GREMLIN Database
TF2B3 - Transcription initiation factor IIB 3
UniProt: Q9HHK5 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 317 (280)
Sequences: 1053 (675)
Seq/√Len: 40.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
236_A275_I6.3791.00
25_C45_C4.0011.00
242_S284_E3.9361.00
142_A181_L3.8891.00
42_C45_C3.8061.00
305_R308_E3.7041.00
248_K282_C3.5481.00
134_A159_Y3.1781.00
288_Q303_R3.1751.00
25_C28_C3.0331.00
33_V40_R2.9271.00
142_A152_R2.8511.00
141_M181_L2.7621.00
137_E140_R2.7361.00
28_C42_C2.7081.00
33_V49_L2.6851.00
135_L156_S2.4721.00
289_R299_E2.4681.00
25_C42_C2.4221.00
181_L197_V2.4091.00
299_E307_Q2.2341.00
59_E63_F2.2081.00
141_M200_V2.1740.99
155_A184_A2.1670.99
61_R73_R2.0480.99
272_A295_A2.0310.99
205_Q209_G2.0010.99
249_A271_A1.9560.99
59_E73_R1.9200.99
32_N44_D1.8700.98
248_K251_E1.8640.98
170_G267_P1.8480.98
249_A278_A1.8340.98
28_C45_C1.8120.98
216_A223_I1.7960.98
83_H86_G1.7920.98
147_V181_L1.7820.98
252_I278_A1.7630.97
192_R196_E1.7440.97
25_C29_N1.7360.97
62_A65_S1.6990.97
60_W63_F1.6880.97
151_V184_A1.6760.97
197_V200_V1.6620.96
235_F239_L1.6620.96
245_V284_E1.6610.96
159_Y168_I1.6480.96
183_A221_L1.6010.96
154_V187_Q1.5780.95
289_R302_I1.5200.94
235_F275_I1.5180.94
57_G60_W1.4920.93
36_D179_A1.4890.93
32_N43_E1.4890.93
186_R209_G1.4860.93
134_A210_R1.4790.93
60_W73_R1.4470.92
35_T40_R1.4320.92
111_M114_L1.4210.92
269_G301_T1.4100.91
273_A301_T1.4070.91
253_I270_F1.4060.91
161_R165_E1.4010.91
157_V160_R1.3930.91
252_I274_A1.3920.91
134_A163_L1.3800.90
288_Q300_V1.3770.90
42_C46_G1.3710.90
274_A278_A1.3690.90
227_D230_E1.3610.90
62_A67_E1.3600.90
253_I274_A1.3490.89
54_I59_E1.3220.88
255_T259_Q1.3000.88
110_Q114_L1.2970.87
279_S294_V1.2700.86
196_E234_R1.2560.86
44_D142_A1.2560.86
47_L87_L1.2450.85
241_L286_K1.2430.85
245_V282_C1.2430.85
54_I60_W1.2360.85
217_Q290_E1.2320.85
27_E30_S1.2280.84
229_K254_D1.2270.84
30_S44_D1.2230.84
27_E47_L1.2190.84
132_Q136_S1.2190.84
159_Y173_I1.1990.83
154_V188_E1.1860.82
40_R252_I1.1830.82
131_L156_S1.1830.82
112_N116_K1.1780.82
287_T290_E1.1700.81
209_G235_F1.1660.81
183_A279_S1.1550.81
286_K290_E1.1530.80
297_V302_I1.1470.80
269_G273_A1.1440.80
64_N67_E1.1420.80
41_V294_V1.1280.79
229_K257_A1.1270.79
227_D253_I1.1170.78
88_T179_A1.1120.78
272_A302_I1.1080.78
154_V157_V1.0970.77
286_K299_E1.0920.77
183_A186_R1.0920.77
26_P49_L1.0910.77
25_C30_S1.0900.77
197_V260_G1.0810.76
178_T185_C1.0760.76
194_L209_G1.0750.75
194_L205_Q1.0730.75
300_V303_R1.0670.75
260_G265_K1.0660.75
176_V215_V1.0660.75
60_W77_P1.0620.75
246_I250_R1.0600.74
285_K290_E1.0600.74
292_A295_A1.0490.74
272_A277_A1.0450.73
156_S163_L1.0360.73
35_T38_S1.0330.73
59_E71_K1.0280.72
83_H303_R1.0260.72
79_T269_G1.0180.71
275_I295_A1.0140.71
244_E282_C1.0080.71
151_V190_I1.0040.70
120_R171_R1.0030.70
232_L253_I1.0030.70
192_R234_R1.0030.70
94_K128_E0.9960.70
138_I144_A0.9800.68
206_K307_Q0.9770.68
227_D257_A0.9760.68
151_V257_A0.9760.68
239_L275_I0.9720.68
48_V180_C0.9720.68
145_L258_E0.9720.68
182_Y226_T0.9680.68
44_D148_P0.9680.68
34_I43_E0.9650.67
77_P84_D0.9630.67
77_P83_H0.9600.67
164_K289_R0.9550.66
193_T196_E0.9540.66
24_Q43_E0.9540.66
117_W159_Y0.9530.66
134_A138_I0.9520.66
142_A270_F0.9500.66
253_I271_A0.9430.65
169_R299_E0.9400.65
134_A273_A0.9400.65
138_I177_A0.9380.65
137_E210_R0.9310.64
152_R181_L0.9270.64
113_R171_R0.9270.64
248_K281_L0.9110.63
90_Q118_Q0.9060.62
269_G305_R0.9050.62
119_E132_Q0.9050.62
254_D258_E0.9000.62
138_I156_S0.8970.62
231_Y236_A0.8960.61
172_S213_R0.8930.61
241_L245_V0.8930.61
128_E165_E0.8920.61
279_S285_K0.8910.61
92_D140_R0.8890.61
41_V307_Q0.8880.61
234_R266_S0.8880.61
176_V211_T0.8850.60
162_A221_L0.8840.60
41_V59_E0.8820.60
84_D87_L0.8820.60
170_G301_T0.8780.60
191_P230_E0.8770.60
193_T197_V0.8740.60
134_A302_I0.8720.59
160_R184_A0.8700.59
49_L266_S0.8670.59
197_V223_I0.8660.59
290_E294_V0.8650.59
34_I272_A0.8640.59
289_R297_V0.8620.58
35_T39_E0.8600.58
147_V185_C0.8530.58
145_L256_S0.8520.58
130_N183_A0.8520.58
35_T50_E0.8470.57
159_Y222_E0.8470.57
29_N34_I0.8450.57
207_E210_R0.8400.56
121_I186_R0.8370.56
204_D207_E0.8360.56
212_Y269_G0.8340.56
156_S160_R0.8340.56
182_Y185_C0.8310.56
138_I159_Y0.8260.55
209_G266_S0.8230.55
26_P45_C0.8210.55
279_S284_E0.8190.55
58_P62_A0.8180.54
155_A180_C0.8170.54
265_K285_K0.8160.54
79_T94_K0.8060.53
113_R117_W0.8060.53
26_P275_I0.8020.53
201_A306_Y0.8000.53
89_T192_R0.7990.53
55_D60_W0.7980.53
283_N287_T0.7980.53
73_R77_P0.7950.52
40_R43_E0.7920.52
97_D139_D0.7900.52
55_D59_E0.7790.51
134_A172_S0.7750.51
97_D111_M0.7710.50
265_K270_F0.7700.50
182_Y223_I0.7680.50
75_G160_R0.7590.49
181_L260_G0.7590.49
297_V301_T0.7500.48
261_L272_A0.7490.48
249_A253_I0.7490.48
86_G92_D0.7450.48
134_A171_R0.7440.48
252_I264_G0.7440.48
59_E239_L0.7420.47
29_N45_C0.7420.47
281_L306_Y0.7380.47
126_A308_E0.7370.47
97_D117_W0.7350.47
241_L264_G0.7330.47
133_F257_A0.7280.46
147_V179_A0.7260.46
37_Q295_A0.7240.46
198_T203_I0.7230.46
29_N224_Q0.7230.46
28_C31_A0.7230.46
79_T83_H0.7180.45
149_R153_E0.7170.45
212_Y215_V0.7140.45
215_V238_D0.7140.45
123_T138_I0.7140.45
161_R187_Q0.7130.45
243_E247_A0.7120.45
119_E204_D0.7110.45
137_E141_M0.7060.44
128_E152_R0.7040.44
201_A226_T0.7040.44
60_W71_K0.7040.44
165_E290_E0.7030.44
73_R89_T0.7020.44
129_R137_E0.7020.44
146_G183_A0.7020.44
119_E173_I0.6990.44
269_G297_V0.6980.43
156_S210_R0.6950.43
229_K296_N0.6900.43
34_I252_I0.6890.43
266_S302_I0.6880.43
120_R264_G0.6880.43
24_Q29_N0.6840.42
155_A261_L0.6840.42
134_A162_A0.6830.42
138_I155_A0.6820.42
252_I281_L0.6810.42
68_R76_A0.6810.42
159_Y305_R0.6790.42
155_A183_A0.6780.42
179_A232_L0.6710.41
158_I180_C0.6700.41
134_A173_I0.6690.41
208_I254_D0.6660.41
86_G156_S0.6650.40
271_A295_A0.6640.40
272_A276_Y0.6640.40
149_R222_E0.6610.40
159_Y212_Y0.6610.40
185_C253_I0.6540.40
38_S53_Q0.6540.40
49_L203_I0.6540.40
126_A214_Y0.6540.40
220_S272_A0.6530.39
51_D220_S0.6520.39
169_R270_F0.6500.39
289_R304_N0.6480.39
65_S70_Q0.6450.39
275_I296_N0.6450.39
270_F295_A0.6440.39
50_E56_H0.6390.38
209_G212_Y0.6360.38
84_D88_T0.6360.38
287_T299_E0.6350.38
95_D245_V0.6350.38
81_T138_I0.6320.38
153_E166_D0.6320.38
60_W89_T0.6300.37
162_A215_V0.6280.37
147_V311_E0.6210.37
177_A181_L0.6200.37
127_G240_E0.6170.36
62_A68_R0.6170.36
147_V158_I0.6170.36
130_N159_Y0.6170.36
24_Q258_E0.6160.36
35_T138_I0.6150.36
256_S262_L0.6150.36
85_K167_L0.6150.36
175_G179_A0.6130.36
77_P270_F0.6130.36
62_A70_Q0.6120.36
232_L304_N0.6120.36
224_Q236_A0.6080.36
150_S237_S0.6080.36
151_V188_E0.6070.35
33_V38_S0.6070.35
126_A179_A0.6060.35
63_F235_F0.6040.35
56_H206_K0.6000.35
261_L308_E0.6000.35
275_I291_V0.5990.35
215_V268_S0.5980.35
64_N193_T0.5970.35
153_E156_S0.5960.35
270_F292_A0.5960.35
225_P287_T0.5950.34
261_L279_S0.5950.34
92_D95_D0.5930.34
202_R272_A0.5930.34
35_T41_V0.5910.34
51_D56_H0.5880.34
240_E294_V0.5880.34
235_F265_K0.5850.34
135_L206_K0.5830.33
191_P274_A0.5830.33
141_M157_V0.5810.33
178_T201_A0.5790.33
174_E306_Y0.5780.33
79_T156_S0.5770.33
49_L207_E0.5760.33
172_S267_P0.5730.33
75_G89_T0.5710.32
74_V81_T0.5710.32
212_Y264_G0.5700.32
272_A292_A0.5700.32
46_G264_G0.5690.32
159_Y162_A0.5670.32
287_T292_A0.5660.32
141_M187_Q0.5660.32
118_Q142_A0.5650.32
86_G113_R0.5650.32
52_D201_A0.5650.32
165_E225_P0.5610.32
265_K278_A0.5610.32
83_H88_T0.5610.32
181_L246_I0.5610.32
70_Q73_R0.5590.32
180_C283_N0.5580.31
252_I307_Q0.5570.31
163_L197_V0.5560.31
138_I217_Q0.5560.31
70_Q262_L0.5550.31
185_C226_T0.5540.31
57_G76_A0.5530.31
214_Y252_I0.5530.31
162_A167_L0.5530.31
27_E44_D0.5520.31
94_K118_Q0.5520.31
128_E169_R0.5520.31
165_E168_I0.5520.31
277_A291_V0.5510.31
236_A239_L0.5510.31
115_R137_E0.5490.31
162_A228_P0.5490.31
74_V83_H0.5490.31
117_W158_I0.5470.31
160_R300_V0.5470.31
31_A215_V0.5450.30
37_Q253_I0.5440.30
245_V249_A0.5420.30
134_A142_A0.5420.30
294_V302_I0.5410.30
219_L301_T0.5360.30
131_L191_P0.5340.30
204_D208_I0.5310.29
78_T125_D0.5310.29
48_V190_I0.5290.29
76_A85_K0.5290.29
261_L310_I0.5280.29
207_E232_L0.5250.29
48_V174_E0.5250.29
276_Y280_L0.5250.29
182_Y212_Y0.5250.29
25_C33_V0.5240.29
199_E296_N0.5230.29
78_T302_I0.5190.28
110_Q135_L0.5180.28
145_L200_V0.5150.28
211_T302_I0.5140.28
245_V274_A0.5140.28
24_Q49_L0.5130.28
64_N205_Q0.5130.28
235_F294_V0.5110.28
215_V285_K0.5100.28
81_T160_R0.5090.28
72_S180_C0.5080.28
191_P253_I0.5080.28
109_N112_N0.5080.28
81_T156_S0.5070.28
52_D58_P0.5060.27
203_I238_D0.5060.27
173_I177_A0.5050.27
70_Q143_S0.5020.27
245_V264_G0.5000.27
161_R221_L0.5000.27
61_R71_K0.5000.27
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  
4bbrM 1 0.5899 100 0.265 Contact Map
1aisB 1 0.5931 100 0.584 Contact Map
1c9bA 1 0.6025 100 0.608 Contact Map
2pk2A 3 0.6814 99.9 0.708 Contact Map
2w96A 1 0.7161 99.9 0.718 Contact Map
4f6uB 1 0.7161 99.9 0.719 Contact Map
3g33B 2 0.6814 99.9 0.728 Contact Map
2i53A 1 0.7035 99.9 0.73 Contact Map
2b9rA 1 0.6877 99.9 0.73 Contact Map
4eojB 1 0.7003 99.9 0.732 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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