GREMLIN Database
YQKD - Uncharacterized protein YqkD
UniProt: P54567 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 305 (239)
Sequences: 17081 (12755)
Seq/√Len: 825.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
155_G180_F4.0221.00
117_R136_D3.4081.00
170_A181_Y3.3261.00
61_V69_D3.1611.00
247_K274_E2.7561.00
63_P69_D2.7061.00
107_L294_Q2.6361.00
271_Y292_T2.6061.00
261_Y268_K2.6001.00
74_H110_N2.4371.00
254_V272_I2.3451.00
269_A292_T2.3401.00
60_F72_G2.3191.00
65_A139_K2.2941.00
247_K272_I2.1861.00
166_A181_Y2.1841.00
273_A292_T2.1421.00
155_G297_L2.1241.00
183_A186_P2.0951.00
269_A299_N2.0841.00
83_T110_N2.0751.00
142_S177_G2.0341.00
143_L147_K1.9711.00
76_A110_N1.9341.00
167_L183_A1.8511.00
156_I166_A1.7861.00
143_L146_N1.7771.00
107_L298_D1.7531.00
233_V236_K1.7351.00
258_E272_I1.6931.00
75_V113_I1.6861.00
285_N288_T1.6341.00
241_V264_K1.6231.00
128_S131_F1.6151.00
69_D123_G1.6121.00
81_P110_N1.6081.00
182_I293_V1.5991.00
254_V258_E1.5891.00
62_I140_V1.5821.00
138_N142_S1.5651.00
87_C137_L1.5601.00
150_H153_L1.5521.00
273_A288_T1.5371.00
245_H254_V1.5311.00
59_A71_K1.5271.00
145_K177_G1.5221.00
291_K295_E1.5211.00
141_V154_I1.5031.00
288_T292_T1.4971.00
112_L140_V1.4811.00
101_M113_I1.4531.00
109_W298_D1.4361.00
65_A135_D1.4301.00
73_Y94_V1.4181.00
221_G224_R1.4111.00
292_T295_E1.3961.00
88_H119_H1.3891.00
103_L107_L1.3811.00
138_N169_Y1.3791.00
258_E262_E1.3751.00
245_H257_T1.3681.00
182_I297_L1.3651.00
74_H112_L1.3571.00
66_Y117_R1.3551.00
60_F143_L1.3461.00
135_D172_A1.3301.00
61_V71_K1.3291.00
247_K254_V1.3241.00
71_K121_Q1.3171.00
163_A186_P1.3171.00
261_Y270_L1.3161.00
86_I157_H1.2961.00
104_F157_H1.2961.00
114_Y140_V1.2821.00
168_L172_A1.2731.00
247_K275_N1.2651.00
129_Y133_E1.2601.00
259_R263_K1.2521.00
242_L271_Y1.2521.00
235_D263_K1.2511.00
87_C166_A1.2411.00
248_D275_N1.2391.00
71_K122_S1.2361.00
273_A276_G1.2181.00
181_Y241_V1.2141.00
128_S132_Y1.2101.00
62_I72_G1.2101.00
153_L179_D1.2091.00
72_G112_L1.1761.00
182_I242_L1.1651.00
89_G160_S1.1611.00
87_C116_H1.1611.00
157_H184_D1.1581.00
82_N109_W1.1581.00
83_T112_L1.1571.00
184_D289_Y1.1521.00
128_S133_E1.1511.00
244_I289_Y1.1501.00
243_F257_T1.1431.00
127_T130_G1.1431.00
102_H106_D1.1341.00
258_E270_L1.1311.00
83_T144_L1.1311.00
181_Y239_K1.1271.00
100_Y290_R1.1261.00
103_L294_Q1.1221.00
159_E185_C1.1191.00
289_Y293_V1.1171.00
87_C114_Y1.1141.00
244_I273_A1.1081.00
243_F260_L1.1061.00
82_N153_L1.1001.00
159_E184_D1.0941.00
257_T270_L1.0891.00
84_I109_W1.0791.00
170_A239_K1.0681.00
91_T160_S1.0671.00
72_G140_V1.0661.00
185_C249_D1.0611.00
226_R232_A1.0601.00
140_V144_L1.0571.00
103_L290_R1.0471.00
168_L171_G1.0461.00
138_N174_C1.0441.00
223_Y227_E1.0421.00
294_Q298_D1.0411.00
276_G285_N1.0411.00
112_L144_L1.0321.00
171_G233_V1.0301.00
244_I271_Y1.0261.00
127_T131_F1.0161.00
229_S232_A1.0131.00
255_S258_E1.0121.00
68_Y123_G1.0091.00
105_L111_V1.0001.00
138_N172_A0.9861.00
71_K94_V0.9791.00
94_V113_I0.9681.00
115_D120_G0.9681.00
183_A243_F0.9651.00
139_K142_S0.9651.00
224_R227_E0.9641.00
167_L186_P0.9611.00
222_G226_R0.9561.00
168_L233_V0.9551.00
142_S146_N0.9491.00
92_M96_N0.9471.00
145_K148_T0.9401.00
85_I141_V0.9391.00
88_H116_H0.9341.00
68_Y117_R0.9341.00
87_C156_I0.9331.00
156_I169_Y0.9221.00
137_L169_Y0.9191.00
70_I122_S0.9131.00
155_G182_I0.9111.00
59_A121_Q0.9081.00
116_H165_T0.9081.00
90_V161_M0.9071.00
129_Y134_K0.9051.00
94_V121_Q0.8991.00
71_K115_D0.8931.00
103_L106_D0.8911.00
295_E299_N0.8901.00
155_G179_D0.8861.00
135_D139_K0.8811.00
75_V105_L0.8781.00
180_F297_L0.8781.00
287_H291_K0.8711.00
271_Y288_T0.8711.00
62_I139_K0.8541.00
180_F296_F0.8481.00
76_A81_P0.8471.00
57_K75_V0.8471.00
243_F261_Y0.8451.00
64_S68_Y0.8391.00
101_M105_L0.8391.00
182_I244_I0.8381.00
141_V178_A0.8381.00
188_A260_L0.8371.00
185_C245_H0.8341.00
257_T261_Y0.8301.00
264_K268_K0.8221.00
205_P208_P0.8171.00
75_V101_M0.8171.00
220_R224_R0.8151.00
130_G133_E0.8121.00
231_L234_I0.8091.00
185_C280_M0.8071.00
250_D277_E0.7991.00
57_K73_Y0.7981.00
276_G280_M0.7931.00
86_I111_V0.7901.00
84_I111_V0.7861.00
160_S278_H0.7841.00
157_H182_I0.7831.00
176_D238_E0.7811.00
91_T161_M0.7811.00
189_C229_S0.7801.00
184_D244_I0.7801.00
174_C177_G0.7791.00
288_T291_K0.7761.00
85_I112_L0.7761.00
191_D226_R0.7761.00
187_F252_I0.7751.00
169_Y174_C0.7751.00
64_S139_K0.7671.00
245_H272_I0.7671.00
171_G237_I0.7531.00
145_K151_R0.7521.00
64_S117_R0.7511.00
59_A73_Y0.7501.00
94_V115_D0.7471.00
84_I157_H0.7431.00
157_H293_V0.7281.00
99_K102_H0.7281.00
164_V187_F0.7271.00
161_M165_T0.7251.00
156_I178_A0.7241.00
114_Y137_L0.7211.00
172_A233_V0.7201.00
243_F264_K0.7201.00
160_S249_D0.7151.00
232_A235_D0.7111.00
58_T147_K0.7051.00
170_A237_I0.7031.00
132_Y135_D0.7001.00
295_E298_D0.6981.00
164_V167_L0.6971.00
142_S145_K0.6961.00
192_E259_R0.6941.00
163_A252_I0.6941.00
127_T133_E0.6921.00
116_H119_H0.6921.00
223_Y226_R0.6901.00
127_T132_Y0.6901.00
222_G225_A0.6901.00
278_H281_S0.6881.00
189_C192_E0.6841.00
109_W155_G0.6841.00
84_I104_F0.6831.00
86_I113_I0.6821.00
218_K221_G0.6821.00
219_L223_Y0.6811.00
62_I114_Y0.6811.00
142_S174_C0.6791.00
109_W297_L0.6771.00
259_R262_E0.6751.00
83_T154_I0.6721.00
238_E266_G0.6721.00
138_N177_G0.6641.00
194_L198_L0.6641.00
180_F240_P0.6611.00
221_G225_A0.6581.00
194_L197_R0.6551.00
60_F74_H0.6551.00
115_D122_S0.6541.00
134_K168_L0.6541.00
62_I65_A0.6521.00
166_A170_A0.6481.00
242_L296_F0.6401.00
86_I101_M0.6401.00
192_E256_S0.6401.00
269_A295_E0.6401.00
265_R268_K0.6381.00
154_I178_A0.6341.00
167_L260_L0.6311.00
159_E279_A0.6301.00
140_V143_L0.6291.00
186_P252_I0.6291.00
158_G166_A0.6281.00
185_C279_A0.6261.00
245_H270_L0.6241.00
101_M111_V0.6181.00
243_F270_L0.6171.00
91_T119_H0.6161.00
85_I114_Y0.6151.00
144_L147_K0.6141.00
186_P245_H0.6141.00
60_F63_P0.6131.00
152_G179_D0.6111.00
193_Q196_Y0.6081.00
134_K165_T0.6061.00
62_I143_L0.6041.00
269_A296_F0.6031.00
131_F134_K0.6011.00
218_K222_G0.6001.00
230_P233_V0.5991.00
160_S279_A0.5981.00
167_L188_A0.5971.00
83_T109_W0.5971.00
116_H161_M0.5971.00
84_I297_L0.5951.00
129_Y190_F0.5941.00
197_R200_A0.5941.00
255_S259_R0.5931.00
61_V72_G0.5911.00
85_I178_A0.5901.00
258_E261_Y0.5891.00
234_I263_K0.5891.00
163_A183_A0.5841.00
267_P299_N0.5831.00
199_R203_R0.5821.00
86_I104_F0.5821.00
64_S70_I0.5821.00
189_C259_R0.5801.00
220_R225_A0.5791.00
176_D239_K0.5741.00
225_A228_V0.5731.00
141_V177_G0.5721.00
80_T110_N0.5721.00
237_I264_K0.5691.00
187_F190_F0.5671.00
135_D138_N0.5611.00
134_K172_A0.5591.00
234_I264_K0.5591.00
97_S100_Y0.5571.00
65_A68_Y0.5561.00
175_S178_A0.5551.00
141_V169_Y0.5501.00
186_P257_T0.5491.00
277_E283_T0.5481.00
138_N178_A0.5471.00
254_V270_L0.5471.00
85_I137_L0.5461.00
170_A241_V0.5461.00
249_D252_I0.5451.00
90_V119_H0.5411.00
170_A178_A0.5401.00
137_L165_T0.5391.00
202_Y208_P0.5381.00
220_R223_Y0.5371.00
144_L148_T0.5341.00
87_C165_T0.5331.00
100_Y157_H0.5321.00
98_L102_H0.5241.00
220_R226_R0.5221.00
184_D280_M0.5201.00
82_N155_G0.5201.00
188_A256_S0.5191.00
78_H81_P0.5141.00
218_K225_A0.5131.00
195_A198_L0.5111.00
82_N152_G0.5111.00
161_M164_V0.5101.00
64_S67_G0.5101.00
269_A272_I0.5091.00
75_V111_V0.5091.00
157_H297_L0.5091.00
116_H137_L0.5091.00
148_T151_R0.5081.00
245_H252_I0.5071.00
73_Y113_I0.5061.00
219_L222_G0.5051.00
110_N149_N0.5021.00
100_Y159_E0.5021.00
58_T74_H0.5011.00
86_I97_S0.5001.00
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  
2wtmA 2 0.7902 100 0.376 Contact Map
2hdwA 2 0.859 100 0.383 Contact Map
1k8qA 1 0.8754 100 0.392 Contact Map
3pe6A 1 0.8262 100 0.402 Contact Map
4ns4A 1 0.7902 100 0.404 Contact Map
2y6uA 2 0.859 100 0.412 Contact Map
1zoiA 3 0.7574 100 0.415 Contact Map
3fobA 3 0.7803 100 0.415 Contact Map
3fnbA 2 0.9049 100 0.422 Contact Map
1mtzA 1 0.777 100 0.422 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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