GREMLIN Database
VPS13_mid_rpt - Repeating coiled region of VPS13
PFAM: PF16910 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 235 (229)
Sequences: 1065 (750)
Seq/√Len: 49.6
META: 0.174

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
106_L159_L4.5751.00
84_D110_H3.8941.00
113_V152_V3.8501.00
76_H115_S3.6301.00
27_P31_N3.5981.00
191_L207_V3.1031.00
87_A109_G2.9771.00
156_D186_N2.9311.00
49_A52_E2.4171.00
15_S82_D2.4031.00
33_L210_H2.3851.00
87_A107_D2.3571.00
125_E128_S2.2551.00
17_K84_D2.2151.00
158_Q184_P2.2131.00
192_E206_K2.1811.00
94_E102_N2.1691.00
190_Q208_S2.1591.00
57_T60_G2.1411.00
207_V216_V2.1171.00
223_Y227_M1.9220.99
88_P107_D1.8130.99
48_E54_A1.8040.99
83_I113_V1.7660.99
12_Q79_L1.7620.99
94_E228_K1.7490.99
90_I126_I1.7450.99
10_A80_D1.7320.99
48_E51_T1.6870.98
22_E94_E1.6840.98
147_Y202_L1.6490.98
16_V135_S1.6240.98
206_K219_S1.6170.98
90_I113_V1.6080.98
58_L62_K1.6000.98
121_S124_K1.5950.98
147_Y150_F1.5740.97
16_V83_I1.5730.97
209_G230_L1.5650.97
65_T69_L1.5570.97
19_Q86_K1.5540.97
122_T125_E1.5410.97
166_E180_H1.5280.97
14_L64_Q1.5220.97
39_P43_A1.5190.97
43_A46_S1.5180.97
19_Q186_N1.5170.97
189_L209_G1.4920.96
200_P218_L1.4800.96
153_K188_D1.4700.96
25_Y32_S1.4690.96
160_L216_V1.4020.95
165_I168_W1.3960.95
202_L205_F1.3950.95
186_N226_L1.3870.95
22_E89_V1.3760.94
60_G90_I1.3690.94
29_F168_W1.3340.93
106_L178_E1.3300.93
94_E104_L1.3280.93
33_L155_T1.3190.93
76_H195_I1.3180.93
194_S202_L1.3130.93
73_L84_D1.3100.93
59_E111_L1.3090.93
124_K128_S1.2980.92
54_A64_Q1.2900.92
53_A81_L1.2900.92
47_I50_L1.2780.92
183_E212_P1.2770.92
194_S199_D1.2720.92
148_D154_L1.2670.91
183_E217_N1.2650.91
164_S167_D1.2370.90
104_L219_S1.2340.90
16_V208_S1.2250.90
73_L214_L1.2240.90
26_N96_S1.2170.90
162_G223_Y1.2140.89
14_L79_L1.2110.89
5_P11_D1.1990.89
30_V112_S1.1950.89
9_K15_S1.1900.89
157_L163_R1.1880.88
115_S195_I1.1610.87
2_E23_I1.1600.87
23_I68_G1.1500.87
11_D92_I1.1310.86
89_V223_Y1.1190.85
160_L222_K1.1130.85
211_L222_K1.1110.85
42_S105_V1.1090.85
26_N29_F1.1050.84
76_H204_K1.0850.83
150_F161_I1.0800.83
157_L185_I1.0790.83
137_E226_L1.0770.83
113_V230_L1.0740.83
104_L181_L1.0730.83
192_E216_V1.0670.82
111_L174_S1.0670.82
14_L177_S1.0620.82
3_T218_L1.0590.82
88_P108_L1.0570.82
92_I106_L1.0440.81
193_R203_P1.0410.81
57_T179_L1.0380.81
150_F160_L1.0370.80
183_E192_E1.0350.80
160_L177_S1.0280.80
129_K132_Q1.0230.80
22_E104_L1.0210.79
18_L168_W1.0190.79
47_I52_E1.0180.79
26_N182_L1.0150.79
33_L197_P1.0110.79
180_H222_K1.0060.78
208_S211_L0.9970.78
3_T12_Q0.9960.78
134_Y137_E0.9930.78
12_Q20_P0.9820.77
171_A174_S0.9760.76
146_M152_V0.9740.76
142_L149_K0.9740.76
38_K151_D0.9670.76
106_L217_N0.9630.75
92_I221_E0.9580.75
90_I223_Y0.9470.74
219_S222_K0.9470.74
25_Y158_Q0.9440.74
88_P109_G0.9430.74
15_S33_L0.9380.73
7_D40_P0.9330.73
113_V171_A0.9270.72
115_S147_Y0.9250.72
10_A36_F0.9190.72
105_V112_S0.9150.71
91_I226_L0.9140.71
146_M202_L0.9130.71
183_E215_H0.9120.71
54_A66_R0.9110.71
77_K115_S0.9100.71
91_I103_L0.9010.70
166_E225_A0.8900.69
205_F227_M0.8870.69
206_K218_L0.8860.69
71_Y91_I0.8850.69
89_V197_P0.8850.69
50_L53_A0.8830.69
18_L89_V0.8820.69
152_V174_S0.8810.69
34_L164_S0.8770.68
206_K220_D0.8750.68
137_E179_L0.8720.68
130_Q133_Q0.8700.68
95_S98_S0.8690.68
82_D114_T0.8680.67
160_L180_H0.8680.67
168_W203_P0.8650.67
9_K80_D0.8650.67
68_G172_L0.8610.67
149_K190_Q0.8600.67
12_Q25_Y0.8580.67
21_L32_S0.8580.67
92_I104_L0.8570.66
127_Q131_S0.8540.66
66_R70_E0.8470.66
182_L185_I0.8460.65
102_N218_L0.8450.65
36_F107_D0.8450.65
154_L158_Q0.8330.64
83_I184_P0.8310.64
64_Q68_G0.8290.64
135_S138_D0.8210.63
78_R195_I0.8200.63
125_E210_H0.8200.63
17_K153_K0.8150.63
48_E52_E0.8140.62
161_I226_L0.8070.62
56_A113_V0.8060.62
21_L156_D0.8050.62
34_L156_D0.8040.61
185_I219_S0.8030.61
111_L154_L0.7990.61
104_L161_I0.7960.61
149_K192_E0.7950.61
36_F43_A0.7940.60
30_V38_K0.7880.60
2_E5_P0.7850.60
75_E144_S0.7850.60
152_V167_D0.7840.59
73_L195_I0.7810.59
65_T162_G0.7810.59
80_D194_S0.7790.59
60_G64_Q0.7780.59
29_F105_V0.7730.58
77_K103_L0.7710.58
105_V108_L0.7680.58
78_R108_L0.7670.58
104_L229_L0.7670.58
68_G146_M0.7660.58
11_D88_P0.7650.58
147_Y206_K0.7630.57
72_A76_H0.7610.57
30_V79_L0.7570.57
15_S111_L0.7540.57
22_E204_K0.7530.56
68_G204_K0.7500.56
34_L113_V0.7480.56
101_S179_L0.7430.55
28_K32_S0.7430.55
54_A65_T0.7400.55
65_T87_A0.7380.55
33_L92_I0.7370.55
56_A106_L0.7360.55
59_E62_K0.7350.55
63_E163_R0.7310.54
99_K178_E0.7310.54
211_L214_L0.7250.54
92_I124_K0.7230.53
61_L187_L0.7220.53
121_S131_S0.7200.53
147_Y222_K0.7060.52
131_S136_E0.7040.51
124_K127_Q0.7010.51
192_E212_P0.6990.51
106_L190_Q0.6980.51
106_L211_L0.6970.51
128_S132_Q0.6960.51
83_I172_L0.6940.50
37_F187_L0.6930.50
120_K123_L0.6900.50
68_G71_Y0.6860.50
55_G62_K0.6860.50
150_F191_L0.6850.50
25_Y30_V0.6850.50
218_L223_Y0.6840.49
208_S218_L0.6780.49
14_L35_N0.6780.49
104_L200_P0.6770.49
59_E92_I0.6750.48
67_A214_L0.6730.48
96_S187_L0.6720.48
137_E140_E0.6700.48
170_S176_S0.6650.47
9_K14_L0.6640.47
91_I215_H0.6620.47
31_N229_L0.6590.47
108_L182_L0.6580.47
50_L59_E0.6570.47
126_I136_E0.6480.46
41_E55_G0.6470.46
92_I114_T0.6430.45
90_I103_L0.6420.45
91_I105_V0.6410.45
132_Q141_E0.6390.45
33_L93_P0.6380.45
183_E211_L0.6380.45
144_S191_L0.6350.44
6_L26_N0.6330.44
120_K124_K0.6330.44
145_L195_I0.6280.44
218_L226_L0.6270.44
158_Q180_H0.6220.43
84_D149_K0.6210.43
150_F167_D0.6200.43
20_P32_S0.6180.43
22_E214_L0.6160.43
173_S226_L0.6160.43
25_Y187_L0.6140.42
42_S113_V0.6120.42
23_I173_S0.6080.42
177_S181_L0.6070.42
135_S140_E0.6060.42
131_S176_S0.6050.41
159_L189_L0.5980.41
135_S177_S0.5960.41
59_E110_H0.5930.40
10_A26_N0.5880.40
112_S229_L0.5840.39
167_D181_L0.5840.39
36_F189_L0.5840.39
171_A180_H0.5810.39
91_I156_D0.5790.39
47_I103_L0.5750.38
18_L66_R0.5750.38
89_V168_W0.5730.38
75_E216_V0.5720.38
12_Q196_V0.5720.38
153_K163_R0.5710.38
127_Q130_Q0.5690.38
137_E176_S0.5690.38
21_L87_A0.5680.38
90_I104_L0.5670.38
28_K186_N0.5670.38
114_T176_S0.5660.38
46_S50_L0.5620.37
33_L196_V0.5590.37
104_L149_K0.5590.37
20_P37_F0.5580.37
84_D212_P0.5560.37
26_N194_S0.5550.37
30_V180_H0.5520.36
35_N100_S0.5490.36
103_L162_G0.5470.36
24_V99_K0.5430.35
145_L223_Y0.5420.35
87_A108_L0.5420.35
61_L99_K0.5420.35
3_T79_L0.5410.35
102_N124_K0.5400.35
126_I131_S0.5400.35
22_E26_N0.5400.35
73_L194_S0.5400.35
154_L182_L0.5370.35
220_D223_Y0.5350.35
11_D81_L0.5340.35
30_V53_A0.5340.35
7_D39_P0.5300.34
34_L178_E0.5270.34
152_V218_L0.5250.34
116_D218_L0.5240.34
170_S173_S0.5220.34
94_E180_H0.5210.33
6_L9_K0.5180.33
77_K195_I0.5150.33
102_N225_A0.5150.33
187_L214_L0.5150.33
24_V193_R0.5150.33
212_P216_V0.5140.33
60_G229_L0.5120.33
27_P87_A0.5110.33
115_S194_S0.5100.32
153_K214_L0.5100.32
53_A223_Y0.5080.32
123_L126_I0.5070.32
90_I112_S0.5070.32
13_R80_D0.5070.32
155_T194_S0.5060.32
65_T107_D0.5040.32
116_D119_D0.5040.32
26_N40_P0.5010.32
89_V105_V0.5000.32
63_E184_P0.5000.32
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  
2ymyA 2 0.1745 4.6 0.951 Contact Map
2fy7A 1 0.3404 4.4 0.952 Contact Map
1s16A 2 0.2298 3.1 0.955 Contact Map
3ayhA 1 0.5319 2.3 0.958 Contact Map
3lnuA 1 0.2128 2.3 0.958 Contact Map
4bjsA 3 0.1021 2.1 0.959 Contact Map
1knzA 2 0.4894 2 0.96 Contact Map
4g1gA 2 0.2553 1.9 0.96 Contact Map
4d2gD 1 0.0894 1.7 0.961 Contact Map
4e0tA 4 0.3617 1.6 0.961 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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