GREMLIN Database
CCDA - Cytochrome c-type biogenesis protein CcdA
UniProt: P45706 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 235 (206)
Sequences: 4952 (3151)
Seq/√Len: 219.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
65_V131_V5.2381.00
196_L200_K3.7891.00
100_G207_I3.3531.00
6_Y169_L3.2361.00
58_C127_F3.1491.00
10_F176_V3.0291.00
60_L175_A2.8831.00
104_L207_I2.8541.00
197_F200_K2.7891.00
197_F201_A2.7181.00
68_I168_M2.5941.00
100_G104_L2.3781.00
189_K192_R2.3611.00
101_F106_V2.3311.00
126_G129_G2.2931.00
97_I210_G2.2831.00
53_L183_F2.2421.00
11_G15_L2.2391.00
56_T182_S2.1931.00
7_F11_G2.1801.00
87_A91_I2.1751.00
87_A90_Q2.1691.00
97_I207_I2.0931.00
16_S170_Y2.0911.00
64_S171_V2.0861.00
93_A210_G2.0741.00
60_L179_L1.8971.00
99_F206_M1.8661.00
68_I171_V1.8501.00
57_L61_L1.8021.00
50_K54_F1.7881.00
72_Y164_V1.7681.00
203_G207_I1.7291.00
204_V208_V1.7151.00
71_G163_A1.6921.00
66_I135_M1.6791.00
75_S161_G1.6551.00
54_F127_F1.6431.00
86_D90_Q1.5891.00
84_Y87_A1.5501.00
200_K204_V1.5471.00
54_F57_L1.5261.00
9_T152_V1.5141.00
73_G76_F1.4661.00
194_N197_F1.4641.00
93_A214_F1.4451.00
105_G108_R1.4371.00
55_H130_S1.4321.00
75_S78_G1.4051.00
62_G131_V1.3921.00
57_L179_L1.3861.00
192_R195_Q1.3691.00
159_N162_S1.3671.00
94_L98_L1.3601.00
190_W194_N1.3561.00
107_F110_E1.3551.00
49_Q52_S1.3371.00
10_F172_L1.3301.00
64_S68_I1.3281.00
97_I214_F1.3151.00
64_S168_M1.2821.00
6_Y165_P1.2791.00
9_T166_Y1.2701.00
65_V135_M1.2661.00
61_L131_V1.2551.00
100_G203_G1.2551.00
58_C130_S1.2401.00
212_L217_W1.2321.00
153_I157_G1.2321.00
104_L203_G1.2271.00
12_A148_I1.2111.00
212_L215_F1.2071.00
16_S19_S1.2041.00
51_R55_H1.2001.00
198_I202_G1.1891.00
189_K194_N1.1881.00
51_R54_F1.1871.00
191_I194_N1.1831.00
19_S22_C1.1671.00
63_F66_I1.1501.00
58_C62_G1.1331.00
10_F169_L1.1261.00
56_T60_L1.1251.00
72_Y76_F1.1031.00
196_L199_M1.0961.00
90_Q94_L1.0921.00
117_R120_F1.0791.00
96_I213_L1.0761.00
49_Q187_K1.0751.00
71_G153_I1.0731.00
59_F137_F1.0631.00
190_W193_K1.0551.00
102_I107_F1.0531.00
135_M139_A1.0481.00
146_G149_L1.0441.00
99_F150_A1.0301.00
25_L28_A1.0251.00
164_V167_M1.0011.00
211_V215_F0.9941.00
217_W220_L0.9911.00
21_C144_C0.9901.00
20_P23_L0.9891.00
191_I195_Q0.9871.00
152_V166_Y0.9841.00
71_G167_M0.9791.00
194_N198_I0.9731.00
154_T157_G0.9711.00
165_P169_L0.9551.00
97_I101_F0.9401.00
161_G164_V0.9401.00
12_A147_P0.9341.00
97_I211_V0.9341.00
90_Q214_F0.9190.99
58_C131_V0.9160.99
193_K197_F0.9080.99
53_L57_L0.8900.99
98_L107_F0.8880.99
176_V180_L0.8850.99
48_L51_R0.8840.99
195_Q198_I0.8790.99
112_M115_E0.8740.99
116_R120_F0.8720.99
204_V207_I0.8720.99
56_T179_L0.8590.99
148_I152_V0.8560.99
70_L153_I0.8560.99
79_S82_R0.8540.99
181_L184_F0.8540.99
111_A115_E0.8510.99
71_G75_S0.8460.99
188_L192_R0.8450.99
53_L56_T0.8450.99
74_T157_G0.8420.99
153_I167_M0.8420.99
201_A204_V0.8380.99
131_V135_M0.8290.99
71_G78_G0.8270.99
104_L107_F0.8200.99
191_I198_I0.8160.99
208_V212_L0.8140.99
88_I92_G0.8130.99
68_I164_V0.8020.99
27_P31_S0.8000.98
62_G134_G0.7940.98
162_S166_Y0.7930.98
59_F130_S0.7880.98
195_Q199_M0.7830.98
82_R85_H0.7730.98
36_V55_H0.7720.98
89_R216_N0.7720.98
29_F33_I0.7720.98
116_R119_H0.7690.98
151_A154_T0.7680.98
53_L179_L0.7650.98
17_F29_F0.7630.98
108_R199_M0.7630.98
104_L204_V0.7620.98
120_F124_P0.7590.98
72_Y161_G0.7590.98
69_A72_Y0.7570.98
86_D89_R0.7570.98
71_G74_T0.7560.98
156_A167_M0.7520.98
94_L214_F0.7450.98
210_G214_F0.7400.98
74_T77_I0.7390.97
91_I111_A0.7320.97
141_W145_T0.7270.97
183_F186_T0.7260.97
19_S24_P0.7230.97
184_F188_L0.7220.97
61_L168_M0.7210.97
78_G81_F0.7190.97
70_L85_H0.7180.97
73_G77_I0.7170.97
19_S25_L0.7160.97
22_C145_T0.7150.97
188_L195_Q0.7130.97
174_F178_F0.7070.97
34_T181_L0.7060.97
36_V124_P0.7020.97
156_A163_A0.7020.97
171_V175_A0.6990.96
206_M210_G0.6980.96
55_H59_F0.6980.96
96_I206_M0.6960.96
59_F67_F0.6950.96
166_Y184_F0.6950.96
142_T146_G0.6940.96
101_F181_L0.6890.96
16_S148_I0.6890.96
101_F207_I0.6880.96
181_L190_W0.6870.96
106_V203_G0.6850.96
17_F142_T0.6830.96
77_I177_P0.6800.96
150_A154_T0.6770.96
150_A167_M0.6760.96
151_A156_A0.6750.96
92_G136_A0.6720.96
66_I138_A0.6720.96
164_V168_M0.6690.96
108_R111_A0.6690.96
56_T59_F0.6620.95
29_F145_T0.6610.95
75_S164_V0.6600.95
124_P129_G0.6590.95
26_Y181_L0.6580.95
132_L135_M0.6570.95
115_E118_I0.6550.95
179_L183_F0.6550.95
138_A174_F0.6520.95
110_E114_K0.6520.95
75_S157_G0.6480.95
77_I80_L0.6450.95
12_A15_L0.6400.94
184_F202_G0.6390.94
103_T202_G0.6360.94
23_L213_L0.6320.94
162_S165_P0.6290.94
72_Y75_S0.6260.94
63_F174_F0.6210.93
63_F67_F0.6190.93
61_L87_A0.6160.93
101_F105_G0.6100.93
17_F174_F0.6090.93
8_L12_A0.6080.93
110_E113_M0.6080.93
149_L163_A0.6080.93
60_L63_F0.6080.93
157_G167_M0.6060.93
128_L132_L0.6060.93
31_S202_G0.6060.93
123_K126_G0.6050.92
151_A155_L0.6050.92
190_W195_Q0.6020.92
14_F177_P0.6000.92
14_F176_V0.5920.92
212_L216_N0.5910.92
135_M138_A0.5870.91
52_S182_S0.5870.91
168_M172_L0.5870.91
75_S209_I0.5860.91
137_F143_P0.5850.91
33_I135_M0.5850.91
111_A114_K0.5820.91
58_C61_L0.5820.91
119_H122_H0.5810.91
214_F220_L0.5810.91
61_L65_V0.5780.91
108_R196_L0.5770.91
28_A93_A0.5770.91
55_H151_A0.5760.91
12_A146_G0.5750.90
145_T174_F0.5730.90
67_F149_L0.5720.90
55_H127_F0.5710.90
49_Q53_L0.5680.90
17_F206_M0.5640.90
129_G151_A0.5610.89
29_F178_F0.5580.89
91_I180_L0.5580.89
60_L172_L0.5560.89
17_F24_P0.5510.89
193_K196_L0.5500.88
8_L15_L0.5500.88
17_F177_P0.5500.88
28_A31_S0.5490.88
9_T156_A0.5470.88
17_F146_G0.5460.88
34_T206_M0.5460.88
122_H126_G0.5430.88
23_L29_F0.5410.88
81_F139_A0.5410.88
122_H128_L0.5400.88
114_K117_R0.5390.87
75_S160_P0.5390.87
64_S103_T0.5370.87
19_S133_I0.5370.87
23_L184_F0.5360.87
122_H132_L0.5350.87
134_G173_G0.5340.87
33_I55_H0.5330.87
60_L64_S0.5330.87
14_F17_F0.5330.87
127_F180_L0.5320.87
146_G150_A0.5230.86
96_I210_G0.5210.86
155_L163_A0.5210.86
102_I113_M0.5190.85
12_A67_F0.5180.85
34_T37_S0.5170.85
70_L74_T0.5170.85
70_L118_I0.5150.85
102_I112_M0.5140.85
124_P128_L0.5130.85
30_L185_I0.5120.85
182_S186_T0.5120.85
102_I106_V0.5120.85
74_T164_V0.5120.85
160_P206_M0.5100.84
78_G160_P0.5060.84
88_I138_A0.5040.84
9_T170_Y0.5040.84
52_S138_A0.5040.84
82_R170_Y0.5020.83
116_R165_P0.5020.83
141_W146_G0.5010.83
99_F151_A0.5000.83
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  
2jlnA 1 0.8128 9.5 0.951 Contact Map
3dh4A 3 0.4426 7.3 0.953 Contact Map
3l1lA 2 0.7149 7 0.954 Contact Map
3tx3A 2 0.2213 6.5 0.955 Contact Map
2wdqD 2 0.1745 5.7 0.956 Contact Map
2gfpA 2 0.8851 5.5 0.956 Contact Map
4xnjA 1 0.8851 4.5 0.958 Contact Map
4q65A 1 0.6213 4.5 0.958 Contact Map
4xp4A 1 0.9064 4.2 0.958 Contact Map
3v5uA 1 0.7915 3.6 0.96 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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