GREMLIN Database
RPIR - HTH-type transcriptional regulator RpiR
UniProt: P0ACS7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12459
Length: 296 (261)
Sequences: 8698 (6112)
Seq/√Len: 378.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
142_R189_G4.8201.00
220_C233_A4.0811.00
209_E232_L3.1561.00
194_V208_V2.9261.00
24_Q36_E2.8551.00
137_F217_K2.7571.00
200_R228_P2.7211.00
51_K70_L2.6491.00
142_R187_Q2.6211.00
143_Q169_R2.6101.00
117_R121_E2.5241.00
208_V218_I2.4901.00
212_K234_D2.4451.00
134_A219_I2.3641.00
134_A235_Y2.3461.00
250_N253_A2.2361.00
186_L216_A2.2231.00
142_R190_D2.1811.00
187_Q190_D2.1341.00
41_P44_L2.1301.00
210_L213_K2.1281.00
192_V211_A2.0791.00
135_A267_S2.0391.00
136_R271_L2.0351.00
116_L120_M2.0141.00
73_F82_A1.9441.00
36_E40_K1.9361.00
195_V261_L1.8811.00
159_V163_F1.8731.00
191_V219_I1.8701.00
217_K234_D1.8501.00
137_F235_Y1.8421.00
37_W41_P1.8351.00
141_A191_V1.8151.00
194_V204_V1.7891.00
139_Y271_L1.7871.00
208_V229_I1.7721.00
23_K26_G1.7611.00
196_T229_I1.7121.00
237_I260_L1.7071.00
195_V221_I1.6981.00
211_A216_A1.6941.00
72_G75_G1.6911.00
146_L193_L1.6741.00
217_K235_Y1.6741.00
81_S84_E1.6421.00
130_E133_R1.6401.00
192_V216_A1.6191.00
53_V66_K1.6081.00
127_N130_E1.5461.00
119_I259_T1.5131.00
220_C229_I1.4951.00
31_E70_L1.4941.00
146_L159_V1.4861.00
53_V69_K1.4671.00
112_F119_I1.4591.00
48_P56_A1.4491.00
279_N282_K1.4471.00
230_A236_I1.4431.00
35_V67_V1.4391.00
34_I67_V1.4371.00
218_I233_A1.4341.00
68_S79_L1.4191.00
193_L221_I1.4111.00
272_N275_Q1.4021.00
267_S271_L1.3981.00
76_F80_R1.3941.00
53_V70_L1.3941.00
74_S78_N1.3701.00
139_Y268_V1.3621.00
24_Q32_S1.3591.00
133_R235_Y1.3441.00
220_C236_I1.3431.00
78_N81_S1.3411.00
147_Y192_V1.3281.00
122_G240_P1.3281.00
80_R84_E1.3191.00
146_L156_C1.3121.00
194_V218_I1.3071.00
202_S206_A1.2941.00
22_M26_G1.2821.00
78_N88_S1.2721.00
30_N33_R1.2711.00
239_S257_Q1.2701.00
32_S36_E1.2671.00
136_R140_Q1.2581.00
20_L23_K1.2471.00
270_Q280_M1.2431.00
76_F79_L1.2351.00
212_K232_L1.2301.00
143_Q190_D1.2291.00
151_G250_N1.2251.00
139_Y272_N1.2231.00
137_F191_V1.2201.00
155_I261_L1.2101.00
206_A209_E1.2091.00
194_V211_A1.2081.00
27_M53_V1.1921.00
30_N63_M1.1881.00
276_A279_N1.1821.00
50_I65_V1.1731.00
79_L83_L1.1701.00
266_V283_T1.1671.00
156_C195_V1.1561.00
140_Q217_K1.1401.00
138_F191_V1.1351.00
73_F76_F1.1331.00
22_M25_E1.1251.00
73_F79_L1.1221.00
102_E110_K1.1201.00
37_W57_L1.1101.00
122_G239_S1.1101.00
118_T256_L1.1071.00
19_Y23_K1.1051.00
27_M69_K1.1041.00
267_S270_Q1.1011.00
103_A106_D1.1001.00
138_F268_V1.0931.00
24_Q35_V1.0891.00
190_D216_A1.0791.00
277_N281_Q1.0761.00
157_A174_P1.0571.00
186_L190_D1.0571.00
82_A86_Y1.0501.00
78_N86_Y1.0471.00
133_R137_F1.0471.00
44_L56_A1.0401.00
145_D190_D1.0401.00
158_D162_K1.0321.00
130_E235_Y1.0201.00
42_G46_C1.0131.00
144_R168_V1.0041.00
145_D186_L1.0001.00
210_L214_N0.9961.00
144_R191_V0.9941.00
34_I57_L0.9911.00
76_F86_Y0.9861.00
159_V262_D0.9861.00
134_A137_F0.9831.00
20_L25_E0.9821.00
85_D88_S0.9791.00
82_A85_D0.9751.00
165_R185_L0.9711.00
68_S86_Y0.9701.00
159_V193_L0.9681.00
146_L160_Q0.9581.00
33_R65_V0.9581.00
135_A271_L0.9571.00
279_N283_T0.9571.00
44_L48_P0.9551.00
209_E213_K0.9511.00
109_N113_N0.9411.00
162_K183_A0.9401.00
137_F140_Q0.9351.00
50_I54_A0.9291.00
25_E32_S0.9191.00
120_M124_S0.9191.00
159_V261_L0.9181.00
48_P52_D0.9151.00
65_V75_G0.9131.00
45_S83_L0.9081.00
214_N282_K0.9021.00
186_L192_V0.9011.00
38_L79_L0.8991.00
116_L119_I0.8981.00
37_W48_P0.8981.00
205_K228_P0.8951.00
160_Q171_Q0.8921.00
160_Q164_L0.8921.00
109_N123_Q0.8901.00
230_A238_C0.8841.00
106_D109_N0.8831.00
75_G79_L0.8801.00
221_I261_L0.8781.00
138_F193_L0.8751.00
153_N172_A0.8721.00
20_L26_G0.8711.00
141_A190_D0.8661.00
134_A237_I0.8591.00
205_K209_E0.8551.00
79_L86_Y0.8541.00
129_D132_H0.8531.00
222_T230_A0.8511.00
138_F144_R0.8431.00
160_Q170_C0.8431.00
134_A264_F0.8421.00
105_Q109_N0.8381.00
121_E124_S0.8381.00
78_N82_A0.8371.00
117_R120_M0.8301.00
30_N69_K0.8291.00
37_W56_A0.8261.00
155_I195_V0.8161.00
133_R136_R0.8131.00
144_R193_L0.8131.00
158_D254_R0.8101.00
160_Q172_A0.8101.00
28_T31_E0.8051.00
93_V97_E0.8021.00
132_H271_L0.7991.00
143_Q171_Q0.7881.00
160_Q265_F0.7861.00
37_W44_L0.7821.00
130_E134_A0.7811.00
79_L87_F0.7791.00
171_Q179_M0.7761.00
104_P113_N0.7701.00
108_V128_V0.7681.00
53_V64_I0.7651.00
122_G256_L0.7651.00
211_A218_I0.7631.00
225_Y238_C0.7631.00
136_R139_Y0.7601.00
77_R80_R0.7601.00
143_Q187_Q0.7591.00
75_G78_N0.7591.00
160_Q268_V0.7581.00
27_M70_L0.7541.00
84_E88_S0.7501.00
46_C49_A0.7471.00
93_V96_S0.7431.00
159_V162_K0.7421.00
46_C84_E0.7391.00
132_H267_S0.7361.00
115_T259_T0.7351.00
275_Q280_M0.7291.00
81_S85_D0.7291.00
146_L170_C0.7241.00
66_K70_L0.7221.00
205_K229_I0.7211.00
23_K27_M0.7181.00
183_A214_N0.7151.00
62_A65_V0.7111.00
51_K61_E0.7111.00
256_L259_T0.7111.00
145_D192_V0.7111.00
49_A52_D0.7111.00
146_L163_F0.7101.00
165_R183_A0.7091.00
83_L87_F0.7071.00
104_P132_H0.7061.00
125_I240_P0.7040.99
49_A54_A0.7030.99
153_N157_A0.6970.99
53_V76_F0.6960.99
149_A201_T0.6930.99
135_A139_Y0.6890.99
157_A160_Q0.6880.99
177_H203_D0.6850.99
189_G217_K0.6850.99
129_D133_R0.6840.99
112_F259_T0.6830.99
142_R169_R0.6810.99
160_Q168_V0.6800.99
138_F141_A0.6790.99
34_I64_I0.6790.99
38_L67_V0.6790.99
245_P248_G0.6780.99
278_I282_K0.6780.99
200_R223_H0.6750.99
235_Y238_C0.6730.99
278_I281_Q0.6720.99
34_I63_M0.6720.99
67_V71_L0.6710.99
47_A50_I0.6700.99
128_V132_H0.6690.99
222_T227_S0.6680.99
154_A157_A0.6680.99
155_I257_Q0.6670.99
196_T199_G0.6630.99
121_E125_I0.6620.99
137_F141_A0.6600.99
194_V207_A0.6590.99
275_Q279_N0.6590.99
63_M66_K0.6580.99
265_F269_A0.6570.99
208_V232_L0.6560.99
191_V217_K0.6530.99
33_R58_A0.6520.99
66_K69_K0.6520.99
105_Q128_V0.6500.99
177_H206_A0.6480.99
156_C159_V0.6460.99
98_L102_E0.6450.99
83_L86_Y0.6440.99
72_G79_L0.6440.99
247_L250_N0.6440.99
251_A254_R0.6420.99
152_S257_Q0.6410.99
25_E29_E0.6410.99
33_R61_E0.6400.99
45_S48_P0.6390.99
27_M66_K0.6370.99
80_R87_F0.6370.99
76_F81_S0.6350.99
239_S256_L0.6350.99
163_F268_V0.6310.99
122_G260_L0.6310.99
77_R81_S0.6300.99
266_V280_M0.6270.99
157_A169_R0.6250.99
254_R257_Q0.6240.99
20_L67_V0.6230.99
27_M54_A0.6210.99
132_H135_A0.6190.99
19_Y22_M0.6190.99
28_T70_L0.6180.99
78_N87_F0.6180.99
168_V173_Y0.6180.99
277_N280_M0.6150.99
193_L219_I0.6120.99
115_T255_I0.6090.99
270_Q277_N0.6090.99
48_P53_V0.6050.98
20_L27_M0.6040.98
227_S230_A0.6030.98
107_V110_K0.6030.98
131_I263_A0.6020.98
184_S210_L0.6010.98
140_Q189_G0.5970.98
233_A236_I0.5960.98
52_D55_E0.5950.98
38_L45_S0.5890.98
111_V115_T0.5880.98
135_A268_V0.5850.98
228_P232_L0.5850.98
179_M183_A0.5840.98
33_R64_I0.5840.98
121_E240_P0.5830.98
157_A161_H0.5800.98
147_Y186_L0.5800.98
112_F115_T0.5780.98
68_S75_G0.5770.98
194_V220_C0.5770.98
145_D171_Q0.5740.98
80_R83_L0.5730.98
183_A216_A0.5690.98
148_G152_S0.5670.98
220_C227_S0.5630.98
206_A210_L0.5620.98
165_R184_S0.5600.98
254_R258_L0.5590.97
94_L99_A0.5590.97
161_H164_L0.5560.97
146_L195_V0.5540.97
212_K218_I0.5540.97
237_I264_F0.5530.97
43_N47_A0.5490.97
169_R173_Y0.5490.97
221_I239_S0.5460.97
196_T220_C0.5420.97
79_L84_E0.5400.97
198_S201_T0.5400.97
205_K232_L0.5400.97
56_A66_K0.5390.97
147_Y194_V0.5380.97
111_V259_T0.5370.97
183_A210_L0.5360.97
61_E65_V0.5360.97
259_T262_D0.5360.97
230_A233_A0.5330.97
149_A203_D0.5330.97
222_T236_I0.5320.97
174_P178_I0.5320.97
27_M35_V0.5310.97
94_L97_E0.5310.97
221_I260_L0.5310.97
239_S260_L0.5280.96
148_G203_D0.5270.96
188_E215_G0.5270.96
112_F122_G0.5270.96
147_Y207_A0.5230.96
250_N255_I0.5230.96
151_G161_H0.5220.96
42_G45_S0.5220.96
113_N117_R0.5210.96
113_N116_L0.5200.96
20_L35_V0.5180.96
72_G76_F0.5160.96
269_A280_M0.5160.96
274_E278_I0.5150.96
76_F88_S0.5140.96
145_D183_A0.5110.96
141_A217_K0.5080.96
113_N120_M0.5070.96
71_L85_D0.5070.96
80_R88_S0.5060.96
266_V269_A0.5060.96
116_L123_Q0.5060.96
273_I276_A0.5050.95
219_I235_Y0.5020.95
123_Q263_A0.5000.95
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  
4ivnA 2 0.8919 100 0.202 Contact Map
3shoA 4 0.6284 100 0.545 Contact Map
2xhzA 4 0.5777 100 0.561 Contact Map
3fxaA 4 0.6419 100 0.566 Contact Map
3etnA 4 0.6318 100 0.571 Contact Map
1m3sA 4 0.6014 100 0.583 Contact Map
1vimA 4 0.6182 100 0.586 Contact Map
2pocA 4 0.6486 100 0.59 Contact Map
1jeoA 4 0.5811 100 0.59 Contact Map
4s12A 2 0.7264 99.9 0.595 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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