GREMLIN Database
SIGZ - RNA polymerase sigma factor SigZ
UniProt: O05409 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 176 (154)
Sequences: 38609 (29202)
Seq/√Len: 2353.1

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_K63_T3.1981.00
118_T128_L2.7501.00
13_P53_D2.4611.00
126_K136_Y2.3651.00
111_Y149_K2.2051.00
106_R153_L2.1841.00
18_I60_T2.1171.00
103_T153_L2.0851.00
61_R65_I2.0481.00
35_V60_T1.9641.00
110_K142_R1.9531.00
135_S138_G1.8941.00
123_L131_K1.8691.00
137_S140_K1.8101.00
26_S29_D1.6971.00
17_Y57_Y1.6841.00
63_T66_D1.6801.00
66_D69_R1.6731.00
42_H45_N1.6681.00
21_R64_I1.6531.00
27_I67_F1.6441.00
51_K54_S1.5961.00
111_Y142_R1.5951.00
119_D147_R1.5801.00
134_I142_R1.5781.00
39_I56_I1.5391.00
4_E8_D1.5241.00
124_S127_E1.5081.00
24_D27_I1.5001.00
125_Q136_Y1.4911.00
144_Q148_G1.4781.00
108_P111_Y1.4771.00
138_G142_R1.4721.00
19_S25_Q1.4701.00
38_K66_D1.4681.00
125_Q143_V1.4621.00
62_N65_I1.4471.00
31_L67_F1.4261.00
14_L60_T1.4191.00
125_Q140_K1.4101.00
34_I63_T1.4031.00
134_I139_A1.4011.00
117_L131_K1.3971.00
138_G141_S1.3841.00
58_R61_R1.3711.00
13_P57_Y1.3701.00
5_D9_Q1.3541.00
18_I64_I1.3501.00
114_A143_V1.3361.00
112_R116_E1.3321.00
149_K153_L1.3271.00
10_F36_F1.2971.00
136_Y140_K1.2751.00
141_S144_Q1.2691.00
58_R62_N1.2371.00
53_D57_Y1.2321.00
105_K112_R1.2291.00
22_V31_L1.2181.00
10_F53_D1.2151.00
46_L49_E1.2101.00
35_V59_I1.2061.00
117_L123_L1.2051.00
22_V64_I1.2021.00
15_K25_Q1.1881.00
27_I71_K1.1871.00
114_A142_R1.1871.00
14_L32_L1.1821.00
141_S145_R1.1821.00
37_M41_V1.1741.00
7_W36_F1.1741.00
15_K19_S1.1731.00
18_I31_L1.1721.00
126_K130_E1.1691.00
31_L63_T1.1691.00
38_K42_H1.1691.00
114_A146_G1.1691.00
18_I32_L1.1381.00
7_W11_H1.1251.00
50_Q54_S1.0901.00
17_Y61_R1.0791.00
143_V147_R1.0741.00
92_F95_E1.0701.00
118_T125_Q1.0631.00
64_I68_Y1.0551.00
25_Q29_D1.0491.00
65_I68_Y1.0451.00
128_L139_A1.0401.00
111_Y146_G1.0391.00
15_K29_D1.0361.00
137_S141_S1.0281.00
123_L127_E1.0261.00
125_Q139_A1.0221.00
10_F56_I1.0191.00
35_V63_T1.0021.00
67_F71_K0.9971.00
11_H15_K0.9911.00
39_I55_W0.9821.00
137_S144_Q0.9641.00
111_Y114_A0.9641.00
119_D143_V0.9591.00
70_T73_T0.9441.00
103_T150_L0.9421.00
14_L56_I0.9371.00
15_K28_V0.9311.00
63_T67_F0.9241.00
3_I40_Q0.9231.00
15_K32_L0.9221.00
31_L64_I0.9081.00
148_G152_Q0.9061.00
116_E120_F0.9021.00
109_E113_E0.8911.00
11_H32_L0.8881.00
10_F13_P0.8851.00
19_S28_V0.8831.00
16_T20_H0.8711.00
12_Q16_T0.8641.00
114_A134_I0.8581.00
116_E121_Q0.8581.00
38_K41_V0.8481.00
14_L35_V0.8451.00
66_D70_T0.8431.00
111_Y145_R0.8381.00
117_L128_L0.8341.00
115_L119_D0.8341.00
58_R65_I0.8281.00
127_E130_E0.8221.00
18_I28_V0.8181.00
88_E92_F0.8151.00
43_L52_I0.8011.00
117_L132_L0.7941.00
55_W59_I0.7851.00
103_T106_R0.7831.00
70_T74_S0.7811.00
75_E78_P0.7801.00
71_K74_S0.7801.00
6_L52_I0.7751.00
17_Y21_R0.7711.00
28_V32_L0.7711.00
126_K140_K0.7691.00
124_S128_L0.7691.00
128_L132_L0.7691.00
134_I138_G0.7661.00
113_E116_E0.7641.00
118_T143_V0.7631.00
97_T101_R0.7621.00
110_K134_I0.7581.00
33_Q37_M0.7561.00
110_K113_E0.7561.00
151_K155_E0.7531.00
34_I37_M0.7511.00
129_S136_Y0.7291.00
13_P17_Y0.7261.00
19_S23_N0.7251.00
72_K76_I0.7231.00
115_L146_G0.7221.00
73_T77_L0.7201.00
98_V102_S0.7161.00
47_I50_Q0.7121.00
74_S78_P0.7101.00
101_R105_K0.7091.00
99_C102_S0.7081.00
103_T154_L0.6971.00
46_L50_Q0.6951.00
5_D8_D0.6831.00
95_E98_V0.6701.00
91_N95_E0.6691.00
91_N94_K0.6631.00
114_A132_L0.6631.00
68_Y72_K0.6601.00
57_Y61_R0.6521.00
18_I22_V0.6451.00
21_R65_I0.6451.00
145_R148_G0.6421.00
31_L60_T0.6391.00
88_E91_N0.6361.00
60_T64_I0.6341.00
96_A99_C0.6301.00
118_T147_R0.6281.00
65_I69_R0.6281.00
34_I67_F0.6261.00
49_E52_I0.6191.00
95_E99_C0.6171.00
61_R113_E0.6101.00
22_V67_F0.6071.00
22_V28_V0.6031.00
22_V27_I0.5991.00
17_Y64_I0.5961.00
30_D33_Q0.5961.00
21_R61_R0.5941.00
94_K97_T0.5901.00
145_R149_K0.5871.00
40_Q43_L0.5871.00
67_F70_T0.5871.00
71_K75_E0.5871.00
8_D11_H0.5791.00
46_L51_K0.5751.00
13_P16_T0.5681.00
35_V39_I0.5661.00
149_K152_Q0.5651.00
48_D51_K0.5621.00
117_L121_Q0.5601.00
94_K98_V0.5591.00
24_D29_D0.5571.00
87_A90_E0.5561.00
46_L54_S0.5551.00
109_E112_R0.5511.00
125_Q128_L0.5491.00
72_K75_E0.5451.00
92_F96_A0.5411.00
115_L150_L0.5391.00
86_S89_E0.5321.00
39_I59_I0.5291.00
89_E93_T0.5261.00
129_S132_L0.5251.00
129_S139_A0.5251.00
104_I116_E0.5241.00
7_W33_Q0.5241.00
142_R145_R0.5231.00
147_R151_K0.5201.00
24_D28_V0.5191.00
32_L36_F0.5191.00
54_S57_Y0.5181.00
101_R104_I0.5151.00
102_S106_R0.5141.00
93_T96_A0.5131.00
140_K144_Q0.5111.00
74_S77_L0.5091.00
18_I21_R0.5081.00
150_L154_L0.5051.00
108_P149_K0.5011.00
73_T76_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 0.7898 100 0.22 Contact Map
1or7A 2 0.8523 100 0.235 Contact Map
2lfwA 1 0.892 100 0.249 Contact Map
4g97A 1 0.767 100 0.259 Contact Map
2q1zA 1 0.875 100 0.265 Contact Map
4nqwA 1 0.7614 100 0.27 Contact Map
3n0rA 1 0.892 100 0.288 Contact Map
4qicA 2 0.8636 100 0.293 Contact Map
1rp3A 1 0.892 100 0.309 Contact Map
4yfkF 1 0.9375 100 0.315 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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