GREMLIN Database
YRKJ - UPF0721 transmembrane protein YrkJ
UniProt: P54437 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 261 (242)
Sequences: 9685 (6698)
Seq/√Len: 430.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
92_G153_F3.7891.00
18_F232_V3.6861.00
99_F157_G3.0371.00
78_N184_V2.9521.00
10_F221_T2.7321.00
72_R79_K2.5481.00
239_K243_W2.5461.00
66_G223_L2.4251.00
151_L173_I2.3791.00
62_F219_M2.3661.00
12_I34_M2.3461.00
86_G195_L2.3241.00
240_F243_W2.3061.00
121_I125_I2.2561.00
231_S235_K2.2541.00
66_G227_P2.1981.00
88_S149_S2.1911.00
57_A200_A2.1681.00
82_I191_A2.1641.00
181_P184_V2.1171.00
94_V203_G2.0481.00
113_G253_A2.0231.00
120_V253_A1.9931.00
254_I258_L1.9211.00
55_I215_A1.9161.00
51_E54_G1.9121.00
81_L180_I1.8941.00
237_N240_F1.8571.00
78_N81_L1.8051.00
71_Y76_L1.7861.00
58_I215_A1.7831.00
14_F224_I1.7581.00
120_V250_G1.7441.00
80_T83_I1.7431.00
16_G30_I1.7341.00
70_A230_A1.7161.00
13_G218_L1.7111.00
14_F225_A1.6811.00
35_L218_L1.6751.00
6_I217_V1.6621.00
117_I253_A1.6271.00
155_I169_I1.6011.00
124_F246_A1.5881.00
98_Y102_Y1.5761.00
18_F228_I1.5681.00
71_Y233_G1.5651.00
83_I87_S1.5501.00
90_L199_G1.5471.00
80_T84_Y1.5361.00
153_F157_G1.5321.00
211_L214_P1.5241.00
120_V246_A1.5201.00
250_G254_I1.5101.00
74_S234_Q1.4691.00
83_I86_G1.4671.00
216_L220_I1.4621.00
82_I188_S1.4611.00
11_I15_I1.4361.00
107_G111_I1.4291.00
243_W247_Q1.4171.00
114_I118_I1.4051.00
68_V191_A1.3871.00
202_V206_I1.3851.00
227_P231_S1.3751.00
13_G221_T1.3731.00
128_K131_K1.3611.00
205_V212_F1.3601.00
92_G96_G1.3501.00
220_I224_I1.3471.00
95_L153_F1.3451.00
67_G190_L1.3441.00
61_F198_I1.3351.00
113_G257_W1.3211.00
170_L192_I1.3091.00
213_V217_V1.3091.00
115_L162_L1.3061.00
76_L187_A1.3051.00
76_L234_Q1.3001.00
7_T11_I1.2971.00
247_Q251_A1.2961.00
65_L194_F1.2951.00
69_W73_K1.2791.00
51_E211_L1.2721.00
94_V98_Y1.2661.00
68_V72_R1.2581.00
88_S152_A1.2501.00
225_A229_G1.2471.00
146_W150_S1.2421.00
36_L49_A1.2401.00
93_S200_A1.2351.00
79_K83_I1.2291.00
79_K82_I1.2161.00
171_V185_T1.2121.00
10_F217_V1.1991.00
89_I196_S1.1981.00
48_T51_E1.1981.00
113_G117_I1.1961.00
88_S92_G1.1651.00
203_G207_T1.1581.00
97_S203_G1.1561.00
103_I161_I1.1541.00
65_L69_W1.1531.00
193_T196_S1.1501.00
67_G226_S1.1441.00
71_Y230_A1.1421.00
92_G157_G1.1271.00
123_M245_L1.1111.00
183_R233_G1.1091.00
125_I128_K1.1081.00
148_A178_L1.1081.00
175_L185_T1.1051.00
10_F220_I1.1041.00
221_T225_A1.1011.00
53_S204_K1.1001.00
225_A228_I1.0761.00
87_S91_L1.0661.00
209_Q213_V1.0541.00
47_L214_P1.0541.00
68_V79_K1.0511.00
146_W149_S1.0431.00
85_M174_M1.0311.00
164_A168_F1.0271.00
144_N147_L1.0131.00
150_S154_I1.0101.00
175_L182_V0.9891.00
70_A227_P0.9891.00
31_N218_L0.9881.00
128_K132_G0.9861.00
95_L98_Y0.9831.00
54_G210_V0.9801.00
68_V194_F0.9751.00
23_I244_V0.9721.00
10_F14_F0.9711.00
71_Y187_A0.9691.00
233_G241_L0.9661.00
166_G170_L0.9601.00
171_V189_S0.9561.00
63_A222_S0.9551.00
106_K110_F0.9541.00
89_I192_I0.9501.00
9_L214_P0.9491.00
182_V186_V0.9461.00
56_G60_V0.9421.00
110_F114_I0.9421.00
8_T11_I0.9411.00
9_L217_V0.9381.00
97_S200_A0.9361.00
240_F244_V0.9331.00
66_G226_S0.9251.00
231_S234_Q0.9211.00
85_M192_I0.9201.00
216_L219_M0.9191.00
72_R77_I0.9071.00
251_A254_I0.9001.00
95_L157_G0.8991.00
28_A160_G0.8971.00
77_I188_S0.8971.00
152_A170_L0.8901.00
74_S231_S0.8871.00
51_E55_I0.8841.00
70_A74_S0.8831.00
61_F201_T0.8791.00
9_L218_L0.8791.00
107_G110_F0.8761.00
72_R75_G0.8751.00
121_I250_G0.8621.00
36_L52_V0.8611.00
255_K258_L0.8611.00
171_V186_V0.8601.00
166_G172_P0.8601.00
118_I122_L0.8541.00
21_G230_A0.8431.00
32_Y56_G0.8411.00
16_G31_N0.8411.00
224_I227_P0.8371.00
117_I121_I0.8361.00
55_I210_V0.8281.00
226_S230_A0.8271.00
147_L150_S0.8271.00
91_L95_L0.8261.00
98_Y101_H0.8241.00
126_P129_G0.8191.00
217_V221_T0.8151.00
96_G157_G0.8121.00
97_S199_G0.8111.00
117_I250_G0.8101.00
126_P242_Q0.8091.00
14_F221_T0.8051.00
77_I82_I0.8041.00
191_A195_L0.8001.00
14_F228_I0.7981.00
64_T163_G0.7961.00
70_A73_K0.7921.00
31_N35_L0.7911.00
55_I211_L0.7911.00
70_A231_S0.7901.00
170_L174_M0.7901.00
22_M229_G0.7891.00
251_A255_K0.7871.00
21_G67_G0.7841.00
245_L249_I0.7821.00
173_I177_I0.7791.00
66_G70_A0.7731.00
159_S196_S0.7691.00
99_F102_Y0.7621.00
64_T193_T0.7571.00
236_V240_F0.7511.00
29_V116_A0.7451.00
14_F18_F0.7421.00
47_L51_E0.7421.00
155_I166_G0.7411.00
20_S28_A0.7351.00
100_S204_K0.7321.00
159_S166_G0.7321.00
95_L99_F0.7301.00
89_I170_L0.7281.00
20_S159_S0.7271.00
60_V166_G0.7231.00
253_A257_W0.7221.00
79_K191_A0.7201.00
54_G201_T0.7161.00
184_V187_A0.7161.00
84_Y145_K0.7141.00
213_V216_L0.7121.00
62_F223_L0.7101.00
105_E109_N0.7091.00
59_Q222_S0.7081.00
47_L211_L0.7061.00
106_K109_N0.7011.00
49_A53_S0.6991.00
88_S91_L0.6971.00
17_A27_G0.6971.00
93_S97_S0.6961.00
117_I257_W0.6961.00
50_H108_I0.6951.00
20_S25_I0.6941.00
57_A163_G0.6941.00
166_G193_T0.6911.00
110_F113_G0.6901.00
13_G31_N0.6891.00
20_S30_I0.6891.00
204_K209_Q0.6881.00
13_G17_A0.6871.00
28_A60_V0.6851.00
8_T12_I0.6811.00
104_S107_G0.6811.00
101_H207_T0.6711.00
10_F13_G0.6681.00
142_I146_W0.6681.00
84_Y87_S0.6661.00
163_G189_S0.6661.00
53_S100_S0.6651.00
98_Y207_T0.6641.00
97_S204_K0.6631.00
223_L227_P0.6631.00
82_I192_I0.6621.00
60_V197_S0.6621.00
163_G166_G0.6611.00
246_A250_G0.6601.00
38_I47_L0.6601.00
22_M241_L0.6580.99
58_I201_T0.6560.99
201_T215_A0.6560.99
228_I231_S0.6550.99
16_G34_M0.6540.99
18_F225_A0.6520.99
50_H54_G0.6510.99
190_L193_T0.6510.99
120_V124_F0.6490.99
150_S153_F0.6480.99
159_S164_A0.6440.99
119_A168_F0.6420.99
105_E161_I0.6410.99
13_G214_P0.6330.99
98_Y203_G0.6320.99
210_V215_A0.6310.99
19_I30_I0.6300.99
85_M152_A0.6290.99
169_I172_P0.6270.99
155_I170_L0.6250.99
64_T194_F0.6230.99
182_V245_L0.6230.99
22_M236_V0.6230.99
103_I107_G0.6170.99
166_G189_S0.6170.99
201_T205_V0.6150.99
39_P52_V0.6120.99
20_S63_A0.6050.99
60_V64_T0.6050.99
180_I184_V0.6040.99
142_I145_K0.6020.99
111_I162_L0.6020.99
215_A219_M0.5970.99
232_V236_V0.5970.99
99_F103_I0.5930.99
37_Y256_I0.5920.99
185_T189_S0.5920.99
60_V159_S0.5870.99
183_R238_T0.5850.99
36_L39_P0.5830.99
10_F224_I0.5820.99
23_I248_L0.5810.99
65_L68_V0.5800.99
69_W72_R0.5780.99
91_L153_F0.5760.99
189_S193_T0.5730.99
20_S193_T0.5720.99
80_T145_K0.5720.99
53_S57_A0.5690.99
147_L173_I0.5690.99
17_A222_S0.5690.99
58_I219_M0.5690.99
57_A60_V0.5690.99
14_F17_A0.5680.99
212_F216_L0.5680.99
120_V249_I0.5630.98
205_V210_V0.5620.98
123_M246_A0.5620.98
78_N83_I0.5560.98
84_Y149_S0.5550.98
22_M232_V0.5530.98
237_N241_L0.5520.98
197_S200_A0.5520.98
23_I226_S0.5460.98
232_V235_K0.5450.98
222_S226_S0.5430.98
50_H53_S0.5430.98
124_F243_W0.5400.98
76_L184_V0.5340.98
29_V162_L0.5340.98
53_S108_I0.5330.98
152_A156_G0.5310.98
31_N56_G0.5270.98
60_V193_T0.5260.98
114_I257_W0.5260.98
112_Y256_I0.5250.98
117_I254_I0.5230.97
60_V245_L0.5190.97
20_S60_V0.5170.97
99_F161_I0.5170.97
149_S152_A0.5150.97
58_I212_F0.5150.97
21_G226_S0.5140.97
84_Y88_S0.5130.97
37_Y255_K0.5130.97
130_Q133_Q0.5130.97
63_A163_G0.5130.97
32_Y52_V0.5100.97
228_I232_V0.5090.97
125_I129_G0.5080.97
49_A108_I0.5050.97
13_G55_I0.5050.97
34_M38_I0.5050.97
18_F22_M0.5050.97
116_A249_I0.5050.97
101_H209_Q0.5040.97
31_N60_V0.5030.97
238_T242_Q0.5020.97
26_G33_P0.5020.97
30_I33_P0.5020.97
39_P218_L0.5000.97
47_L52_V0.5000.97
148_A174_M0.5000.97
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  
3o7qA 1 0.8659 82.9 0.906 Contact Map
1pw4A 1 0.8391 77.8 0.911 Contact Map
4rp9A 2 0.4789 72.6 0.915 Contact Map
2gfpA 2 0.8391 69.8 0.916 Contact Map
4j05A 3 0.751 64.8 0.919 Contact Map
2cfqA 1 0.8391 55.2 0.924 Contact Map
3wdoA 1 0.8467 43.5 0.929 Contact Map
4m64A 1 0.8429 40.4 0.93 Contact Map
4pypA 1 0.8276 35.6 0.932 Contact Map
4zw9A 1 0.7893 30.3 0.934 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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