GREMLIN Database
CITR - HTH-type transcriptional regulator CitR
UniProt: P39127 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 291 (282)
Sequences: 79461 (57849)
Seq/√Len: 3444.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_R74_D3.6191.00
15_Y24_T3.4181.00
158_H287_S2.6761.00
96_A141_A2.6181.00
67_Y81_E2.4581.00
230_I237_S2.3311.00
11_T24_T2.2661.00
173_K189_Q2.2381.00
164_P241_L2.2201.00
159_C162_K2.2051.00
162_K264_P2.1951.00
92_T123_A2.1951.00
20_K23_E2.1281.00
92_T121_E2.1071.00
14_K69_L2.0911.00
159_C264_P2.0801.00
182_D185_E2.0611.00
45_C60_E2.0571.00
8_T35_H2.0451.00
227_K247_E2.0141.00
10_V65_L2.0111.00
162_K262_Q2.0101.00
94_Q123_A1.9871.00
67_Y74_D1.9801.00
112_R285_F1.9661.00
10_V69_L1.9571.00
11_T14_K1.9231.00
231_K252_Q1.9211.00
8_T32_V1.9041.00
10_V14_K1.9031.00
11_T15_Y1.8941.00
192_L235_G1.8911.00
71_L75_Y1.8821.00
13_A57_L1.8811.00
166_V241_L1.8651.00
18_F36_I1.8361.00
65_L69_L1.8221.00
169_A256_I1.7761.00
49_E56_Q1.7401.00
64_Y78_S1.7371.00
231_K247_E1.7361.00
190_Y217_T1.7151.00
63_A81_E1.6731.00
157_C266_A1.6621.00
178_D185_E1.6581.00
166_V255_R1.6481.00
135_L140_E1.6261.00
13_A65_L1.6231.00
14_K24_T1.6091.00
113_Y282_F1.5921.00
15_Y20_K1.5871.00
9_F65_L1.5841.00
10_V68_A1.5641.00
156_S271_I1.5591.00
8_T27_L1.5541.00
88_G119_E1.5411.00
113_Y120_T1.5191.00
201_W205_L1.5161.00
5_W35_H1.5121.00
19_R29_Q1.5021.00
134_S138_A1.4961.00
59_D62_R1.4951.00
28_S31_T1.4791.00
5_W42_E1.4601.00
5_W38_Q1.4581.00
17_N20_K1.4511.00
158_H269_Y1.4491.00
67_Y70_R1.4431.00
46_K49_E1.4401.00
11_T25_L1.4231.00
10_V72_L1.4221.00
275_E279_E1.4001.00
71_L78_S1.3891.00
146_S268_A1.3861.00
156_S269_Y1.3841.00
67_Y77_N1.3841.00
148_L266_A1.3791.00
103_D224_H1.3571.00
171_P252_Q1.3501.00
90_S119_E1.3471.00
94_Q125_T1.3371.00
137_K154_S1.3311.00
143_I279_E1.3271.00
267_G283_L1.3241.00
136_I144_G1.3121.00
64_Y79_M1.3061.00
135_L141_A1.3061.00
283_L287_S1.3001.00
51_K56_Q1.2961.00
163_D242_S1.2931.00
281_K284_D1.2831.00
42_E79_M1.2821.00
74_D77_N1.2771.00
189_Q236_V1.2751.00
169_A236_V1.2721.00
226_T237_S1.2721.00
143_I267_G1.2701.00
114_T217_T1.2661.00
269_Y283_L1.2641.00
3_F75_Y1.2631.00
112_R116_M1.2531.00
228_R231_K1.2231.00
66_P70_R1.2171.00
241_L245_K1.2131.00
67_Y78_S1.2091.00
37_K41_K1.2061.00
62_R66_P1.2031.00
114_T190_Y1.2011.00
241_L255_R1.1971.00
63_A66_P1.1951.00
247_E252_Q1.1891.00
159_C266_A1.1821.00
9_F48_F1.1791.00
179_N254_I1.1761.00
111_K115_A1.1751.00
174_R189_Q1.1691.00
245_K249_A1.1671.00
116_M285_F1.1651.00
27_L31_T1.1641.00
208_V212_F1.1411.00
9_F13_A1.1391.00
192_L226_T1.1361.00
112_R115_A1.1331.00
157_C268_A1.1321.00
9_F47_L1.1291.00
34_V38_Q1.1261.00
93_L282_F1.1261.00
34_V37_K1.1151.00
111_K232_E1.1071.00
123_A219_K1.1061.00
33_T37_K1.0991.00
18_F55_I1.0981.00
127_F135_L1.0931.00
190_Y215_V1.0931.00
117_N281_K1.0921.00
171_P254_I1.0911.00
102_A126_I1.0911.00
70_R77_N1.0891.00
12_A21_T1.0841.00
7_H76_E1.0821.00
220_V226_T1.0741.00
6_L68_A1.0731.00
113_Y285_F1.0711.00
11_T21_T1.0601.00
71_L74_D1.0581.00
181_I185_E1.0551.00
57_L61_G1.0491.00
202_D205_L1.0431.00
63_A67_Y1.0421.00
108_S232_E1.0381.00
280_K284_D1.0381.00
227_K231_K1.0341.00
35_H38_Q1.0321.00
284_D287_S1.0311.00
170_P233_G1.0301.00
4_K7_H1.0231.00
228_R232_E1.0171.00
137_K152_S1.0101.00
158_H283_L1.0051.00
109_V286_L1.0041.00
79_M83_H0.9981.00
8_T25_L0.9951.00
168_V255_R0.9871.00
27_L32_V0.9821.00
246_R250_E0.9811.00
76_E80_A0.9811.00
76_E79_M0.9751.00
113_Y117_N0.9721.00
167_L236_V0.9721.00
13_A48_F0.9691.00
168_V244_V0.9661.00
169_A173_K0.9641.00
180_E259_Q0.9611.00
64_Y68_A0.9601.00
164_P262_Q0.9551.00
12_A18_F0.9541.00
73_D77_N0.9541.00
9_F57_L0.9411.00
220_V229_F0.9381.00
135_L138_A0.9341.00
276_N279_E0.9301.00
21_T32_V0.9241.00
193_L216_R0.9231.00
125_T135_L0.9201.00
48_F55_I0.9171.00
38_Q41_K0.9161.00
9_F39_L0.9141.00
109_V285_F0.9131.00
96_A144_G0.9061.00
191_L214_F0.9051.00
202_D206_R0.8951.00
45_C82_L0.8941.00
13_A61_G0.8931.00
63_A85_V0.8911.00
173_K190_Y0.8881.00
141_A144_G0.8871.00
20_K24_T0.8841.00
244_V247_E0.8831.00
121_E215_V0.8821.00
169_A174_R0.8801.00
96_A146_S0.8791.00
154_S271_I0.8721.00
173_K176_I0.8711.00
66_P69_L0.8701.00
99_P222_Q0.8621.00
270_A273_L0.8601.00
174_R179_N0.8591.00
185_E188_E0.8551.00
19_R23_E0.8511.00
190_Y216_R0.8511.00
70_R73_D0.8511.00
120_T278_K0.8481.00
133_A137_K0.8471.00
177_E190_Y0.8451.00
16_E56_Q0.8451.00
148_L264_P0.8391.00
155_L268_A0.8371.00
95_L143_I0.8361.00
25_L32_V0.8341.00
51_K54_Q0.8331.00
60_E85_V0.8311.00
168_V237_S0.8281.00
204_L208_V0.8211.00
156_S159_C0.8121.00
91_Q278_K0.8091.00
16_E62_R0.8071.00
257_P260_S0.8071.00
275_E280_K0.8071.00
9_F64_Y0.8071.00
13_A16_E0.8061.00
125_T141_A0.8041.00
37_K46_K0.8031.00
12_A36_I0.7991.00
60_E82_L0.7951.00
247_E250_E0.7941.00
29_Q33_T0.7931.00
248_L251_K0.7871.00
111_K234_L0.7851.00
184_K187_L0.7821.00
89_Y117_N0.7821.00
12_A48_F0.7811.00
170_P234_L0.7771.00
75_Y78_S0.7741.00
182_D259_Q0.7731.00
74_D78_S0.7711.00
173_K177_E0.7701.00
14_K65_L0.7701.00
4_K35_H0.7671.00
91_Q120_T0.7661.00
175_F189_Q0.7641.00
172_D176_I0.7621.00
175_F178_D0.7591.00
60_E63_A0.7591.00
143_I282_F0.7561.00
77_N81_E0.7561.00
114_T234_L0.7551.00
16_E54_Q0.7541.00
75_Y79_M0.7531.00
15_Y21_T0.7521.00
3_F72_L0.7481.00
229_F234_L0.7451.00
5_W8_T0.7451.00
83_H86_R0.7341.00
68_A71_L0.7301.00
187_L212_F0.7271.00
168_V239_L0.7261.00
137_K155_L0.7231.00
78_S82_L0.7211.00
7_H11_T0.7191.00
240_P243_T0.7181.00
277_K281_K0.7171.00
94_Q141_A0.7161.00
56_Q62_R0.7151.00
49_E58_T0.7151.00
57_L62_R0.7121.00
31_T35_H0.7111.00
113_Y281_K0.7111.00
201_W219_K0.7081.00
248_L255_R0.7061.00
12_A32_V0.7061.00
18_F32_V0.7041.00
168_V248_L0.7041.00
97_V102_A0.7021.00
206_R210_M0.7021.00
205_L209_R0.7001.00
231_K250_E0.6981.00
170_P173_K0.6951.00
222_Q225_I0.6911.00
244_V248_L0.6901.00
60_E64_Y0.6881.00
40_E45_C0.6871.00
69_L73_D0.6871.00
116_M281_K0.6861.00
145_L286_L0.6811.00
195_H219_K0.6771.00
49_E54_Q0.6761.00
94_Q142_D0.6741.00
62_R65_L0.6731.00
218_M229_F0.6661.00
174_R178_D0.6631.00
246_R249_A0.6611.00
164_P257_P0.6611.00
188_E215_V0.6611.00
97_V106_L0.6601.00
207_Q210_M0.6581.00
169_A175_F0.6561.00
59_D63_A0.6541.00
169_A254_I0.6531.00
203_D207_Q0.6531.00
73_D76_E0.6501.00
142_D279_E0.6501.00
194_T226_T0.6481.00
77_N80_A0.6471.00
68_A72_L0.6461.00
64_Y82_L0.6451.00
40_E50_R0.6441.00
18_F54_Q0.6431.00
191_L236_V0.6421.00
206_R209_R0.6421.00
139_G270_A0.6401.00
281_K285_F0.6381.00
7_H10_V0.6381.00
172_D175_F0.6341.00
121_E219_K0.6341.00
99_P128_E0.6341.00
93_L278_K0.6321.00
126_I221_T0.6301.00
23_E26_F0.6281.00
172_D233_G0.6261.00
12_A17_N0.6261.00
36_I40_E0.6241.00
103_D228_R0.6221.00
21_T25_L0.6211.00
252_Q255_R0.6181.00
67_Y71_L0.6131.00
167_L186_V0.6091.00
4_K38_Q0.6081.00
176_I254_I0.6081.00
277_K280_K0.6041.00
136_I268_A0.6041.00
273_L276_N0.6031.00
80_A84_R0.6021.00
167_L238_F0.6011.00
63_A82_L0.6011.00
203_D206_R0.6001.00
90_S121_E0.6001.00
180_E185_E0.5991.00
93_L143_I0.5981.00
106_L109_V0.5941.00
143_I283_L0.5941.00
167_L191_L0.5931.00
171_P251_K0.5931.00
172_D254_I0.5881.00
175_F181_I0.5861.00
126_I222_Q0.5831.00
226_T230_I0.5821.00
282_F286_L0.5791.00
161_Y265_Y0.5771.00
201_W207_Q0.5761.00
165_V238_F0.5741.00
195_H221_T0.5741.00
204_L207_Q0.5741.00
108_S111_K0.5731.00
30_P34_V0.5731.00
136_I155_L0.5721.00
156_S272_A0.5721.00
31_T34_V0.5711.00
57_L65_L0.5711.00
96_A127_F0.5711.00
208_V214_F0.5671.00
205_L208_V0.5671.00
7_H72_L0.5641.00
147_C263_L0.5631.00
48_F57_L0.5621.00
28_S34_V0.5621.00
110_M122_M0.5611.00
201_W204_L0.5581.00
269_Y280_K0.5581.00
43_I64_Y0.5571.00
4_K8_T0.5561.00
229_F235_G0.5551.00
45_C49_E0.5541.00
163_D263_L0.5541.00
220_V225_I0.5531.00
43_I82_L0.5531.00
108_S112_R0.5501.00
239_L244_V0.5421.00
91_Q119_E0.5401.00
196_N219_K0.5381.00
173_K236_V0.5381.00
96_A125_T0.5381.00
8_T36_I0.5371.00
66_P81_E0.5371.00
72_L76_E0.5361.00
43_I46_K0.5351.00
160_L267_G0.5331.00
101_I105_V0.5331.00
174_R177_E0.5261.00
117_N120_T0.5241.00
9_F61_G0.5221.00
223_T240_P0.5211.00
72_L75_Y0.5211.00
169_A176_I0.5211.00
202_D207_Q0.5201.00
148_L157_C0.5191.00
8_T21_T0.5191.00
279_E283_L0.5181.00
36_I48_F0.5171.00
46_K60_E0.5161.00
18_F29_Q0.5131.00
184_K212_F0.5131.00
91_Q117_N0.5111.00
18_F50_R0.5101.00
84_R89_Y0.5101.00
6_L64_Y0.5101.00
108_S228_R0.5081.00
68_A75_Y0.5081.00
16_E55_I0.5071.00
183_A258_Y0.5061.00
67_Y82_L0.5031.00
71_L79_M0.5021.00
105_V109_V0.5001.00
97_V124_V0.5001.00
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  
4x6gA 4 1 100 0.104 Contact Map
1uthA 2 0.7526 100 0.104 Contact Map
1ixcA 4 0.9897 100 0.104 Contact Map
2esnA 3 0.9931 100 0.105 Contact Map
3fxqA 3 0.9931 100 0.107 Contact Map
2h98A 2 0.6838 100 0.108 Contact Map
2h9bA 2 0.6907 100 0.111 Contact Map
1al3A 1 0.7045 100 0.111 Contact Map
3fzvA 4 0.9725 100 0.115 Contact Map
3szpA 3 0.9863 100 0.126 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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