GREMLIN Database
FLIA - RNA polymerase sigma factor FliA
UniProt: P0AEM6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11355
Length: 239 (223)
Sequences: 7403 (4484)
Seq/√Len: 300.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
13_K57_E3.6241.00
107_L111_L3.5931.00
110_E123_R3.5331.00
113_R119_E3.2081.00
24_V48_G3.1891.00
194_K198_T3.0611.00
118_T128_I2.9301.00
106_Q123_R2.8521.00
216_V221_V2.6311.00
14_H18_Q2.6211.00
199_L213_V2.2781.00
220_R223_Q2.2671.00
103_A123_R2.2641.00
188_T235_K2.2441.00
117_E132_R2.2001.00
200_Y225_H2.1581.00
193_E231_R2.1491.00
199_L205_L2.1121.00
23_L68_T2.0741.00
195_L213_V2.0561.00
208_K212_A1.9491.00
127_D130_D1.9381.00
60_D63_Q1.9321.00
187_E194_K1.9111.00
219_S222_S1.8841.00
205_L213_V1.8561.00
21_V49_G1.8191.00
47_A82_E1.8151.00
195_L199_L1.8021.00
27_E72_V1.7891.00
195_L214_L1.7761.00
66_A69_T1.7551.00
106_Q110_E1.7251.00
15_S19_R1.7061.00
120_V131_Y1.7001.00
196_V224_L1.6891.00
103_A106_Q1.6781.00
196_V228_A1.6741.00
107_L115_A1.6501.00
170_L174_L1.6501.00
118_T122_E1.6491.00
117_E135_L1.6461.00
214_L221_V1.6461.00
117_E128_I1.6381.00
190_P231_R1.5841.00
27_E79_M1.5811.00
163_D166_R1.5801.00
28_A79_M1.5761.00
10_V14_H1.5451.00
205_L209_E1.5401.00
100_V120_V1.5361.00
45_L49_G1.5351.00
100_V134_M1.5321.00
25_R45_L1.5171.00
58_R70_Y1.5101.00
147_D158_E1.4871.00
17_W53_L1.4751.00
48_G79_M1.4381.00
117_E131_Y1.4291.00
56_V67_F1.4271.00
107_L113_R1.4221.00
28_A45_L1.3911.00
220_R224_L1.3801.00
107_L123_R1.3721.00
128_I132_R1.3661.00
190_P193_E1.3581.00
103_A107_L1.3371.00
34_R38_S1.3191.00
67_F71_A1.3141.00
24_V52_L1.3091.00
28_A41_L1.3071.00
103_A124_L1.3061.00
104_I135_L1.2971.00
193_E227_Q1.2891.00
121_A131_Y1.2581.00
121_A128_I1.2561.00
96_N130_D1.2431.00
95_R99_E1.2401.00
126_I134_M1.2191.00
197_L232_L1.2161.00
100_V124_L1.2141.00
174_L177_N1.2121.00
201_Y225_H1.2031.00
126_I131_Y1.2021.00
9_G12_D1.2001.00
11_M14_H1.1991.00
96_N134_M1.1951.00
199_L210_I1.1661.00
116_T119_E1.1361.00
191_E194_K1.1321.00
177_N181_R1.1301.00
29_L41_L1.1251.00
55_A71_A1.1251.00
219_S223_Q1.1231.00
192_R224_L1.1221.00
115_A119_E1.1201.00
168_N171_Q1.1141.00
96_N126_I1.1121.00
100_V131_Y1.1101.00
111_L115_A1.0961.00
195_L198_T1.0911.00
102_Q106_Q1.0821.00
224_L228_A1.0801.00
51_G55_A1.0551.00
208_K218_E1.0541.00
207_L211_G1.0521.00
39_V82_E1.0471.00
17_W56_V1.0351.00
33_V38_S1.0241.00
87_D94_R1.0181.00
176_S180_Q1.0161.00
11_M15_S1.0151.00
89_V97_A1.0091.00
159_L162_D1.0041.00
179_R183_M1.0011.00
45_L48_G0.9981.00
207_L222_S0.9961.00
207_L219_S0.9961.00
29_L32_Q0.9921.00
108_E115_A0.9781.00
193_E224_L0.9741.00
192_R220_R0.9571.00
20_Y68_T0.9511.00
15_S18_Q0.9491.00
54_N58_R0.9491.00
104_I120_V0.9451.00
207_L218_E0.9441.00
54_N78_A0.9381.00
70_Y74_R0.9351.00
121_A126_I0.9301.00
76_R80_L0.9271.00
181_R184_E0.9211.00
200_Y210_I0.9081.00
151_E155_D0.8961.00
107_L120_V0.8921.00
16_L56_V0.8911.00
25_R49_G0.8891.00
191_E195_L0.8861.00
156_S160_V0.8761.00
192_R196_V0.8731.00
230_K234_T0.8731.00
144_F148_E0.8731.00
103_A120_V0.8721.00
81_D85_S0.8721.00
41_L45_L0.8661.00
170_L173_L0.8651.00
27_E76_R0.8621.00
24_V49_G0.8621.00
108_E111_L0.8581.00
171_Q174_L0.8531.00
49_G53_L0.8501.00
151_E154_G0.8501.00
198_T203_E0.8491.00
111_L119_E0.8481.00
74_R77_G0.8451.00
25_R41_L0.8431.00
90_P93_V0.8381.00
146_Y158_E0.8371.00
82_E86_R0.8311.00
32_Q41_L0.8301.00
132_R136_L0.8291.00
8_E12_D0.8281.00
21_V24_V0.8281.00
111_L123_R0.8261.00
217_G220_R0.8251.00
208_K211_G0.8211.00
152_E156_S0.8141.00
58_R74_R0.8121.00
100_V135_L0.8081.00
225_H228_A0.8021.00
52_L71_A0.8011.00
175_D179_R0.8001.00
173_L177_N0.7961.00
196_V214_L0.7951.00
130_D133_Q0.7900.99
150_R160_V0.7820.99
186_I198_T0.7790.99
96_N99_E0.7780.99
185_A235_K0.7720.99
184_E187_E0.7700.99
210_I225_H0.7700.99
169_P173_L0.7680.99
31_L79_M0.7640.99
26_H29_L0.7620.99
16_L20_Y0.7610.99
69_T72_V0.7520.99
200_Y207_L0.7440.99
108_E114_N0.7420.99
217_G223_Q0.7410.99
84_R91_R0.7400.99
55_A67_F0.7380.99
13_K56_V0.7330.99
201_Y229_I0.7320.99
101_A104_I0.7320.99
196_V216_V0.7310.99
207_L223_Q0.7310.99
65_T69_T0.7280.99
172_Q176_S0.7280.99
192_R223_Q0.7270.99
77_G81_D0.7270.99
131_Y135_L0.7270.99
185_A232_L0.7220.99
183_M198_T0.7070.99
197_L229_I0.7040.99
61_A64_G0.6980.99
173_L176_S0.6970.99
209_E212_A0.6970.99
97_A134_M0.6890.99
23_L72_V0.6880.99
77_G84_R0.6820.99
107_L119_E0.6780.98
93_V97_A0.6780.98
121_A124_L0.6750.98
149_W155_D0.6740.98
193_E228_A0.6690.98
22_P25_R0.6680.98
19_R22_P0.6670.98
185_A228_A0.6640.98
13_K17_W0.6640.98
192_R216_V0.6620.98
180_Q184_E0.6600.98
183_M187_E0.6600.98
51_G79_M0.6580.98
98_R101_A0.6560.98
94_R98_R0.6560.98
43_D46_Q0.6550.98
71_A75_I0.6540.98
133_Q136_L0.6520.98
104_I114_N0.6510.98
26_H30_R0.6510.98
169_P172_Q0.6470.98
200_Y218_E0.6410.98
50_I53_L0.6340.98
207_L220_R0.6340.98
124_L131_Y0.6320.98
211_G218_E0.6300.97
39_V83_L0.6270.97
59_Y63_Q0.6270.97
158_E161_T0.6250.97
167_E175_D0.6220.97
74_R222_S0.6200.97
74_R81_D0.6200.97
97_A138_T0.6160.97
133_Q137_D0.6160.97
190_P228_A0.6140.97
74_R219_S0.6130.97
122_E125_G0.6130.97
115_A120_V0.6120.97
81_D95_R0.6080.97
151_E156_S0.6060.97
185_A188_T0.6040.97
112_G115_A0.6040.97
56_V61_A0.5980.97
207_L225_H0.5950.96
23_L69_T0.5950.96
53_L56_V0.5930.96
7_A12_D0.5920.96
216_V220_R0.5860.96
25_R28_A0.5850.96
97_A100_V0.5810.96
167_E172_Q0.5800.96
150_R159_L0.5800.96
185_A236_L0.5790.96
59_Y65_T0.5790.96
203_E213_V0.5750.96
104_I108_E0.5740.96
80_L91_R0.5700.96
186_I190_P0.5700.96
176_S179_R0.5690.95
21_V45_L0.5690.95
157_I161_T0.5680.95
39_V44_L0.5670.95
21_V25_R0.5660.95
182_V185_A0.5650.95
210_I214_L0.5630.95
160_V163_D0.5630.95
93_V134_M0.5610.95
25_R42_D0.5600.95
103_A111_L0.5590.95
157_I162_D0.5530.95
10_V13_K0.5520.95
107_L110_E0.5510.95
117_E124_L0.5490.95
218_E223_Q0.5490.95
83_L94_R0.5490.95
134_M137_D0.5490.95
99_E103_A0.5480.94
54_N94_R0.5480.94
157_I160_V0.5450.94
54_N57_E0.5440.94
119_E123_R0.5440.94
25_R29_L0.5420.94
182_V236_L0.5400.94
26_H46_Q0.5380.94
78_A82_E0.5370.94
105_G109_Q0.5330.94
145_S148_E0.5320.94
70_Y73_Q0.5310.94
102_Q105_G0.5250.93
175_D183_M0.5230.93
47_A86_R0.5230.93
44_L82_E0.5230.93
116_T120_V0.5220.93
54_N70_Y0.5180.93
131_Y137_D0.5180.93
100_V126_I0.5180.93
27_E75_I0.5160.93
229_I233_R0.5150.92
190_P224_L0.5150.92
24_V56_V0.5140.92
177_N180_Q0.5140.92
46_Q50_I0.5130.92
121_A127_D0.5130.92
8_E11_M0.5130.92
189_L232_L0.5110.92
221_V236_L0.5110.92
120_V124_L0.5110.92
81_D200_Y0.5090.92
117_E121_A0.5090.92
48_G75_I0.5090.92
227_Q230_K0.5080.92
98_R102_Q0.5080.92
28_A40_E0.5070.92
178_L185_A0.5050.92
211_G219_S0.5050.92
144_F149_W0.5030.92
136_L139_N0.5020.92
96_N124_L0.5020.92
52_L67_F0.5010.91
227_Q231_R0.5010.91
200_Y206_N0.5010.91
144_F147_D0.5010.91
150_R156_S0.5000.91
218_E222_S0.5000.91
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  
2a6hF 1 0.9582 100 0.244 Contact Map
1l9zH 1 0.9456 100 0.244 Contact Map
4yfkF 1 0.9791 100 0.292 Contact Map
1rp3A 1 0.9749 100 0.384 Contact Map
1l0oC 1 0.2301 100 0.436 Contact Map
3ugoA 1 0.3515 99.9 0.576 Contact Map
4nqwA 1 0.6025 99.9 0.599 Contact Map
2q1zA 1 0.6987 99.9 0.633 Contact Map
4cxfA 1 0.6192 99.9 0.633 Contact Map
1or7A 2 0.7155 99.8 0.634 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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