GREMLIN Database
SIGV - RNA polymerase sigma factor SigV
UniProt: O05404 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 166 (152)
Sequences: 41204 (30533)
Seq/√Len: 2476.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
46_K71_T3.1641.00
124_R134_I2.7331.00
21_D61_K2.4391.00
132_E142_T2.3251.00
117_Y155_L2.1781.00
112_E159_Q2.1721.00
109_A159_Q2.1181.00
69_V73_I2.0791.00
26_A68_L2.0761.00
43_S68_L1.9631.00
116_R148_R1.9461.00
129_L137_I1.9121.00
141_N144_T1.8151.00
143_N146_K1.8111.00
59_T62_S1.6941.00
25_L65_Y1.6871.00
74_D77_R1.6851.00
71_T74_D1.6771.00
34_D37_L1.6511.00
50_S53_T1.6351.00
29_Y72_A1.6091.00
117_Y148_R1.5991.00
12_V16_T1.5971.00
35_D75_F1.5871.00
125_F153_L1.5491.00
140_E148_R1.5431.00
47_A64_F1.5271.00
130_K133_E1.5251.00
114_P117_Y1.5121.00
131_L142_T1.4931.00
123_L137_I1.4861.00
150_Y154_K1.4701.00
144_T148_R1.4701.00
32_N35_D1.4681.00
13_T17_D1.4581.00
46_K74_D1.4491.00
131_L149_L1.4491.00
131_L146_K1.4411.00
27_F33_Q1.4301.00
70_R73_I1.4261.00
39_I75_F1.4031.00
140_E145_V1.3981.00
144_T147_T1.3941.00
42_E71_T1.3901.00
22_F68_L1.3651.00
66_K69_V1.3521.00
118_K122_I1.3421.00
155_L159_Q1.3391.00
21_D65_Y1.3361.00
26_A72_A1.3241.00
66_K70_R1.2791.00
120_I149_L1.2771.00
123_L129_L1.2731.00
18_H44_I1.2691.00
54_V57_P1.2631.00
142_T146_K1.2291.00
147_T150_Y1.2291.00
61_K65_Y1.2281.00
120_I148_R1.2111.00
55_R58_E1.2081.00
120_I152_A1.2081.00
18_H61_K1.2071.00
46_K50_S1.1981.00
111_D118_K1.1881.00
132_E136_E1.1821.00
39_I71_T1.1811.00
30_V72_A1.1661.00
23_Y27_F1.1621.00
45_K49_S1.1591.00
147_T151_R1.1581.00
30_V39_I1.1531.00
15_I44_I1.1481.00
43_S67_I1.1481.00
23_Y33_Q1.1461.00
26_A40_V1.1431.00
26_A39_I1.1421.00
15_I19_K1.1331.00
22_F40_V1.1171.00
35_D79_Q1.1071.00
117_Y152_A1.1021.00
11_L48_L1.0951.00
25_L69_V1.0861.00
98_E101_Y1.0821.00
149_L153_L1.0691.00
129_L133_E1.0651.00
124_R131_L1.0391.00
33_Q37_L1.0371.00
134_I145_V1.0291.00
73_I76_L1.0001.00
131_L145_V0.9981.00
75_F79_Q0.9921.00
143_N147_T0.9901.00
19_K23_Y0.9811.00
18_H64_F0.9811.00
43_S71_T0.9801.00
72_A76_L0.9791.00
23_Y37_L0.9781.00
78_K81_K0.9771.00
47_A63_W0.9681.00
125_F149_L0.9561.00
143_N150_Y0.9511.00
58_E62_S0.9411.00
71_T75_F0.9381.00
115_Y119_T0.9351.00
23_Y40_V0.9351.00
117_Y120_I0.9181.00
83_R86_D0.9031.00
109_A156_M0.9011.00
122_I127_E0.9001.00
122_I126_F0.9001.00
22_F64_F0.8931.00
22_F43_S0.8921.00
74_D78_K0.8881.00
24_R28_S0.8791.00
18_H21_D0.8781.00
23_Y36_A0.8661.00
39_I72_A0.8621.00
19_K40_V0.8611.00
123_L134_I0.8601.00
120_I140_E0.8561.00
20_Q24_R0.8551.00
46_K49_S0.8511.00
117_Y151_R0.8431.00
26_A36_A0.8371.00
154_K158_I0.8321.00
27_F36_A0.8301.00
84_V87_D0.8261.00
66_K73_I0.8141.00
116_R140_E0.8091.00
79_Q82_I0.8081.00
63_W67_I0.8071.00
121_I125_F0.8031.00
119_T122_I0.8021.00
109_A112_E0.7991.00
124_R149_L0.7931.00
14_C60_I0.7881.00
78_K82_I0.7871.00
133_E136_E0.7861.00
94_S98_E0.7841.00
103_D107_H0.7611.00
134_I138_T0.7581.00
116_R119_T0.7551.00
41_Q45_K0.7541.00
104_T108_E0.7511.00
123_L138_T0.7491.00
109_A160_L0.7481.00
13_T16_T0.7461.00
130_K134_I0.7451.00
140_E144_T0.7421.00
42_E45_K0.7361.00
21_D25_L0.7311.00
36_A40_V0.7301.00
25_L29_Y0.7211.00
135_A142_T0.7181.00
9_A12_V0.7161.00
107_H111_D0.7111.00
132_E146_K0.7081.00
97_K100_H0.7071.00
105_D108_E0.6971.00
54_V58_E0.6881.00
121_I152_A0.6851.00
27_F31_K0.6841.00
120_I138_T0.6831.00
29_Y73_I0.6601.00
51_V60_I0.6551.00
101_Y104_T0.6491.00
42_E75_F0.6471.00
76_L80_K0.6441.00
94_S97_K0.6431.00
25_L72_A0.6321.00
83_R87_D0.6291.00
68_L72_A0.6261.00
124_R153_L0.6241.00
101_Y105_D0.6241.00
102_K105_D0.6201.00
97_K101_Y0.6171.00
73_I77_R0.6121.00
93_L96_G0.6061.00
39_I68_L0.6061.00
40_V44_I0.6051.00
151_R154_K0.6011.00
123_L127_E0.5961.00
30_V75_F0.5931.00
65_Y69_V0.5931.00
16_T19_K0.5901.00
75_F78_K0.5891.00
151_R155_L0.5851.00
11_L15_I0.5731.00
115_Y118_K0.5711.00
30_V35_D0.5701.00
54_V62_S0.5701.00
43_S47_A0.5701.00
56_N59_T0.5641.00
48_L51_V0.5621.00
38_D41_Q0.5571.00
30_V36_A0.5551.00
131_L134_I0.5551.00
21_D24_R0.5531.00
26_A30_V0.5521.00
146_K150_Y0.5471.00
10_L51_V0.5451.00
29_Y69_V0.5441.00
100_H104_T0.5431.00
69_V119_T0.5391.00
100_H103_D0.5391.00
92_F95_K0.5361.00
155_L158_I0.5321.00
54_V59_T0.5311.00
110_L122_I0.5291.00
9_A13_T0.5291.00
135_A145_V0.5271.00
108_E112_E0.5251.00
98_E102_K0.5241.00
32_N37_L0.5201.00
135_A138_T0.5191.00
10_L13_T0.5171.00
153_L157_R0.5161.00
148_R152_A0.5161.00
19_K44_I0.5141.00
119_T138_T0.5131.00
96_G100_H0.5131.00
121_I156_M0.5131.00
148_R151_R0.5121.00
95_K99_D0.5091.00
62_S65_Y0.5091.00
113_L152_A0.5061.00
107_H110_L0.5051.00
119_T137_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 0.8855 100 0.174 Contact Map
1or7A 2 0.9458 100 0.191 Contact Map
2q1zA 1 0.9639 100 0.211 Contact Map
4nqwA 1 0.8494 100 0.213 Contact Map
4yfkF 1 1 100 0.235 Contact Map
2lfwA 1 0.8855 100 0.244 Contact Map
4g97A 1 0.7169 100 0.25 Contact Map
1rp3A 1 0.9819 100 0.25 Contact Map
3n0rA 1 0.8554 100 0.257 Contact Map
1l0oC 1 0.0602 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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