OPENSEQ.org - 1512244940 - GREMLIN Submission

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C1_rep

ID:	1512244940	Query Sequence SLIDQSQWLPPKRFKIQAKNYFITYPQCSLTKEEALSQIQAINTPSNKKYIKLCRELHEDGSPHLHVLIQFEGKFVCTNNRFFDLVSPTRSAHLLPNIQEAKSSPDVQAYIAKDGGTPNWGEFRIHGRSPRGRQQTATDAFAAALNASSKSEAFKVHKELAPKDFLLPFHYLNANLDRIFQEPPAPHISPFSPSSFDQVPEELEVWAIDNVVEAAARPLRPRCIVIEGDSRTGKTMWARSLGP	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	243 (229)
Sequences:	1105 (648.5)
Seq/Len:	4.825
Nf(neff/√len):	42.9

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: 4.825).

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 > 50% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

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.

i	j	Scaled score	Prob
23_I	67_V	3.247	1.00
101_A	107_V	3.146	1.00
26_P	62_S	2.476	1.00
27_Q	62_S	2.457	1.00
235_T	238_A	2.118	1.00
54_C	117_T	2.083	1.00
52_K	112_A	2.076	1.00
136_T	139_D	2.074	1.00
19_K	74_K	2.061	1.00
107_V	112_A	2.049	1.00
54_C	116_G	1.989	1.00
50_Y	119_N	1.979	1.00
103_S	106_D	1.958	1.00
58_H	62_S	1.881	1.00
108_Q	112_A	1.877	1.00
226_I	237_W	1.814	1.00
70_Q	104_S	1.751	1.00
54_C	115_G	1.722	1.00
26_P	58_H	1.674	0.99
70_Q	101_A	1.625	0.99
17_Q	74_K	1.573	0.99
110_Y	113_K	1.532	0.99
228_G	234_K	1.517	0.99
236_M	240_S	1.504	0.98
204_E	209_D	1.501	0.98
143_A	160_L	1.483	0.98
101_A	104_S	1.478	0.98
201_E	204_E	1.412	0.97
84_D	95_L	1.408	0.97
131_R	136_T	1.398	0.97
25_Y	96_P	1.391	0.97
204_E	208_I	1.368	0.97
112_A	119_N	1.361	0.97
168_P	171_Y	1.356	0.96
200_P	207_A	1.353	0.96
25_Y	32_K	1.349	0.96
162_P	175_N	1.340	0.96
106_D	109_A	1.329	0.96
18_A	21_Y	1.316	0.96
171_Y	175_N	1.313	0.95
15_K	76_V	1.309	0.95
193_P	198_Q	1.294	0.95
175_N	178_R	1.286	0.95
77_C	98_I	1.279	0.95
169_F	173_N	1.250	0.94
56_E	64_H	1.245	0.93
198_Q	204_E	1.238	0.93
87_S	90_R	1.233	0.93
221_P	230_S	1.232	0.93
90_R	93_H	1.228	0.93
192_S	207_A	1.224	0.93
169_F	175_N	1.223	0.93
105_P	109_A	1.213	0.92
193_P	204_E	1.210	0.92
197_D	204_E	1.206	0.92
53_L	67_V	1.206	0.92
22_F	66_H	1.198	0.92
81_R	84_D	1.193	0.91
239_R	242_G	1.192	0.91
150_K	173_N	1.188	0.91
228_G	233_G	1.180	0.91
189_S	208_I	1.180	0.91
169_F	174_A	1.170	0.90
192_S	212_V	1.164	0.90
161_A	164_D	1.155	0.90
26_P	63_P	1.139	0.89
28_C	65_L	1.134	0.88
54_C	111_I	1.132	0.88
104_S	108_Q	1.130	0.88
207_A	212_V	1.112	0.87
68_L	104_S	1.107	0.87
217_R	220_R	1.106	0.87
217_R	221_P	1.102	0.86
203_L	212_V	1.099	0.86
205_V	209_D	1.097	0.86
197_D	202_E	1.095	0.86
161_A	167_L	1.095	0.86
55_R	116_G	1.095	0.86
193_P	209_D	1.092	0.86
54_C	66_H	1.090	0.86
112_A	117_T	1.085	0.85
189_S	211_V	1.084	0.85
182_E	185_A	1.080	0.85
189_S	193_P	1.080	0.85
192_S	208_I	1.079	0.85
68_L	111_I	1.077	0.85
142_A	162_P	1.071	0.84
203_L	211_V	1.068	0.84
68_L	101_A	1.061	0.84
89_T	92_A	1.060	0.83
204_E	210_N	1.060	0.83
28_C	62_S	1.053	0.83
35_A	65_L	1.051	0.83
150_K	177_D	1.048	0.82
205_V	208_I	1.039	0.82
87_S	93_H	1.039	0.82
189_S	204_E	1.036	0.81
227_E	239_R	1.035	0.81
204_E	212_V	1.031	0.81
189_S	198_Q	1.030	0.81
209_D	213_E	1.029	0.81
232_T	238_A	1.029	0.81
185_A	202_E	1.028	0.81
186_P	189_S	1.025	0.81
29_S	32_K	1.019	0.80
237_W	241_L	1.017	0.80
202_E	209_D	1.013	0.79
76_V	79_N	1.013	0.79
235_T	239_R	1.012	0.79
17_Q	76_V	1.011	0.79
231_R	235_T	1.010	0.79
204_E	211_V	1.009	0.79
186_P	209_D	1.008	0.79
25_Y	28_C	1.008	0.79

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)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

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
1l2mA	1	0.4856	100	0.515	Contact Map
2hw0A	1	0.4568	99.9	0.618	Contact Map
2hwtA	1	0.3621	99.8	0.627	Contact Map
4blpA	6	0.5103	98.8	0.803	Contact Map
3cf0A	14	0.2922	95.8	0.886	Contact Map
1sxjA	1	0.2716	95.7	0.887	Contact Map
3pvsA	4	0.2346	95.5	0.888	Contact Map
1ofhA	3	0.2922	95.5	0.888	Contact Map
3ec2A	1	0.2469	95.5	0.888	Contact Map
4ww0A	3	0	95.5	0.889	Contact 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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