GREMLIN Database
SIGX - RNA polymerase sigma factor SigX
UniProt: P35165 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 194 (159)
Sequences: 40468 (30369)
Seq/√Len: 2408.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
40_R65_V3.2181.00
129_R139_T2.7861.00
15_D55_K2.5191.00
137_Q147_E2.4381.00
117_Q164_H2.2971.00
122_Q160_V2.2451.00
20_L62_A2.1381.00
114_A164_H2.0631.00
63_R67_I2.0461.00
37_V62_A2.0401.00
134_Y142_A1.9681.00
146_S149_K1.9621.00
121_D153_T1.9571.00
148_S151_K1.8331.00
44_S47_T1.7431.00
19_F59_L1.7211.00
28_N31_E1.7111.00
68_D71_R1.6941.00
6_Q10_D1.6851.00
23_M66_A1.6601.00
53_S56_T1.6531.00
65_V68_D1.6451.00
41_V58_L1.6211.00
122_Q153_T1.6191.00
29_Q69_W1.6191.00
130_F158_L1.5871.00
145_F153_T1.5671.00
26_D29_Q1.5631.00
135_S138_E1.5531.00
149_K153_T1.5071.00
119_T122_Q1.5061.00
136_I154_Q1.5001.00
21_F27_K1.4941.00
136_I147_E1.4751.00
7_L11_T1.4691.00
149_K152_T1.4671.00
136_I151_K1.4591.00
64_H67_I1.4511.00
40_R68_D1.4481.00
128_L142_A1.4381.00
155_H159_K1.4301.00
33_L69_W1.4181.00
123_R127_I1.4091.00
125_V154_Q1.4081.00
145_F150_V1.4031.00
60_S63_R1.4021.00
16_L62_A1.3861.00
36_E65_V1.3681.00
20_L66_A1.3631.00
160_V164_H1.3471.00
15_D59_L1.3331.00
12_Y38_Y1.3111.00
60_S64_H1.3081.00
137_Q141_K1.2971.00
116_D123_R1.2641.00
16_L34_L1.2591.00
152_T155_H1.2551.00
125_V157_G1.2401.00
125_V153_T1.2391.00
128_L134_Y1.2321.00
147_E151_K1.2201.00
55_K59_L1.2111.00
33_L65_V1.2091.00
20_L33_L1.2081.00
20_L34_L1.1991.00
9_Y38_Y1.1981.00
52_S56_T1.1981.00
24_V33_L1.1901.00
12_Y55_K1.1881.00
17_Y21_F1.1851.00
37_V61_I1.1701.00
48_F51_R1.1701.00
9_Y13_H1.1641.00
152_T156_R1.1631.00
29_Q73_Q1.1521.00
39_I43_N1.1361.00
17_Y27_K1.1351.00
40_R44_S1.1351.00
24_V66_A1.1261.00
103_V106_E1.1211.00
19_F63_R1.1111.00
5_F42_L1.0821.00
139_T150_V1.0771.00
134_Y138_E1.0741.00
12_Y58_L1.0661.00
41_V57_W1.0661.00
27_K31_E1.0601.00
154_Q158_L1.0571.00
67_I70_F1.0481.00
122_Q157_G1.0391.00
66_A70_F1.0311.00
37_V65_V1.0281.00
129_R136_I1.0161.00
17_Y31_E1.0091.00
148_S152_T1.0071.00
136_I150_V1.0031.00
114_A161_L0.9921.00
69_W73_Q0.9911.00
148_S155_H0.9771.00
16_L37_V0.9661.00
159_K163_K0.9571.00
72_K75_T0.9541.00
13_H17_Y0.9521.00
120_I124_A0.9481.00
130_F154_Q0.9381.00
33_L66_A0.9301.00
122_Q125_V0.9261.00
125_V145_F0.9221.00
17_Y30_T0.9171.00
16_L58_L0.9151.00
68_D72_K0.9151.00
127_I132_Q0.9101.00
17_Y34_L0.9071.00
127_I131_I0.9051.00
65_V69_W0.9051.00
12_Y15_D0.8841.00
99_D103_V0.8831.00
122_Q156_R0.8811.00
18_Q22_Y0.8751.00
14_Q18_Q0.8651.00
128_L139_T0.8611.00
40_R43_N0.8601.00
57_W61_I0.8521.00
13_H34_L0.8411.00
60_S67_I0.8341.00
20_L30_T0.8341.00
19_F23_M0.8251.00
138_E141_K0.8201.00
21_F30_T0.8121.00
72_K76_I0.8051.00
126_I130_F0.8011.00
128_L143_L0.7901.00
77_R80_I0.7881.00
124_A127_I0.7851.00
35_Q39_I0.7851.00
8_L54_E0.7841.00
121_D124_A0.7741.00
135_S139_T0.7721.00
110_E113_A0.7641.00
129_R154_Q0.7631.00
162_R166_E0.7601.00
30_T34_L0.7541.00
145_F149_K0.7541.00
73_Q76_I0.7521.00
7_L10_D0.7511.00
15_D19_F0.7491.00
121_D145_F0.7461.00
114_A117_Q0.7381.00
49_E52_S0.7361.00
107_N110_E0.7331.00
114_A165_M0.7311.00
112_Y116_D0.7281.00
139_T143_L0.7271.00
106_E109_R0.7261.00
137_Q151_K0.7251.00
126_I157_G0.7241.00
36_E39_I0.7161.00
48_F52_S0.7161.00
45_Y54_E0.7151.00
140_A147_E0.7071.00
74_Q78_Q0.7021.00
75_T79_R0.6971.00
97_L100_E0.6961.00
33_L62_A0.6931.00
21_F25_K0.6921.00
98_P101_L0.6891.00
109_R113_A0.6771.00
156_R159_K0.6761.00
108_V112_Y0.6721.00
105_H108_V0.6661.00
125_V143_L0.6511.00
24_V69_W0.6501.00
129_R158_L0.6451.00
4_T45_Y0.6411.00
77_R81_L0.6331.00
20_L24_V0.6281.00
19_F66_A0.6281.00
70_F74_Q0.6251.00
120_I123_R0.6241.00
76_I80_I0.6231.00
67_I71_R0.6231.00
104_Q107_N0.6221.00
78_Q81_L0.6201.00
48_F56_T0.6151.00
105_H109_R0.6141.00
62_A66_A0.6141.00
24_V29_Q0.6091.00
5_F9_Y0.6031.00
59_L63_R0.6001.00
106_E110_E0.6001.00
36_E69_W0.5981.00
24_V30_T0.5961.00
63_R124_A0.5941.00
37_V41_V0.5931.00
51_R54_E0.5911.00
15_D18_Q0.5911.00
23_M67_I0.5901.00
102_A105_H0.5881.00
101_L105_H0.5871.00
103_V107_N0.5841.00
34_L38_Y0.5821.00
32_D35_Q0.5801.00
160_V163_K0.5711.00
69_W72_K0.5671.00
26_D31_E0.5641.00
42_L45_Y0.5631.00
156_R160_V0.5601.00
78_Q82_G0.5571.00
136_I139_T0.5561.00
9_Y35_Q0.5481.00
119_T160_V0.5481.00
10_D13_H0.5471.00
153_T156_R0.5451.00
23_M63_R0.5451.00
158_L162_R0.5411.00
126_I161_L0.5401.00
151_K155_H0.5391.00
128_L132_Q0.5381.00
50_G53_S0.5361.00
74_Q77_R0.5361.00
73_Q77_R0.5361.00
48_F53_S0.5341.00
112_Y115_L0.5331.00
115_L127_I0.5331.00
102_A106_E0.5321.00
113_A117_Q0.5321.00
79_R82_G0.5271.00
48_F54_E0.5231.00
118_C157_G0.5201.00
56_T59_L0.5201.00
140_A150_V0.5181.00
140_A143_L0.5151.00
124_A143_L0.5131.00
100_E103_V0.5101.00
124_A142_A0.5081.00
26_D30_T0.5051.00
76_I79_R0.5011.00
96_L104_Q0.5001.00
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 0.7268 100 0.245 Contact Map
1or7A 2 0.8299 100 0.261 Contact Map
2q1zA 1 0.8144 100 0.285 Contact Map
2lfwA 1 0.8093 100 0.289 Contact Map
4nqwA 1 0.701 100 0.291 Contact Map
4g97A 1 0.732 100 0.32 Contact Map
1rp3A 1 0.8608 100 0.321 Contact Map
4yfkF 1 0.9072 100 0.328 Contact Map
3n0rA 1 0.8505 100 0.349 Contact Map
4qicA 2 0.8196 100 0.353 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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