May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

PhyB_BAC

ID: 1434653918 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 503 (486)
Sequences: 562 (398.8)
Seq/Len: 1.156
Nf(neff/√len): 18.1

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.156).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
158_T172_L4.3461.00
213_Y271_S3.4251.00
363_G440_P3.1741.00
375_T385_V2.8551.00
162_R187_A2.8021.00
176_A180_T2.7251.00
24_E254_S2.6491.00
53_L230_P2.4790.99
261_L266_V2.4410.99
233_P237_P2.3610.99
272_V306_G2.3200.99
261_L285_A2.3030.99
221_T253_T2.2780.99
259_Q459_D2.2730.99
366_I438_L2.1940.98
167_F270_L2.1410.98
447_A468_T2.1140.98
21_C24_E2.0460.97
19_E22_E2.0390.97
40_T243_T1.9960.97
422_L436_V1.9910.96
233_P240_N1.9890.96
157_A309_L1.9570.96
50_Q233_P1.9430.96
154_A184_I1.9150.95
403_D476_Y1.8730.95
26_I209_A1.8560.94
420_A440_P1.7990.93
263_N465_S1.7820.92
34_P226_A1.7300.91
40_T202_A1.7100.90
198_H446_V1.6610.88
21_C256_M1.6590.88
259_Q464_H1.6380.87
226_A252_A1.6300.87
26_I273_S1.6190.87
339_A348_T1.6090.86
258_M262_R1.5970.86
364_G380_P1.5810.85
375_T379_V1.5560.84
208_Q271_S1.5510.83
412_G415_L1.5500.83
171_M261_L1.5500.83
245_L248_A1.5410.83
36_G250_L1.5310.82
208_Q213_Y1.5310.82
194_A200_F1.5300.82
462_P465_S1.5270.82
42_D45_S1.5220.82
462_P466_F1.5060.81
213_Y273_S1.4780.79
233_P236_N1.4770.79
450_G466_F1.4720.79
335_V348_T1.4620.78
236_N239_T1.4480.77
257_H269_S1.4430.77
110_L123_F1.4380.76
25_P30_G1.4360.76
208_Q254_S1.4300.76
24_E208_Q1.4210.75
182_E199_R1.4160.75
357_L362_A1.4120.75
463_R466_F1.4050.74
428_G449_G1.4020.74
213_Y253_T1.4010.74
167_F492_R1.3950.73
221_T264_M1.3910.73
381_P384_A1.3870.73
25_P28_I1.3760.72
171_M266_V1.3750.72
30_G254_S1.3660.71
208_Q273_S1.3600.71
302_L420_A1.3580.70
24_E454_D1.3540.70
214_T275_V1.3520.70
41_A172_L1.3370.69
263_N462_P1.3310.68
364_G438_L1.3300.68
428_G434_C1.3300.68
109_S285_A1.3240.68
124_E299_R1.3160.67
263_N466_F1.3020.66
233_P239_T1.2990.65
167_F222_A1.2960.65
419_A440_P1.2940.65
405_L412_G1.2900.65
48_V66_L1.2900.65
33_Q36_G1.2850.64
192_L200_F1.2740.63
116_G241_A1.2730.63
26_I208_Q1.2630.62
216_H286_C1.2620.62
204_D263_N1.2610.62
204_D260_Y1.2550.61
216_H271_S1.2550.61
263_N463_R1.2500.61
165_T449_G1.2460.61
224_T261_L1.2440.60
154_A172_L1.2430.60
20_N23_R1.2350.60
203_S245_L1.2200.58
112_V125_P1.2180.58
151_R155_E1.2180.58
340_A427_V1.2140.58
213_Y252_A1.2130.58
335_V477_A1.2120.57
69_Q73_A1.2120.57
291_P479_P1.2110.57
231_L410_P1.2060.57
114_R301_T1.2010.56
21_C25_P1.1980.56
154_A187_A1.1930.56
209_A257_H1.1890.55
79_W172_L1.1880.55
205_I209_A1.1880.55
141_M308_L1.1870.55
29_P208_Q1.1850.55
171_M285_A1.1840.55
74_L388_L1.1830.55
32_I229_V1.1810.55
205_I263_N1.1810.55
226_A270_L1.1740.54
294_L392_L1.1740.54
188_R191_G1.1730.54
24_E255_P1.1700.53
255_P273_S1.1570.52
450_G465_S1.1540.52
215_R247_G1.1520.52
392_L422_L1.1490.51
162_R189_R1.1480.51
145_E307_R1.1470.51
219_R260_Y1.1470.51
19_E23_R1.1450.51
28_I208_Q1.1370.50
39_L55_A1.1370.50
43_G114_R1.1370.50
192_L289_Q1.1350.50
307_R310_S1.1300.50
450_G462_P1.1280.49
55_A59_L1.1260.49
174_K275_V1.1250.49
204_D465_S1.1220.49
181_G263_N1.1220.49
263_N450_G1.1220.49
168_D192_L1.1210.49
309_L313_V1.1210.49
257_H273_S1.1190.49
112_V330_E1.1180.48
164_L184_I1.1180.48
111_T296_P1.1140.48
171_M200_F1.1120.48
27_H30_G1.1110.48
200_F360_M1.1080.48
241_A477_A1.1080.48
25_P208_Q1.1070.47
354_L358_G1.1050.47
231_L443_R1.1020.47
208_Q257_H1.1000.47
173_Y181_G1.1000.47
51_M55_A1.0980.47
179_A279_Q1.0970.46
168_D189_R1.0960.46
412_G420_A1.0960.46
481_H484_E1.0950.46
364_G379_V1.0940.46
110_L274_V1.0910.46
403_D471_E1.0900.46
209_A263_N1.0900.46
41_A71_L1.0900.46
115_V120_I1.0880.46
24_E30_G1.0860.45
226_A253_T1.0840.45
231_L274_V1.0830.45
209_A462_P1.0800.45
50_Q237_P1.0790.45
79_W158_T1.0770.45
211_A214_T1.0720.44
21_C208_Q1.0710.44
200_F268_S1.0710.44
268_S469_Y1.0700.44
181_G466_F1.0700.44
336_A495_L1.0690.44
365_L376_L1.0680.44
71_L449_G1.0670.44
26_I205_I1.0670.44
181_G465_S1.0660.43
86_L279_Q1.0640.43
402_T405_L1.0620.43
200_F461_G1.0590.43
56_A62_E1.0580.43
204_D257_H1.0550.42
204_D448_W1.0530.42
204_D466_F1.0520.42
26_I29_P1.0520.42
75_L79_W1.0510.42
145_E158_T1.0510.42
438_L484_E1.0500.42
150_L356_L1.0490.42
252_A273_S1.0480.42
24_E212_L1.0470.42
264_M466_F1.0470.42
180_T461_G1.0460.42
221_T245_L1.0450.42
48_V267_G1.0440.41
274_V356_L1.0410.41
21_C254_S1.0390.41
41_A121_L1.0390.41
181_G204_D1.0390.41
50_Q236_N1.0350.41
331_H435_L1.0330.40
50_Q240_N1.0310.40
80_P84_A1.0300.40
427_V493_D1.0280.40
37_A58_F1.0270.40
164_L243_T1.0250.40
21_C213_Y1.0250.40
35_H252_A1.0240.40
221_T257_H1.0230.39
43_G119_L1.0220.39
173_Y465_S1.0190.39
254_S454_D1.0190.39
59_L491_L1.0170.39
324_F328_L1.0170.39
182_E285_A1.0160.39
204_D462_P1.0160.39
415_L420_A1.0160.39
31_S252_A1.0150.39
266_V285_A1.0130.39
35_H226_A1.0130.39
264_M287_H1.0120.38
391_W409_W1.0120.38
459_D464_H1.0120.38
207_A211_A1.0090.38
168_D487_E1.0080.38
149_N152_A1.0080.38
291_P424_A1.0050.38
450_G463_R1.0040.38
25_P254_S1.0040.38
406_G475_G1.0030.38
274_V416_A1.0030.38
178_D199_R1.0020.38
278_G444_L1.0020.38
133_G259_Q1.0000.37
218_L242_P1.0000.37
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (31Jan15)
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-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4q0jA10.97611000.234Contact Map
4ourA10.84891000.264Contact Map
3zq5A10.98011000.327Contact Map
3nhqA80.93641000.356Contact Map
4gw9A40.97221000.402Contact Map
4bwiA20.71571000.542Contact Map
4cqhA10.59641000.555Contact Map
4e04A20.60241000.584Contact Map
2oolA20.59641000.588Contact Map
2k2nA10.3499.90.856Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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.

Page generated in 0.6157 seconds.