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arpc1b

ID: 1501024353 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 372 (354)
Sequences: 2624 (2187.3)
Seq/Len: 7.412
Nf(neff/√len): 116.3

Jackhmmer Results: (2016_04)
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: 7.412).

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
141_I159_A3.6211.00
95_I113_V3.5461.00
51_H69_T3.4071.00
32_V69_T3.2681.00
101_C114_G3.1031.00
159_A169_F3.0991.00
24_A67_I3.0551.00
113_V123_C2.9351.00
147_S160_G2.9101.00
25_I35_Y2.8781.00
112_A157_L2.7911.00
120_I159_A2.7781.00
201_S219_W2.7771.00
68_V111_F2.7381.00
51_H73_D2.6141.00
219_W229_A2.5631.00
24_A60_W2.5271.00
58_I69_T2.3761.00
112_A150_W2.3711.00
158_A217_V2.3651.00
57_G70_C2.3441.00
71_G75_N2.3291.00
201_S223_D2.0831.00
26_C30_H1.9971.00
220_V224_S1.9441.00
163_D167_R1.8311.00
68_V78_V1.7691.00
141_I161_S1.7671.00
68_V104_W1.7581.00
25_I29_N1.7561.00
69_T79_W1.7441.00
95_I123_C1.7381.00
160_G164_F1.7081.00
218_A252_F1.7061.00
68_V102_V1.7061.00
166_C219_W1.7011.00
59_D103_R1.6811.00
207_G220_V1.6691.00
141_I163_D1.6601.00
17_N21_T1.6311.00
50_E79_W1.5941.00
298_A301_R1.5751.00
297_T301_R1.5701.00
24_A34_I1.5591.00
117_S121_S1.5551.00
76_A113_V1.5331.00
58_I67_I1.5271.00
95_I115_S1.5170.99
114_G145_V1.5120.99
211_S214_G1.4920.99
51_H71_G1.4680.99
13_C26_C1.4640.99
141_I169_F1.4620.99
7_L25_I1.4520.99
95_I99_A1.4420.99
50_E77_Y1.4270.99
99_A113_V1.4170.99
159_A163_D1.3830.99
253_I256_N1.3770.99
112_A122_I1.3760.99
160_G205_V1.3680.99
301_R304_N1.3640.99
158_A168_I1.3310.98
152_P210_F1.3270.98
62_P108_E1.3190.98
289_K293_Q1.3190.98
309_A313_G1.3180.98
25_I33_H1.3150.98
56_T72_T1.3090.98
27_P33_H1.3070.98
220_V247_L1.3070.98
95_I117_S1.3070.98
106_P150_W1.3050.98
69_T73_D1.3010.98
219_W223_D1.2940.98
105_A150_W1.2920.98
208_V219_W1.2880.98
70_C99_A1.2730.98
208_V217_V1.2660.97
346_C356_I1.2650.97
348_T354_M1.2650.97
114_G118_R1.2600.97
61_A104_W1.2570.97
296_L299_R1.2570.97
115_S119_V1.2500.97
303_Q308_K1.2430.97
306_D310_S1.2420.97
161_S165_K1.2420.97
288_P292_S1.2410.97
243_E264_D1.2370.97
303_Q307_K1.2310.97
298_A302_F1.2310.97
158_A210_F1.2280.97
36_E39_G1.2020.96
305_L308_K1.2000.96
27_P31_E1.1980.96
300_E303_Q1.1860.96
51_H79_W1.1860.96
160_G208_V1.1820.96
282_G285_L1.1810.96
311_S314_G1.1790.96
295_G300_E1.1780.96
27_P30_H1.1750.96
303_Q306_D1.1640.95
288_P291_S1.1590.95
261_A265_C1.1470.95
35_Y44_K1.1470.95
301_R307_K1.1440.95
16_W23_I1.1420.95
300_E304_N1.1400.95
115_S118_R1.1350.94
332_I347_T1.1270.94
299_R310_S1.1220.94
103_R149_D1.1160.94
79_W86_W1.1150.94
318_G321_L1.1140.94
299_R302_F1.1140.94
29_N33_H1.1040.93
60_W67_I1.1030.93
290_Q293_Q1.0880.93
124_Y127_Q1.0870.93
291_S294_R1.0870.93
205_V208_V1.0830.92
289_K292_S1.0830.92
57_G101_C1.0810.92
17_N60_W1.0800.92
301_R308_K1.0780.92
260_A264_D1.0780.92
285_L288_P1.0760.92
223_D227_C1.0720.92
113_V121_S1.0710.92
201_S221_S1.0690.92
298_A303_Q1.0670.92
299_R304_N1.0670.92
289_K295_G1.0650.92
218_A250_L1.0640.91
32_V55_V1.0590.91
102_V113_V1.0580.91
243_E247_L1.0580.91
158_A169_F1.0550.91
299_R303_Q1.0530.91
51_H55_V1.0520.91
149_D208_V1.0510.91
259_V269_L1.0500.91
324_L328_S1.0480.91
307_K310_S1.0460.91
115_S121_S1.0430.90
296_L301_R1.0370.90
118_R144_T1.0350.90
170_S173_I1.0350.90
138_K141_I1.0280.89
71_G77_Y1.0240.89
285_L291_S1.0230.89
325_H329_V1.0200.89
287_V290_Q1.0190.89
290_Q294_R1.0180.89
325_H347_T1.0160.89
295_G299_R1.0150.89
303_Q309_A1.0110.88
284_R287_V1.0100.88
56_T100_R1.0090.88
301_R310_S1.0030.88
98_A116_G1.0000.88
287_V294_R1.0000.88
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: (06Aug15)
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  
1k8kC10.95161000.249Contact Map
3dwlC20.85751000.287Contact Map
1vyhC100.77151000.306Contact Map
3dm0A10.7931000.338Contact Map
3fm0A10.8281000.343Contact Map
4wjuA20.81991000.344Contact Map
3sfzA10.95431000.345Contact Map
4bpeR10.83061000.346Contact Map
3j60g10.82261000.346Contact Map
3ow8A40.78231000.35Contact 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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