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OPENSEQ.org
HYFD - Hydrogenase-4 component D
UniProt: P77416 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG14212
Length: 479 (469)
Sequences: 6096
Seq/Len: 13.00
HYFD
Paralog alert: 0.84 [within 20: 0.58] - ratio of genomes with paralogs
Cluster includes: HYCC HYFB HYFD HYFF NUOL NUOM NUON
GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
128_G 141_F 4.868 1.00
75_D 259_R 4.516 1.00
194_A 197_A 3.634 1.00
342_L 379_A 3.395 1.00
335_N 390_N 3.384 1.00
167_K 232_D 3.374 1.00
295_D 357_R 3.196 1.00
192_T 197_A 2.926 1.00
82_L 131_L 2.905 1.00
287_F 306_T 2.822 1.00
13_F 124_G 2.737 1.00
356_T 361_R 2.7 1.00
89_G 123_I 2.69 1.00
332_Y 394_S 2.668 1.00
234_M 250_V 2.632 1.00
294_Q 360_P 2.548 1.00
154_S 165_A 2.508 1.00
85_V 130_V 2.507 1.00
96_S 115_Y 2.426 1.00
299_L 359_L 2.397 1.00
223_Q 312_F 2.317 1.00
15_G 34_F 2.234 1.00
358_L 361_R 2.212 1.00
238_T 241_S 2.15 1.00
135_L 260_A 2.148 1.00
258_A 315_L 2.084 1.00
291_L 428_A 2.058 1.00
315_L 329_S 2.057 1.00
250_V 304_T 2.005 1.00
132_S 137_G 1.99 1.00
78_S 255_Y 1.941 1.00
42_M 86_V 1.931 1.00
84_V 337_A 1.925 1.00
328_G 401_A 1.918 1.00
381_L 386_V 1.881 1.00
373_G 439_P 1.878 1.00
80_L 334_V 1.873 1.00
182_A 216_A 1.868 1.00
372_P 451_P 1.859 1.00
359_L 437_V 1.845 1.00
369_L 372_P 1.836 1.00
125_A 144_I 1.829 1.00
237_P 241_S 1.818 1.00
377_C 434_F 1.816 1.00
454_G 458_L 1.812 1.00
224_L 281_V 1.792 1.00
135_L 198_M 1.788 1.00
366_L 373_G 1.773 1.00
234_M 241_S 1.764 1.00
279_A 316_S 1.741 1.00
273_G 277_V 1.735 1.00
160_K 235_E 1.729 1.00
331_A 394_S 1.714 1.00
294_Q 358_L 1.708 1.00
82_L 127_A 1.701 1.00
9_L 124_G 1.656 1.00
351_S 357_R 1.651 1.00
376_F 380_A 1.647 1.00
74_I 131_L 1.641 1.00
303_S 429_W 1.639 1.00
182_A 212_G 1.636 1.00
426_S 429_W 1.636 1.00
216_A 219_G 1.621 1.00
314_G 398_L 1.619 1.00
317_L 402_G 1.606 1.00
133_S 196_S 1.605 1.00
453_P 456_M 1.594 1.00
86_V 127_A 1.589 1.00
257_F 312_F 1.585 1.00
237_P 240_I 1.583 1.00
36_A 90_L 1.576 1.00
192_T 198_M 1.575 1.00
425_A 429_W 1.567 1.00
88_L 341_S 1.547 1.00
236_A 241_S 1.54 1.00
163_R 167_K 1.535 1.00
373_G 434_F 1.525 1.00
300_L 347_A 1.51 1.00
171_I 228_A 1.504 1.00
43_L 47_S 1.494 1.00
293_Q 298_R 1.483 1.00
276_M 316_S 1.468 1.00
371_L 461_I 1.459 1.00
380_A 430_F 1.456 1.00
136_L 193_F 1.446 1.00
88_L 247_A 1.44 1.00
138_Q 256_I 1.431 1.00
73_V 76_R 1.429 1.00
283_I 422_E 1.427 1.00
422_E 425_A 1.403 0.99
287_F 303_S 1.394 0.99
98_G 455_S 1.39 0.99
335_N 394_S 1.374 0.99
432_R 436_R 1.372 0.99
80_L 330_I 1.368 0.99
71_G 194_A 1.366 0.99
376_F 438_V 1.365 0.99
39_T 43_L 1.364 0.99
75_D 78_S 1.364 0.99
129_L 252_V 1.364 0.99
277_V 281_V 1.364 0.99
223_Q 278_M 1.363 0.99
222_A 230_L 1.361 0.99
81_I 333_I 1.36 0.99
135_L 183_A 1.346 0.99
61_L 66_D 1.342 0.99
296_M 433_W 1.337 0.99
230_L 234_M 1.327 0.99
429_W 432_R 1.322 0.99
276_M 313_F 1.318 0.99
232_D 298_R 1.316 0.99
184_A 188_L 1.316 0.99
120_L 124_G 1.303 0.99
73_V 133_S 1.302 0.99
33_L 37_L 1.284 0.99
376_F 433_W 1.282 0.99
192_T 195_L 1.28 0.99
338_F 466_M 1.263 0.99
30_W 34_F 1.251 0.99
197_A 200_E 1.249 0.99
39_T 86_V 1.248 0.99
214_L 218_W 1.246 0.98
350_L 365_V 1.243 0.98
304_T 336_H 1.241 0.98
71_G 133_S 1.241 0.98
311_M 329_S 1.239 0.98
465_V 469_I 1.235 0.98
234_M 304_T 1.232 0.98
37_L 41_C 1.227 0.98
375_G 461_I 1.218 0.98
458_L 462_V 1.213 0.98
265_G 268_P 1.212 0.98
214_L 275_G 1.202 0.98
187_F 193_F 1.202 0.98
258_A 329_S 1.201 0.98
95_Y 348_G 1.199 0.98
336_H 340_K 1.197 0.98
231_P 293_Q 1.195 0.98
39_T 87_F 1.19 0.98
152_L 240_I 1.183 0.98
314_G 325_A 1.182 0.98
459_V 462_V 1.177 0.98
118_F 151_A 1.176 0.98
339_A 382_A 1.175 0.98
454_G 457_R 1.168 0.97
238_T 242_A 1.168 0.97
9_L 131_L 1.166 0.97
322_S 401_A 1.164 0.97
31_G 116_Y 1.163 0.97
461_I 465_V 1.158 0.97
88_L 337_A 1.153 0.97
190_T 198_M 1.152 0.97
314_G 328_G 1.146 0.97
374_V 378_V 1.144 0.97
158_S 161_A 1.144 0.97
285_Y 289_M 1.142 0.97
36_A 40_L 1.14 0.97
46_I 83_F 1.135 0.97
90_L 94_I 1.135 0.97
237_P 242_A 1.134 0.97
139_L 180_Y 1.124 0.97
373_G 377_C 1.117 0.96
353_S 369_L 1.111 0.96
378_V 464_I 1.111 0.96
451_P 456_M 1.11 0.96
466_M 470_S 1.106 0.96
352_Y 450_A 1.099 0.96
294_Q 303_S 1.093 0.96
85_V 127_A 1.092 0.96
149_S 249_M 1.088 0.96
142_F 252_V 1.085 0.96
31_G 35_A 1.082 0.96
428_A 432_R 1.082 0.96
457_R 461_I 1.079 0.95
83_F 87_F 1.076 0.95
234_M 297_K 1.076 0.95
462_V 466_M 1.075 0.95
122_F 249_M 1.073 0.95
307_Q 429_W 1.071 0.95
213_I 216_A 1.07 0.95
255_Y 259_R 1.068 0.95
161_A 235_E 1.066 0.95
95_Y 345_L 1.066 0.95
122_F 126_M 1.061 0.95
150_W 172_T 1.06 0.95
46_I 50_Y 1.058 0.95
254_V 311_M 1.057 0.95
444_E 447_A 1.057 0.95
349_A 452_L 1.056 0.95
186_L 198_M 1.054 0.95
153_I 233_A 1.054 0.95
60_T 68_A 1.052 0.95
400_A 404_A 1.051 0.94
235_E 298_R 1.048 0.94
349_A 372_P 1.043 0.94
354_C 362_L 1.043 0.94
63_N 68_A 1.038 0.94
63_N 66_D 1.036 0.94
343_F 379_A 1.036 0.94
452_L 457_R 1.034 0.94
307_Q 340_K 1.032 0.94
31_G 93_T 1.031 0.94
133_S 194_A 1.031 0.94
74_I 79_T 1.025 0.93
231_P 302_W 1.025 0.93
371_L 374_V 1.025 0.93
162_Q 165_A 1.023 0.93
296_M 437_V 1.021 0.93
281_V 285_Y 1.018 0.93
361_R 445_A 1.017 0.93
258_A 326_L 1.016 0.93
332_Y 339_A 1.013 0.93
179_L 183_A 1.012 0.93
96_S 99_Y 1.01 0.93
280_L 313_F 1.01 0.93
279_A 312_F 1.008 0.93
93_T 119_L 1.007 0.93
60_T 63_N 1.006 0.93
332_Y 335_N 1.006 0.93
451_P 457_R 1.006 0.93
230_L 250_V 1.005 0.93
40_L 44_S 1.005 0.93
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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 P(%) HHΔ   Acc
4he8L20.94361000.193Contact Map0.735
3rkoL20.95621000.204Contact Map0.746
3rkoM20.95621000.206Contact Map0.687
4he8M20.93111000.208Contact Map0.645
3rkoN20.94571000.249Contact Map0.62
4he8N20.87471000.335Contact Map0.609
4he8K20.192145.30.966Contact Map0.762
3rkoK20.198330.50.969Contact Map0.46
3arcX20.07932.50.981Contact Map0.429
2l0nA10.06262.30.982Contact Map0.154
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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