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OPENSEQ.org

rbcL -force run

ID: 1429047077 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 479 (465)
Sequences: 458 (204.2)
Seq/Len: 0.985
Nf(neff/√len): 9.5

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: 0.985).

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_E3.3871.00
411_W457_A3.1271.00
38_A135_L2.7531.00
224_A228_S2.3660.99
448_A452_S2.3490.99
257_A262_V2.3090.98
422_V452_S2.2000.98
258_R289_L2.1860.98
187_R191_E2.0330.96
257_A265_V2.0310.96
455_L458_A1.9760.95
190_Y228_S1.8900.93
35_D102_A1.8870.93
195_G417_A1.8400.92
404_G408_G1.8180.91
137_D316_K1.8090.91
145_T320_L1.8080.91
384_V419_A1.7380.89
450_K456_A1.7270.88
137_D150_G1.6970.87
407_L413_N1.6610.85
116_M140_I1.6320.84
412_G416_G1.5850.82
295_R327_H1.5700.81
256_F260_L1.5670.80
447_E450_K1.5520.80
170_L387_M1.5270.78
191_E414_A1.5000.76
71_T74_L1.4990.76
202_D217_R1.4740.75
190_Y227_K1.4710.74
292_H295_R1.4700.74
37_L100_Y1.4510.73
148_F411_W1.4500.73
385_W463_K1.4470.73
452_S460_E1.4360.72
319_R322_G1.4360.72
277_N314_L1.4340.72
292_H327_H1.4130.70
171_G295_R1.4090.70
295_R334_K1.4050.69
144_Y147_T1.4020.69
405_G409_H1.3950.69
182_A212_M1.3840.68
338_D344_G1.3790.67
50_P99_A1.3790.67
50_P97_F1.3760.67
254_A333_G1.3690.67
114_T243_T1.3580.66
112_S115_N1.3530.65
292_H334_K1.3380.64
190_Y224_A1.3380.64
182_A373_G1.3370.64
435_R448_A1.3340.64
435_R447_E1.3280.63
59_A62_S1.3220.63
327_H379_S1.3150.62
189_V380_G1.3100.61
116_M144_Y1.3080.61
123_N327_H1.3070.61
52_E169_L1.3060.61
295_R303_R1.3050.61
381_G404_G1.3020.61
242_A419_A1.2990.61
64_G402_F1.2940.60
456_A460_E1.2930.60
236_K239_Y1.2930.60
118_T268_D1.2910.60
189_V225_I1.2770.59
254_A280_L1.2740.58
84_C101_V1.2730.58
298_H329_G1.2700.58
61_S176_P1.2670.58
49_P323_G1.2670.58
58_A62_S1.2630.57
126_G333_G1.2590.57
60_E123_N1.2580.57
64_G104_P1.2510.56
53_A60_E1.2490.56
177_K329_G1.2390.55
128_K236_K1.2290.54
335_L383_H1.2250.54
171_G334_K1.2240.54
244_A253_R1.2180.53
409_H412_G1.2170.53
278_T282_H1.2160.53
113_V242_A1.2120.53
377_V405_G1.2110.53
126_G177_K1.2110.53
419_A462_W1.2060.52
39_A100_Y1.2050.52
115_N207_N1.2040.52
60_E327_H1.1950.51
36_I98_I1.1890.51
227_K231_E1.1870.50
124_V379_S1.1860.50
37_L139_R1.1850.50
171_G327_H1.1820.50
44_P47_G1.1820.50
217_R397_D1.1800.50
327_H334_K1.1800.50
296_A383_H1.1770.49
103_Y108_F1.1750.49
455_L459_C1.1740.49
73_G289_L1.1720.49
53_A130_L1.1720.49
115_N209_Q1.1700.49
164_K200_T1.1680.49
191_E216_D1.1660.48
159_R397_D1.1650.48
297_M309_M1.1580.48
112_S210_P1.1560.47
203_D217_R1.1510.47
262_V265_V1.1510.47
108_F401_Q1.1510.47
40_F57_V1.1510.47
173_T402_F1.1480.47
62_S82_G1.1460.47
57_V62_S1.1460.47
423_A434_G1.1420.46
409_H416_G1.1420.46
350_R456_A1.1410.46
235_I419_A1.1360.46
15_A18_K1.1330.45
171_G292_H1.1310.45
422_V448_A1.1310.45
319_R404_G1.1290.45
208_S213_R1.1260.45
17_V20_Y1.1260.45
177_K268_D1.1260.45
104_P118_T1.1250.45
103_Y333_G1.1240.45
183_K216_D1.1170.44
379_S405_G1.1160.44
412_G426_A1.1160.44
154_G217_R1.1150.44
155_I227_K1.1140.44
443_E460_E1.1140.44
135_L167_R1.1140.44
204_E416_G1.1120.43
292_H325_H1.1110.43
205_N266_M1.1100.43
205_N401_Q1.1090.43
102_A388_P1.1060.43
157_V324_D1.1050.43
126_G329_G1.1030.43
329_G380_G1.0990.42
123_N334_K1.0990.42
211_F399_V1.0980.42
249_E252_K1.0940.42
142_P183_K1.0910.42
16_G20_Y1.0900.41
295_R298_H1.0900.41
213_R216_D1.0890.41
53_A333_G1.0890.41
113_V116_M1.0890.41
252_K289_L1.0880.41
309_M326_I1.0880.41
360_R365_T1.0840.41
85_Y102_A1.0830.41
118_T269_Y1.0790.40
44_P61_S1.0780.40
274_F281_S1.0780.40
41_R136_E1.0750.40
123_N266_M1.0740.40
204_E412_G1.0730.40
327_H330_T1.0700.40
156_Q373_G1.0700.40
66_W382_I1.0700.40
194_R228_S1.0690.40
291_L311_F1.0660.39
267_H277_N1.0660.39
152_P289_L1.0640.39
402_F420_N1.0630.39
339_R343_L1.0600.39
169_L394_F1.0600.39
123_N205_N1.0570.39
223_E227_K1.0560.38
86_H100_Y1.0560.38
227_K230_A1.0550.38
265_V290_L1.0540.38
156_Q160_D1.0520.38
228_S243_T1.0520.38
195_G257_A1.0500.38
208_S212_M1.0490.38
249_E253_R1.0490.38
23_T26_T1.0460.38
123_N171_G1.0460.38
209_Q242_A1.0450.37
421_R425_E1.0440.37
37_L85_Y1.0430.37
198_D201_K1.0430.37
329_G378_A1.0420.37
189_V311_F1.0420.37
150_G316_K1.0420.37
429_Q456_A1.0420.37
115_N118_T1.0410.37
234_E239_Y1.0380.37
154_G261_G1.0350.37
219_L256_F1.0350.37
452_S457_A1.0330.36
115_N206_V1.0330.36
408_G421_R1.0330.36
195_G224_A1.0330.36
142_P146_K1.0320.36
37_L102_A1.0310.36
458_A462_W1.0300.36
112_S268_D1.0280.36
375_L399_V1.0280.36
177_K298_H1.0280.36
412_G423_A1.0280.36
195_G407_L1.0270.36
372_P422_V1.0240.36
396_D428_V1.0230.36
133_L136_E1.0200.35
237_G240_L1.0200.35
359_S365_T1.0190.35
390_L398_S1.0180.35
132_A307_H1.0180.35
126_G129_A1.0170.35
259_E446_R1.0160.35
307_H314_L1.0150.35
270_L298_H1.0150.35
254_A424_L1.0150.35
103_Y170_L1.0140.35
152_P281_S1.0130.35
292_H303_R1.0130.35
299_A321_S1.0130.35
121_V178_L1.0120.35
55_A69_V1.0110.35
435_R451_W1.0090.34
118_T271_T1.0090.34
217_R324_D1.0080.34
419_A423_A1.0070.34
95_T316_K1.0070.34
107_L205_N1.0060.34
176_P182_A1.0060.34
266_M295_R1.0060.34
223_E230_A1.0040.34
124_V127_F1.0040.34
39_A139_R1.0020.34
42_V350_R1.0020.34
163_N198_D1.0010.34
177_K244_A1.0010.34
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: (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  
1wddA20.96871000.056Contact Map
4f0hA10.9291000.07Contact Map
3kdnA100.90611000.176Contact Map
2d69A40.88731000.185Contact Map
2oemA20.83511000.225Contact Map
4nasA40.82881000.228Contact Map
3fk4A20.79961000.23Contact Map
1ykwA20.82881000.234Contact Map
3nwrA10.79541000.24Contact Map
5rubA20.87271000.242Contact 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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