GREMLIN Database
YLAC - RNA polymerase sigma factor YlaC
UniProt: O07627 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 173 (158)
Sequences: 40727 (30663)
Seq/√Len: 2439.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
42_K67_T3.2261.00
128_R138_I2.7751.00
17_E57_R2.4771.00
136_E146_L2.3571.00
116_K163_N2.3211.00
121_H159_E2.2691.00
65_H69_I2.2021.00
113_E163_N2.1381.00
22_L64_A2.0061.00
133_L141_I1.9721.00
120_Q152_T1.9671.00
39_T64_A1.9251.00
147_S150_N1.7851.00
21_Y61_Y1.7151.00
70_N73_R1.7131.00
145_S148_K1.7051.00
30_E33_K1.6951.00
46_G49_S1.6941.00
67_T70_N1.6761.00
31_T71_W1.6581.00
55_S58_T1.6331.00
144_W152_T1.6321.00
121_H152_T1.6131.00
8_E12_R1.6121.00
134_S137_E1.6071.00
25_R68_F1.5701.00
135_Y146_L1.5491.00
43_A60_L1.5491.00
154_H158_L1.5391.00
118_K121_H1.5331.00
127_L141_I1.5171.00
23_F29_L1.4951.00
42_K70_N1.4921.00
66_H69_I1.4901.00
9_D13_Q1.4771.00
129_E157_R1.4751.00
38_D67_T1.4721.00
148_K152_T1.4671.00
135_Y153_L1.4631.00
144_W149_V1.4521.00
135_Y150_N1.4421.00
17_E61_Y1.4361.00
28_H31_T1.4241.00
159_E163_N1.4151.00
35_L71_W1.3941.00
18_I64_A1.3631.00
148_K151_T1.3411.00
127_L133_L1.3351.00
22_L68_F1.3281.00
122_Q126_I1.3261.00
62_T65_H1.3241.00
14_Y57_R1.3141.00
146_L150_N1.3101.00
151_T154_H1.3061.00
57_R61_Y1.2971.00
41_V45_N1.2801.00
42_K46_G1.2761.00
124_V153_L1.2661.00
14_Y40_F1.2641.00
62_T66_H1.2601.00
124_V156_A1.2401.00
115_L122_Q1.2371.00
124_V152_T1.2341.00
151_T155_R1.2141.00
39_T63_I1.2031.00
19_L29_L1.1991.00
19_L23_F1.1891.00
35_L67_T1.1831.00
26_T68_F1.1731.00
136_E140_E1.1671.00
31_T75_D1.1601.00
11_Y15_Y1.1551.00
50_F53_H1.1551.00
121_H156_A1.1441.00
11_Y40_F1.1441.00
22_L36_A1.1201.00
128_R135_Y1.1121.00
133_L137_E1.1061.00
102_S105_V1.1031.00
26_T35_L1.1021.00
22_L35_L1.1001.00
7_I44_L1.0901.00
129_E153_L1.0881.00
29_L33_K1.0841.00
71_W75_D1.0741.00
21_Y65_H1.0591.00
153_L157_R1.0481.00
147_S151_T1.0471.00
138_I149_V1.0371.00
69_I72_Y1.0361.00
15_Y19_L1.0271.00
68_F72_Y1.0261.00
18_I36_A1.0191.00
135_Y149_V1.0181.00
19_L33_K1.0101.00
39_T67_T1.0041.00
67_T71_W1.0031.00
14_Y60_L0.9941.00
19_L36_A0.9841.00
74_R77_K0.9711.00
126_I130_F0.9681.00
147_S154_H0.9591.00
18_I60_L0.9511.00
121_H124_V0.9501.00
119_D123_S0.9491.00
54_S58_T0.9411.00
126_I131_Q0.9391.00
113_E160_L0.9351.00
70_N74_R0.9271.00
15_Y36_A0.9251.00
14_Y17_E0.9251.00
158_L162_K0.9221.00
19_L32_A0.9101.00
20_N24_R0.9011.00
113_E116_K0.8821.00
42_K45_N0.8781.00
35_L68_F0.8761.00
123_S126_I0.8761.00
16_Q20_N0.8711.00
43_A59_W0.8701.00
23_F32_A0.8691.00
62_T69_I0.8641.00
22_L32_A0.8541.00
107_S111_R0.8511.00
127_L138_I0.8511.00
124_V144_W0.8461.00
120_Q144_W0.8431.00
121_H155_R0.8431.00
18_I39_T0.8391.00
10_L56_I0.8381.00
75_D78_Y0.8341.00
137_E140_E0.8271.00
128_R153_L0.8241.00
98_E102_S0.8171.00
161_K165_T0.8091.00
127_L142_L0.8071.00
120_Q123_S0.8021.00
144_W148_K0.8011.00
138_I142_L0.7911.00
125_L129_E0.7901.00
136_E150_N0.7891.00
139_A146_L0.7801.00
37_Q41_V0.7741.00
111_R115_L0.7711.00
38_D41_V0.7681.00
134_S138_I0.7651.00
59_W63_I0.7621.00
125_L156_A0.7611.00
103_R106_K0.7571.00
32_A36_A0.7521.00
9_D12_R0.7501.00
109_T112_Q0.7501.00
74_R78_Y0.7481.00
108_E112_Q0.7421.00
113_E164_M0.7411.00
17_E21_Y0.7341.00
21_Y25_R0.7231.00
23_F27_H0.7121.00
124_V142_L0.6951.00
83_I86_N0.6941.00
51_R54_S0.6901.00
106_K109_T0.6791.00
5_D8_E0.6671.00
38_D71_W0.6651.00
25_R69_I0.6601.00
76_V80_F0.6601.00
72_Y76_V0.6541.00
155_R158_L0.6531.00
97_P100_Y0.6491.00
104_T107_S0.6471.00
36_A40_F0.6401.00
69_I73_R0.6311.00
127_L131_Q0.6281.00
61_Y65_H0.6281.00
155_R159_E0.6281.00
75_D79_Q0.6261.00
128_R157_R0.6231.00
105_V108_E0.6231.00
12_R15_Y0.6191.00
25_R65_H0.6161.00
52_G55_S0.6161.00
26_T32_A0.6151.00
71_W74_R0.6141.00
53_H56_I0.6051.00
64_A68_F0.6051.00
102_S106_K0.6031.00
17_E20_N0.6011.00
119_D122_Q0.5991.00
47_L56_I0.5991.00
105_V109_T0.5921.00
34_D37_Q0.5851.00
76_V79_Q0.5841.00
35_L64_A0.5831.00
26_T31_T0.5791.00
96_Q99_Q0.5781.00
101_L105_V0.5771.00
100_Y104_T0.5681.00
50_F54_S0.5661.00
101_L104_T0.5621.00
159_E162_K0.5621.00
26_T71_W0.5611.00
21_Y68_F0.5611.00
77_K81_T0.5591.00
112_Q116_K0.5581.00
150_N154_H0.5561.00
28_H33_K0.5561.00
139_A149_V0.5541.00
5_D9_D0.5541.00
104_T108_E0.5531.00
72_Y75_D0.5521.00
135_Y138_I0.5521.00
39_T43_A0.5491.00
125_L160_L0.5441.00
7_I11_Y0.5441.00
44_L47_L0.5421.00
123_S142_L0.5391.00
65_H123_S0.5391.00
6_S9_D0.5381.00
139_A142_L0.5361.00
152_T156_A0.5321.00
6_S47_L0.5311.00
15_Y40_F0.5301.00
50_F55_S0.5291.00
114_L126_I0.5271.00
99_Q103_R0.5231.00
115_L126_I0.5181.00
117_L156_A0.5161.00
157_R161_K0.5161.00
58_T61_Y0.5151.00
109_T113_E0.5111.00
22_L26_T0.5111.00
118_K159_E0.5071.00
111_R114_L0.5061.00
123_S127_L0.5061.00
28_H32_A0.5031.00
112_Q115_L0.5031.00
43_A63_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  
4cxfA 1 0.8266 100 0.175 Contact Map
1or7A 2 0.9249 100 0.188 Contact Map
4nqwA 1 0.7919 100 0.216 Contact Map
2q1zA 1 0.9249 100 0.217 Contact Map
2lfwA 1 0.8671 100 0.254 Contact Map
4g97A 1 0.6763 100 0.258 Contact Map
1rp3A 1 0.9595 100 0.262 Contact Map
4yfkF 1 1 100 0.278 Contact Map
3n0rA 1 0.8092 100 0.281 Contact Map
1l0oC 1 0.0809 100 0.29 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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