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OPENSEQ.org

sst3a_deltaC

ID: 1410244395 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 480 (472)
Sequences: 642 (474.2)
Seq/Len: 1.360
Nf(neff/√len): 21.8

Jackhmmer Results: (2014_04_16)
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: 1.360).

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
135_T144_G2.1630.99
55_R73_D2.0770.98
176_M215_L2.0110.98
135_T143_A1.9930.97
133_H181_Y1.9830.97
167_D405_R1.9420.97
132_Y136_K1.8250.95
96_S166_Y1.7870.94
54_Y58_R1.7480.94
77_W82_R1.7370.93
348_S352_H1.7110.93
168_N403_M1.6420.90
130_V178_L1.6200.90
461_I465_A1.6020.89
132_Y141_A1.6000.89
146_L419_G1.5940.89
126_F174_F1.5210.85
453_K458_S1.5200.85
186_A198_C1.5130.85
135_T416_I1.5090.85
466_F469_I1.5030.84
73_D167_D1.4980.84
169_E172_A1.4440.81
115_V189_T1.4390.81
137_E185_K1.4260.80
133_H178_L1.4170.79
59_F63_E1.4170.79
373_V421_G1.4150.79
450_Y456_V1.4140.79
465_A469_I1.4090.79
232_F236_I1.3970.78
446_Q464_M1.3950.78
120_A124_S1.3950.78
448_S462_L1.3710.76
117_V163_A1.3590.75
47_E352_H1.3560.75
445_Q448_S1.3530.75
186_A199_A1.3500.74
360_Y400_S1.3400.74
443_K446_Q1.3370.73
27_A125_S1.3330.73
476_T479_T1.3230.72
303_I308_F1.3200.72
135_T139_K1.3190.72
48_F165_S1.3170.72
172_A392_Y1.3160.72
232_F298_L1.3140.72
205_M212_Y1.3130.71
100_Y104_H1.3090.71
136_K144_G1.3090.71
168_N172_A1.3060.71
449_T460_M1.3010.70
449_T454_N1.2900.69
68_F73_D1.2900.69
439_D442_S1.2890.69
183_W222_H1.2880.69
348_S351_E1.2810.69
116_C166_Y1.2790.69
452_I462_L1.2770.68
453_K457_A1.2720.68
99_I103_L1.2610.67
446_Q449_T1.2600.67
443_K463_V1.2540.66
169_E403_M1.2520.66
461_I466_F1.2510.66
168_N405_R1.2490.66
49_D79_P1.2490.66
143_A419_G1.2460.66
447_D462_L1.2450.66
140_D143_A1.2360.65
133_H152_A1.2350.65
457_A470_T1.2340.65
142_G427_S1.2330.64
469_I473_F1.2320.64
198_C246_L1.2320.64
379_F382_L1.2270.64
470_T473_F1.2260.64
447_D454_N1.2260.64
450_Y463_V1.2250.64
121_P125_S1.2230.63
435_I438_P1.2230.63
465_A470_T1.2230.63
169_E408_L1.2200.63
439_D458_S1.2190.63
128_T148_A1.2160.63
446_Q452_I1.2140.63
452_I464_M1.2090.62
455_E458_S1.2070.62
278_Q290_L1.2050.62
156_G330_F1.2050.62
126_F130_V1.2040.62
448_S456_V1.2040.62
111_D376_Y1.1960.61
447_D452_I1.1960.61
443_K461_I1.1900.60
461_I464_M1.1900.60
443_K452_I1.1900.60
206_V257_V1.1860.60
205_M399_F1.1850.60
76_A84_I1.1820.60
443_K458_S1.1760.59
45_I53_N1.1730.59
447_D451_P1.1680.58
210_G329_R1.1650.58
53_N124_S1.1620.58
187_V377_Y1.1600.57
443_K451_P1.1590.57
450_Y455_E1.1550.57
76_A83_I1.1530.57
23_L34_R1.1530.57
345_I348_S1.1510.57
451_P463_V1.1510.57
457_A460_M1.1500.56
26_A149_A1.1480.56
150_M418_S1.1460.56
146_L422_V1.1400.55
31_F34_R1.1390.55
44_V51_Y1.1370.55
55_R78_Y1.1310.55
293_Q448_S1.1260.54
449_T453_K1.1250.54
448_S458_S1.1230.54
47_E57_T1.1220.54
50_P161_S1.1210.54
443_K467_F1.1200.53
180_Y388_F1.1190.53
144_G148_A1.1170.53
77_W210_G1.1170.53
450_Y453_K1.1150.53
150_M196_A1.1130.53
150_M414_M1.1130.53
305_L313_V1.1120.53
445_Q459_G1.1110.53
48_F352_H1.1080.52
399_F406_L1.1070.52
55_R161_S1.1040.52
465_A473_F1.1030.52
438_P448_S1.1020.52
161_S170_G1.1010.52
392_Y399_F1.1000.51
50_P57_T1.0980.51
452_I470_T1.0980.51
178_L181_Y1.0980.51
438_P465_A1.0970.51
445_Q456_V1.0970.51
403_M408_L1.0940.51
218_L395_T1.0930.51
443_K465_A1.0930.51
50_P210_G1.0920.51
131_T275_G1.0910.51
440_K454_N1.0900.50
352_H403_M1.0890.50
57_T352_H1.0870.50
466_F472_T1.0870.50
444_K465_A1.0840.50
149_A194_W1.0840.50
439_D447_D1.0810.50
449_T459_G1.0790.49
460_M464_M1.0790.49
71_W90_P1.0790.49
448_S454_N1.0780.49
344_P348_S1.0770.49
306_V452_I1.0770.49
451_P454_N1.0770.49
438_P441_K1.0760.49
436_S439_D1.0750.49
446_Q461_I1.0740.49
451_P455_E1.0740.49
444_K470_T1.0720.49
456_V462_L1.0660.48
20_L282_F1.0650.48
125_S411_A1.0630.48
93_M211_G1.0620.48
454_N458_S1.0610.48
235_R384_D1.0600.47
442_S446_Q1.0590.47
443_K448_S1.0580.47
260_Q268_M1.0580.47
169_E210_G1.0570.47
445_Q452_I1.0570.47
127_T132_Y1.0560.47
436_S443_K1.0560.47
441_K456_V1.0550.47
438_P444_K1.0540.47
246_L250_L1.0540.47
464_M472_T1.0520.47
446_Q466_F1.0520.47
458_S465_A1.0500.46
442_S467_F1.0500.46
103_L191_S1.0490.46
92_L95_T1.0490.46
458_S462_L1.0490.46
55_R72_F1.0480.46
443_K450_Y1.0480.46
453_K462_L1.0440.46
309_V453_K1.0430.46
455_E465_A1.0410.46
192_I222_H1.0410.46
456_V465_A1.0400.45
444_K450_Y1.0400.45
441_K453_K1.0370.45
442_S452_I1.0370.45
451_P467_F1.0370.45
118_F377_Y1.0370.45
439_D452_I1.0360.45
458_S467_F1.0360.45
452_I455_E1.0350.45
137_E188_K1.0340.45
120_A227_M1.0330.45
24_S311_L1.0330.45
346_I352_H1.0320.45
101_H105_F1.0310.45
446_Q454_N1.0310.45
72_F167_D1.0310.45
76_A88_I1.0310.45
447_D463_V1.0300.44
447_D466_F1.0290.44
172_A408_L1.0270.44
163_A166_Y1.0260.44
169_E352_H1.0230.44
438_P447_D1.0220.44
438_P449_T1.0220.44
437_R465_A1.0220.44
453_K470_T1.0200.43
451_P464_M1.0200.43
453_K456_V1.0200.43
454_N465_A1.0170.43
169_E346_I1.0150.43
184_I188_K1.0150.43
459_G465_A1.0150.43
453_K467_F1.0130.43
57_T60_L1.0120.43
236_I277_C1.0120.43
51_Y61_A1.0110.43
147_A407_M1.0100.42
167_D408_L1.0080.42
290_L298_L1.0080.42
139_K144_G1.0070.42
451_P456_V1.0070.42
230_G254_I1.0070.42
85_G167_D1.0060.42
443_K449_T1.0060.42
172_A210_G1.0040.42
155_P354_P1.0030.42
442_S456_V1.0030.42
121_P357_W1.0020.42
306_V314_G1.0010.42
230_G233_S1.0010.42
283_V333_L1.0010.42
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: (17Jul14)
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  
3wajA10.80631000.429Contact Map
3rceA10.82291000.56Contact Map
3pe5A2026.90.969Contact Map
4tq3A40.208313.60.973Contact Map
3mk7C40.16259.80.974Contact Map
4od4A60.28.30.975Contact Map
3rkoJ20.33756.10.977Contact Map
2m8rA10.07924.80.978Contact Map
4av3A20.15423.80.979Contact Map
2qsfA10.08133.70.979Contact 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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