GREMLIN Database
RPSF - RNA polymerase sigma-F factor
UniProt: P07860 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 255 (227)
Sequences: 7365 (4386)
Seq/√Len: 291.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
127_L131_L3.7521.00
34_R75_D3.6161.00
133_R139_E3.3421.00
130_T143_H3.2491.00
45_V66_G3.1321.00
208_K212_Y3.0001.00
126_E143_H2.8961.00
230_I235_V2.8251.00
138_Q148_A2.8181.00
25_Q30_D2.7981.00
35_D39_E2.6331.00
123_A143_H2.4291.00
213_L227_R2.2611.00
207_E245_Q2.2471.00
234_Q237_R2.2101.00
202_D249_Q2.1351.00
213_L219_Q2.1111.00
214_R239_E2.1031.00
137_V152_V2.0911.00
209_L227_R2.0211.00
222_S226_E1.9951.00
44_L86_S1.9571.00
201_S208_K1.9571.00
147_E150_D1.9561.00
127_L135_P1.8261.00
78_D81_Y1.8211.00
219_Q227_R1.8181.00
48_V90_V1.8131.00
209_L213_L1.7751.00
210_I238_L1.7661.00
126_E130_T1.7581.00
210_I242_I1.7491.00
42_M67_C1.7451.00
65_I100_F1.7451.00
209_L228_L1.7221.00
233_V236_S1.7141.00
204_E245_Q1.7101.00
36_L40_K1.6841.00
165_H177_T1.6521.00
140_I151_V1.6401.00
84_R87_T1.6261.00
228_L235_V1.6201.00
120_I140_I1.6111.00
48_V97_I1.5951.00
137_V148_A1.5841.00
138_Q142_D1.5771.00
76_K88_Y1.5681.00
137_V155_Q1.5681.00
123_A127_L1.5481.00
63_F67_C1.5461.00
123_A126_E1.5391.00
46_W63_F1.5221.00
31_Q35_D1.5211.00
38_I71_L1.5091.00
49_V97_I1.4941.00
120_I154_A1.4851.00
66_G97_I1.4781.00
219_Q223_E1.4731.00
137_V151_V1.4281.00
27_Q80_T1.4141.00
124_K155_Q1.4061.00
74_V85_F1.4061.00
204_E207_E1.3991.00
127_L143_H1.3921.00
148_A152_V1.3761.00
165_H179_L1.3721.00
234_Q238_L1.3711.00
127_L133_R1.3541.00
49_V63_F1.3541.00
116_L146_I1.3361.00
85_F89_A1.3361.00
49_V59_P1.3131.00
115_E119_K1.3101.00
123_A144_L1.2901.00
141_A151_V1.2801.00
207_E241_K1.2771.00
45_V70_L1.2601.00
146_I151_V1.2541.00
141_A148_A1.2351.00
211_V246_I1.2351.00
23_I26_S1.2281.00
146_I154_A1.2261.00
32_Q35_D1.2061.00
116_L154_A1.1811.00
215_Y239_E1.1771.00
191_F195_A1.1681.00
120_I144_L1.1671.00
136_T139_E1.1611.00
50_Q59_P1.1501.00
23_I27_Q1.1431.00
188_E191_F1.1431.00
27_Q79_L1.1211.00
193_K197_K1.1011.00
205_E208_K1.1001.00
238_L242_I1.0811.00
57_Y100_F1.0781.00
135_P139_E1.0771.00
120_I151_V1.0721.00
38_I74_V1.0701.00
24_K80_T1.0681.00
73_S89_A1.0681.00
25_Q28_N1.0601.00
209_L212_Y1.0561.00
221_Q225_A1.0551.00
213_L224_V1.0521.00
206_R238_L1.0431.00
141_A146_I1.0381.00
24_K28_N1.0351.00
116_L150_D1.0291.00
233_V237_R1.0241.00
50_Q53_L1.0171.00
105_G114_K1.0111.00
128_S135_P1.0101.00
69_G73_S1.0091.00
222_S232_Q0.9991.00
183_A186_S0.9851.00
244_K248_V0.9781.00
122_R126_E0.9731.00
221_Q233_V0.9721.00
123_A140_I0.9711.00
124_K140_I0.9581.00
26_S29_G0.9521.00
221_Q232_Q0.9481.00
32_Q36_L0.9451.00
63_F66_G0.9441.00
221_Q236_S0.9411.00
206_R234_Q0.9381.00
94_I98_Q0.9341.00
189_K193_K0.9301.00
25_Q36_L0.9301.00
164_I179_L0.9291.00
195_A198_E0.9251.00
53_L59_P0.9201.00
184_D187_E0.9161.00
128_S134_V0.9151.00
72_K76_K0.9131.00
37_L74_V0.9131.00
222_S225_A0.9051.00
25_Q33_A0.9041.00
174_D181_Q0.9031.00
131_L135_P0.9011.00
190_W194_I0.9001.00
207_E238_L0.8991.00
127_L140_I0.8931.00
48_V94_I0.8881.00
214_R224_V0.8881.00
45_V67_C0.8801.00
41_N86_S0.8751.00
59_P63_F0.8731.00
210_I230_I0.8731.00
88_Y92_M0.8691.00
131_L139_E0.8681.00
30_D33_A0.8621.00
72_K96_E0.8561.00
24_K79_L0.8561.00
152_V156_E0.8481.00
36_L39_E0.8471.00
109_V117_G0.8471.00
70_L89_A0.8431.00
212_Y217_K0.8381.00
67_C71_L0.8351.00
162_S166_E0.8321.00
46_W59_P0.8311.00
76_K92_M0.8301.00
46_W67_C0.8301.00
200_I212_Y0.8271.00
92_M95_G0.8261.00
205_E209_L0.8201.00
210_I228_L0.8201.00
206_R210_I0.8181.00
110_S113_L0.8151.00
128_S131_L0.8101.00
47_S50_Q0.7940.99
99_R103_D0.7840.99
120_I155_Q0.7820.99
100_F104_D0.7800.99
42_M45_V0.7790.99
231_S234_Q0.7750.99
29_G33_A0.7670.99
150_D153_L0.7660.99
224_V239_E0.7590.99
22_L26_S0.7590.99
117_G154_A0.7560.99
26_S37_L0.7550.99
102_R111_R0.7550.99
37_L41_N0.7520.99
27_Q30_D0.7490.99
22_L36_L0.7490.99
73_S85_F0.7380.99
214_R221_Q0.7370.99
83_V87_T0.7320.99
211_V243_L0.7320.99
239_E242_I0.7290.99
34_R74_V0.7270.99
22_L33_A0.7270.99
119_K122_R0.7260.99
131_L143_H0.7250.99
113_L117_G0.7250.99
199_A249_Q0.7190.99
116_L119_K0.7180.99
52_F97_I0.7170.99
198_E201_S0.7130.99
89_A93_I0.7090.99
168_V181_Q0.7080.99
207_E242_I0.7030.99
116_L144_L0.6980.99
151_V155_Q0.6970.99
221_Q237_R0.6930.99
87_T90_V0.6890.98
114_K118_N0.6870.98
197_K212_Y0.6870.98
197_K201_S0.6840.98
44_L90_V0.6810.98
47_S51_R0.6810.98
117_G158_V0.6800.98
221_Q234_Q0.6790.98
199_A246_I0.6760.98
95_G99_R0.6750.98
231_S237_R0.6740.98
68_I71_L0.6730.98
177_T180_D0.6660.98
118_N121_R0.6650.98
106_T161_P0.6640.98
95_G102_R0.6640.98
69_G97_I0.6630.98
154_A157_A0.6580.98
215_Y243_L0.6550.98
24_K27_Q0.6540.98
44_L87_T0.6510.98
79_L82_D0.6470.98
27_Q78_D0.6450.98
141_A144_L0.6430.98
77_F81_Y0.6420.98
223_E226_E0.6410.98
163_S167_T0.6390.97
178_L181_Q0.6380.97
121_R124_K0.6360.97
177_T181_Q0.6340.97
206_R230_I0.6330.97
132_G135_P0.6320.97
194_I198_E0.6300.97
190_W193_K0.6280.97
103_D108_K0.6260.97
217_K227_R0.6260.97
23_I79_L0.6230.97
40_K43_R0.6220.97
43_R46_W0.6220.97
92_M233_V0.6210.97
153_L156_E0.6210.97
127_L139_E0.6210.97
153_L157_A0.6180.97
199_A242_I0.6180.97
214_R220_T0.6120.97
230_I234_Q0.6110.97
206_R237_R0.6110.97
124_K134_V0.6100.97
77_F83_V0.6090.97
61_D64_Q0.6080.97
92_M236_S0.6080.97
199_A202_D0.6070.97
112_S115_E0.6050.96
120_I146_I0.6040.96
72_K88_Y0.6030.96
144_L151_V0.6030.96
225_A232_Q0.6010.96
46_W60_D0.6010.96
57_Y101_I0.6000.96
28_N33_A0.6000.96
243_L247_K0.5990.96
119_K123_A0.5960.96
62_L100_F0.5930.96
221_Q239_E0.5930.96
99_R214_R0.5920.96
204_E242_I0.5920.96
47_S64_Q0.5910.96
46_W49_V0.5900.96
42_M46_W0.5900.96
72_K75_D0.5900.96
214_R232_Q0.5890.96
224_V228_L0.5860.96
169_Y181_Q0.5850.96
42_M63_F0.5800.96
71_L74_V0.5780.95
139_E143_H0.5770.95
203_L246_I0.5740.95
135_P140_I0.5710.95
113_L154_A0.5650.95
191_F194_I0.5640.95
151_V154_A0.5620.95
142_D145_E0.5620.95
26_S33_A0.5610.95
225_A233_V0.5600.95
66_G93_I0.5590.95
196_L250_M0.5590.95
168_V174_D0.5580.95
65_I104_D0.5570.94
34_R38_I0.5570.94
169_Y172_D0.5550.94
226_E229_G0.5540.94
22_L25_Q0.5520.94
45_V97_I0.5500.94
232_Q237_R0.5500.94
92_M99_R0.5490.94
64_Q68_I0.5490.94
124_K135_P0.5430.94
141_A147_E0.5430.94
192_D199_A0.5420.94
95_G236_S0.5420.94
183_A187_E0.5410.94
163_S166_E0.5360.93
204_E238_L0.5360.93
179_L182_I0.5340.93
169_Y173_G0.5330.93
161_P165_H0.5320.93
188_E192_D0.5320.93
162_S165_H0.5320.93
160_A165_H0.5260.93
117_G120_I0.5250.93
46_W50_Q0.5240.93
57_Y62_L0.5240.93
168_V177_T0.5230.92
136_T140_I0.5210.92
49_V62_L0.5200.92
137_V144_L0.5200.92
69_G93_I0.5190.92
200_I204_E0.5190.92
98_Q111_R0.5130.92
101_I114_K0.5130.92
69_G89_A0.5120.92
104_D110_S0.5110.92
124_K128_S0.5100.91
74_V79_L0.5100.91
31_Q34_R0.5090.91
196_L199_A0.5080.91
41_N44_L0.5060.91
186_S189_K0.5050.91
60_D67_C0.5050.91
232_Q236_S0.5020.91
156_E159_R0.5010.91
241_K244_K0.5000.91
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 0.9725 100 0.224 Contact Map
1l9zH 1 0.9569 100 0.224 Contact Map
4yfkF 1 0.9922 100 0.305 Contact Map
1l0oC 1 0.2235 100 0.4 Contact Map
1rp3A 1 0.8784 100 0.488 Contact Map
3ugoA 1 0.4118 100 0.526 Contact Map
4nqwA 1 0.5804 99.9 0.608 Contact Map
4cxfA 1 0.6039 99.9 0.653 Contact Map
1or7A 2 0.7216 99.9 0.654 Contact Map
2q1zA 1 0.6863 99.9 0.658 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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