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DHH

ID: 1518200821 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (292)
Sequences: 1111 (783.9)
Seq/Len: 3.805
Nf(neff/√len): 45.9

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: 3.805).

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
145_C155_H4.7881.00
131_C141_H3.3311.00
145_C162_C3.1151.00
155_H162_C2.9791.00
141_H148_C2.8071.00
131_C148_C2.6321.00
142_C145_C2.6131.00
168_Y231_H2.6081.00
264_S268_R2.4861.00
272_G278_W2.4721.00
267_W271_F2.3951.00
141_H145_C2.2461.00
235_V267_W2.2231.00
159_V163_V2.2011.00
169_K173_L2.1781.00
142_C162_C2.1591.00
142_C155_H2.1401.00
172_L235_V2.0191.00
172_L232_C2.0091.00
131_C145_C1.9821.00
164_G167_N1.9771.00
76_S147_S1.9481.00
153_D156_C1.9261.00
148_C155_H1.8581.00
135_K140_H1.8271.00
141_H155_H1.7670.99
72_T159_V1.7670.99
231_H241_T1.7570.99
131_C155_H1.7420.99
278_W281_P1.7330.99
128_C131_C1.7260.99
289_G292_F1.6220.99
238_N269_Q1.5930.98
151_K168_Y1.5880.98
212_F215_F1.5400.98
272_G281_P1.5340.98
128_C141_H1.5220.98
145_C148_C1.5080.97
30_Y59_H1.4980.97
128_C140_H1.4790.97
34_V59_H1.4680.97
120_S123_K1.4660.97
231_H234_L1.4560.97
230_Y234_L1.4540.97
208_F212_F1.4340.96
126_R135_K1.4280.96
32_A62_F1.4200.96
128_C138_R1.3910.95
60_L64_M1.3860.95
67_W71_M1.3720.95
233_W237_K1.3650.95
260_S266_N1.3550.94
151_K270_V1.3520.94
126_R137_D1.3500.94
170_F173_L1.3480.94
176_L228_F1.3480.94
262_G266_N1.3480.94
268_R273_D1.3350.94
140_H152_M1.3160.93
179_L225_L1.3090.93
71_M170_F1.2990.93
30_Y34_V1.2970.92
77_P164_G1.2950.92
17_V21_F1.2800.92
62_F181_Y1.2770.92
140_H154_H1.2730.92
225_L229_S1.2720.91
152_M158_W1.2700.91
173_L277_Y1.2470.90
156_C171_F1.2390.90
288_D291_S1.2380.90
224_V229_S1.2350.90
148_C154_H1.2340.90
138_R156_C1.2290.90
131_C135_K1.2260.89
236_G263_C1.2230.89
138_R141_H1.2220.89
178_S224_V1.2140.89
152_M242_I1.2120.89
61_F184_F1.2090.88
153_D171_F1.2070.88
64_M68_S1.1930.88
131_C140_H1.1900.87
67_W231_H1.1800.87
172_L184_F1.1680.86
123_K137_D1.1660.86
179_L228_F1.1580.85
136_P145_C1.1550.85
168_Y241_T1.1490.85
128_C154_H1.1480.85
190_L194_I1.1420.84
14_V17_V1.1390.84
78_A164_G1.1380.84
17_V22_I1.1380.84
232_C236_G1.1230.83
149_I152_M1.1160.82
259_F266_N1.1120.82
21_F24_F1.1090.82
70_W74_F1.1060.82
148_C153_D1.1050.82
128_C135_K1.0980.81
185_V188_T1.0950.81
78_A166_S1.0950.81
168_Y270_V1.0920.80
152_M157_P1.0900.80
238_N266_N1.0900.80
240_T243_E1.0870.80
154_H157_P1.0840.80
81_S84_F1.0760.79
28_W31_Y1.0720.79
26_V65_F1.0680.78
98_F101_E1.0670.78
152_M164_G1.0670.78
7_W10_C1.0670.78
173_L177_Y1.0660.78
158_W163_V1.0600.78
176_L180_L1.0580.78
262_G265_K1.0580.78
135_K141_H1.0570.77
269_Q293_P1.0530.77
128_C148_C1.0480.77
57_A184_F1.0470.76
32_A37_L1.0470.76
7_W11_Q1.0450.76
69_Y159_V1.0390.76
69_Y174_F1.0370.76
138_R154_H1.0360.75
61_F177_Y1.0330.75
80_P139_A1.0300.75
148_C156_C1.0290.75
15_G18_P1.0270.75
119_T123_K1.0260.74
163_V242_I1.0260.74
142_C243_E1.0250.74
158_W161_N1.0240.74
50_K54_Y1.0210.74
140_H153_D1.0180.74
64_M67_W1.0160.73
231_H271_F1.0100.73
261_L265_K1.0090.73
173_L271_F1.0080.73
174_F230_Y1.0070.72
19_V30_Y1.0060.72
61_F181_Y1.0010.72
141_H154_H1.0010.72
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  
2rowA10.246713.80.967Contact Map
4c7rA30.3533120.968Contact Map
2fnfX10.176711.20.968Contact Map
3j21g10.156.60.971Contact Map
4xp4A106.20.972Contact Map
1wflA10.22676.10.972Contact Map
1qleD10.14335.60.972Contact Map
4ujrZ10.16335.40.972Contact Map
1faqA10.15674.50.973Contact Map
3uejA20.194.50.974Contact 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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