GREMLIN Database
RADA - DNA repair and recombination protein RadA
UniProt: Q55075 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 324 (249)
Sequences: 2560 (1065)
Seq/√Len: 67.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
104_I127_L5.5671.00
168_D171_N5.5581.00
285_I297_A4.9371.00
127_L206_L4.3971.00
259_A275_H4.3721.00
110_T250_A3.9911.00
104_I250_A3.9621.00
124_C254_T3.7111.00
91_T104_I3.5581.00
100_L283_I3.3361.00
285_I299_V3.1721.00
195_Q243_L3.0561.00
127_L252_I2.8651.00
89_I250_A2.8601.00
128_S144_A2.8151.00
131_V144_A2.6431.00
297_A312_F2.6411.00
131_V206_L2.6221.00
287_L297_A2.5231.00
294_R311_V2.4651.00
244_A251_V2.4381.00
144_A206_L2.4041.00
128_S208_V2.3881.00
142_G205_K2.3191.00
70_D75_T2.2791.00
183_N187_Q2.1611.00
112_F252_I2.1341.00
147_I194_L2.1211.00
150_E256_Q2.0941.00
91_T127_L2.0601.00
290_S296_I2.0301.00
90_S140_L1.9951.00
237_L277_L1.9691.00
184_T220_Y1.9631.00
315_T320_R1.9521.00
164_A317_E1.9521.00
273_G277_L1.9251.00
244_A250_A1.9051.00
121_T125_H1.7731.00
112_F123_L1.7351.00
60_K63_K1.7241.00
317_E320_R1.6800.99
128_S146_Y1.6520.99
104_I110_T1.6480.99
145_V204_I1.6280.99
217_R221_P1.5960.99
123_L287_L1.5910.99
93_S321_D1.5630.99
294_R313_A1.5550.99
261_P270_V1.5300.99
89_I131_V1.5250.99
296_I309_E1.5240.99
144_A208_V1.4810.99
111_E284_R1.4670.99
113_F300_V1.4270.98
63_K67_D1.4270.98
206_L250_A1.4060.98
62_I66_R1.4020.98
112_F285_I1.3570.98
145_V197_L1.3290.97
61_I65_A1.3030.97
291_R294_R1.2830.97
194_L198_V1.2820.97
187_Q236_H1.2630.96
122_Q146_Y1.2600.96
99_L308_G1.2390.96
56_S59_Q1.2380.96
194_L207_I1.2300.96
131_V250_A1.2210.95
129_V161_M1.2170.95
194_L251_V1.1910.95
198_V244_A1.1900.95
243_L249_I1.1890.95
255_N274_G1.1800.94
64_E67_D1.1680.94
274_G284_R1.1670.94
225_N235_K1.1570.94
118_S312_F1.1480.94
60_K64_E1.1450.93
68_A72_R1.1370.93
262_D268_P1.1230.93
104_I252_I1.1130.92
207_I249_I1.0950.92
95_A98_G1.0910.92
290_S294_R1.0780.91
313_A320_R1.0620.91
57_T60_K1.0600.91
183_N186_H1.0550.90
229_R272_V1.0420.90
272_V275_H1.0320.89
95_A321_D1.0210.89
267_D286_Q1.0210.89
87_K248_D1.0070.88
265_Y268_P1.0060.88
264_F270_V1.0030.88
121_T144_A1.0000.88
146_Y179_I0.9930.87
296_I311_V0.9890.87
213_T272_V0.9880.87
150_E219_E0.9870.87
95_A310_V0.9800.87
286_Q290_S0.9770.87
206_L252_I0.9750.86
143_K204_I0.9680.86
263_M268_P0.9680.86
224_E235_K0.9660.86
217_R229_R0.9560.85
124_C146_Y0.9520.85
218_A225_N0.9460.85
106_T131_V0.9420.85
212_V277_L0.9400.84
241_T282_G0.9380.84
111_E255_N0.9330.84
243_L247_Y0.9280.84
202_P316_E0.9270.84
245_E248_D0.9250.83
257_V286_Q0.9220.83
151_G180_R0.9210.83
77_L81_K0.9210.83
241_T245_E0.9140.83
287_L295_R0.9130.83
289_K298_R0.9100.82
91_T97_D0.9090.82
150_E213_T0.9090.82
287_L312_F0.9060.82
277_L295_R0.9030.82
226_L229_R0.8980.82
87_K106_T0.8970.81
148_D154_R0.8930.81
58_A62_I0.8930.81
212_V236_H0.8920.81
212_V253_I0.8910.81
132_Q144_A0.8890.81
111_E274_G0.8850.81
187_Q215_H0.8810.80
181_A190_I0.8810.80
264_F268_P0.8770.80
61_I64_E0.8740.80
115_E286_Q0.8710.80
119_G210_D0.8700.79
92_G97_D0.8650.79
123_L251_V0.8610.79
199_S247_Y0.8590.79
126_Q319_I0.8580.79
104_I312_F0.8540.78
106_T140_L0.8540.78
263_M267_D0.8490.78
283_I302_A0.8470.78
145_V173_M0.8460.78
120_K210_D0.8380.77
150_E217_R0.8360.77
161_M165_L0.8310.76
216_F242_R0.8300.76
234_N280_V0.8290.76
115_E288_K0.8210.75
148_D152_T0.8210.75
107_R248_D0.8190.75
191_V236_H0.8180.75
81_K169_I0.8120.75
263_M266_G0.8090.74
110_T254_T0.8090.74
240_L251_V0.8010.74
116_F271_A0.8000.74
59_Q63_K0.7980.73
215_H236_H0.7960.73
75_T78_E0.7920.73
261_P275_H0.7860.72
184_T187_Q0.7790.72
292_G295_R0.7780.71
139_G142_G0.7750.71
125_H153_F0.7730.71
109_M241_T0.7710.71
225_N228_V0.7690.71
193_D252_I0.7630.70
217_R254_T0.7600.70
123_L252_I0.7590.70
187_Q192_D0.7570.69
93_S319_I0.7550.69
148_D153_F0.7530.69
80_K171_N0.7510.69
209_V236_H0.7470.68
273_G276_T0.7440.68
146_Y153_F0.7410.68
55_L59_Q0.7400.68
126_Q161_M0.7380.67
94_Q98_G0.7360.67
206_L244_A0.7330.67
286_Q296_I0.7330.67
195_Q294_R0.7300.67
218_A228_V0.7260.66
208_V263_M0.7250.66
289_K292_G0.7240.66
249_I306_P0.7230.66
302_A305_L0.7220.66
94_Q321_D0.7170.65
131_V139_G0.7130.65
253_I277_L0.7130.65
279_H301_D0.7110.64
261_P291_R0.7090.64
60_K312_F0.7050.64
184_T217_R0.7040.64
106_T205_K0.7040.64
237_L273_G0.7030.64
93_S123_L0.6980.63
68_A146_Y0.6980.63
186_H190_I0.6960.63
145_V194_L0.6950.63
161_M316_E0.6940.63
194_L209_V0.6940.63
124_C252_I0.6920.62
220_Y233_L0.6920.62
89_I104_I0.6920.62
130_N165_L0.6920.62
240_L244_A0.6890.62
125_H129_V0.6860.62
122_Q271_A0.6850.62
117_G147_I0.6840.61
126_Q130_N0.6790.61
288_K296_I0.6780.61
294_R312_F0.6710.60
183_N242_R0.6710.60
216_F232_K0.6700.60
148_D301_D0.6690.60
100_L285_I0.6690.60
59_Q143_K0.6650.59
217_R256_Q0.6630.59
260_R270_V0.6620.59
208_V266_G0.6590.59
252_I314_L0.6580.59
197_L200_K0.6580.59
214_S256_Q0.6550.58
210_D255_N0.6550.58
257_V275_H0.6540.58
104_I243_L0.6540.58
65_A73_F0.6520.58
216_F226_L0.6510.58
100_L299_V0.6480.57
59_Q250_A0.6460.57
257_V270_V0.6460.57
112_F124_C0.6440.57
153_F225_N0.6420.57
146_Y190_I0.6400.56
116_F301_D0.6390.56
59_Q67_D0.6380.56
108_T283_I0.6380.56
81_K84_M0.6230.54
84_M316_E0.6230.54
213_T230_Q0.6210.54
95_A317_E0.6210.54
163_K169_I0.6200.54
113_F272_V0.6200.54
256_Q303_P0.6190.54
96_L285_I0.6180.54
84_M315_T0.6150.53
106_T250_A0.6140.53
230_Q276_T0.6130.53
108_T304_H0.6120.53
312_F320_R0.6120.53
220_Y229_R0.6110.53
184_T221_P0.6110.53
87_K194_L0.6100.53
90_S93_S0.6090.53
289_K296_I0.6080.53
219_E256_Q0.6070.53
295_R312_F0.6040.52
59_Q64_E0.6030.52
64_E248_D0.6030.52
106_T139_G0.6020.52
69_L77_L0.6020.52
213_T277_L0.6010.52
80_K85_N0.6010.52
64_E84_M0.6010.52
114_G119_G0.6000.52
224_E240_L0.5990.52
209_V320_R0.5990.52
234_N307_E0.5980.51
63_K94_Q0.5970.51
58_A61_I0.5970.51
163_K316_E0.5950.51
99_L299_V0.5920.51
268_P286_Q0.5900.51
117_G287_L0.5890.50
114_G120_K0.5870.50
232_K237_L0.5840.50
150_E212_V0.5840.50
264_F267_D0.5830.50
118_S163_K0.5810.49
65_A70_D0.5810.49
71_I251_V0.5810.49
162_A172_V0.5790.49
125_H179_I0.5790.49
62_I65_A0.5790.49
62_I203_S0.5750.49
150_E303_P0.5750.49
224_E257_V0.5740.49
103_G211_S0.5730.48
116_F273_G0.5710.48
89_I130_N0.5710.48
187_Q212_V0.5700.48
99_L181_A0.5700.48
61_I75_T0.5690.48
96_L100_L0.5690.48
88_K104_I0.5690.48
98_G104_I0.5680.48
55_L61_I0.5670.48
258_M272_V0.5670.48
105_E283_I0.5650.48
212_V220_Y0.5650.48
299_V317_E0.5620.47
57_T83_R0.5610.47
226_L261_P0.5580.47
93_S121_T0.5540.46
91_T252_I0.5530.46
65_A68_A0.5530.46
108_T282_G0.5520.46
258_M276_T0.5520.46
102_G150_E0.5500.46
65_A199_S0.5490.46
79_V82_E0.5480.46
194_L240_L0.5470.45
258_M270_V0.5470.45
55_L69_L0.5460.45
128_S206_L0.5450.45
279_H282_G0.5410.45
63_K171_N0.5410.45
69_L85_N0.5400.45
257_V291_R0.5380.44
77_L85_N0.5370.44
164_A316_E0.5370.44
107_R114_G0.5350.44
211_S256_Q0.5340.44
163_K209_V0.5340.44
145_V199_S0.5330.44
163_K315_T0.5320.44
122_Q295_R0.5310.44
186_H212_V0.5310.44
274_G302_A0.5310.44
144_A250_A0.5290.43
124_C128_S0.5290.43
84_M88_K0.5280.43
93_S312_F0.5270.43
229_R233_L0.5250.43
226_L230_Q0.5240.43
149_T209_V0.5230.43
149_T272_V0.5230.43
122_Q303_P0.5210.42
228_V260_R0.5200.42
77_L321_D0.5190.42
117_G259_A0.5190.42
59_Q290_S0.5180.42
92_G214_S0.5170.42
226_L259_A0.5140.42
72_R84_M0.5130.41
216_F229_R0.5120.41
91_T100_L0.5120.41
127_L140_L0.5110.41
246_V260_R0.5110.41
202_P247_Y0.5110.41
277_L281_P0.5080.41
125_H165_L0.5080.41
99_L305_L0.5080.41
144_A207_I0.5070.41
59_Q66_R0.5060.41
216_F275_H0.5050.40
181_A186_H0.5040.40
197_L204_I0.5040.40
292_G309_E0.5040.40
251_V259_A0.5040.40
118_S289_K0.5040.40
230_Q234_N0.5020.40
117_G145_V0.5010.40
298_R309_E0.5010.40
153_F179_I0.5000.40
63_K208_V0.5000.40
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  
2z43A 1 0.8951 100 0.324 Contact Map
2i1qA 1 0.929 100 0.357 Contact Map
1v5wA 5 0.7346 100 0.362 Contact Map
3ldaA 1 0.9043 100 0.386 Contact Map
1pznA 5 0.9105 100 0.386 Contact Map
1n0wA 1 0.6481 100 0.526 Contact Map
4hyyA 4 0.7407 100 0.55 Contact Map
4b3bA 1 0.679 100 0.583 Contact Map
2cvhA 1 0.6728 100 0.592 Contact Map
3cmuA 1 0.6821 100 0.613 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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