GREMLIN Database
YPOP - Uncharacterized HTH-type transcriptional regulator YpoP
UniProt: P54182 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 141 (129)
Sequences: 22949 (17006)
Seq/√Len: 1497.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
83_I95_H3.1501.00
126_E136_K2.8551.00
85_S93_R2.7501.00
52_K91_I2.7311.00
50_P95_H2.6861.00
81_T95_H2.6521.00
123_T126_E2.4401.00
129_T132_E2.3251.00
129_T133_L2.2731.00
46_S104_L2.1021.00
84_R92_I2.0681.00
52_K55_E2.0591.00
38_E77_K1.9821.00
122_Y133_L1.9001.00
85_S91_I1.8361.00
46_S96_I1.8071.00
126_E129_T1.7731.00
75_V82_R1.6851.00
99_A103_V1.6771.00
78_E99_A1.6131.00
38_E73_A1.5951.00
14_L135_S1.5781.00
130_L133_L1.5461.00
53_V71_T1.5421.00
48_Q59_I1.4821.00
35_S38_E1.4821.00
72_D76_E1.4681.00
46_S101_E1.4541.00
126_E132_E1.4501.00
103_V106_H1.4491.00
99_A102_K1.4491.00
71_T94_I1.4481.00
41_I70_V1.4461.00
133_L136_K1.4161.00
44_I59_I1.3451.00
14_L131_I1.3421.00
14_L138_D1.2831.00
55_E58_P1.2691.00
29_I110_K1.2621.00
50_P93_R1.2611.00
72_D89_R1.2521.00
54_T64_A1.2391.00
41_I67_I1.2311.00
102_K106_H1.2051.00
53_V92_I1.1761.00
132_E136_K1.1731.00
63_S66_H1.1651.00
82_R92_I1.1571.00
62_V66_H1.1381.00
53_V94_I1.1341.00
48_Q51_K1.1021.00
127_L131_I1.1011.00
125_A129_T1.0961.00
79_W103_V1.0891.00
131_I135_S1.0861.00
126_E133_L1.0801.00
54_T58_P1.0791.00
17_K138_D1.0651.00
51_K55_E1.0611.00
27_N31_D1.0581.00
53_V64_A1.0521.00
53_V67_I1.0411.00
18_V138_D1.0101.00
68_T72_D1.0101.00
16_R19_F0.9891.00
65_S68_T0.9881.00
45_L80_I0.9851.00
81_T97_T0.9811.00
50_P83_I0.9721.00
72_D75_V0.9681.00
110_K113_E0.9641.00
96_I100_G0.9561.00
55_E59_I0.9501.00
51_K59_I0.9471.00
98_E101_E0.9421.00
49_G101_E0.9411.00
19_F23_R0.9241.00
77_K103_V0.9161.00
62_V67_I0.9161.00
96_I101_E0.9151.00
79_W99_A0.9111.00
29_I114_Y0.9051.00
33_E77_K0.9041.00
37_N70_V0.9021.00
101_E105_Q0.8971.00
115_F118_R0.8931.00
83_I93_R0.8901.00
66_H69_A0.8871.00
98_E102_K0.8781.00
11_M131_I0.8761.00
77_K99_A0.8691.00
29_I117_K0.8661.00
111_K115_F0.8641.00
63_S69_A0.8581.00
84_R89_R0.8541.00
71_T80_I0.8521.00
46_S108_N0.8521.00
41_I56_F0.8511.00
18_V134_F0.8371.00
129_T136_K0.8371.00
124_D128_A0.8331.00
25_E114_Y0.8311.00
46_S105_Q0.8311.00
39_F107_F0.8221.00
122_Y137_L0.8191.00
109_E113_E0.8181.00
21_Q138_D0.8171.00
75_V80_I0.8151.00
69_A73_A0.7971.00
88_D91_I0.7951.00
48_Q55_E0.7861.00
44_I48_Q0.7771.00
16_R20_K0.7751.00
29_I113_E0.7731.00
75_V81_T0.7631.00
69_A72_D0.7581.00
42_L104_L0.7561.00
123_T127_L0.7521.00
106_H110_K0.7481.00
73_A76_E0.7441.00
102_K105_Q0.7421.00
114_Y117_K0.7411.00
40_T60_L0.7361.00
71_T75_V0.7351.00
86_K93_R0.7281.00
113_E116_F0.7251.00
14_L17_K0.7241.00
117_K120_D0.7221.00
32_K110_K0.7191.00
57_A67_I0.7191.00
20_K24_N0.7171.00
128_A131_I0.7081.00
44_I60_L0.7061.00
49_G95_H0.7051.00
109_E112_T0.6981.00
53_V68_T0.6961.00
27_N36_R0.6901.00
85_S88_D0.6901.00
39_F111_K0.6811.00
72_D82_R0.6751.00
15_L19_F0.6741.00
128_A132_E0.6731.00
125_A128_A0.6711.00
44_I51_K0.6671.00
37_N66_H0.6651.00
113_E117_K0.6591.00
45_L51_K0.6561.00
67_I71_T0.6551.00
112_T116_F0.6541.00
119_F127_L0.6541.00
74_L79_W0.6491.00
43_R47_E0.6441.00
44_I56_F0.6421.00
41_I60_L0.6411.00
106_H109_E0.6381.00
57_A64_A0.6361.00
73_A77_K0.6131.00
45_L96_I0.6111.00
29_I32_K0.6021.00
10_D131_I0.5981.00
18_V137_L0.5931.00
25_E117_K0.5901.00
56_F94_I0.5851.00
122_Y127_L0.5801.00
40_T44_I0.5771.00
132_E135_S0.5771.00
25_E28_E0.5751.00
15_L18_V0.5741.00
23_R26_I0.5721.00
38_E70_V0.5711.00
108_N112_T0.5681.00
17_K21_Q0.5611.00
26_I29_I0.5611.00
39_F104_L0.5601.00
23_R27_N0.5601.00
97_T100_G0.5551.00
122_Y136_K0.5481.00
105_Q109_E0.5441.00
80_I94_I0.5441.00
78_E81_T0.5431.00
11_M130_L0.5341.00
104_L108_N0.5331.00
54_T57_A0.5311.00
103_V107_F0.5271.00
133_L137_L0.5251.00
42_L46_S0.5251.00
122_Y126_E0.5131.00
43_R108_N0.5131.00
15_L134_F0.5121.00
105_Q108_N0.5111.00
26_I111_K0.5071.00
83_I86_K0.5041.00
74_L80_I0.5021.00
82_R94_I0.5001.00
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  
3bj6A 2 1 99.9 0.276 Contact Map
4rguA 4 0.9716 99.9 0.277 Contact Map
3fm5A 4 1 99.9 0.278 Contact Map
3cdhA 4 0.9362 99.9 0.283 Contact Map
2nnnA 2 0.9433 99.9 0.285 Contact Map
3cjnA 2 0.9504 99.9 0.287 Contact Map
1s3jA 2 0.9929 99.9 0.288 Contact Map
2gxgA 2 0.9574 99.9 0.291 Contact Map
3jw4A 2 0.9078 99.9 0.293 Contact Map
3boqA 2 0.922 99.9 0.295 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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