GREMLIN Database
YPDB - Transcriptional regulatory protein YpdB
UniProt: P0AE39 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14149
Length: 244 (187)
Sequences: 50227 (39005)
Seq/√Len: 2852.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
13_Q31_T3.8671.00
13_Q33_D3.4521.00
17_S31_T3.3481.00
6_V38_V2.8361.00
39_L67_N2.5231.00
30_G47_V2.4281.00
59_L67_N2.4181.00
36_L58_S2.4171.00
32_F41_F2.3971.00
35_G59_L2.3121.00
34_D58_S2.2781.00
19_L105_E2.0961.00
30_G41_F2.0201.00
87_A107_R1.9701.00
79_F95_A1.9621.00
30_G45_N1.9491.00
41_F45_N1.9321.00
65_A77_I1.9311.00
17_S21_K1.8801.00
55_N83_W1.8531.00
60_D63_L1.8451.00
52_L64_L1.7941.00
33_D37_D1.7851.00
4_I32_F1.7541.00
97_D111_M1.6961.00
2_K28_I1.6921.00
23_H109_T1.6841.00
43_Q71_F1.6801.00
79_F90_A1.6791.00
165_T169_T1.6541.00
34_D37_D1.6281.00
135_E138_T1.6051.00
65_A79_F1.5611.00
165_T168_Y1.5581.00
50_I75_P1.5361.00
67_N71_F1.5211.00
69_S96_F1.5161.00
54_I79_F1.5151.00
35_G64_L1.5131.00
83_W86_H1.4551.00
7_E13_Q1.4531.00
41_F44_H1.4481.00
39_L64_L1.4461.00
36_L59_L1.4401.00
42_L68_I1.4391.00
59_L63_L1.4331.00
174_Y177_P1.3911.00
54_I62_V1.3881.00
2_K30_G1.3721.00
96_F118_A1.3591.00
2_K27_E1.3481.00
63_L66_Q1.3461.00
52_L65_A1.3031.00
39_L59_L1.2711.00
164_M167_V1.2661.00
109_T113_Q1.2581.00
67_N70_Q1.2501.00
41_F47_V1.2381.00
8_D53_D1.2361.00
168_Y171_R1.2341.00
32_F38_V1.2281.00
166_F169_T1.2241.00
20_I112_L1.2141.00
6_V56_I1.2101.00
78_V115_L1.2081.00
66_Q89_E1.2041.00
167_V171_R1.1911.00
66_Q93_L1.1851.00
164_M168_Y1.1841.00
40_K44_H1.1811.00
36_L40_K1.1791.00
4_I41_F1.1711.00
62_V89_E1.1651.00
163_K166_F1.1621.00
23_H113_Q1.1441.00
179_N182_E1.1351.00
39_L43_Q1.1331.00
4_I47_V1.1211.00
142_V145_E1.1201.00
96_F115_L1.1151.00
10_F33_D1.1111.00
147_I155_I1.1101.00
4_I38_V1.0981.00
37_D40_K1.0891.00
37_D41_F1.0861.00
43_Q72_A1.0771.00
49_A112_L1.0751.00
76_F118_A1.0721.00
38_V64_L1.0631.00
87_A100_L1.0541.00
163_K168_Y1.0461.00
182_E185_S1.0411.00
72_A75_P1.0391.00
89_E93_L1.0171.00
38_V42_L1.0071.00
14_Q31_T1.0051.00
76_F96_F1.0051.00
10_F14_Q1.0011.00
4_I30_G1.0011.00
78_V111_M0.9951.00
16_L80_I0.9941.00
89_E92_E0.9941.00
107_R110_G0.9801.00
84_K100_L0.9761.00
56_I64_L0.9671.00
92_E113_Q0.9631.00
2_K45_N0.9571.00
65_A93_L0.9531.00
15_E19_L0.9501.00
131_T144_D0.9431.00
4_I42_L0.9391.00
50_I77_I0.9381.00
178_M182_E0.9341.00
165_T171_R0.9331.00
97_D114_K0.9321.00
11_L15_E0.9291.00
52_L79_F0.9231.00
139_I156_Y0.9221.00
153_N156_Y0.9171.00
88_V92_E0.9161.00
164_M169_T0.9151.00
110_G114_K0.9151.00
62_V90_A0.9141.00
92_E110_G0.9141.00
62_V93_L0.9101.00
142_V147_I0.9091.00
6_V50_I0.8991.00
55_N82_A0.8941.00
54_I60_D0.8821.00
178_M181_T0.8801.00
137_D141_L0.8761.00
6_V32_F0.8751.00
49_A116_E0.8731.00
103_Y108_I0.8661.00
63_L67_N0.8621.00
16_L108_I0.8611.00
14_Q17_S0.8571.00
50_I68_I0.8551.00
40_K43_Q0.8481.00
163_K169_T0.8461.00
163_K167_V0.8451.00
42_L72_A0.8351.00
164_M171_R0.8301.00
158_A162_E0.8291.00
51_F108_I0.8291.00
105_E109_T0.8271.00
140_N147_I0.8271.00
32_F37_D0.8261.00
54_I86_H0.8261.00
65_A95_A0.8241.00
51_F80_I0.8191.00
5_I16_L0.8191.00
9_E12_A0.8141.00
159_E162_E0.8121.00
42_L50_I0.8101.00
150_T154_D0.8001.00
5_I17_S0.7981.00
10_F13_Q0.7941.00
133_T142_V0.7941.00
161_H164_M0.7911.00
166_F170_R0.7891.00
18_W22_E0.7891.00
151_P155_I0.7831.00
80_I103_Y0.7801.00
86_H89_E0.7781.00
107_R111_M0.7661.00
5_I13_Q0.7581.00
7_E56_I0.7551.00
90_A95_A0.7551.00
52_L77_I0.7491.00
160_A164_M0.7451.00
42_L47_V0.7431.00
151_P154_D0.7431.00
42_L75_P0.7401.00
64_L68_I0.7351.00
91_F111_M0.7341.00
6_V64_L0.7231.00
134_R162_E0.7211.00
24_S27_E0.7211.00
14_Q18_W0.7141.00
76_F119_W0.7121.00
68_I77_I0.7021.00
59_L64_L0.7011.00
167_V170_R0.6981.00
122_Q126_S0.6981.00
158_A163_K0.6971.00
66_Q70_Q0.6901.00
43_Q67_N0.6811.00
115_L118_A0.6791.00
114_K117_A0.6771.00
176_M185_S0.6721.00
164_M170_R0.6701.00
166_F171_R0.6671.00
68_I75_P0.6651.00
143_K146_R0.6641.00
177_P181_T0.6641.00
148_I151_P0.6641.00
134_R141_L0.6641.00
161_H168_Y0.6631.00
78_V97_D0.6621.00
51_F78_V0.6611.00
35_G39_L0.6601.00
181_T185_S0.6601.00
32_F35_G0.6591.00
51_F112_L0.6571.00
42_L64_L0.6541.00
111_M115_L0.6511.00
184_C188_P0.6501.00
104_Q107_R0.6471.00
76_F122_Q0.6461.00
152_I156_Y0.6451.00
65_A69_S0.6401.00
158_A161_H0.6391.00
13_Q17_S0.6371.00
88_V106_S0.6351.00
174_Y178_M0.6341.00
119_W123_Q0.6251.00
21_K24_S0.6221.00
92_E97_D0.6201.00
180_I183_F0.6191.00
160_A163_K0.6151.00
116_E119_W0.6131.00
106_S110_G0.6121.00
180_I184_C0.6091.00
185_S189_P0.6081.00
39_L42_L0.6071.00
54_I83_W0.6071.00
113_Q116_E0.6061.00
4_I50_I0.6021.00
175_V179_N0.5991.00
88_V91_F0.5991.00
87_A104_Q0.5971.00
114_K119_W0.5951.00
5_I31_T0.5941.00
150_T160_A0.5931.00
162_E166_F0.5931.00
165_T170_R0.5921.00
15_E18_W0.5901.00
81_T87_A0.5861.00
12_A103_Y0.5831.00
35_G56_I0.5821.00
161_H165_T0.5811.00
62_V86_H0.5801.00
3_V49_A0.5771.00
122_Q127_T0.5771.00
2_K48_D0.5751.00
6_V35_G0.5741.00
35_G58_S0.5721.00
54_I90_A0.5621.00
150_T157_Y0.5611.00
110_G113_Q0.5611.00
138_T142_V0.5581.00
154_D157_Y0.5551.00
2_K47_V0.5531.00
76_F115_L0.5451.00
86_H90_A0.5441.00
6_V52_L0.5401.00
136_N139_I0.5401.00
134_R155_I0.5391.00
124_T127_T0.5391.00
17_S29_V0.5351.00
114_K118_A0.5341.00
141_L148_I0.5341.00
128_P133_T0.5291.00
123_Q126_S0.5291.00
120_Q123_Q0.5281.00
141_L155_I0.5281.00
116_E120_Q0.5271.00
106_S109_T0.5261.00
113_Q117_A0.5251.00
69_S75_P0.5241.00
159_E163_K0.5191.00
3_V20_I0.5191.00
27_E113_Q0.5171.00
134_R137_D0.5171.00
74_K122_Q0.5141.00
118_A122_Q0.5121.00
49_A115_L0.5051.00
92_E107_R0.5021.00
139_I142_V0.5001.00
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  
4cbvA 2 0.959 100 0.287 Contact Map
4gvpA 1 0.791 100 0.386 Contact Map
4g97A 1 0.5205 100 0.39 Contact Map
3n0rA 1 0.4877 100 0.393 Contact Map
1yioA 1 0.7664 100 0.395 Contact Map
1a04A 1 0.7828 100 0.401 Contact Map
4ldzA 2 0.7623 100 0.406 Contact Map
3c3wA 2 0.791 100 0.407 Contact Map
3rqiA 2 0.668 99.9 0.423 Contact Map
4hyeA 2 0.7869 99.9 0.425 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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