GREMLIN Database
MCR_D - Methyl-coenzyme M reductase operon protein D
PFAM: PF02505 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 142 (140)
Sequences: 582 (267)
Seq/√Len: 22.5
META: 0.888

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
94_E101_F6.6081.00
83_E105_E4.2591.00
21_E95_E3.3121.00
3_E75_R3.1701.00
90_R94_E2.7520.99
61_K64_G2.6660.99
18_L76_I2.5470.98
15_T36_P2.2600.97
104_Q108_F2.1940.96
26_E116_T2.0720.94
123_P126_A2.0090.93
87_E90_R1.9470.92
25_I92_A1.9040.91
126_A129_R1.7950.89
34_N75_R1.7930.89
15_T33_I1.7270.87
88_E91_A1.7140.86
4_I78_L1.7060.86
62_V95_E1.6870.85
34_N71_V1.6670.85
69_L73_V1.6560.84
3_E34_N1.6060.82
37_R70_Q1.6010.82
48_K55_P1.5640.81
13_E68_E1.5570.80
19_L62_V1.5550.80
23_Y31_I1.5520.80
59_V68_E1.5220.79
92_A96_V1.5030.78
6_P10_L1.4810.77
16_E20_N1.4710.76
27_G85_V1.4660.76
42_V45_G1.4660.76
54_H58_K1.4530.75
54_H57_R1.4460.75
42_V46_P1.4370.75
41_T51_P1.3560.70
136_P139_K1.3360.69
64_G67_V1.3290.68
118_Y127_D1.2910.66
61_K66_E1.2780.65
18_L32_V1.2670.65
3_E77_L1.2620.64
7_E100_G1.2550.64
22_L28_I1.2070.61
56_D133_L1.1790.59
112_K115_V1.1730.59
113_P123_P1.1710.58
94_E98_P1.1610.58
45_G49_G1.1610.58
18_L97_L1.1270.55
132_G135_D1.0940.53
107_R111_T1.0740.52
129_R138_A1.0630.51
36_P43_P1.0620.51
116_T126_A1.0510.50
22_L25_I1.0500.50
15_T73_V1.0480.50
3_E104_Q1.0400.49
89_I107_R1.0380.49
17_K85_V1.0370.49
1_Q119_A1.0260.49
119_A126_A1.0190.48
10_L19_L1.0170.48
43_P48_K1.0130.48
3_E109_M1.0120.48
80_L97_L1.0030.47
56_D72_K0.9810.45
78_L89_I0.9810.45
1_Q27_G0.9800.45
44_Y47_A0.9790.45
56_D128_K0.9720.45
68_E107_R0.9700.45
32_V36_P0.9630.44
67_V89_I0.9560.44
111_T139_K0.9460.43
29_R107_R0.9430.43
14_T19_L0.9270.42
127_D136_P0.9020.40
18_L53_P0.8980.40
2_I82_D0.8880.39
4_I8_R0.8870.39
58_K113_P0.8820.39
59_V66_E0.8780.39
24_E116_T0.8780.39
45_G48_K0.8680.38
1_Q12_P0.8670.38
9_L130_L0.8660.38
27_G81_E0.8630.38
11_N67_V0.8630.38
5_F102_E0.8620.38
111_T127_D0.8600.37
16_E77_L0.8560.37
78_L88_E0.8550.37
26_E76_I0.8540.37
1_Q7_E0.8520.37
77_L110_K0.8410.36
6_P18_L0.8380.36
16_E58_K0.8370.36
84_E88_E0.8330.36
36_P99_F0.8290.35
12_P36_P0.8230.35
80_L131_L0.8220.35
76_I133_L0.8200.35
70_Q134_V0.8200.35
22_L55_P0.8140.34
96_V116_T0.8120.34
10_L14_T0.8080.34
41_T46_P0.8070.34
36_P78_L0.7940.33
80_L140_S0.7920.33
6_P115_V0.7920.33
115_V131_L0.7770.32
53_P80_L0.7710.32
24_E63_G0.7640.31
117_D120_K0.7620.31
44_Y48_K0.7620.31
34_N98_P0.7460.30
72_K89_I0.7350.30
32_V51_P0.7350.30
119_A123_P0.7320.30
68_E108_F0.7270.29
28_I128_K0.7250.29
15_T38_L0.7240.29
40_A67_V0.7230.29
68_E130_L0.7190.29
32_V133_L0.7190.29
17_K84_E0.7190.29
115_V140_S0.7170.29
37_R93_C0.7130.28
112_K128_K0.7110.28
38_L138_A0.7100.28
7_E102_E0.7090.28
77_L104_Q0.7050.28
80_L92_A0.7010.28
34_N72_K0.6930.27
5_F97_L0.6910.27
91_A95_E0.6840.27
57_R60_I0.6830.27
51_P61_K0.6800.27
33_I52_N0.6790.27
134_V139_K0.6700.26
11_N72_K0.6690.26
37_R55_P0.6680.26
4_I45_G0.6630.26
1_Q126_A0.6590.26
1_Q137_K0.6570.25
37_R76_I0.6570.25
47_A108_F0.6510.25
42_V47_A0.6480.25
26_E87_E0.6470.25
32_V77_L0.6420.25
71_V89_I0.6380.24
119_A137_K0.6370.24
28_I85_V0.6360.24
18_L38_L0.6340.24
29_R66_E0.6340.24
68_E78_L0.6300.24
32_V47_A0.6300.24
6_P76_I0.6290.24
2_I26_E0.6260.24
36_P85_V0.6210.24
87_E92_A0.6200.24
103_I138_A0.6130.23
40_A77_L0.6090.23
124_D128_K0.6090.23
6_P116_T0.6080.23
40_A65_Q0.6070.23
6_P71_V0.6050.23
10_L25_I0.6020.23
4_I18_L0.5980.22
42_V52_N0.5960.22
48_K109_M0.5930.22
40_A95_E0.5910.22
23_Y62_V0.5880.22
20_N67_V0.5860.22
20_N103_I0.5850.22
3_E29_R0.5820.22
23_Y47_A0.5790.22
20_N108_F0.5760.21
113_P126_A0.5740.21
81_E130_L0.5720.21
79_E109_M0.5710.21
78_L83_E0.5670.21
21_E28_I0.5630.21
45_G52_N0.5550.20
73_V118_Y0.5490.20
54_H60_I0.5470.20
33_I65_Q0.5470.20
21_E96_V0.5470.20
22_L31_I0.5470.20
36_P58_K0.5450.20
91_A94_E0.5450.20
34_N109_M0.5440.20
17_K78_L0.5430.20
21_E24_E0.5430.20
81_E128_K0.5410.20
107_R133_L0.5390.20
84_E91_A0.5270.19
100_G109_M0.5250.19
83_E100_G0.5200.19
12_P15_T0.5160.19
34_N119_A0.5160.19
39_P42_V0.5160.19
103_I108_F0.5130.19
33_I51_P0.5130.19
90_R105_E0.5110.19
20_N33_I0.5090.19
19_L133_L0.5070.18
6_P64_G0.5000.18
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  
1vw4K 1 0.8803 32.5 0.947 Contact Map
5c1zA 2 0.5 27.1 0.949 Contact Map
1uelA 1 0.5 24 0.95 Contact Map
1oqyA 1 0.5211 17.9 0.953 Contact Map
4k95A 4 0.4577 17.3 0.954 Contact Map
2kjrA 1 0.5634 15.5 0.954 Contact Map
3bboO 1 0.4789 15.5 0.954 Contact Map
2mrpA 1 0.5 15 0.955 Contact Map
2kdbA 1 0.4648 14 0.955 Contact Map
2kanA 1 0.6268 14 0.955 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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