GREMLIN Database
HYFD - Hydrogenase-4 component D
UniProt: P77416 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14212
Length: 479 (447)
Sequences: 20297 (12584)
Seq/√Len: 595.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
75_D259_R4.8841.00
342_L379_A4.7401.00
128_G141_F4.6231.00
194_A197_A3.8751.00
82_L131_L3.7231.00
154_S165_A3.6201.00
167_K232_D3.3401.00
295_D357_R3.3321.00
335_N390_N3.2751.00
89_G123_I3.1351.00
332_Y394_S3.1271.00
283_I422_E2.9181.00
192_T197_A2.8371.00
279_A316_S2.8121.00
294_Q360_P2.7701.00
300_L347_A2.7051.00
85_V130_V2.6721.00
377_C434_F2.6381.00
182_A212_G2.5561.00
125_A144_I2.5551.00
13_F124_G2.5071.00
15_G34_F2.4981.00
82_L127_A2.4831.00
223_Q312_F2.4801.00
358_L361_R2.3561.00
96_S115_Y2.2761.00
234_M250_V2.2321.00
299_L359_L2.2291.00
73_V133_S2.2231.00
250_V304_T2.2121.00
234_M241_S2.1981.00
380_A430_F2.1231.00
291_L428_A2.1111.00
314_G398_L2.0791.00
86_V127_A2.0631.00
313_F419_L2.0571.00
218_W223_Q1.9481.00
303_S429_W1.9171.00
273_G277_V1.9101.00
284_L422_E1.8891.00
197_A200_E1.8451.00
287_F306_T1.8431.00
317_L325_A1.8371.00
36_A90_L1.7931.00
20_S23_P1.7881.00
432_R436_R1.7831.00
369_L372_P1.7711.00
135_L198_M1.7611.00
331_A394_S1.7531.00
296_M433_W1.7501.00
294_Q358_L1.7481.00
222_A230_L1.7461.00
75_D78_S1.7451.00
399_F419_L1.7281.00
185_T209_V1.7261.00
214_L218_W1.7231.00
328_G401_A1.7091.00
356_T361_R1.6971.00
138_Q256_I1.6891.00
133_S196_S1.6661.00
276_M316_S1.6511.00
293_Q298_R1.6411.00
132_S137_G1.6401.00
454_G458_L1.6261.00
258_A315_L1.6201.00
84_V337_A1.6141.00
135_L260_A1.5831.00
224_L281_V1.5801.00
25_R28_A1.5781.00
78_S255_Y1.5751.00
36_A40_L1.5701.00
280_L418_L1.5661.00
338_F466_M1.5641.00
39_T87_F1.5631.00
9_L12_P1.5571.00
189_Q209_V1.5451.00
372_P451_P1.4971.00
465_V469_I1.4891.00
366_L373_G1.4881.00
160_K235_E1.4841.00
217_A256_I1.4741.00
73_V76_R1.4731.00
402_G416_M1.4711.00
400_A404_A1.4581.00
275_G316_S1.4581.00
134_T194_A1.4551.00
118_F151_A1.4531.00
80_L334_V1.4471.00
287_F422_E1.4471.00
46_I50_Y1.4231.00
204_D208_L1.4211.00
315_L329_S1.4201.00
152_L240_I1.4181.00
187_F193_F1.4181.00
38_T45_L1.4131.00
376_F380_A1.4131.00
223_Q278_M1.4121.00
311_M329_S1.4101.00
9_L124_G1.4091.00
317_L402_G1.4081.00
60_T63_N1.4071.00
182_A216_A1.3981.00
376_F433_W1.3741.00
453_P456_M1.3721.00
134_T193_F1.3681.00
232_D298_R1.3641.00
164_S235_E1.3571.00
214_L275_G1.3541.00
378_V464_I1.3531.00
93_T119_L1.3411.00
257_F312_F1.3381.00
40_L44_S1.3381.00
184_A188_L1.3351.00
111_G114_R1.3301.00
88_L341_S1.3301.00
35_A38_T1.3261.00
45_L49_F1.3241.00
38_T42_M1.3151.00
42_M45_L1.3141.00
93_T116_Y1.2991.00
42_M86_V1.2951.00
8_T12_P1.2881.00
314_G325_A1.2851.00
74_I131_L1.2841.00
31_G35_A1.2831.00
343_F379_A1.2831.00
339_A382_A1.2741.00
35_A39_T1.2741.00
129_L252_V1.2721.00
182_A209_V1.2711.00
182_A213_I1.2711.00
47_S51_Q1.2691.00
461_I465_V1.2681.00
313_F402_G1.2631.00
407_V410_W1.2611.00
138_Q195_L1.2611.00
462_V466_M1.2581.00
375_G464_I1.2511.00
258_A329_S1.2491.00
71_G133_S1.2421.00
314_G329_S1.2411.00
43_L47_S1.2271.00
81_I333_I1.2241.00
171_I228_A1.2221.00
373_G439_P1.2171.00
26_R29_E1.2101.00
379_A464_I1.2051.00
454_G457_R1.2011.00
16_A20_S1.1991.00
279_A309_G1.1951.00
270_V273_G1.1941.00
88_L337_A1.1901.00
80_L330_I1.1881.00
25_R29_E1.1871.00
277_V281_V1.1861.00
234_M304_T1.1831.00
95_Y345_L1.1781.00
373_G434_F1.1681.00
285_Y289_M1.1641.00
61_L64_V1.1591.00
139_L180_Y1.1581.00
183_A213_I1.1581.00
179_L216_A1.1571.00
336_H340_K1.1551.00
45_L48_A1.1551.00
16_A19_V1.1551.00
459_V462_V1.1521.00
325_A401_A1.1491.00
163_R167_K1.1461.00
359_L437_V1.1461.00
133_S194_A1.1431.00
63_N66_D1.1401.00
377_C438_V1.1371.00
335_N394_S1.1321.00
380_A434_F1.1301.00
455_S459_V1.1301.00
426_S429_W1.1271.00
27_A30_W1.1231.00
218_W278_M1.1181.00
39_T43_L1.1181.00
32_V35_A1.1161.00
185_T205_A1.1131.00
122_F126_M1.1111.00
346_V376_F1.1101.00
175_G219_G1.1071.00
98_G101_T1.1061.00
12_P16_A1.1041.00
219_G226_M1.1031.00
351_S357_R1.1031.00
286_G309_G1.1031.00
78_S259_R1.0981.00
383_I430_F1.0981.00
371_L374_V1.0961.00
346_V460_L1.0951.00
16_A121_V1.0941.00
328_G397_P1.0921.00
23_P113_N1.0911.00
90_L94_I1.0861.00
247_A251_K1.0811.00
353_S369_L1.0801.00
306_T426_S1.0771.00
33_L37_L1.0751.00
158_S161_A1.0701.00
230_L234_M1.0671.00
86_V90_L1.0661.00
149_S249_M1.0621.00
371_L461_I1.0621.00
179_L183_A1.0611.00
190_T198_M1.0591.00
397_P400_A1.0521.00
37_L41_C1.0511.00
135_L183_A1.0491.00
34_F38_T1.0451.00
464_I468_L1.0441.00
38_T44_S1.0411.00
221_S254_V1.0371.00
375_G460_L1.0271.00
231_P302_W1.0211.00
19_V23_P1.0201.00
372_P452_L1.0181.00
74_I79_T1.0161.00
466_M470_S1.0141.00
136_L193_F1.0131.00
91_L462_V1.0111.00
352_Y450_A1.0101.00
381_L386_V1.0081.00
39_T86_V1.0051.00
224_L285_Y1.0041.00
85_V123_I1.0021.00
44_S47_S1.0021.00
403_F416_M1.0011.00
60_T68_A0.9981.00
121_V148_C0.9971.00
77_V258_A0.9961.00
189_Q205_A0.9931.00
307_Q332_Y0.9911.00
304_T336_H0.9871.00
120_L124_G0.9851.00
161_A235_E0.9821.00
8_T20_S0.9791.00
354_C362_L0.9791.00
295_D358_L0.9751.00
417_I421_I0.9741.00
287_F425_A0.9721.00
251_K255_Y0.9691.00
371_L375_G0.9691.00
38_T41_C0.9651.00
95_Y348_G0.9641.00
349_A372_P0.9641.00
87_F91_L0.9561.00
254_V311_M0.9521.00
88_L247_A0.9511.00
119_L243_Y0.9501.00
279_A313_F0.9501.00
72_L131_L0.9491.00
77_V330_I0.9481.00
273_G276_M0.9421.00
125_A148_C0.9421.00
272_G276_M0.9411.00
396_F400_A0.9401.00
42_M46_I0.9401.00
283_I313_F0.9391.00
196_S200_E0.9351.00
186_L198_M0.9351.00
162_Q165_A0.9351.00
376_F438_V0.9331.00
242_A345_L0.9331.00
446_V449_A0.9321.00
314_G328_G0.9321.00
209_V213_I0.9321.00
469_I473_I0.9291.00
28_A31_G0.9281.00
207_Y271_I0.9271.00
283_I309_G0.9261.00
374_V438_V0.9221.00
47_S50_Y0.9201.00
178_G212_G0.9201.00
159_D163_R0.9181.00
307_Q426_S0.9171.00
331_A335_N0.9161.00
307_Q429_W0.9161.00
153_I233_A0.9151.00
44_S48_A0.9141.00
296_M347_A0.9141.00
287_F429_W0.9121.00
186_L209_V0.9121.00
353_S456_M0.9071.00
98_G455_S0.9071.00
288_L425_A0.9051.00
373_G438_V0.9041.00
187_F190_T0.9041.00
48_A51_Q0.9011.00
71_G194_A0.9001.00
258_A326_L0.8971.00
178_G215_F0.8911.00
214_L257_F0.8901.00
287_F303_S0.8901.00
236_A243_Y0.8891.00
375_G461_I0.8891.00
422_E425_A0.8891.00
350_L365_V0.8891.00
276_M279_A0.8881.00
139_L143_E0.8881.00
57_V60_T0.8871.00
8_T23_P0.8831.00
339_A391_G0.8821.00
122_F149_S0.8801.00
78_S82_L0.8791.00
204_D207_Y0.8791.00
195_L199_S0.8781.00
125_A141_F0.8731.00
257_F315_L0.8721.00
211_G215_F0.8721.00
145_T249_M0.8711.00
246_A250_V0.8701.00
236_A241_S0.8671.00
299_L433_W0.8661.00
126_M145_T0.8641.00
192_T195_L0.8641.00
16_A117_A0.8631.00
11_L15_G0.8621.00
173_H176_S0.8621.00
12_P15_G0.8611.00
92_V345_L0.8611.00
342_L463_L0.8601.00
434_F439_P0.8601.00
311_M333_I0.8601.00
17_L20_S0.8601.00
359_L436_R0.8571.00
9_L24_Q0.8561.00
41_C45_L0.8561.00
254_V333_I0.8531.00
281_V285_Y0.8531.00
430_F433_W0.8491.00
126_M249_M0.8461.00
31_G42_M0.8441.00
84_V334_V0.8431.00
457_R461_I0.8411.00
238_T297_K0.8391.00
310_W398_L0.8381.00
199_S262_I0.8371.00
139_L183_A0.8361.00
276_M280_L0.8331.00
208_L212_G0.8331.00
46_I83_F0.8311.00
250_V255_Y0.8301.00
29_E32_V0.8281.00
382_A389_F0.8261.00
290_Y429_W0.8251.00
89_G119_L0.8251.00
390_N470_S0.8241.00
91_L459_V0.8221.00
286_G289_M0.8201.00
127_A131_L0.8191.00
29_E34_F0.8191.00
126_M248_S0.8161.00
30_W34_F0.8151.00
363_R443_S0.8151.00
367_H370_P0.8151.00
28_A32_V0.8121.00
142_F179_L0.8121.00
98_G453_P0.8101.00
31_G116_Y0.8101.00
21_F24_Q0.8091.00
349_A460_L0.8091.00
248_S251_K0.8081.00
12_P23_P0.8081.00
276_M313_F0.8061.00
192_T198_M0.8061.00
29_E33_L0.8041.00
296_M362_L0.8031.00
349_A452_L0.8021.00
332_Y339_A0.7981.00
207_Y211_G0.7961.00
254_V312_F0.7941.00
363_R436_R0.7931.00
150_W165_A0.7931.00
307_Q340_K0.7931.00
310_W422_E0.7901.00
464_I467_S0.7901.00
185_T189_Q0.7881.00
15_G120_L0.7861.00
49_F53_D0.7791.00
374_V378_V0.7781.00
390_N467_S0.7761.00
19_V24_Q0.7761.00
325_A329_S0.7751.00
9_L72_L0.7751.00
279_A312_F0.7711.00
10_L14_I0.7711.00
279_A283_I0.7671.00
431_I435_G0.7661.00
130_V255_Y0.7631.00
424_V428_A0.7621.00
64_V67_V0.7611.00
303_S336_H0.7571.00
15_G19_V0.7571.00
48_A52_A0.7571.00
284_L288_L0.7561.00
373_G377_C0.7551.00
286_G306_T0.7551.00
452_L457_R0.7541.00
26_R30_W0.7531.00
246_A336_H0.7511.00
368_T442_P0.7481.00
12_P124_G0.7481.00
300_L343_F0.7471.00
385_G395_K0.7441.00
71_G134_T0.7441.00
35_A42_M0.7431.00
255_Y259_R0.7421.00
85_V126_M0.7381.00
238_T348_G0.7381.00
293_Q302_W0.7361.00
122_F249_M0.7321.00
160_K163_R0.7321.00
8_T41_C0.7321.00
369_L451_P0.7311.00
150_W172_T0.7311.00
399_F416_M0.7301.00
280_L313_F0.7291.00
293_Q299_L0.7281.00
449_A452_L0.7251.00
115_Y239_P0.7241.00
389_F393_F0.7201.00
458_L462_V0.7191.00
31_G34_F0.7181.00
246_A340_K0.7181.00
231_P305_I0.7141.00
287_F426_S0.7111.00
317_L405_L0.7111.00
113_N117_A0.7101.00
384_T427_F0.7081.00
145_T252_V0.7051.00
388_P472_V0.7041.00
58_T71_G0.7031.00
382_A391_G0.7021.00
9_L23_P0.6991.00
280_L284_L0.6991.00
236_A240_I0.6981.00
43_L83_F0.6971.00
134_T137_G0.6951.00
97_T455_S0.6951.00
254_V308_L0.6941.00
201_L206_R0.6931.00
83_F87_F0.6921.00
303_S340_K0.6921.00
142_F252_V0.6921.00
20_S117_A0.6911.00
14_I18_V0.6901.00
250_V254_V0.6881.00
427_F431_I0.6841.00
374_V377_C0.6841.00
363_R440_G0.6841.00
385_G389_F0.6831.00
380_A433_W0.6831.00
460_L464_I0.6831.00
16_A124_G0.6831.00
289_M302_W0.6811.00
11_L37_L0.6811.00
274_V277_V0.6791.00
74_I78_S0.6781.00
62_V67_V0.6761.00
13_F17_L0.6711.00
368_T447_A0.6711.00
180_Y184_A0.6701.00
31_G38_T0.6691.00
9_L16_A0.6671.00
345_L459_V0.6671.00
399_F423_S0.6671.00
143_E220_K0.6661.00
8_T11_L0.6651.00
58_T68_A0.6631.00
8_T24_Q0.6611.00
133_S137_G0.6601.00
260_A263_D0.6601.00
451_P457_R0.6591.00
208_L211_G0.6591.00
175_G216_A0.6571.00
418_L422_E0.6571.00
387_P392_F0.6551.00
234_M301_A0.6541.00
241_S250_V0.6521.00
205_A209_V0.6521.00
303_S307_Q0.6521.00
228_A231_P0.6511.00
35_A93_T0.6501.00
68_A71_G0.6491.00
99_Y239_P0.6471.00
283_I310_W0.6461.00
35_A41_C0.6431.00
234_M247_A0.6431.00
39_T46_I0.6431.00
371_L457_R0.6431.00
458_L461_I0.6411.00
166_L170_L0.6401.00
11_L23_P0.6401.00
138_Q179_L0.6321.00
240_I243_Y0.6311.00
115_Y240_I0.6311.00
377_C439_P0.6291.00
304_T308_L0.6291.00
247_A250_V0.6271.00
79_T83_F0.6271.00
251_K308_L0.6261.00
86_V123_I0.6251.00
91_L341_S0.6251.00
122_F243_Y0.6241.00
37_L42_M0.6231.00
378_V468_L0.6221.00
43_L46_I0.6221.00
41_C44_S0.6211.00
92_V239_P0.6211.00
83_F86_V0.6211.00
206_R267_I0.6131.00
59_L62_V0.6131.00
153_I236_A0.6131.00
346_V379_A0.6131.00
27_A31_G0.6121.00
92_V119_L0.6111.00
9_L131_L0.6101.00
31_G46_I0.6101.00
210_Y264_G0.6071.00
34_F41_C0.6071.00
49_F79_T0.6061.00
234_M297_K0.6061.00
339_A383_I0.6061.00
186_L213_I0.6051.00
349_A456_M0.6051.00
241_S244_L0.6031.00
12_P20_S0.6031.00
118_F148_C0.6031.00
307_Q310_W0.6021.00
206_R209_V0.6021.00
112_T116_Y0.6021.00
73_V196_S0.6011.00
339_A467_S0.6011.00
45_L50_Y0.6001.00
346_V375_G0.5991.00
452_L456_M0.5981.00
139_L176_S0.5971.00
81_I255_Y0.5971.00
149_S152_L0.5951.00
289_M293_Q0.5951.00
133_S259_R0.5941.00
85_V127_A0.5931.00
49_F52_A0.5931.00
85_V89_G0.5921.00
323_R327_E0.5921.00
50_Y53_D0.5911.00
89_G243_Y0.5901.00
149_S246_A0.5881.00
269_H272_G0.5881.00
9_L20_S0.5871.00
32_V46_I0.5871.00
294_Q303_S0.5861.00
342_L460_L0.5851.00
36_A44_S0.5851.00
366_L438_V0.5841.00
81_I85_V0.5841.00
205_A208_L0.5821.00
236_A244_L0.5811.00
212_G216_A0.5801.00
32_V94_I0.5791.00
230_L250_V0.5791.00
336_H344_F0.5761.00
132_S141_F0.5751.00
238_T241_S0.5741.00
375_G379_A0.5741.00
193_F197_A0.5731.00
266_N269_H0.5731.00
84_V333_I0.5701.00
241_S297_K0.5701.00
364_G370_P0.5691.00
304_T340_K0.5681.00
149_S153_I0.5671.00
92_V242_A0.5671.00
428_A432_R0.5651.00
32_V97_T0.5651.00
289_M292_P0.5641.00
395_K423_S0.5631.00
375_G457_R0.5631.00
77_V81_I0.5621.00
223_Q226_M0.5621.00
13_F16_A0.5621.00
153_I244_L0.5611.00
230_L233_A0.5611.00
10_L13_F0.5601.00
115_Y155_Y0.5591.00
135_L186_L0.5580.99
235_E298_R0.5570.99
18_V21_F0.5570.99
434_F438_V0.5570.99
246_A251_K0.5560.99
368_T449_A0.5560.99
266_N270_V0.5530.99
181_L185_T0.5520.99
20_S24_Q0.5520.99
288_L292_P0.5510.99
366_L377_C0.5510.99
241_S336_H0.5510.99
463_L467_S0.5490.99
250_V308_L0.5490.99
32_V38_T0.5490.99
77_V255_Y0.5480.99
460_L463_L0.5470.99
42_M82_L0.5460.99
296_M350_L0.5450.99
332_Y335_N0.5420.99
401_A405_L0.5390.99
251_K254_V0.5390.99
284_L418_L0.5390.99
349_A353_S0.5380.99
399_F420_M0.5380.99
15_G20_S0.5370.99
31_G41_C0.5370.99
163_R232_D0.5360.99
207_Y270_V0.5340.99
18_V23_P0.5340.99
282_T312_F0.5330.99
61_L67_V0.5310.99
224_L286_G0.5310.99
48_A53_D0.5310.99
237_P240_I0.5300.99
419_L423_S0.5290.99
185_T208_L0.5290.99
247_A341_S0.5280.99
42_M83_F0.5280.99
31_G120_L0.5270.99
377_C380_A0.5270.99
190_T194_A0.5250.99
455_S458_L0.5230.99
123_I127_A0.5210.99
9_L21_F0.5200.99
362_L437_V0.5200.99
435_G440_G0.5190.99
373_G437_V0.5180.99
146_G172_T0.5180.99
36_A39_T0.5160.99
94_I459_V0.5160.99
377_C381_L0.5160.99
430_F434_F0.5150.99
301_A304_T0.5150.99
96_S99_Y0.5140.99
454_G459_V0.5130.99
202_H206_R0.5130.99
296_M437_V0.5130.99
141_F144_I0.5120.99
67_V136_L0.5120.99
32_V36_A0.5120.99
334_V470_S0.5110.99
171_I219_G0.5110.99
341_S463_L0.5110.99
307_Q383_I0.5090.99
393_F397_P0.5090.99
234_M246_A0.5090.99
384_T431_I0.5080.99
15_G18_V0.5060.99
9_L19_V0.5050.99
269_H273_G0.5050.99
210_Y214_L0.5050.99
85_V300_L0.5050.99
407_V411_I0.5050.99
96_S239_P0.5040.99
421_I425_A0.5040.99
365_V370_P0.5020.99
359_L433_W0.5020.99
146_G149_S0.5010.99
91_L463_L0.5010.99
338_F390_N0.5000.99
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  
3rkoL 1 0.9541 100 0.159 Contact Map
3rkoM 1 0.9562 100 0.169 Contact Map
4he8L 1 0.9457 100 0.173 Contact Map
4he8M 1 0.9248 100 0.196 Contact Map
3rkoN 1 0.9311 100 0.212 Contact Map
4he8N 1 0.8768 100 0.267 Contact Map
4he8K 1 0.1921 63.2 0.956 Contact Map
3rkoK 1 0.2004 60.6 0.957 Contact Map
3wu2X 1 0.0772 4.5 0.976 Contact Map
2gfpA 2 0.7182 3 0.978 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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