GREMLIN Database
YYCF - Transcriptional regulatory protein YycF
UniProt: P37478 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 235 (201)
Sequences: 73933 (51998)
Seq/√Len: 3667.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_A31_C3.7761.00
15_A33_H3.2941.00
19_E31_C3.2891.00
8_V38_A2.7811.00
39_V67_E2.7441.00
36_N58_N2.5631.00
30_H47_P2.4151.00
59_K67_E2.3991.00
35_G59_K2.3211.00
43_E71_K2.3151.00
34_D58_N2.3111.00
4_K30_H2.2061.00
25_E110_L2.1191.00
19_E23_R2.0921.00
21_N106_T2.0671.00
32_A41_M2.0421.00
4_K28_E1.9901.00
55_M82_K1.9281.00
52_L64_V1.8791.00
33_H37_E1.8271.00
30_H41_M1.8261.00
88_K108_E1.8161.00
196_R199_D1.7911.00
65_C76_I1.7811.00
34_D37_E1.7621.00
41_M45_L1.7441.00
161_R164_E1.7441.00
78_M91_G1.7061.00
69_R97_D1.7031.00
67_E71_K1.6901.00
6_L32_A1.6651.00
30_H45_L1.6531.00
78_M96_A1.6021.00
66_R94_I1.6011.00
168_Y185_T1.5991.00
179_R199_D1.5891.00
59_K63_E1.5881.00
85_E105_S1.5781.00
35_G64_V1.5701.00
98_D112_R1.5541.00
167_H171_K1.5191.00
82_K87_D1.5151.00
42_V68_V1.5021.00
22_L113_V1.4891.00
60_D63_E1.4871.00
177_M185_T1.4771.00
41_M44_E1.4621.00
36_N59_K1.4521.00
50_I74_M1.4431.00
67_E70_K1.4391.00
136_H141_V1.4361.00
201_T204_R1.4201.00
49_L113_V1.3781.00
178_T181_H1.3591.00
12_K33_H1.3571.00
77_I116_N1.3491.00
65_C78_M1.3431.00
63_E66_R1.3361.00
54_I62_V1.3281.00
39_V64_V1.2951.00
134_E141_V1.2641.00
41_M47_P1.2611.00
4_K45_L1.2531.00
27_Y114_K1.2521.00
162_E208_K1.2311.00
8_V56_L1.2301.00
39_V59_K1.2301.00
97_D119_R1.2291.00
139_S152_R1.2251.00
62_V91_G1.2141.00
168_Y172_H1.2021.00
84_S87_D1.1981.00
110_L114_K1.1911.00
40_E44_E1.1881.00
97_D116_N1.1861.00
10_D53_D1.1811.00
6_L47_P1.1801.00
9_D15_A1.1731.00
32_A38_A1.1561.00
90_I94_I1.1541.00
37_E40_E1.1541.00
141_V150_S1.1511.00
37_E41_M1.1491.00
148_V155_T1.1461.00
52_L65_C1.1421.00
54_I78_M1.1381.00
181_H185_T1.1321.00
62_V90_I1.1171.00
36_N40_E1.1161.00
26_G114_K1.1111.00
25_E114_K1.1101.00
212_N216_P1.1061.00
168_Y177_M1.0881.00
6_L38_A1.0821.00
85_E89_V1.0811.00
200_V203_R1.0681.00
180_E195_V1.0671.00
108_E111_A1.0661.00
5_I27_Y1.0581.00
93_E114_K1.0491.00
86_I90_I1.0471.00
39_V43_E1.0461.00
49_L117_L1.0461.00
32_A37_E1.0441.00
6_L41_M1.0401.00
111_A115_A1.0391.00
143_F146_A1.0381.00
163_F167_H1.0261.00
7_V18_L1.0251.00
133_N145_D1.0211.00
89_V93_E1.0131.00
38_A64_V1.0061.00
19_E29_V1.0021.00
144_P167_H0.9961.00
4_K48_D0.9771.00
177_M181_H0.9731.00
38_A42_V0.9651.00
88_K101_T0.9621.00
16_D31_C0.9541.00
66_R90_I0.9541.00
54_I60_D0.9511.00
212_N215_H0.9451.00
50_I68_V0.9431.00
13_P17_I0.9421.00
18_L79_L0.9331.00
8_V32_A0.9321.00
197_T201_T0.9321.00
12_K16_D0.9231.00
196_R200_V0.9231.00
6_L42_V0.9231.00
65_C96_A0.9211.00
62_V94_I0.9121.00
116_N119_R0.9111.00
52_L76_I0.9081.00
65_C94_I0.9061.00
164_E167_H0.9041.00
160_H164_E0.9001.00
150_S155_T0.8931.00
142_I170_A0.8791.00
20_F24_K0.8761.00
63_E67_E0.8751.00
75_P97_D0.8721.00
83_D101_T0.8581.00
196_R203_R0.8571.00
40_E43_E0.8571.00
52_L78_M0.8551.00
202_V206_R0.8541.00
8_V50_I0.8481.00
85_E88_K0.8481.00
27_Y110_L0.8371.00
16_D19_E0.8361.00
12_K15_A0.8351.00
50_I76_I0.8341.00
195_V199_D0.8301.00
134_E143_F0.8261.00
142_I163_F0.8211.00
54_I82_K0.8131.00
7_V29_V0.8121.00
147_Y164_E0.8111.00
211_D217_N0.8071.00
203_R207_E0.8061.00
108_E112_R0.8041.00
51_L109_L0.7981.00
115_A120_Q0.7961.00
77_I112_R0.7941.00
42_V74_M0.7931.00
90_I93_E0.7841.00
105_S108_E0.7791.00
89_V107_R0.7771.00
56_L64_V0.7761.00
64_V68_V0.7741.00
54_I87_D0.7721.00
106_T110_L0.7681.00
79_L104_F0.7651.00
179_R195_V0.7651.00
59_K64_V0.7631.00
168_Y171_K0.7631.00
159_T208_K0.7581.00
14_I104_F0.7531.00
68_V72_Y0.7511.00
51_L79_L0.7471.00
136_H139_S0.7461.00
87_D90_I0.7431.00
4_K47_P0.7371.00
16_D20_F0.7361.00
168_Y182_L0.7351.00
42_V47_P0.7351.00
204_R207_E0.7331.00
200_V204_R0.7331.00
181_H184_Q0.7201.00
66_R70_K0.7171.00
86_I107_R0.7171.00
8_V64_V0.7121.00
55_M81_A0.7001.00
35_G39_V0.6981.00
5_I49_L0.6961.00
165_L169_L0.6921.00
18_L109_L0.6881.00
140_L151_K0.6871.00
115_A118_R0.6871.00
39_V71_K0.6841.00
21_N110_L0.6801.00
51_L113_V0.6781.00
42_V50_I0.6741.00
180_E184_Q0.6731.00
35_G58_N0.6691.00
39_V42_V0.6691.00
210_E216_P0.6661.00
117_L120_Q0.6661.00
17_I21_N0.6651.00
92_L112_R0.6651.00
112_R116_N0.6591.00
98_D115_A0.6561.00
73_D122_T0.6551.00
91_G96_A0.6541.00
9_D56_L0.6531.00
137_I140_L0.6521.00
23_R29_V0.6501.00
211_D220_V0.6481.00
69_R75_P0.6481.00
210_E217_N0.6461.00
150_S153_D0.6441.00
35_G56_L0.6401.00
206_R211_D0.6381.00
120_Q124_A0.6381.00
15_A19_E0.6381.00
104_F108_E0.6361.00
88_K105_S0.6341.00
75_P117_L0.6331.00
104_F109_L0.6321.00
171_K177_M0.6321.00
199_D202_V0.6321.00
135_I139_S0.6271.00
171_K185_T0.6261.00
43_E67_E0.6261.00
7_V31_C0.6251.00
93_E111_A0.6231.00
147_Y163_F0.6221.00
68_V76_I0.6161.00
144_P171_K0.6041.00
135_I144_P0.6031.00
54_I91_G0.6021.00
169_L202_V0.6001.00
62_V87_D0.5991.00
164_E168_Y0.5971.00
11_E81_A0.5961.00
22_L27_Y0.5941.00
11_E14_I0.5931.00
75_P119_R0.5931.00
107_R111_A0.5921.00
21_N25_E0.5901.00
7_V19_E0.5891.00
53_D102_K0.5891.00
216_P219_I0.5881.00
85_E107_R0.5881.00
5_I22_L0.5861.00
133_N144_P0.5811.00
65_C69_R0.5801.00
77_I98_D0.5781.00
51_L77_I0.5751.00
73_D123_T0.5741.00
151_K210_E0.5741.00
111_A114_K0.5731.00
194_D197_T0.5701.00
161_R201_T0.5681.00
134_E138_G0.5661.00
69_R74_M0.5621.00
142_I149_V0.5611.00
10_D80_T0.5601.00
52_L56_L0.5551.00
151_K154_E0.5541.00
49_L116_N0.5521.00
139_S151_K0.5511.00
119_R123_T0.5491.00
86_I89_V0.5471.00
37_E58_N0.5451.00
14_I17_I0.5421.00
46_Q72_Y0.5371.00
27_Y117_L0.5371.00
193_G198_V0.5361.00
114_K118_R0.5311.00
151_K212_N0.5301.00
42_V71_K0.5291.00
89_V92_L0.5251.00
162_E165_L0.5251.00
143_F148_V0.5241.00
135_I138_G0.5221.00
215_H218_W0.5211.00
133_N136_H0.5211.00
17_I20_F0.5191.00
83_D103_P0.5181.00
80_T88_K0.5151.00
142_I167_H0.5131.00
23_R28_E0.5121.00
42_V64_V0.5121.00
68_V74_M0.5101.00
20_F23_R0.5071.00
75_P120_Q0.5051.00
179_R202_V0.5051.00
5_I113_V0.5051.00
52_L68_V0.5031.00
8_V52_L0.5001.00
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  
2gwrA 1 0.9489 100 0.195 Contact Map
2oqrA 2 0.9617 100 0.211 Contact Map
4b09A 2 0.9106 100 0.217 Contact Map
1ys7A 2 0.9574 100 0.22 Contact Map
3r0jA 2 0.9362 100 0.222 Contact Map
4kfcA 2 0.9532 100 0.224 Contact Map
1kgsA 1 0.9277 100 0.234 Contact Map
1p2fA 1 0.9191 100 0.25 Contact Map
3q9sA 1 0.8894 100 0.264 Contact Map
2hqrA 2 0.9277 100 0.274 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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