GREMLIN Database
Q9HRJ9 - Cytochrome c oxidase subunit II
UniProt: Q9HRJ9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 255 (210)
Sequences: 5850 (3092)
Seq/√Len: 213.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
237_D240_T4.0741.00
238_R242_D3.8611.00
165_V236_V3.7741.00
176_T196_A3.5911.00
170_T238_R3.4911.00
129_V164_L3.3841.00
134_V139_N3.1011.00
168_A235_V3.0911.00
208_D235_V2.9361.00
166_L208_D2.8451.00
211_E237_D2.6991.00
168_A211_E2.6121.00
132_E177_E2.4631.00
163_P234_H2.3261.00
174_I206_T2.2991.00
130_T141_D2.2111.00
45_L97_V2.1371.00
128_T173_T2.0551.00
193_K220_E2.0431.00
126_S170_T1.9951.00
236_V240_T1.9741.00
211_E235_V1.9501.00
218_C222_C1.9421.00
130_T175_Q1.9001.00
134_V179_N1.8961.00
176_T194_M1.8751.00
145_S241_Y1.8641.00
168_A238_R1.8391.00
171_E207_N1.8221.00
186_H219_A1.7961.00
184_A219_A1.7941.00
184_A193_K1.7871.00
213_T234_H1.7831.00
166_L233_I1.7591.00
213_T232_K1.7091.00
133_G196_A1.7091.00
132_E141_D1.6931.00
240_T243_A1.6841.00
128_T175_Q1.6561.00
127_A241_Y1.6541.00
43_S47_A1.6471.00
195_D220_E1.6441.00
36_E209_L1.5861.00
173_T203_H1.5591.00
216_L231_S1.5581.00
165_V234_H1.5171.00
147_V245_I1.5041.00
131_V174_I1.4901.00
33_A207_N1.4901.00
160_G232_K1.4751.00
172_V208_D1.4651.00
175_Q201_Q1.4541.00
190_L233_I1.4471.00
134_V137_Y1.4391.00
37_L40_N1.4171.00
163_P232_K1.3971.00
184_A220_E1.3911.00
109_Y112_S1.3871.00
191_G206_T1.3841.00
126_S171_E1.3811.00
194_M204_L1.3661.00
190_L208_D1.3591.00
183_H218_C1.3581.00
81_R85_T1.3231.00
187_A233_I1.3191.00
222_C226_H1.3131.00
140_Y164_L1.3011.00
140_Y231_S1.2661.00
211_E240_T1.2601.00
163_P213_T1.2561.00
183_H222_C1.2441.00
88_V92_V1.2361.00
130_T177_E1.2141.00
129_V166_L1.2071.00
215_Q232_K1.2061.00
30_Y35_E1.1981.00
31_Q210_D1.1831.00
218_C226_H1.1811.00
166_L206_T1.1561.00
193_K219_A1.1481.00
58_G62_Y1.1331.00
61_V65_W1.1211.00
99_V103_S1.1191.00
217_Y230_L1.1151.00
129_V174_I1.1101.00
168_A237_D1.1091.00
174_I204_L1.0961.00
123_N126_S1.0781.00
53_T57_E1.0711.00
31_Q189_E1.0691.00
33_A209_L1.0671.00
23_P26_A1.0641.00
62_Y66_K1.0501.00
92_V96_F1.0481.00
218_C229_M1.0451.00
31_Q214_Y1.0401.00
36_E40_N1.0401.00
44_Q48_A1.0181.00
215_Q230_L1.0171.00
242_D246_N1.0141.00
175_Q203_H1.0111.00
169_D209_L1.0051.00
82_L86_W0.9991.00
37_L104_A0.9851.00
214_Y235_V0.9811.00
50_I54_L0.9771.00
131_V140_Y0.9701.00
86_W90_T0.9671.00
44_Q96_F0.9611.00
35_E39_R0.9551.00
166_L235_V0.9521.00
243_A246_N0.9521.00
139_N148_S0.9511.00
44_Q51_T0.9481.00
194_M202_N0.9451.00
83_E86_W0.9410.99
135_Q181_V0.9390.99
166_L172_V0.9340.99
39_R43_S0.9330.99
187_A190_L0.9120.99
135_Q180_D0.9060.99
32_S190_L0.8990.99
40_N44_Q0.8960.99
79_N83_E0.8930.99
243_A247_D0.8920.99
208_D211_E0.8880.99
160_G163_P0.8830.99
52_I56_V0.8790.99
84_I88_V0.8780.99
225_G228_K0.8770.99
226_H229_M0.8720.99
169_D238_R0.8600.99
83_E87_T0.8500.99
164_L174_I0.8480.99
222_C229_M0.8460.99
197_L200_Q0.8400.99
128_T144_G0.8360.99
25_A28_S0.8330.99
185_F233_I0.8300.99
137_Y161_N0.8290.99
140_Y185_F0.8270.99
26_A30_Y0.8240.99
103_S110_L0.8240.99
192_L204_L0.8230.99
211_E236_V0.8220.99
142_Y241_Y0.8200.99
21_V24_A0.8140.99
211_E214_Y0.8130.99
182_I197_L0.8020.98
167_P172_V0.7870.98
123_N205_V0.7840.98
178_S182_I0.7820.98
57_E61_V0.7810.98
27_S30_Y0.7740.98
136_W181_V0.7700.98
145_S245_I0.7680.98
43_S46_V0.7580.98
129_V142_Y0.7570.98
180_D183_H0.7530.98
28_S31_Q0.7520.98
190_L235_V0.7510.98
35_E38_I0.7510.98
122_A205_V0.7490.97
131_V176_T0.7490.97
162_Q248_P0.7460.97
47_A51_T0.7440.97
195_D219_A0.7400.97
41_L45_L0.7330.97
95_L99_V0.7310.97
33_A37_L0.7290.97
28_S32_S0.7280.97
177_E201_Q0.7270.97
183_H226_H0.7270.97
93_V96_F0.7210.97
239_D243_A0.7180.97
57_E60_L0.7170.97
142_Y164_L0.7050.96
145_S149_M0.7050.96
83_E90_T0.7020.96
80_R84_I0.6980.96
140_Y216_L0.6930.96
22_D25_A0.6890.96
164_L233_I0.6840.96
28_S189_E0.6800.96
36_E39_R0.6790.96
123_N171_E0.6770.95
55_L59_I0.6740.95
31_Q35_E0.6700.95
42_N46_V0.6700.95
135_Q221_F0.6690.95
159_V163_P0.6680.95
171_E205_V0.6680.95
34_T38_I0.6610.95
44_Q103_S0.6600.95
241_Y245_I0.6590.95
127_A170_T0.6580.95
181_V222_C0.6580.95
208_D233_I0.6560.95
40_N43_S0.6550.95
174_I185_F0.6490.94
172_V206_T0.6480.94
186_H193_K0.6450.94
187_A214_Y0.6420.94
216_L233_I0.6410.94
125_D128_T0.6400.94
186_H192_L0.6380.94
47_A50_I0.6360.94
73_A76_T0.6350.94
176_T204_L0.6330.94
131_V185_F0.6320.93
24_A29_G0.6300.93
91_A94_L0.6280.93
21_V25_A0.6270.93
122_A171_E0.6260.93
29_G39_R0.6200.93
21_V26_A0.6200.93
168_A209_L0.6150.93
155_N159_V0.6130.92
133_G137_Y0.6120.92
98_G102_Y0.6120.92
173_T205_V0.6110.92
27_S39_R0.6110.92
48_A97_V0.6100.92
39_R191_G0.6100.92
127_A172_V0.6090.92
126_S238_R0.6090.92
94_L100_S0.6090.92
180_D218_C0.6040.92
44_Q100_S0.6030.92
133_G178_S0.6020.92
128_T131_V0.6010.92
41_L104_A0.6010.92
168_A208_D0.5990.92
186_H217_Y0.5980.91
90_T248_P0.5970.91
98_G101_A0.5960.91
125_D170_T0.5960.91
32_S36_E0.5960.91
77_K82_L0.5950.91
33_A36_E0.5940.91
178_S196_A0.5910.91
132_E179_N0.5900.91
168_A210_D0.5900.91
217_Y221_F0.5870.91
76_T90_T0.5860.91
180_D198_P0.5810.90
30_Y34_T0.5780.90
130_T143_A0.5780.90
85_T89_A0.5770.90
49_A53_T0.5770.90
76_T79_N0.5770.90
50_I57_E0.5760.90
191_G216_L0.5730.90
181_V220_E0.5730.90
59_I84_I0.5720.90
182_I198_P0.5720.90
82_L90_T0.5710.89
137_Y225_G0.5700.89
35_E191_G0.5670.89
232_K235_V0.5660.89
133_G185_F0.5650.89
80_R85_T0.5610.89
132_E139_N0.5580.88
26_A29_G0.5570.88
72_E75_P0.5570.88
30_Y39_R0.5570.88
156_D160_G0.5550.88
84_I87_T0.5530.88
244_Y248_P0.5530.88
32_S35_E0.5520.88
169_D235_V0.5510.88
44_Q91_A0.5510.88
186_H204_L0.5490.88
42_N45_L0.5480.88
61_V64_V0.5470.87
81_R84_I0.5450.87
32_S206_T0.5440.87
62_Y127_A0.5430.87
66_K71_D0.5420.87
49_A59_I0.5410.87
138_W196_A0.5410.87
129_V145_S0.5390.87
34_T37_L0.5390.87
141_D148_S0.5370.86
50_I53_T0.5360.86
94_L98_G0.5330.86
70_A73_A0.5330.86
136_W221_F0.5320.86
146_N149_M0.5320.86
170_T242_D0.5300.86
220_E226_H0.5300.86
183_H220_E0.5290.86
90_T101_A0.5240.85
125_D171_E0.5230.85
83_E98_G0.5230.85
192_L206_T0.5200.85
24_A27_S0.5200.85
101_A104_A0.5200.85
63_T66_K0.5190.85
112_S194_M0.5180.84
219_A226_H0.5180.84
239_D242_D0.5170.84
158_V245_I0.5170.84
185_F192_L0.5170.84
169_D207_N0.5140.84
158_V217_Y0.5120.84
32_S192_L0.5090.83
89_A92_V0.5090.83
124_E169_D0.5080.83
137_Y140_Y0.5080.83
49_A97_V0.5040.83
139_N179_N0.5020.83
204_L207_N0.5000.82
52_I101_A0.5000.82
140_Y161_N0.5000.82
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  
3hb3B 1 0.902 100 0.141 Contact Map
2gsmB 1 0.8902 100 0.167 Contact Map
1fftB 1 0.8392 100 0.171 Contact Map
1v54B 1 0.851 100 0.199 Contact Map
2yevB 1 0.8314 100 0.203 Contact Map
4txvB 1 0.5412 100 0.378 Contact Map
1cyxA 1 0.4706 100 0.421 Contact Map
3s8fB 1 0.6118 100 0.494 Contact Map
2cuaA 1 0.502 100 0.651 Contact Map
3sbqA 2 0.7608 99.9 0.679 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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