GREMLIN Database
RADA - DNA repair and recombination protein RadA
UniProt: Q9HMM4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 343 (300)
Sequences: 1236 (782)
Seq/√Len: 45.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
151_I193_I6.1331.00
124_V137_A4.5671.00
120_L273_L4.2251.00
121_A137_A4.0031.00
105_V273_L3.8351.00
127_P132_G3.7761.00
306_M318_V3.6721.00
117_T275_T3.6391.00
308_L318_V3.4341.00
258_L298_L3.4081.00
143_E277_Q3.0841.00
45_I50_A3.0821.00
97_V271_A2.9231.00
120_L227_M2.8871.00
103_T271_A2.8751.00
82_L271_A2.8101.00
137_A229_T2.7911.00
84_W97_V2.7681.00
105_V306_M2.6861.00
204_Q257_H2.5351.00
294_G298_L2.4911.00
97_V103_T2.4881.00
276_N295_G2.4681.00
135_G226_R2.4551.00
114_S118_H2.4131.00
264_V270_A2.3981.00
115_Q150_R2.2231.00
117_T273_L2.2131.00
106_Y321_V2.2031.00
128_T134_H2.1971.00
336_Q341_K2.0961.00
115_Q139_F2.0300.99
238_R250_R2.0030.99
338_E341_K1.9910.99
265_G271_A1.9750.99
105_V116_V1.9730.99
136_R192_K1.9440.99
228_L270_A1.9330.99
143_E238_R1.8930.99
97_V273_L1.8700.99
125_Q192_K1.8600.99
153_D337_D1.8140.99
14_P18_E1.8020.99
25_F30_S1.7830.98
121_A229_T1.7620.98
261_L272_V1.7590.98
247_L250_R1.7520.98
138_V225_V1.7510.98
315_K332_V1.7480.98
126_L132_G1.7350.98
204_Q236_H1.7220.98
234_T293_I1.7120.98
104_E305_R1.6870.98
127_P131_G1.6810.98
141_D146_F1.6580.97
138_V211_A1.6160.97
122_V154_M1.6120.97
68_T71_T1.6090.97
141_D147_R1.6050.97
144_D197_K1.5680.96
211_A228_L1.4950.95
88_E91_D1.4950.95
84_W90_D1.4840.95
97_V120_L1.4710.95
233_L298_L1.4520.94
304_F323_A1.4340.94
99_T271_A1.4090.94
200_N263_K1.3920.93
216_S268_Y1.3790.93
119_Q154_M1.3660.92
306_M320_L1.3650.92
308_L333_M1.3630.92
227_M271_A1.3330.91
238_R277_Q1.3310.91
274_V298_L1.3310.91
318_V333_M1.3270.91
111_A333_M1.3250.91
116_V306_M1.3100.91
18_E21_R1.3100.91
127_P130_Y1.3050.91
12_V18_E1.2980.90
298_L316_R1.2840.90
92_L329_G1.2830.90
13_G16_T1.2690.89
114_S137_A1.2680.89
31_L56_A1.2550.89
140_I229_T1.2300.88
39_L44_D1.2280.88
37_A47_E1.2250.88
143_E234_T1.2240.87
86_I340_L1.2070.87
277_Q324_P1.2060.87
121_A139_F1.2000.86
45_I53_V1.1930.86
143_E240_E1.1840.86
118_H151_I1.1740.85
101_S304_F1.1640.85
19_K24_G1.1620.85
255_N301_K1.1560.84
139_F278_V1.1530.84
136_R194_H1.1510.84
200_N203_H1.1430.84
138_V196_A1.1390.83
127_P133_L1.1380.83
54_I57_A1.1320.83
143_E324_P1.1200.82
124_V227_M1.1130.82
198_G207_L1.1100.82
237_F247_L1.1090.82
46_G49_T1.0970.81
214_I218_H1.0890.81
136_R230_V1.0880.80
77_E337_D1.0810.80
310_K319_K1.0800.80
115_Q232_S1.0790.80
150_R193_I1.0760.80
100_Q269_N1.0730.80
54_I58_R1.0680.79
67_E75_R1.0600.79
193_I228_L1.0580.79
101_S325_N1.0420.77
116_V208_A1.0330.77
31_L54_I1.0290.77
240_E277_Q1.0280.77
12_V19_K1.0250.76
241_Y254_L1.0200.76
285_F335_V1.0200.76
74_E77_E1.0160.76
262_E303_T1.0140.76
125_Q137_A1.0050.75
230_V338_E0.9990.74
47_E51_A0.9980.74
108_E322_D0.9960.74
126_L130_Y0.9960.74
84_W93_L0.9930.74
70_A320_L0.9880.74
210_K273_L0.9870.74
17_A21_R0.9860.73
15_A19_K0.9810.73
29_Q216_S0.9730.72
119_Q340_L0.9700.72
47_E53_V0.9640.72
35_N38_E0.9630.72
149_E154_M0.9610.72
124_V132_G0.9580.71
234_T298_L0.9540.71
233_L274_V0.9510.71
141_D145_T0.9500.71
25_F31_L0.9450.70
156_R337_D0.9400.70
237_F253_K0.9240.68
294_G297_I0.9230.68
90_D93_L0.9190.68
233_L257_H0.9180.68
257_H262_E0.9170.68
123_N158_L0.9160.68
37_A335_V0.9050.67
117_T229_T0.9030.67
141_D197_K0.9010.67
309_R331_A0.9010.67
84_W273_L0.8920.66
89_V327_A0.8890.65
103_T124_V0.8870.65
95_G143_E0.8870.65
232_S275_T0.8870.65
16_T24_G0.8770.64
148_P195_V0.8760.64
109_F292_P0.8740.64
249_D281_N0.8740.64
247_L251_Q0.8730.64
288_D307_Y0.8690.64
115_Q316_R0.8680.64
111_A310_K0.8580.63
141_D322_D0.8510.62
295_G305_R0.8490.62
102_I218_H0.8470.62
154_M158_L0.8440.61
203_H207_L0.8360.61
131_G135_G0.8360.61
300_H322_D0.8340.60
90_D231_D0.8310.60
201_S241_Y0.8280.60
143_E278_V0.8280.60
39_L272_V0.8260.60
281_N291_K0.8230.59
33_V36_S0.8210.59
136_R224_P0.8210.59
98_E304_F0.8140.59
230_V257_H0.8110.58
102_I198_G0.8100.58
250_R254_L0.8090.58
136_R218_H0.8060.58
265_G272_V0.8060.58
18_E22_D0.8050.58
68_T229_T0.8020.57
91_D229_T0.8010.57
143_E232_S0.8010.57
227_M273_L0.8010.57
124_V133_L0.8000.57
71_T74_E0.7990.57
150_R316_R0.7980.57
119_Q254_L0.7950.57
86_I114_S0.7920.57
15_A30_S0.7880.56
251_Q297_I0.7830.56
215_A325_N0.7830.56
129_E134_H0.7830.56
56_A59_E0.7820.56
23_N31_L0.7750.55
235_A278_V0.7750.55
335_V339_G0.7740.55
279_Q293_I0.7680.54
298_L302_S0.7670.54
332_V340_L0.7640.54
101_S303_T0.7630.54
53_V61_A0.7570.53
210_K213_E0.7570.53
85_N123_N0.7560.53
201_S205_M0.7550.53
51_A54_I0.7530.53
315_K334_R0.7500.52
43_A51_A0.7490.52
25_F54_I0.7450.52
93_L306_M0.7440.52
215_A225_V0.7430.52
117_T264_V0.7400.51
276_N323_A0.7390.51
38_E116_V0.7390.51
102_I336_Q0.7350.51
81_K97_V0.7340.51
13_G17_A0.7320.51
13_G21_R0.7300.51
215_A268_Y0.7280.50
104_E276_N0.7270.50
115_Q193_I0.7260.50
139_F318_V0.7260.50
255_N292_P0.7250.50
241_Y250_R0.7240.50
41_N49_T0.7240.50
127_P134_H0.7240.50
274_V320_L0.7230.50
97_V264_V0.7230.50
106_Y299_G0.7230.50
50_A54_I0.7220.50
141_D296_N0.7190.49
127_P146_F0.7190.49
107_G113_K0.7180.49
296_N300_H0.7130.49
155_V189_F0.7130.49
214_I229_T0.7130.49
250_R300_H0.7100.49
138_V194_H0.7100.49
12_V21_R0.7090.48
187_D191_D0.7080.48
36_S42_T0.7080.48
92_L292_P0.7070.48
232_S277_Q0.7060.48
51_A59_E0.7050.48
25_F53_V0.7040.48
37_A48_S0.7030.48
25_F42_T0.7000.48
88_E130_Y0.6990.47
85_N90_D0.6980.47
25_F50_A0.6900.47
200_N239_A0.6900.47
143_E233_L0.6890.47
236_H257_H0.6880.46
258_L302_S0.6860.46
215_A226_R0.6840.46
99_T200_N0.6810.46
76_R79_I0.6790.46
47_E61_A0.6790.46
299_G302_S0.6780.45
250_R277_Q0.6760.45
25_F129_E0.6710.45
53_V56_A0.6690.45
190_L297_I0.6690.45
29_Q121_A0.6680.44
320_L327_A0.6670.44
192_K333_M0.6660.44
46_G246_E0.6660.44
251_Q300_H0.6650.44
92_L326_L0.6640.44
258_L294_G0.6630.44
141_D148_P0.6620.44
49_T53_V0.6610.44
49_T52_D0.6600.44
16_T49_T0.6590.44
77_E306_M0.6590.44
269_N283_D0.6560.43
191_D320_L0.6560.43
70_A191_D0.6540.43
144_D211_A0.6530.43
86_I116_V0.6510.43
286_F289_P0.6490.43
335_V341_K0.6470.42
249_D253_K0.6470.42
119_Q270_A0.6460.42
44_D50_A0.6430.42
151_I154_M0.6420.42
189_F280_S0.6410.42
15_A18_E0.6410.42
71_T130_Y0.6400.42
102_I246_E0.6390.42
264_V335_V0.6390.42
200_N212_K0.6390.42
52_D55_Q0.6360.41
127_P135_G0.6360.41
17_A22_D0.6360.41
88_E338_E0.6350.41
284_A315_K0.6340.41
32_A35_N0.6340.41
76_R99_T0.6340.41
43_A48_S0.6320.41
105_V153_D0.6300.41
307_Y321_V0.6300.41
115_Q125_Q0.6290.41
106_Y203_H0.6290.41
16_T19_K0.6290.41
309_R317_I0.6280.41
38_E41_N0.6260.40
116_V308_L0.6250.40
115_Q278_V0.6240.40
26_D82_L0.6240.40
116_V340_L0.6230.40
148_P275_T0.6210.40
108_E280_S0.6210.40
75_R78_Q0.6200.40
150_R298_L0.6200.40
208_A257_H0.6190.40
75_R146_F0.6180.40
120_L193_I0.6170.40
317_I332_V0.6170.40
285_F289_P0.6160.40
131_G134_H0.6160.40
299_G335_V0.6150.39
12_V27_A0.6150.39
70_A74_E0.6140.39
113_K232_S0.6140.39
234_T251_Q0.6140.39
205_M253_K0.6130.39
145_T251_Q0.6130.39
155_V200_N0.6120.39
50_A212_K0.6100.39
195_V262_E0.6100.39
48_S51_A0.6090.39
122_V296_N0.6070.39
244_R251_Q0.6050.39
57_A62_D0.6030.38
48_S242_V0.6030.38
27_A55_Q0.6010.38
85_N310_K0.5990.38
81_K326_L0.5960.38
217_E265_G0.5960.38
273_L335_V0.5960.38
252_Q282_P0.5940.38
25_F45_I0.5930.37
279_Q291_K0.5920.37
39_L59_E0.5920.37
251_Q254_L0.5920.37
125_Q193_I0.5920.37
258_L261_L0.5910.37
84_W265_G0.5900.37
125_Q238_R0.5890.37
29_Q33_V0.5870.37
233_L242_V0.5840.37
38_E91_D0.5840.37
327_A340_L0.5780.36
72_V87_P0.5750.36
58_R62_D0.5720.36
14_P226_R0.5720.36
114_S130_Y0.5720.36
264_V333_M0.5700.35
194_H225_V0.5690.35
208_A260_D0.5680.35
211_A297_I0.5660.35
100_Q265_G0.5650.35
284_A314_D0.5650.35
324_P333_M0.5640.35
25_F34_A0.5640.35
211_A335_V0.5630.35
111_A315_K0.5630.35
132_G144_D0.5630.35
112_G231_D0.5620.35
84_W120_L0.5620.35
257_H319_K0.5610.35
83_T86_I0.5600.34
196_A202_N0.5600.34
50_A57_A0.5590.34
132_G238_R0.5590.34
117_T265_G0.5590.34
122_V300_H0.5590.34
42_T45_I0.5560.34
324_P327_A0.5560.34
240_E278_V0.5500.34
52_D59_E0.5490.34
12_V111_A0.5480.33
311_S317_I0.5480.33
82_L227_M0.5480.33
49_T56_A0.5470.33
105_V256_K0.5450.33
254_L297_I0.5450.33
311_S314_D0.5440.33
53_V217_E0.5430.33
39_L43_A0.5420.33
59_E62_D0.5370.32
138_V212_K0.5370.32
18_E31_L0.5360.32
31_L39_L0.5350.32
279_Q297_I0.5340.32
153_D335_V0.5340.32
105_V117_T0.5330.32
83_T123_N0.5330.32
120_L131_G0.5320.32
89_V274_V0.5320.32
22_D333_M0.5310.32
55_Q59_E0.5290.32
129_E205_M0.5280.32
111_A234_T0.5280.32
262_E266_N0.5270.32
46_G268_Y0.5270.32
13_G18_E0.5250.31
290_T335_V0.5240.31
51_A55_Q0.5240.31
97_V208_A0.5210.31
203_H267_L0.5210.31
144_D323_A0.5200.31
84_W100_Q0.5190.31
277_Q299_G0.5180.31
70_A73_L0.5180.31
32_A50_A0.5180.31
237_F250_R0.5150.31
258_L316_R0.5140.31
18_E35_N0.5140.31
84_W141_D0.5130.30
141_D280_S0.5120.30
145_T296_N0.5100.30
265_G307_Y0.5100.30
136_R225_V0.5080.30
13_G34_A0.5070.30
235_A277_Q0.5060.30
36_S43_A0.5050.30
87_P205_M0.5040.30
73_L114_S0.5030.30
116_V260_D0.5020.30
35_N117_T0.5020.30
141_D300_H0.5020.30
83_T90_D0.5020.30
249_D259_H0.5010.29
198_G235_A0.5000.29
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 0.8397 100 0.363 Contact Map
2i1qA 1 0.8776 100 0.373 Contact Map
1v5wA 5 0.691 100 0.397 Contact Map
1pznA 5 0.8746 100 0.399 Contact Map
3ldaA 1 0.8426 100 0.409 Contact Map
1n0wA 1 0.6064 100 0.551 Contact Map
4hyyA 4 0.7026 100 0.564 Contact Map
4b3bA 1 0.6531 100 0.598 Contact Map
2cvhA 1 0.6327 100 0.616 Contact Map
3cmuA 1 0.6385 100 0.618 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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