OPENSEQ.org
gremlin_chainA

ID: 1517403186 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 354 (299)
Sequences: 2030 (1289.2)
Seq/Len: 6.789
Nf(neff/√len): 74.6

HHblits Results: (2016_02)
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: 6.789).

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
289_N331_N2.7111.00
67_H71_E2.4591.00
301_L306_A2.4541.00
122_L128_C2.3591.00
287_L328_A2.3521.00
268_L286_T2.3121.00
199_S209_I2.1391.00
166_L171_S2.0771.00
244_N289_N2.0331.00
108_L150_V2.0241.00
209_I215_A2.0211.00
284_C328_A2.0151.00
153_N197_N1.9451.00
56_L107_A1.8781.00
57_M60_S1.8191.00
69_M74_G1.8171.00
239_G286_T1.8021.00
165_T168_E1.7441.00
246_S259_L1.7441.00
53_V107_A1.7191.00
284_C325_S1.6821.00
306_A310_L1.6791.00
207_A211_A1.6681.00
105_G150_V1.6481.00
257_Q261_E1.6151.00
60_S69_M1.6111.00
208_D211_A1.5901.00
199_S244_N1.5891.00
53_V57_M1.5510.99
112_T122_L1.5470.99
310_L328_A1.5450.99
259_L264_C1.5350.99
120_A125_M1.5300.99
79_A128_C1.4840.99
55_V58_K1.4760.99
60_S110_N1.4350.99
285_G288_W1.4330.99
192_L241_I1.4190.99
57_M103_Y1.4110.99
58_K61_F1.3900.99
269_L306_A1.3860.99
299_E303_D1.3720.98
313_L321_I1.3630.98
146_V156_W1.3590.98
54_C58_K1.3390.98
119_K206_K1.3280.98
242_L286_T1.3160.98
155_S166_L1.2880.97
155_S197_N1.2790.97
103_Y109_T1.2670.97
106_M149_S1.2520.97
53_V78_I1.2490.97
68_A72_L1.2480.97
88_M93_N1.2470.97
151_L194_A1.2450.97
78_I107_A1.2390.96
291_S301_L1.2380.96
164_K168_E1.2350.96
240_G243_R1.2350.96
282_N285_G1.2330.96
132_L147_I1.2270.96
145_Q187_T1.2170.96
188_L191_V1.2100.96
280_V321_I1.2080.96
193_S237_S1.2020.96
112_T153_N1.2020.96
149_S190_S1.1930.95
322_A329_L1.1900.95
223_L238_G1.1900.95
240_G282_N1.1750.95
51_P54_C1.1750.95
185_E231_T1.1740.95
143_L150_V1.1680.95
175_L194_A1.1660.95
196_W240_G1.1610.94
124_S162_S1.1600.94
109_T149_S1.1590.94
60_S107_A1.1560.94
113_F153_N1.1530.94
284_C313_L1.1490.94
189_K239_G1.1470.94
88_M91_L1.1380.94
246_S289_N1.1350.93
231_T276_S1.1320.93
106_M109_T1.1310.93
133_V169_V1.1300.93
89_Y93_N1.1250.93
280_V316_S1.1240.93
152_R163_K1.1230.93
90_G93_N1.1190.93
167_R174_A1.1170.93
263_N286_T1.1140.93
294_N297_D1.1130.93
59_L276_S1.1060.92
298_Q335_N1.1060.92
89_Y94_D1.1040.92
192_L234_I1.1030.92
128_C135_Q1.1010.92
56_L78_I1.0990.92
87_E90_G1.0980.92
165_T169_V1.0950.92
88_M94_D1.0940.92
256_R293_R1.0940.92
105_G147_I1.0910.92
109_T119_K1.0830.91
216_L242_L1.0810.91
196_W237_S1.0750.91
184_K187_T1.0740.91
89_Y92_T1.0730.91
291_S331_N1.0690.90
258_I262_N1.0640.90
65_H260_R1.0630.90
245_V255_H1.0630.90
79_A126_K1.0620.90
50_C99_T1.0590.90
136_L148_A1.0580.90
143_L146_V1.0570.90
288_W327_A1.0570.90
133_V171_S1.0540.90
148_A175_L1.0540.90
197_N244_N1.0540.90
154_L175_L1.0520.89
110_N244_N1.0460.89
187_T191_V1.0430.89
87_E92_T1.0420.89
265_L332_L1.0420.89
271_H279_I1.0390.89
77_A81_L1.0380.89
242_L259_L1.0370.89
132_L154_L1.0360.88
273_K309_M1.0350.88
51_P66_R1.0320.88
68_A71_E1.0300.88
259_L295_P1.0270.88
64_E259_L1.0260.88
271_H274_S1.0250.88
243_R285_G1.0220.88
168_E329_L1.0220.88
87_E91_L1.0200.87
59_L75_L1.0200.87
204_E207_A1.0200.87
49_I187_T1.0160.87
76_Q79_A1.0120.87
310_L322_A1.0110.87
54_C106_M1.0040.86
152_R282_N1.0010.86
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  
3nmwA20.92371000.277Contact Map
3nmzA20.94071000.388Contact Map
4plqA10.79941000.43Contact Map
4rxhB101000.431Contact Map
3opbA20.9351000.436Contact Map
4uadA10.92371000.436Contact Map
4uaeA10.84181000.438Contact Map
4uafB10.93221000.443Contact Map
2jdqA20.92661000.447Contact Map
4b8jA10.92091000.456Contact 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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