GREMLIN Database
SIGY - RNA polymerase sigma factor SigY
UniProt: P94370 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 178 (158)
Sequences: 44269 (31871)
Seq/√Len: 2535.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_K81_L3.1601.00
139_R149_I2.6061.00
31_F71_S2.4421.00
132_L170_Q2.3041.00
147_A157_E2.2921.00
127_K174_E2.2571.00
79_S83_L2.1911.00
124_L174_E2.0911.00
144_Y152_M2.0261.00
36_L78_A2.0131.00
131_K163_R1.9771.00
53_T78_A1.9461.00
138_L152_M1.9021.00
158_G161_K1.7871.00
138_L144_Y1.6871.00
155_I163_R1.6751.00
22_T26_H1.6601.00
44_D47_E1.6581.00
69_K72_T1.6341.00
129_D132_L1.6331.00
60_H63_S1.6251.00
132_L163_R1.6031.00
35_Y75_I1.5951.00
23_A27_Y1.5861.00
45_L85_H1.5811.00
81_L84_D1.5781.00
84_D87_K1.5701.00
146_Y157_E1.5621.00
145_T148_E1.5621.00
156_K159_T1.5551.00
57_G74_L1.5381.00
39_L82_Y1.5221.00
42_H45_L1.5221.00
165_H169_Q1.5161.00
31_F75_I1.5141.00
159_T163_R1.4661.00
140_H168_L1.4511.00
56_K84_D1.4471.00
146_Y164_V1.4461.00
146_Y161_K1.4341.00
133_R137_L1.4161.00
52_E81_L1.4111.00
49_L85_H1.3901.00
159_T162_S1.3891.00
32_L78_A1.3781.00
170_Q174_E1.3761.00
37_L43_P1.3711.00
28_H71_S1.3591.00
155_I160_V1.3201.00
71_S75_I1.3041.00
76_S79_S1.3041.00
157_E161_K1.2991.00
36_L82_Y1.2971.00
56_K60_H1.2951.00
80_R83_L1.2781.00
135_P163_R1.2581.00
55_L59_I1.2511.00
162_S165_H1.2471.00
139_R164_V1.2211.00
135_P167_G1.2191.00
33_Y43_P1.1971.00
76_S80_R1.1941.00
135_P164_V1.1921.00
113_A116_A1.1781.00
132_L167_G1.1741.00
144_Y148_E1.1701.00
40_S82_Y1.1391.00
53_T77_I1.1371.00
25_F29_Y1.1371.00
147_A151_V1.1371.00
40_S49_L1.1321.00
33_Y37_L1.1301.00
25_F54_F1.1291.00
126_S133_R1.1281.00
162_S166_K1.1201.00
64_F67_R1.1151.00
139_R146_Y1.1081.00
28_H54_F1.1071.00
140_H164_V1.0901.00
29_Y33_Y1.0891.00
85_H89_R1.0841.00
32_L50_V1.0831.00
36_L49_L1.0791.00
35_Y79_S1.0701.00
21_F58_Y1.0561.00
158_G162_S1.0541.00
164_V168_L1.0511.00
124_L127_K1.0451.00
43_P47_E1.0391.00
45_L89_R1.0321.00
81_L85_H1.0171.00
53_T81_L1.0121.00
49_L81_L1.0041.00
132_L166_K1.0011.00
84_D88_K1.0011.00
36_L50_V1.0001.00
146_Y160_V0.9911.00
149_I160_V0.9901.00
138_L149_I0.9871.00
137_L141_Y0.9841.00
28_H74_L0.9771.00
33_Y47_E0.9751.00
83_L86_Q0.9651.00
82_Y86_Q0.9641.00
37_L46_S0.9571.00
28_H31_F0.9521.00
130_P134_T0.9451.00
118_W122_L0.9421.00
68_S72_T0.9291.00
134_T137_L0.9281.00
33_Y50_V0.9251.00
132_L135_P0.9191.00
18_D22_T0.9101.00
34_K38_K0.9081.00
49_L82_Y0.9061.00
32_L53_T0.9061.00
29_Y50_V0.9051.00
137_L142_Y0.8911.00
131_K155_I0.8911.00
135_P155_I0.8911.00
32_L74_L0.8891.00
36_L46_S0.8821.00
24_L70_F0.8771.00
124_L171_I0.8751.00
158_G165_H0.8731.00
33_Y46_S0.8721.00
88_K91_R0.8641.00
30_S34_K0.8631.00
155_I159_T0.8591.00
56_K59_I0.8551.00
169_Q173_K0.8311.00
134_T138_L0.8191.00
134_T153_L0.8121.00
109_W113_A0.8031.00
23_A26_H0.8021.00
52_E85_H0.8011.00
52_E55_L0.8001.00
136_V140_H0.7961.00
150_G157_E0.7891.00
76_S83_L0.7891.00
124_L175_W0.7871.00
147_A161_K0.7801.00
73_W77_I0.7761.00
136_V167_G0.7751.00
89_R92_E0.7671.00
57_G73_W0.7631.00
19_E22_T0.7631.00
50_V54_F0.7511.00
51_Q55_L0.7441.00
21_F62_R0.7321.00
138_L153_L0.7321.00
93_W96_N0.7301.00
148_E151_V0.7271.00
149_I153_L0.7261.00
119_S123_D0.7231.00
135_P153_L0.7061.00
31_F35_Y0.7041.00
116_A120_E0.7031.00
46_S50_V0.7021.00
120_E123_D0.6971.00
145_T149_I0.6941.00
122_L126_S0.6941.00
117_E120_E0.6911.00
65_Q68_S0.6831.00
35_Y39_L0.6831.00
95_R98_T0.6781.00
39_L83_L0.6731.00
92_E96_N0.6721.00
88_K92_E0.6711.00
109_W112_S0.6701.00
75_I79_S0.6641.00
131_K134_T0.6641.00
116_A119_S0.6611.00
138_L142_Y0.6511.00
29_Y54_F0.6441.00
26_H29_Y0.6421.00
115_G118_W0.6411.00
83_L87_K0.6341.00
112_S116_A0.6331.00
112_S115_G0.6291.00
108_K111_V0.6291.00
39_L79_S0.6251.00
95_R99_V0.6241.00
37_L41_L0.6231.00
166_K170_Q0.6231.00
90_K94_K0.6221.00
91_R95_R0.6221.00
85_H88_K0.6181.00
67_R70_F0.6161.00
86_Q90_K0.6111.00
48_E51_Q0.6101.00
58_Y61_L0.6081.00
57_G77_I0.6021.00
166_K169_Q0.6001.00
89_R93_W0.6001.00
94_K98_T0.5941.00
31_F34_K0.5931.00
163_R167_G0.5911.00
78_A82_Y0.5811.00
115_G119_S0.5781.00
35_Y82_Y0.5731.00
107_I110_D0.5701.00
168_L172_R0.5681.00
94_K97_Q0.5671.00
86_Q89_R0.5641.00
136_V171_I0.5631.00
66_G69_K0.5621.00
82_Y85_H0.5601.00
53_T57_G0.5571.00
128_L167_G0.5561.00
113_A117_E0.5551.00
93_W97_Q0.5551.00
64_F68_S0.5511.00
150_G153_L0.5501.00
114_K117_E0.5481.00
57_G70_F0.5471.00
19_E23_A0.5461.00
130_P133_R0.5461.00
36_L39_L0.5451.00
123_D127_K0.5441.00
134_T152_M0.5411.00
40_S46_S0.5411.00
20_A61_L0.5381.00
146_Y149_I0.5371.00
61_L70_F0.5311.00
111_V115_G0.5311.00
108_K112_S0.5281.00
120_E124_L0.5281.00
40_S45_L0.5261.00
96_N100_T0.5241.00
110_D114_K0.5241.00
90_K93_W0.5181.00
150_G160_V0.5151.00
21_F25_F0.5141.00
129_D170_Q0.5121.00
64_F69_K0.5111.00
161_K165_H0.5001.00
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 0.8596 100 0.137 Contact Map
1or7A 2 0.9494 100 0.15 Contact Map
2q1zA 1 0.9775 100 0.167 Contact Map
4nqwA 1 0.8258 100 0.18 Contact Map
4yfkF 1 1 100 0.2 Contact Map
1l0oC 1 0.073 100 0.22 Contact Map
1rp3A 1 0.9438 100 0.248 Contact Map
2lfwA 1 0.809 100 0.256 Contact Map
4g97A 1 0.6517 100 0.262 Contact Map
2a6hF 1 0.9719 100 0.269 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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