GREMLIN Database
RADB - DNA repair and recombination protein RadB
UniProt: Q9HPF2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 236 (208)
Sequences: 6958 (3650)
Seq/√Len: 253.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
43_A163_T3.9351.00
55_G114_D3.7691.00
47_A57_A3.5141.00
9_P16_D2.9451.00
47_A117_V2.9151.00
28_V150_L2.8821.00
224_T229_D2.7551.00
50_T115_L2.7061.00
6_T25_R2.5931.00
56_L114_D2.5791.00
103_V116_I2.5571.00
10_T23_V2.5461.00
23_V46_T2.5271.00
11_G16_D2.4421.00
153_A160_V2.3971.00
23_V159_A2.2441.00
199_R202_T2.2101.00
226_G229_D2.1931.00
43_A117_V2.1691.00
202_T220_Q2.0951.00
29_T159_A2.0671.00
49_T52_A2.0551.00
116_I160_V2.0281.00
102_A106_T2.0061.00
95_D127_L2.0021.00
58_V113_A1.9861.00
12_C230_A1.8841.00
71_Q75_E1.8481.00
168_T183_H1.7941.00
18_L219_A1.7851.00
56_L87_N1.7451.00
49_T53_A1.7301.00
25_R114_D1.7131.00
152_L158_L1.6841.00
23_V161_V1.6761.00
10_T16_D1.6711.00
69_R73_L1.6541.00
44_L74_L1.6271.00
222_Q229_D1.5871.00
193_L205_A1.5571.00
102_A105_D1.5571.00
187_H190_G1.5471.00
152_L156_H1.5331.00
115_L159_A1.5101.00
50_T55_G1.5031.00
55_G115_L1.5001.00
29_T191_T1.4691.00
50_T57_A1.4501.00
189_T192_V1.4371.00
48_V79_T1.4251.00
9_P53_A1.4171.00
46_T115_L1.4041.00
80_D87_N1.4001.00
43_A161_V1.3901.00
30_Q192_V1.3881.00
194_R208_E1.3721.00
210_H213_K1.3621.00
15_L42_V1.3551.00
108_D113_A1.3461.00
47_A59_Y1.3401.00
95_D98_E1.3301.00
151_S155_K1.3281.00
25_R55_G1.3171.00
14_A17_E1.3121.00
46_T161_V1.3081.00
186_A192_V1.2971.00
13_G230_A1.2891.00
63_E165_Q1.2821.00
190_G193_L1.2571.00
15_L19_L1.2461.00
56_L112_R1.2361.00
65_L68_A1.2301.00
116_I158_L1.2151.00
44_L70_F1.2001.00
100_A104_R1.1991.00
149_L160_V1.1981.00
104_R156_H1.1811.00
23_V29_T1.1691.00
47_A115_L1.1551.00
61_D70_F1.1461.00
56_L111_D1.1391.00
8_L159_A1.1311.00
115_L161_V1.1271.00
98_E101_Q1.1141.00
101_Q104_R1.1091.00
31_L193_L1.1071.00
182_G187_H1.0921.00
56_L89_I1.0851.00
100_A103_V1.0831.00
41_N223_I1.0801.00
73_L77_R1.0771.00
203_R217_E1.0721.00
34_P37_A1.0651.00
51_A57_A1.0621.00
93_A98_E1.0541.00
181_G185_L1.0541.00
7_H213_K1.0411.00
104_R108_D1.0371.00
126_R129_R1.0231.00
195_L205_A1.0161.00
31_L42_V1.0141.00
66_S71_Q1.0081.00
99_Q102_A1.0021.00
204_R218_H1.0011.00
148_H151_S1.0001.00
98_E102_A1.0001.00
118_V124_F0.9891.00
89_I93_A0.9861.00
14_A219_A0.9861.00
187_H192_V0.9851.00
146_I185_L0.9831.00
48_V52_A0.9821.00
131_G135_T0.9811.00
89_I106_T0.9761.00
99_Q124_F0.9751.00
184_T187_H0.9601.00
28_V160_V0.9521.00
104_R152_L0.9461.00
91_S102_A0.9451.00
32_Y194_R0.9401.00
19_L191_T0.9391.00
72_Q75_E0.9361.00
182_G192_V0.9271.00
198_F204_R0.9221.00
103_V152_L0.9131.00
118_V121_V0.9131.00
179_P182_G0.9041.00
126_R130_G0.8961.00
205_A221_F0.8941.00
69_R72_Q0.8891.00
100_A148_H0.8871.00
216_G219_A0.8821.00
96_F100_A0.8761.00
45_T49_T0.8731.00
12_C16_D0.8711.00
59_Y117_V0.8701.00
34_P194_R0.8681.00
180_L183_H0.8671.00
183_H187_H0.8671.00
181_G186_A0.8520.99
182_G186_A0.8470.99
182_G185_L0.8440.99
94_H98_E0.8430.99
8_L115_L0.8410.99
100_A152_L0.8350.99
28_V146_I0.8340.99
186_A190_G0.8220.99
190_G195_L0.8200.99
146_I162_V0.8180.99
190_G196_D0.8110.99
61_D92_D0.8000.99
179_P192_V0.7980.99
42_V228_I0.7950.99
195_L228_I0.7940.99
99_Q103_V0.7930.99
193_L196_D0.7920.99
153_A159_A0.7890.99
61_D65_L0.7860.99
164_N182_G0.7860.99
188_W192_V0.7840.99
105_D108_D0.7800.99
171_D179_P0.7800.99
103_V106_T0.7740.99
25_R157_D0.7730.99
34_P183_H0.7570.99
130_G140_R0.7560.99
100_A106_T0.7520.99
70_F73_L0.7510.99
135_T139_L0.7510.99
57_A115_L0.7500.99
12_C49_T0.7490.99
101_Q108_D0.7480.99
120_S163_T0.7460.99
107_A156_H0.7430.98
24_E210_H0.7390.98
189_T193_L0.7380.98
41_N77_R0.7310.98
73_L76_A0.7300.98
51_A88_V0.7270.98
73_L212_A0.7190.98
89_I95_D0.7190.98
104_R107_A0.7090.98
59_Y123_G0.7000.98
85_S88_V0.6970.98
183_H186_A0.6940.98
46_T50_T0.6930.98
181_G192_V0.6900.98
191_T210_H0.6860.97
20_G214_P0.6840.97
103_V107_A0.6840.97
105_D226_G0.6830.97
196_D206_T0.6810.97
40_T44_L0.6780.97
122_T180_L0.6760.97
78_A226_G0.6730.97
26_G157_D0.6720.97
13_G17_E0.6720.97
48_V80_D0.6700.97
96_F99_Q0.6680.97
26_G33_G0.6680.97
181_G184_T0.6660.97
24_E191_T0.6650.97
167_F180_L0.6650.97
118_V162_V0.6640.97
97_D100_A0.6640.97
186_A191_T0.6600.97
129_R140_R0.6580.97
14_A230_A0.6480.96
12_C221_F0.6450.96
184_T192_V0.6450.96
125_Y128_A0.6400.96
73_L78_A0.6400.96
222_Q225_D0.6370.96
61_D66_S0.6350.96
205_A209_K0.6310.96
89_I92_D0.6310.96
94_H97_D0.6300.96
62_T123_G0.6280.96
99_Q107_A0.6260.96
97_D106_T0.6250.96
90_V93_A0.6240.96
201_G206_T0.6240.96
31_L161_V0.6210.95
202_T222_Q0.6200.95
70_F88_V0.6200.95
63_E123_G0.6170.95
18_L205_A0.6160.95
25_R159_A0.6150.95
122_T164_N0.6140.95
97_D107_A0.6130.95
75_E79_T0.6130.95
18_L216_G0.6130.95
88_V92_D0.6120.95
121_V145_Q0.6080.95
7_H21_G0.6060.95
181_G187_H0.6060.95
150_L188_W0.5970.94
80_D86_A0.5900.94
46_T207_L0.5900.94
97_D101_Q0.5870.94
54_G114_D0.5870.94
88_V95_D0.5870.94
37_A204_R0.5860.94
13_G49_T0.5830.94
61_D69_R0.5830.94
115_L225_D0.5820.94
80_D85_S0.5800.94
6_T53_A0.5740.93
146_I188_W0.5730.93
204_R220_Q0.5730.93
15_L193_L0.5720.93
101_Q105_D0.5720.93
18_L207_L0.5710.93
100_A107_A0.5710.93
97_D126_R0.5670.93
191_T194_R0.5660.93
117_V163_T0.5660.93
68_A72_Q0.5660.93
101_Q107_A0.5640.93
64_G211_R0.5600.92
57_A117_V0.5590.92
93_A102_A0.5580.92
8_L25_R0.5580.92
7_H24_E0.5580.92
10_T15_L0.5560.92
96_F145_Q0.5550.92
150_L162_V0.5550.92
188_W193_L0.5550.92
72_Q225_D0.5530.92
194_R198_F0.5520.92
197_R206_T0.5520.92
131_G138_A0.5500.92
30_Q164_N0.5490.92
16_D49_T0.5480.91
103_V108_D0.5480.91
90_V94_H0.5480.91
193_L207_L0.5470.91
88_V93_A0.5470.91
201_G216_G0.5450.91
147_T151_S0.5450.91
99_Q104_R0.5440.91
188_W191_T0.5420.91
63_E128_A0.5420.91
144_D148_H0.5410.91
60_V103_V0.5400.91
46_T55_G0.5390.91
62_T124_F0.5390.91
61_D64_G0.5380.91
115_L148_H0.5370.91
34_P196_D0.5330.90
165_Q168_T0.5290.90
190_G197_R0.5290.90
75_E80_D0.5280.90
36_A203_R0.5270.90
214_P217_E0.5260.90
63_E121_V0.5260.90
118_V149_L0.5240.90
8_L29_T0.5230.90
135_T138_A0.5180.89
31_L228_I0.5170.89
93_A99_Q0.5150.89
43_A46_T0.5140.89
43_A47_A0.5140.89
64_G73_L0.5130.89
65_L90_V0.5120.89
54_G75_E0.5110.88
195_L207_L0.5080.88
18_L215_D0.5050.88
144_D147_T0.5030.88
166_V194_R0.5030.88
44_L73_L0.5010.87
12_C46_T0.5000.87
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 0.8898 100 0.332 Contact Map
2i1qA 1 0.9449 100 0.359 Contact Map
3ldaA 1 0.8856 100 0.361 Contact Map
1v5wA 5 0.9195 100 0.361 Contact Map
1n0wA 1 0.8517 100 0.363 Contact Map
1pznA 5 0.911 100 0.377 Contact Map
2cvhA 1 0.9195 100 0.4 Contact Map
4hyyA 4 0.9322 100 0.408 Contact Map
2dr3A 3 0.9025 100 0.445 Contact Map
4b3bA 1 0.8898 100 0.447 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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