_L114_W1.2390.99
120_V130_W1.2340.99
88_Y121_A1.2280.99
17_D20_S1.2250.99
6_A130_W1.2210.99
8_G12_F1.2170.99
18_N22_D1.2110.99
82_M113_A1.2060.99
89_V97_L1.2020.99
5_I130_W1.2010.99
102_K107_D1.1900.99
211_R214_M1.1580.98
49_Y90_G1.1300.98
128_I158_H1.1300.98
122_G126_G1.1240.98
6_A28_Q1.1160.98
109_I113_A1.1130.98
37_C87_I1.0980.98
165_R168_A1.0970.98
114_W120_V1.0810.97
132_E152_Q1.0800.97
171_Q175_N1.0790.97
188_A207_A1.0790.97
151_L154_S1.0710.97
123_I186_D1.0660.97
82_M109_I1.0650.97
52_R56_A1.0620.97
6_A9_G1.0600.97
39_L67_L1.0560.97
49_Y52_R1.0500.97
41_T73_P1.0450.97
9_G12_F1.0430.97
81_V109_I1.0300.96
10_G159_Y1.0130.96
8_G11_G0.9910.96
108_H111_R0.9680.95
58_Q61_D0.9670.95
206_G211_R0.9660.95
169_Y173_I0.9480.94
39_L97_L0.9440.94
109_I118_V0.9380.94
107_D111_R0.9330.94
161_G186_D0.9280.94
23_Q60_L0.9240.94
81_V84_M0.9200.93
114_W195_D0.9180.93
154_S181_G0.9160.93
78_V105_G0.9080.93
18_N26_L0.9000.93
21_L189_A0.8950.92
94_T157_P0.8890.92
56_A59_T0.8870.92
38_F90_G0.8840.92
101_W129_C0.8830.92
21_L24_Y0.8820.92
95_R103_E0.8790.92
7_M11_G0.8780.92
160_D163_K0.8780.92
92_G126_G0.8770.92
81_V113_A0.8760.92
190_L197_L0.8710.91
133_E178_L0.8640.91
25_I119_V0.8590.91
194_N197_L0.8580.91
65_S83_E0.8520.90
18_N21_L0.8520.90
20_S24_Y0.8520.90
86_V119_V0.8390.90
191_H199_Q0.8370.90
22_D57_F0.8350.90
105_G109_I0.8260.89
26_L29_S0.8230.89
110_L120_V0.8210.89
97_L158_H0.8200.89
47_Q51_Q0.8190.89
80_F84_M0.8150.88
185_D188_A0.8130.88
166_R210_Y0.8090.88
166_R170_H0.8060.88
128_I168_A0.8040.88
6_A121_A0.8000.88
192_F197_L0.7990.87
128_I134_G0.7990.87
127_A184_A0.7980.87
51_Q54_Y0.7970.87
40_P90_G0.7910.87
91_G126_G0.7890.87
130_W150_F0.7870.87
169_Y183_A0.7800.86
45_D51_Q0.7640.85
57_F88_Y0.7640.85
53_F88_Y0.7610.85
206_G212_V0.7550.84
112_E115_K0.7550.84
123_I163_K0.7490.84
135_V172_L0.7490.84
20_S28_Q0.7390.83
169_Y185_D0.7390.83
204_R207_A0.7350.83
10_G13_S0.7320.82
39_L110_L0.7230.82
10_G186_D0.7220.82
21_L25_I0.7220.82
155_F184_A0.7180.81
43_S49_Y0.7170.81
96_N99_V0.7090.80
100_L103_E0.7080.80
30_K78_V0.7060.80
160_D168_A0.7060.80
95_R145_L0.7020.80
21_L28_Q0.7000.80
94_T123_I0.6980.79
37_C65_S0.6950.79
106_L109_I0.6940.79
102_K105_G0.6930.79
8_G88_Y0.6910.79
48_N51_Q0.6910.79
79_S82_M0.6850.78
160_D169_Y0.6840.78
160_D183_A0.6820.78
18_N25_I0.6770.77
8_G13_S0.6760.77
13_S18_N0.6750.77
4_I9_G0.6720.77
92_G125_A0.6690.76
77_L81_V0.6660.76
43_S94_T0.6620.76
31_R85_D0.6620.76
88_Y189_A0.6590.75
132_E178_L0.6580.75
46_S186_D0.6570.75
123_I160_D0.6570.75
209_A212_V0.6570.75
97_L129_C0.6550.75
96_N100_L0.6540.75
108_H196_Q0.6530.75
53_F123_I0.6520.75
119_V191_H0.6520.75
154_S169_Y0.6500.74
189_A200_T0.6500.74
27_N108_H0.6500.74
54_Y66_H0.6490.74
65_S70_F0.6460.74
98_L129_C0.6460.74
18_N28_Q0.6450.74
157_P168_A0.6450.74
124_S159_Y0.6420.73
35_R84_M0.6420.73
26_L62_C0.6410.73
94_T128_I0.6400.73
7_M158_H0.6380.73
48_N79_S0.6360.73
19_L23_Q0.6350.73
147_S156_C0.6310.72
44_G47_Q0.6310.72
90_G97_L0.6310.72
85_D118_V0.6300.72
24_Y191_H0.6290.72
7_M192_F0.6270.72
81_V87_I0.6240.71
43_S96_N0.6230.71
53_F56_A0.6230.71
54_Y58_Q0.6210.71
42_A158_H0.6200.71
188_A209_A0.6180.71
78_V195_D0.6130.70
159_Y163_K0.6110.70
60_L177_F0.6100.70
94_T158_H0.6080.69
29_S34_P0.6070.69
55_H59_T0.6030.69
4_I7_M0.5990.68
102_K143_T0.5980.68
23_Q27_N0.5930.67
82_M196_Q0.5930.67
111_R114_W0.5900.67
25_I36_I0.5890.67
162_E208_K0.5890.67
38_F94_T0.5870.67
88_Y119_V0.5850.66
12_F18_N0.5820.66
63_V71_K0.5790.66
69_L101_W0.5710.65
68_S155_F0.5710.65
192_F200_T0.5690.64
27_N30_K0.5690.64
162_E167_P0.5670.64
176_K179_C0.5660.64
12_F53_F0.5640.64
55_H214_M0.5630.64
189_A201_V0.5610.63
161_G208_K0.5600.63
134_G138_S0.5590.63
40_P158_H0.5580.63
131_F155_F0.5570.63
201_V204_R0.5570.63
128_I156_C0.5510.62
75_S105_G0.5500.62
143_T146_K0.5500.62
31_R86_V0.5470.61
86_V129_C0.5460.61
134_G149_G0.5460.61
40_P93_N0.5450.61
172_L176_K0.5450.61
149_G152_Q0.5440.61
132_E149_G0.5430.61
207_A210_Y0.5360.60
74_S77_L0.5330.59
8_G121_A0.5310.59
75_S80_F0.5270.58
20_S26_L0.5230.58
82_M214_M0.5210.58
42_A93_N0.5200.57
200_T207_A0.5190.57
76_D152_Q0.5180.57
11_G189_A0.5180.57
83_E175_N0.5170.57
92_G122_G0.5170.57
5_I175_N0.5160.57
137_D156_C0.5160.57
82_M116_N0.5150.57
129_C151_L0.5150.57
33_Q108_H0.5140.57
165_R181_G0.5130.56
4_I191_H0.5110.56
28_Q191_H0.5110.56
159_Y187_G0.5110.56
37_C107_D0.5090.56
76_D79_S0.5070.56
6_A21_L0.5050.55
61_D213_M0.5040.55
32_E55_H0.5040.55
35_R54_Y0.5040.55
93_N123_I0.5040.55
130_W137_D0.5030.55
9_G189_A0.5020.55
94_T159_Y0.5020.55
25_I29_S0.5020.55
98_L117_G0.5000.55
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  
3en0A 2 0.9913 100 0.304 Contact Map
1fy2A 1 0.9261 100 0.481 Contact Map
3l4eA 1 0.8348 100 0.488 Contact Map
1ka9H 1 0.7391 98 0.838 Contact Map
2nv0A 1 0.7217 97.9 0.84 Contact Map
2issD 1 0.7261 97.8 0.845 Contact Map
1jvnA 1 0.7696 97.7 0.847 Contact Map
2ywdA 1 0.7304 97.7 0.847 Contact Map
1q7rA 1 0.7565 97.6 0.851 Contact Map
2abwA 1 0.7565 97.5 0.854 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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