GREMLIN Database
YHBJ - UPF0042 nucleotide-binding protein YhbJ
UniProt: P0A894 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12146
Length: 284 (278)
Sequences: 2249 (1482)
Seq/√Len: 88.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
177_A244_A7.2311.00
203_K207_A5.6671.00
201_L259_E4.9441.00
198_M204_P4.6921.00
164_F258_A3.7221.00
221_Q224_S3.3671.00
198_M202_D3.2321.00
164_F265_F3.0991.00
2_V81_Q3.0761.00
181_F222_T3.0691.00
262_A274_S3.0101.00
89_R117_D2.8161.00
89_R120_S2.7141.00
91_T137_S2.7041.00
227_E264_Y2.6831.00
173_I180_V2.6541.00
227_E268_R2.5211.00
223_R264_Y2.5111.00
142_H191_W2.4771.00
190_H197_P2.3811.00
219_I257_I2.3771.00
210_D256_Y2.3221.00
219_I260_Q2.3201.00
88_D91_T2.3051.00
179_Y233_L2.2851.00
260_Q263_D2.2761.00
226_L261_L2.1111.00
214_E235_T2.0721.00
245_I261_L2.0371.00
209_L256_Y2.0201.00
260_Q264_Y2.0011.00
180_V244_A1.9941.00
259_E263_D1.9541.00
199_T251_K1.9531.00
221_Q228_L1.9351.00
9_R86_D1.9051.00
206_A256_Y1.9031.00
140_S143_E1.8601.00
18_L54_S1.8581.00
217_N221_Q1.8561.00
93_I113_E1.8171.00
29_V40_L1.8141.00
39_D42_R1.8081.00
132_L151_R1.7621.00
220_Y264_Y1.6841.00
147_M150_T1.6201.00
203_K206_A1.6191.00
70_A80_P1.6161.00
162_M243_V1.6061.00
183_V257_I1.5921.00
259_E274_S1.5851.00
6_V83_L1.5811.00
185_F218_F1.5751.00
3_L41_A1.5751.00
127_R133_I1.5741.00
179_Y241_L1.5581.00
17_A148_L1.5571.00
121_D124_E1.5471.00
71_M129_R1.5091.00
219_I264_Y1.5021.00
143_E146_E1.4931.00
258_A274_S1.4811.00
177_A180_V1.4781.00
162_M230_L1.4781.00
118_K121_D1.4660.99
218_F222_T1.4550.99
111_S114_S1.4460.99
223_R227_E1.4180.99
213_T217_N1.4120.99
2_V79_S1.4070.99
88_D138_E1.4070.99
111_S165_E1.4000.99
37_L53_V1.3940.99
86_D127_R1.3710.99
113_E117_D1.3630.99
215_V257_I1.3580.99
124_E128_S1.3430.99
4_M21_L1.3320.99
263_D266_R1.3220.99
141_V191_W1.2910.99
214_E232_M1.2830.99
42_R76_D1.2760.99
24_M148_L1.2720.99
216_H220_Y1.2410.98
169_F183_V1.2310.98
213_T216_H1.2310.98
118_K122_L1.2140.98
37_L55_I1.2070.98
206_A210_D1.2060.98
208_F212_H1.1980.98
74_L129_R1.1980.98
6_V21_L1.1910.98
183_V218_F1.1710.97
183_V245_I1.1590.97
190_H196_R1.1570.97
171_H251_K1.1570.97
38_P72_S1.1540.97
205_V251_K1.1490.97
222_T225_Y1.1460.97
6_V54_S1.1460.97
9_R120_S1.1440.97
16_V98_D1.1380.97
139_M147_M1.1370.97
96_Y99_T1.1340.97
251_K280_E1.1340.97
34_V62_E1.1320.97
206_A260_Q1.1310.97
210_D219_I1.1310.97
68_E71_M1.1210.97
18_L28_C1.1140.97
263_D267_S1.1130.97
163_V275_R1.1110.96
192_D208_F1.1070.96
168_G171_H1.1070.96
168_G278_T1.0920.96
71_M75_P1.0890.96
233_L278_T1.0760.96
187_P212_H1.0560.95
222_T245_I1.0410.95
198_M205_V1.0400.95
165_E244_A1.0360.95
227_E265_F1.0310.95
164_F261_L1.0180.94
147_M151_R1.0160.94
159_E271_N0.9980.94
217_N220_Y0.9940.94
190_H205_V0.9940.94
164_F272_V0.9900.93
140_S191_W0.9820.93
165_E242_T0.9810.93
83_L152_L0.9770.93
62_E115_A0.9770.93
179_Y229_W0.9720.93
34_V63_S0.9670.93
207_A211_R0.9670.93
210_D260_Q0.9670.93
17_A85_L0.9650.92
24_M153_L0.9630.92
193_P196_R0.9610.92
229_W238_R0.9600.92
221_Q225_Y0.9580.92
209_L238_R0.9490.92
86_D120_S0.9450.92
88_D137_S0.9400.91
132_L152_L0.9260.91
3_L78_F0.9240.91
144_L148_L0.9180.90
92_L96_Y0.9140.90
66_I126_L0.9100.90
190_H199_T0.9030.90
69_Q72_S0.9020.90
190_H215_V0.9020.90
71_M74_L0.8990.90
216_H260_Q0.8940.89
192_D196_R0.8930.89
162_M265_F0.8860.89
112_L115_A0.8770.88
68_E72_S0.8710.88
220_Y224_S0.8710.88
166_S276_H0.8670.88
93_I175_I0.8630.88
229_W233_L0.8570.87
97_S242_T0.8560.87
231_P241_L0.8560.87
88_D135_D0.8550.87
245_I257_I0.8490.87
164_F243_V0.8490.87
2_V50_S0.8470.87
4_M26_F0.8460.87
214_E217_N0.8420.86
219_I223_R0.8410.86
44_L51_A0.8270.85
72_S75_P0.8270.85
92_L116_I0.8240.85
15_S19_R0.8230.85
36_L40_L0.8160.84
233_L241_L0.8150.84
206_A263_D0.8120.84
106_S115_A0.8110.84
223_R261_L0.8100.84
245_I258_A0.8050.84
232_M235_T0.7990.83
5_I41_A0.7980.83
32_L53_V0.7970.83
222_T261_L0.7850.82
256_Y259_E0.7810.82
79_S159_E0.7800.82
72_S76_D0.7790.82
42_R46_D0.7780.82
201_L274_S0.7770.81
148_L152_L0.7750.81
145_A149_R0.7750.81
102_L161_T0.7750.81
26_F191_W0.7730.81
214_E226_L0.7680.81
12_S24_M0.7570.80
230_L270_K0.7530.79
190_H251_K0.7480.79
27_Y39_D0.7410.78
159_E234_E0.7390.78
206_A209_L0.7380.78
177_A242_T0.7360.78
257_I261_L0.7360.78
198_M251_K0.7310.77
251_K278_T0.7300.77
97_S236_N0.7280.77
34_V59_N0.7270.77
6_V40_L0.7260.77
98_D191_W0.7220.77
40_L51_A0.7190.76
27_Y87_A0.7170.76
225_Y237_N0.7170.76
12_S85_L0.7150.76
3_L80_P0.7150.76
231_P238_R0.7130.76
109_N115_A0.7120.76
63_S67_F0.7100.75
162_M270_K0.7060.75
81_Q131_D0.7060.75
66_I93_I0.7060.75
32_L56_D0.7050.75
248_T278_T0.7030.75
66_I73_N0.7020.74
190_H242_T0.7000.74
24_M96_Y0.7000.74
174_P244_A0.6980.74
204_P207_A0.6970.74
262_A266_R0.6940.74
18_L181_F0.6930.74
210_D215_V0.6920.73
74_L131_D0.6920.73
109_N118_K0.6880.73
59_N63_S0.6870.73
224_S228_L0.6860.73
89_R115_A0.6850.73
191_W196_R0.6850.73
84_F120_S0.6820.72
65_E68_E0.6810.72
26_F50_S0.6800.72
223_R268_R0.6790.72
126_L150_T0.6790.72
111_S275_R0.6780.72
67_F129_R0.6780.72
228_L232_M0.6770.72
114_S117_D0.6750.72
27_Y32_L0.6730.71
217_N228_L0.6720.71
129_R133_I0.6710.71
111_S115_A0.6670.71
93_I169_F0.6640.70
6_V275_R0.6640.70
106_S111_S0.6630.70
160_L241_L0.6610.70
225_Y238_R0.6610.70
202_D245_I0.6600.70
66_I70_A0.6600.70
266_R269_G0.6580.70
165_E177_A0.6540.69
219_I261_L0.6530.69
134_V147_M0.6520.69
181_F231_P0.6510.69
256_Y260_Q0.6480.68
6_V18_L0.6440.68
90_N94_R0.6430.68
102_L185_F0.6430.68
122_L125_P0.6410.68
31_N278_T0.6400.68
185_F233_L0.6390.67
9_R236_N0.6370.67
111_S163_V0.6320.67
209_L215_V0.6320.67
131_D151_R0.6300.66
48_E64_P0.6290.66
74_L80_P0.6270.66
83_L148_L0.6240.66
99_T115_A0.6240.66
176_D191_W0.6230.65
137_S196_R0.6230.65
149_R238_R0.6230.65
81_Q151_R0.6210.65
82_L126_L0.6200.65
218_F257_I0.6190.65
192_D197_P0.6190.65
70_A82_L0.6180.65
97_S240_Y0.6160.65
19_R96_Y0.6150.64
232_M265_F0.6140.64
36_L96_Y0.6140.64
56_D59_N0.6130.64
66_I71_M0.6120.64
40_L43_T0.6120.64
96_Y240_Y0.6100.64
27_Y187_P0.6100.64
3_L53_V0.6070.63
14_K40_L0.6050.63
3_L81_Q0.6040.63
14_K18_L0.6040.63
145_A231_P0.6030.63
218_F229_W0.5980.62
207_A210_D0.5940.62
32_L58_R0.5940.62
52_A105_L0.5920.62
64_P122_L0.5920.62
98_D231_P0.5920.62
64_P67_F0.5910.61
82_L129_R0.5910.61
82_L272_V0.5910.61
45_A78_F0.5910.61
4_M83_L0.5890.61
28_C98_D0.5880.61
86_D89_R0.5870.61
7_S56_D0.5870.61
40_L44_L0.5870.61
7_S34_V0.5830.60
10_S40_L0.5820.60
94_R179_Y0.5800.60
37_L105_L0.5800.60
154_G216_H0.5800.60
39_D53_V0.5790.60
258_A261_L0.5780.60
191_W240_Y0.5780.60
210_D216_H0.5760.59
48_E79_S0.5760.59
96_Y186_L0.5730.59
62_E73_N0.5730.59
38_P53_V0.5720.59
3_L51_A0.5720.59
97_S176_D0.5720.59
94_R130_A0.5710.59
29_V197_P0.5700.59
145_A237_N0.5700.59
136_T258_A0.5700.59
139_M143_E0.5680.58
30_D178_D0.5670.58
28_C106_S0.5650.58
201_L204_P0.5650.58
114_S275_R0.5640.58
103_H255_V0.5630.58
74_L79_S0.5620.58
14_K99_T0.5610.57
217_N232_M0.5610.57
21_L226_L0.5600.57
32_L40_L0.5600.57
116_I230_L0.5590.57
160_L234_E0.5590.57
37_L69_Q0.5560.57
216_H219_I0.5550.57
46_D180_V0.5510.56
181_F245_I0.5500.56
54_S278_T0.5490.56
165_E176_D0.5470.56
161_T273_Q0.5470.56
59_N191_W0.5470.56
67_F71_M0.5460.55
102_L145_A0.5460.55
41_A80_P0.5450.55
127_R237_N0.5440.55
168_G233_L0.5430.55
181_F241_L0.5430.55
97_S173_I0.5420.55
91_T251_K0.5390.54
92_L255_V0.5380.54
69_Q73_N0.5380.54
226_L243_V0.5380.54
227_E267_S0.5370.54
41_A160_L0.5360.54
99_T231_P0.5350.54
19_R85_L0.5340.54
98_D248_T0.5340.54
88_D175_I0.5310.53
204_P208_F0.5300.53
94_R245_I0.5300.53
81_Q152_L0.5300.53
36_L39_D0.5290.53
230_L237_N0.5290.53
94_R126_L0.5280.53
212_H215_V0.5270.53
54_S130_A0.5270.53
41_A78_F0.5270.53
40_L98_D0.5260.53
97_S142_H0.5250.53
112_L240_Y0.5250.53
4_M42_R0.5250.53
57_V105_L0.5250.53
20_A149_R0.5250.53
226_L244_A0.5240.52
181_F229_W0.5240.52
24_M149_R0.5220.52
20_A152_L0.5200.52
65_E263_D0.5200.52
224_S227_E0.5190.52
168_G176_D0.5190.52
14_K51_A0.5180.52
77_A80_P0.5180.52
35_V43_T0.5180.52
223_R226_L0.5170.51
57_V122_L0.5170.51
27_Y34_V0.5160.51
29_V32_L0.5150.51
69_Q78_F0.5150.51
3_L94_R0.5140.51
12_S163_V0.5140.51
7_S238_R0.5130.51
7_S258_A0.5120.51
215_V256_Y0.5120.51
82_L143_E0.5120.51
44_L251_K0.5110.51
16_V141_V0.5110.51
2_V54_S0.5080.50
206_A259_E0.5050.50
51_A78_F0.5040.50
53_V174_P0.5040.50
91_T94_R0.5030.50
221_Q229_W0.5020.49
226_L230_L0.5010.49
34_V176_D0.5010.49
83_L243_V0.5000.49
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  
3nwjA 2 0.4965 99.7 0.852 Contact Map
3lw7A 2 0.493 99.7 0.859 Contact Map
2if2A 1 0.5246 99.6 0.863 Contact Map
1knqA 2 0.4965 99.6 0.869 Contact Map
3kb2A 2 0.5387 99.6 0.87 Contact Map
3trfA 2 0.5176 99.5 0.874 Contact Map
3vaaA 1 0.5282 99.5 0.874 Contact Map
2grjA 2 0.4824 99.5 0.876 Contact Map
2pezA 2 0.5106 99.5 0.876 Contact Map
1ckeA 1 0.5141 99.5 0.876 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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