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OPENSEQ.org

Rubisco large subunit

ID: 1420831392 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 475 (465)
Sequences: 473 (214.2)
Seq/Len: 1.017
Nf(neff/√len): 9.9

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: 1.017).

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
422_V454_E3.2141.00
411_W457_A3.1081.00
38_A135_L2.7291.00
448_A452_S2.6081.00
224_A228_S2.5000.99
257_A262_V2.3970.99
258_K289_L2.0030.96
422_V452_S1.9910.95
187_R191_E1.9600.95
137_D316_K1.9300.94
257_A265_I1.9180.94
455_L458_A1.9080.94
450_K456_A1.8550.93
190_Y228_S1.8350.92
195_G417_A1.8110.92
35_D102_A1.7810.91
384_V419_A1.7280.89
412_G416_G1.7030.88
137_D150_G1.6780.87
145_A320_L1.6770.87
385_W463_K1.6300.85
116_L140_I1.6230.84
407_L413_N1.6150.84
447_A450_K1.5990.83
191_E414_A1.5470.80
254_A280_L1.5370.80
295_R327_H1.5310.79
202_D217_R1.5180.78
319_R322_G1.5060.78
404_G408_G1.5020.77
190_Y227_K1.4980.77
292_H295_R1.4880.76
114_T243_T1.4860.76
37_L100_Y1.4760.76
73_G289_L1.4390.73
85_Y102_A1.4340.73
170_L387_M1.4330.72
295_R334_K1.4200.71
435_V447_A1.4190.71
148_F411_W1.4160.71
295_R303_R1.3870.69
256_C260_L1.3810.68
292_H327_H1.3710.68
409_H416_G1.3700.68
71_T74_L1.3700.68
171_G295_R1.3640.67
227_K231_E1.3580.67
189_V380_G1.3570.66
381_G404_G1.3510.66
61_S176_P1.3460.66
242_V419_A1.3450.65
84_C101_V1.3390.65
116_L144_Y1.3290.64
435_V448_A1.3260.64
254_A333_G1.3260.64
452_S460_E1.3210.63
64_G402_F1.3190.63
236_K239_Y1.3070.62
377_V405_G1.3030.62
409_H412_G1.3020.62
338_E344_G1.3020.62
60_E123_N1.2930.61
112_S115_N1.2910.61
292_H334_K1.2710.59
182_A212_M1.2630.58
159_R397_D1.2620.58
190_Y224_A1.2610.58
64_G104_P1.2570.58
177_K329_G1.2570.58
456_A460_E1.2530.57
277_N314_L1.2510.57
115_N207_N1.2510.57
244_A253_R1.2490.57
455_L459_C1.2470.57
59_A62_S1.2440.57
327_H334_K1.2430.56
423_A434_G1.2380.56
50_P99_A1.2340.56
123_N327_H1.2330.56
327_H379_S1.2320.55
53_C60_E1.2310.55
173_T402_F1.2290.55
118_T268_D1.2270.55
298_H329_G1.2260.55
252_K289_L1.2250.55
189_V225_I1.2240.55
36_I98_I1.2150.54
335_L383_H1.2140.54
115_N209_Q1.2110.54
135_L167_R1.2100.53
182_A373_G1.2090.53
274_L281_A1.2050.53
164_K200_T1.2010.53
204_E416_G1.2000.52
203_D217_R1.1990.52
190_Y194_R1.1940.52
57_V62_S1.1940.52
297_M309_I1.1910.52
262_V265_I1.1910.52
39_A100_Y1.1890.51
53_C130_L1.1890.51
249_E252_K1.1800.51
60_E327_H1.1780.50
103_Y108_F1.1780.50
204_E412_G1.1760.50
355_E365_T1.1750.50
50_P97_Y1.1730.50
458_A462_W1.1730.50
307_H314_L1.1720.50
104_P118_T1.1720.50
357_D360_R1.1710.50
142_P146_K1.1690.50
217_R397_D1.1690.50
118_T269_Y1.1670.49
144_Y147_T1.1640.49
126_G333_G1.1610.49
195_G224_A1.1580.49
209_Q242_V1.1560.48
113_V242_V1.1480.48
243_T249_E1.1480.48
350_R456_A1.1460.47
177_K268_D1.1450.47
171_G334_K1.1440.47
142_P183_K1.1440.47
211_F399_C1.1420.47
155_I227_K1.1420.47
152_P281_A1.1420.47
235_I419_A1.1410.47
171_G327_H1.1400.47
262_V290_L1.1380.47
208_S213_R1.1360.47
375_M399_C1.1340.46
327_H330_T1.1310.46
213_R216_D1.1310.46
115_N118_T1.1310.46
37_L139_R1.1300.46
40_F57_V1.1280.46
296_A383_H1.1280.46
295_R298_H1.1270.46
107_L205_N1.1260.46
62_S82_G1.1260.46
126_G129_A1.1250.46
154_G217_R1.1240.45
17_V20_Y1.1220.45
319_R404_G1.1210.45
124_V379_S1.1200.45
133_L136_E1.1200.45
171_G292_H1.1160.45
121_V125_F1.1150.45
421_R425_E1.1150.45
265_I290_L1.1140.44
97_Y148_F1.1120.44
53_C333_G1.1120.44
15_A18_K1.1110.44
339_R343_L1.1090.44
419_A462_W1.1090.44
249_E289_L1.1040.44
58_A62_S1.1010.43
292_H325_H1.1000.43
157_V324_D1.1000.43
278_T285_R1.0990.43
126_G177_K1.0970.43
270_L298_H1.0920.42
52_E169_L1.0910.42
44_P61_S1.0900.42
205_N401_Q1.0900.42
132_A307_H1.0900.42
108_F401_Q1.0860.42
16_G20_Y1.0860.42
194_R228_S1.0850.42
412_G426_A1.0840.42
329_G333_G1.0840.42
113_V116_L1.0810.41
254_A287_T1.0780.41
295_R378_A1.0770.41
330_T333_G1.0760.41
118_T271_T1.0760.41
215_R243_T1.0750.41
154_G159_R1.0730.41
208_S212_M1.0730.41
41_R136_E1.0710.41
379_S405_G1.0690.40
454_E460_E1.0680.40
103_Y333_G1.0670.40
183_K216_D1.0670.40
281_A290_L1.0620.40
405_G409_H1.0590.39
188_A212_M1.0540.39
251_M447_A1.0540.39
49_P323_G1.0530.39
467_F473_D1.0520.39
42_M350_R1.0510.39
422_V448_A1.0510.39
329_G380_G1.0460.38
36_I369_C1.0440.38
190_Y216_D1.0430.38
101_V237_G1.0420.38
358_R365_T1.0400.38
329_G378_A1.0400.38
292_H303_R1.0400.38
162_I165_Y1.0370.38
288_G426_A1.0350.37
55_A69_V1.0340.37
38_A167_R1.0340.37
153_H290_L1.0340.37
117_F300_V1.0330.37
37_L85_Y1.0330.37
123_N205_N1.0330.37
254_A463_K1.0320.37
208_S253_R1.0260.37
123_N334_K1.0260.37
237_G240_L1.0250.37
23_T26_T1.0240.36
64_G204_E1.0240.36
86_D100_Y1.0200.36
69_V174_I1.0180.36
37_L102_A1.0180.36
154_G261_G1.0150.36
177_K205_N1.0150.36
143_A215_R1.0150.36
39_A139_R1.0150.36
223_E230_A1.0130.35
452_S457_A1.0110.35
453_P457_A1.0090.35
217_R324_D1.0080.35
49_P52_E1.0080.35
325_H328_S1.0070.35
95_N316_K1.0050.35
112_S325_H1.0040.35
35_D85_Y1.0000.34
418_A454_E1.0000.34
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: (06Sep14)
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  
1wddA20.97681000.033Contact Map
4f0hA10.93681000.067Contact Map
3kdnA100.91371000.155Contact Map
2d69A40.89261000.177Contact Map
2qygA40.86951000.203Contact Map
4nasA40.83581000.211Contact Map
2oemA20.84211000.216Contact Map
3fk4A20.80631000.219Contact Map
5rubA20.87371000.219Contact Map
2zviA40.83581000.22Contact 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.

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