GREMLIN Database
YABD - Uncharacterized deoxyribonuclease YabD
UniProt: P37545 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 255 (251)
Sequences: 7136 (5017)
Seq/√Len: 316.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
79_K120_E3.2721.00
112_R142_E2.9431.00
159_A192_E2.8631.00
228_Q231_E2.7221.00
51_E84_H2.4931.00
97_Y135_D2.4601.00
115_I125_I2.3271.00
24_R218_E2.3201.00
150_G170_F2.2221.00
246_E250_R2.1901.00
227_E237_F2.1851.00
141_K164_E2.1291.00
187_K228_Q2.0511.00
26_K55_F2.0421.00
129_N136_V1.9371.00
108_K135_D1.9181.00
82_S90_I1.9161.00
59_A89_A1.8661.00
195_N233_K1.8471.00
116_A143_E1.8291.00
195_N243_I1.8231.00
235_M240_I1.8071.00
242_S246_E1.7921.00
112_R143_E1.7911.00
17_D216_R1.7861.00
7_A33_I1.7761.00
23_E27_A1.7721.00
97_Y104_K1.7661.00
50_I58_A1.7471.00
190_V229_I1.7451.00
15_D18_L1.7351.00
195_N235_M1.7311.00
134_E138_T1.7281.00
159_A163_R1.7081.00
109_E113_N1.6951.00
141_K168_M1.6801.00
59_A126_I1.6621.00
226_A237_F1.6451.00
32_R57_Y1.6311.00
44_T77_W1.6311.00
58_A87_V1.6301.00
32_R249_K1.6211.00
164_E167_K1.6201.00
152_M165_C1.6111.00
5_T248_A1.5941.00
154_C175_G1.5841.00
93_M114_Q1.5661.00
184_K188_E1.5551.00
200_I226_A1.5551.00
48_E52_E1.5251.00
93_M125_I1.5211.00
113_N116_A1.5191.00
163_R167_K1.5041.00
163_R192_E1.4961.00
19_E52_E1.4951.00
178_V229_I1.4791.00
79_K121_V1.4771.00
174_F190_V1.4721.00
108_K138_T1.4401.00
129_N133_T1.4321.00
3_F32_R1.4221.00
75_L113_N1.4201.00
171_Y250_R1.4191.00
151_I251_L1.4171.00
188_E191_K1.4151.00
162_A172_L1.4151.00
227_E231_E1.4041.00
158_S161_V1.4011.00
223_K227_E1.3881.00
111_F127_I1.3791.00
137_V164_E1.3681.00
171_Y197_R1.3601.00
39_D42_T1.3591.00
245_T249_K1.3481.00
112_R139_I1.3361.00
138_T142_E1.3311.00
108_K112_R1.3071.00
25_A33_I1.3061.00
77_W80_E1.2991.00
184_K187_K1.2991.00
187_K232_L1.2941.00
82_S121_V1.2921.00
224_Y227_E1.2851.00
172_L193_I1.2701.00
122_N149_G1.2681.00
194_P197_R1.2631.00
48_E51_E1.2561.00
3_F34_V1.2451.00
111_F136_V1.2371.00
119_K143_E1.2191.00
239_E242_S1.2151.00
10_N42_T1.2131.00
108_K139_I1.2121.00
46_A58_A1.2101.00
97_Y108_K1.2041.00
34_V88_V1.2001.00
235_M239_E1.1971.00
65_V99_W1.1921.00
3_F245_T1.1891.00
236_T239_E1.1811.00
229_I240_I1.1801.00
212_F221_Y1.1681.00
212_F224_Y1.1671.00
166_M197_R1.1661.00
212_F215_K1.1661.00
37_G43_I1.1641.00
2_L241_A1.1621.00
7_A204_C1.1611.00
104_K108_K1.1511.00
35_V46_A1.1451.00
103_P106_I1.1441.00
245_T248_A1.1431.00
226_A244_T1.1311.00
2_L226_A1.1281.00
199_L251_L1.1251.00
71_T74_D1.1201.00
17_D20_E1.1181.00
19_E23_E1.1181.00
174_F198_L1.1171.00
40_R43_I1.1151.00
105_D109_E1.1101.00
40_R74_D1.0911.00
160_E163_R1.0911.00
47_M58_A1.0891.00
20_E24_R1.0871.00
100_D104_K1.0821.00
79_K83_A1.0811.00
228_Q232_L1.0701.00
244_T248_A1.0661.00
51_E86_K1.0651.00
80_E83_A1.0631.00
133_T161_V1.0621.00
188_E192_E1.0571.00
171_Y251_L1.0541.00
67_A110_V1.0471.00
14_Y216_R1.0411.00
36_V126_I1.0401.00
217_N221_Y1.0361.00
33_I56_I1.0221.00
178_V190_V1.0181.00
47_M84_H1.0141.00
106_I109_E1.0121.00
134_E164_E1.0081.00
24_R220_S1.0051.00
116_A120_E1.0051.00
2_L222_V1.0041.00
157_G161_V1.0041.00
66_D69_D1.0021.00
181_K210_H1.0011.00
35_V56_I1.0001.00
159_A189_V1.0001.00
190_V233_K0.9971.00
3_F248_A0.9941.00
105_D108_K0.9941.00
47_M60_I0.9921.00
65_V102_S0.9861.00
200_I229_I0.9841.00
134_E161_V0.9831.00
200_I222_V0.9751.00
243_I246_E0.9721.00
40_R77_W0.9721.00
44_T48_E0.9621.00
20_E23_E0.9581.00
45_R48_E0.9571.00
226_A241_A0.9441.00
241_A245_T0.9401.00
159_A188_E0.9341.00
44_T81_L0.9251.00
174_F193_I0.9251.00
218_E221_Y0.9181.00
34_V248_A0.9161.00
70_M75_L0.9131.00
79_K117_L0.9121.00
239_E243_I0.9121.00
98_H131_D0.9121.00
190_V232_L0.9111.00
200_I244_T0.9091.00
77_W81_L0.9081.00
180_F208_T0.9021.00
240_I244_T0.8991.00
50_I56_I0.8931.00
173_S199_L0.8891.00
150_G251_L0.8861.00
223_K237_F0.8851.00
5_T199_L0.8771.00
233_K240_I0.8771.00
70_M110_V0.8751.00
137_V165_C0.8751.00
226_A240_I0.8721.00
76_A80_E0.8651.00
47_M51_E0.8641.00
237_F241_A0.8621.00
104_K135_D0.8611.00
19_E53_Y0.8601.00
38_F42_T0.8541.00
74_D77_W0.8531.00
83_A121_V0.8491.00
9_L219_P0.8391.00
67_A106_I0.8381.00
75_L79_K0.8341.00
36_V59_A0.8321.00
195_N240_I0.8301.00
22_I53_Y0.8291.00
151_I252_F0.8251.00
46_A50_I0.8201.00
135_D138_T0.8101.00
127_I152_M0.8061.00
166_M194_P0.8001.00
31_E245_T0.7971.00
76_A79_K0.7951.00
122_N148_V0.7941.00
222_V225_V0.7901.00
119_K144_G0.7901.00
60_I87_V0.7901.00
191_K232_L0.7881.00
117_L121_V0.7831.00
145_A148_V0.7811.00
24_R27_A0.7791.00
62_W70_M0.7781.00
115_I119_K0.7761.00
137_V161_V0.7741.00
119_K146_E0.7731.00
5_T151_I0.7721.00
14_Y18_L0.7710.99
14_Y17_D0.7650.99
127_I136_V0.7640.99
119_K148_V0.7610.99
166_M172_L0.7580.99
10_N45_R0.7550.99
139_I142_E0.7540.99
72_E113_N0.7530.99
246_E249_K0.7520.99
34_V59_A0.7490.99
65_V101_K0.7490.99
238_E242_S0.7490.99
171_Y199_L0.7480.99
100_D103_P0.7440.99
90_I93_M0.7430.99
133_T165_C0.7430.99
226_A230_A0.7370.99
129_N157_G0.7370.99
87_V123_L0.7300.99
191_K234_E0.7290.99
2_L223_K0.7270.99
43_I81_L0.7270.99
2_L245_T0.7220.99
28_E223_K0.7210.99
133_T157_G0.7190.99
112_R116_A0.7170.99
141_K167_K0.7120.99
70_M74_D0.7110.99
119_K145_A0.7010.99
235_M243_I0.7010.99
198_L233_K0.7010.99
15_D45_R0.7000.99
229_I233_K0.7000.99
60_I81_L0.6990.99
198_L240_I0.6930.99
12_E15_D0.6900.99
194_P233_K0.6890.99
42_T46_A0.6890.99
139_I143_E0.6880.99
22_I33_I0.6860.99
23_E26_K0.6830.99
18_L21_V0.6790.99
37_G46_A0.6790.99
151_I173_S0.6720.99
11_A206_F0.6670.99
106_I110_V0.6650.99
186_P189_V0.6640.99
101_K104_K0.6630.98
2_L237_F0.6620.98
177_P207_L0.6610.98
149_G253_R0.6600.98
177_P180_F0.6600.98
89_A126_I0.6530.98
122_N253_R0.6520.98
137_V141_K0.6510.98
243_I250_R0.6500.98
115_I139_I0.6490.98
43_I78_I0.6460.98
166_M193_I0.6450.98
115_I143_E0.6450.98
165_C172_L0.6430.98
22_I26_K0.6350.98
39_D69_D0.6310.98
5_T126_I0.6300.98
155_F161_V0.6280.98
26_K31_E0.6250.98
162_A166_M0.6200.98
43_I60_I0.6180.98
57_Y88_V0.6140.98
67_A102_S0.6120.97
177_P186_P0.6110.97
80_E84_H0.6090.97
162_A193_I0.6080.97
198_L244_T0.6070.97
75_L117_L0.6070.97
95_L132_A0.6060.97
68_I103_P0.6050.97
193_I198_L0.6050.97
129_N165_C0.6040.97
208_T221_Y0.6030.97
93_M110_V0.6020.97
57_Y86_K0.5990.97
2_L200_I0.5980.97
22_I56_I0.5960.97
17_D21_V0.5940.97
184_K191_K0.5940.97
73_E76_A0.5940.97
21_V216_R0.5920.97
196_D250_R0.5920.97
185_K188_E0.5900.97
196_D243_I0.5900.97
126_I252_F0.5870.97
164_E168_M0.5870.97
28_E220_S0.5870.97
162_A189_V0.5860.97
152_M173_S0.5850.97
68_I106_I0.5840.97
133_T137_V0.5840.97
43_I58_A0.5830.97
82_S87_V0.5810.97
116_A119_K0.5810.97
166_M192_E0.5790.96
10_N38_F0.5710.96
137_V168_M0.5690.96
199_L248_A0.5690.96
171_Y247_N0.5690.96
25_A30_V0.5680.96
34_V252_F0.5630.96
98_H130_R0.5610.96
233_K243_I0.5590.96
230_A237_F0.5560.96
127_I150_G0.5560.96
243_I247_N0.5550.96
110_V114_Q0.5550.96
145_A149_G0.5540.95
3_F249_K0.5510.95
47_M81_L0.5500.95
10_N35_V0.5490.95
178_V240_I0.5480.95
41_P45_R0.5470.95
38_F66_D0.5470.95
25_A218_E0.5470.95
231_E234_E0.5430.95
68_I102_S0.5400.95
144_G170_F0.5390.95
22_I55_F0.5360.95
99_W102_S0.5360.95
174_F177_P0.5320.94
179_T210_H0.5310.94
43_I46_A0.5280.94
41_P69_D0.5270.94
83_A120_E0.5270.94
151_I199_L0.5270.94
180_F214_G0.5260.94
176_G179_T0.5240.94
221_Y224_Y0.5210.94
247_N250_R0.5210.94
113_N117_L0.5210.94
47_M50_I0.5200.94
72_E76_A0.5190.94
186_P190_V0.5150.93
97_Y132_A0.5140.93
25_A29_K0.5120.93
32_R245_T0.5120.93
173_S207_L0.5100.93
238_E241_A0.5100.93
21_V24_R0.5060.93
61_G114_Q0.5060.93
179_T228_Q0.5050.93
133_T136_V0.5050.93
200_I240_I0.5020.93
187_K191_K0.5020.93
78_I82_S0.5000.92
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  
3e2vA 1 0.9765 100 0.178 Contact Map
3ipwA 1 0.9922 100 0.24 Contact Map
2xioA 1 0.9922 100 0.306 Contact Map
1j6oA 1 1 100 0.316 Contact Map
3gg7A 1 0.9451 100 0.342 Contact Map
3rcmA 1 1 100 0.358 Contact Map
2gzxA 1 0.9882 100 0.366 Contact Map
1xwyA 1 0.9922 100 0.368 Contact Map
1zzmA 1 0.9961 100 0.388 Contact Map
2y1hA 2 0.9725 100 0.394 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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