GREMLIN Database
SIGM - RNA polymerase sigma factor SigM
UniProt: O07582 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 163 (153)
Sequences: 38349 (29168)
Seq/√Len: 2358.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_R62_A3.2271.00
120_Y130_A2.8081.00
13_D52_K2.4741.00
128_K138_E2.3781.00
113_Y151_R2.2131.00
108_E155_L2.1601.00
105_Y155_L2.1151.00
18_L59_A2.0861.00
60_R64_I2.0631.00
112_N144_V1.9431.00
35_T59_A1.9421.00
125_L133_I1.8851.00
137_S140_N1.8631.00
139_A142_K1.8321.00
17_F56_F1.7161.00
26_H29_E1.7151.00
50_K53_P1.6901.00
65_D68_R1.6811.00
42_H45_S1.6781.00
62_A65_D1.6581.00
21_M63_F1.6511.00
27_L66_Y1.6481.00
113_Y144_V1.6251.00
121_Y149_R1.6081.00
136_I144_V1.6061.00
39_A55_L1.5471.00
126_N129_E1.5231.00
127_Y138_E1.5181.00
146_F150_Q1.5141.00
24_D27_L1.5021.00
4_D8_Q1.4941.00
19_L25_K1.4901.00
38_R65_D1.4831.00
127_Y145_L1.4801.00
61_N64_I1.4681.00
140_N144_V1.4621.00
110_P113_Y1.4551.00
136_I141_F1.4341.00
127_Y142_K1.4271.00
34_E62_A1.4161.00
31_L66_Y1.4091.00
14_V59_A1.3961.00
13_D56_F1.3941.00
119_L133_I1.3891.00
57_Q60_R1.3841.00
140_N143_S1.3761.00
5_E9_M1.3631.00
18_L63_F1.3431.00
116_A145_L1.3331.00
151_R155_L1.3271.00
138_E142_K1.3171.00
10_Y36_F1.3041.00
114_R118_T1.3021.00
143_S146_F1.2931.00
52_K56_F1.2691.00
22_T63_F1.2601.00
10_Y52_K1.2571.00
35_T58_V1.2411.00
57_Q61_N1.2381.00
37_M41_I1.2331.00
143_S147_R1.2251.00
27_L70_H1.2181.00
15_Y25_K1.2131.00
119_L125_L1.2051.00
107_S114_R1.2001.00
22_T31_L1.1991.00
116_A144_V1.1951.00
38_R42_H1.1941.00
15_Y19_L1.1921.00
14_V32_L1.1741.00
116_A148_A1.1731.00
7_Y36_F1.1681.00
31_L62_A1.1671.00
7_Y11_M1.1571.00
18_L31_L1.1371.00
18_L32_L1.1351.00
128_K132_H1.1301.00
94_H97_E1.0991.00
120_Y127_Y1.0891.00
145_L149_R1.0841.00
17_F60_R1.0831.00
25_K29_E1.0821.00
15_Y29_E1.0671.00
130_A141_F1.0621.00
63_F67_V1.0621.00
113_Y148_A1.0521.00
125_L129_E1.0481.00
64_I67_V1.0381.00
66_Y70_H1.0311.00
127_Y141_F1.0291.00
49_S53_P1.0231.00
139_A143_S1.0221.00
10_Y55_L1.0161.00
11_M15_Y1.0081.00
35_T62_A1.0061.00
39_A54_W0.9871.00
121_Y145_L0.9861.00
113_Y116_A0.9671.00
139_A146_F0.9631.00
14_V55_L0.9621.00
15_Y28_A0.9411.00
105_Y152_L0.9391.00
69_K72_K0.9371.00
15_Y32_L0.9311.00
118_T122_L0.9151.00
111_D115_E0.9131.00
62_A66_Y0.9021.00
31_L63_F0.9021.00
10_Y13_D0.9011.00
11_M32_L0.8981.00
118_T123_K0.8771.00
150_Q154_A0.8711.00
19_L28_A0.8701.00
38_R41_I0.8561.00
18_L28_A0.8551.00
65_D69_K0.8541.00
46_Y49_S0.8511.00
12_N16_R0.8461.00
105_Y108_E0.8431.00
117_L121_Y0.8401.00
57_Q64_I0.8401.00
116_A136_I0.8351.00
16_R20_S0.8301.00
129_E132_H0.8131.00
113_Y147_R0.8131.00
70_H73_E0.8111.00
6_I51_V0.8101.00
14_V35_T0.8061.00
115_E118_T0.8011.00
43_I51_V0.7991.00
119_L130_A0.7981.00
54_W58_V0.7951.00
126_N130_A0.7871.00
69_K73_E0.7831.00
33_Q37_M0.7801.00
99_K103_T0.7801.00
128_K142_K0.7791.00
136_I140_N0.7761.00
120_Y145_L0.7751.00
112_N136_I0.7741.00
28_A32_L0.7721.00
130_A134_M0.7681.00
17_F21_M0.7651.00
112_N115_E0.7591.00
131_S138_E0.7521.00
119_L134_M0.7491.00
90_Q94_H0.7431.00
34_E37_M0.7431.00
117_L148_A0.7361.00
101_V104_G0.7291.00
100_E104_G0.7291.00
105_Y156_Y0.7261.00
13_D17_F0.7261.00
71_K75_T0.7251.00
72_K76_I0.7141.00
103_T107_S0.7101.00
5_E8_Q0.6941.00
56_F60_R0.6761.00
67_V71_K0.6751.00
116_A134_M0.6711.00
98_I101_V0.6691.00
64_I68_R0.6671.00
97_E100_E0.6671.00
46_Y50_K0.6651.00
46_Y53_P0.6581.00
21_M64_I0.6581.00
59_A63_F0.6481.00
31_L59_A0.6431.00
120_Y149_R0.6431.00
34_E66_Y0.6421.00
19_L23_K0.6391.00
147_R151_R0.6321.00
40_Y43_I0.6301.00
21_M60_R0.6301.00
97_E101_V0.6201.00
147_R150_Q0.6161.00
119_L123_K0.6101.00
96_V99_K0.6091.00
88_A91_S0.6071.00
22_T66_Y0.6071.00
60_R115_E0.6031.00
93_A97_E0.5981.00
18_L22_T0.5971.00
89_V92_P0.5931.00
127_Y130_A0.5921.00
22_T27_L0.5881.00
8_Q11_M0.5871.00
35_T39_A0.5861.00
66_Y69_K0.5841.00
13_D16_R0.5831.00
30_D33_Q0.5831.00
17_F63_F0.5821.00
22_T28_A0.5751.00
93_A96_V0.5661.00
70_H74_V0.5661.00
90_Q93_A0.5651.00
71_K74_V0.5611.00
111_D114_R0.5581.00
96_V100_E0.5561.00
24_D29_E0.5521.00
106_M118_T0.5431.00
32_L36_F0.5431.00
94_H98_I0.5421.00
92_P96_V0.5381.00
67_V70_H0.5311.00
131_S141_F0.5311.00
103_T106_M0.5311.00
39_A58_V0.5301.00
151_R154_A0.5291.00
46_Y54_W0.5281.00
104_G108_E0.5261.00
53_P56_F0.5221.00
152_L156_Y0.5211.00
18_L21_M0.5211.00
131_S134_M0.5211.00
101_V105_Y0.5211.00
79_D83_S0.5211.00
46_Y51_V0.5201.00
7_Y33_Q0.5201.00
144_V147_R0.5121.00
149_R153_K0.5121.00
95_Q98_I0.5121.00
115_E134_M0.5101.00
91_S95_Q0.5091.00
142_K146_F0.5081.00
36_F40_Y0.5071.00
117_L152_L0.5071.00
72_K75_T0.5071.00
109_L148_A0.5011.00
110_P151_R0.5001.00
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 0.8466 100 0.171 Contact Map
1or7A 2 0.9325 100 0.188 Contact Map
2q1zA 1 0.9509 100 0.2 Contact Map
2lfwA 1 0.9018 100 0.203 Contact Map
4g97A 1 0.7301 100 0.214 Contact Map
4nqwA 1 0.816 100 0.215 Contact Map
3n0rA 1 0.865 100 0.248 Contact Map
4qicA 2 0.8344 100 0.251 Contact Map
4yfkF 1 1 100 0.255 Contact Map
1rp3A 1 0.9816 100 0.273 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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