OPENSEQ.org - 1509666792 - GREMLIN Submission

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ID:	1509666792	Query Sequence MSLFEWVFGKNVTPQERLKKNQRALERTQRELEREKRKLELQDKKLVSEIKKSAKNGQVAAAKVQAKDLVRTRNYIQKFDNMKAQLQAISLRIQAVRSSDQMTRSMSEATGLLAGMNRTMNLPQLQRISMEFEKQSDLMGQRQEFMDEAIDNVMGDEVDEDEEADEIVNKVLDEIGVDLNSQLQSTPQNLVSNAPIAETAMGIAEPIGAGSEFHGNPDDDLQARLNTLKKQT	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	232 (211)
Sequences:	810 (443.2)
Seq/Len:	3.839
Nf(neff/√len):	30.5

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: 3.839).

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.

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
72_T	75_Y	3.339	1.00
225_L	228_L	3.014	1.00
52_K	56_N	2.924	1.00
12_V	20_K	2.659	1.00
222_Q	226_N	2.337	1.00
121_N	124_Q	2.056	1.00
44_K	47_V	1.995	1.00
127_R	131_E	1.900	1.00
42_Q	45_K	1.867	1.00
25_L	86_L	1.861	1.00
40_E	44_K	1.834	1.00
131_E	134_K	1.596	0.98
58_Q	61_A	1.528	0.98
224_R	228_L	1.471	0.97
221_L	224_R	1.469	0.97
12_V	17_R	1.461	0.97
48_S	52_K	1.457	0.97
161_D	165_D	1.444	0.96
168_V	172_L	1.443	0.96
146_M	149_A	1.436	0.96
43_D	47_V	1.434	0.96
113_L	129_S	1.431	0.96
48_S	56_N	1.407	0.96
43_D	73_R	1.405	0.96
94_Q	98_S	1.396	0.95
100_D	104_R	1.388	0.95
114_A	131_E	1.376	0.95
169_N	173_D	1.366	0.95
13_T	17_R	1.363	0.95
13_T	16_E	1.355	0.94
32_L	35_E	1.336	0.94
50_I	69_L	1.331	0.94
226_N	229_K	1.322	0.93
36_K	80_D	1.319	0.93
225_L	229_K	1.314	0.93
9_G	18_L	1.288	0.92
135_Q	138_L	1.278	0.92
64_V	174_E	1.266	0.91
51_K	174_E	1.251	0.91
115_G	118_R	1.225	0.89
184_Q	191_V	1.217	0.89
92_R	140_G	1.208	0.89
38_K	41_L	1.205	0.88
217_P	220_D	1.199	0.88
221_L	228_L	1.192	0.88
223_A	226_N	1.192	0.88
224_R	227_T	1.189	0.88
145_F	148_E	1.184	0.87
35_E	79_F	1.182	0.87
49_E	52_K	1.182	0.87
32_L	66_A	1.174	0.87
45_K	49_E	1.169	0.86
166_E	169_N	1.165	0.86
46_L	68_D	1.156	0.85
79_F	128_I	1.150	0.85
101_Q	113_L	1.145	0.85
138_L	142_R	1.143	0.85
186_T	192_S	1.141	0.84
173_D	179_L	1.140	0.84
54_A	175_I	1.132	0.84
43_D	69_L	1.128	0.84
182_Q	185_S	1.121	0.83
40_E	76_I	1.120	0.83
89_I	113_L	1.120	0.83
166_E	170_K	1.116	0.83
146_M	226_N	1.113	0.82
190_L	193_N	1.111	0.82
194_A	197_A	1.108	0.82
194_A	198_E	1.100	0.81
105_S	112_L	1.097	0.81
29_Q	90_S	1.095	0.81
193_N	197_A	1.086	0.80
140_G	143_Q	1.084	0.80
99_S	109_A	1.079	0.80
22_Q	62_A	1.077	0.79
50_I	105_S	1.069	0.79
32_L	98_S	1.066	0.78
171_V	176_G	1.063	0.78
7_V	20_K	1.063	0.78
106_M	148_E	1.062	0.78
70_V	158_V	1.060	0.78
60_A	75_Y	1.060	0.78
107_S	123_P	1.057	0.78
86_L	93_I	1.054	0.77
106_M	114_A	1.050	0.77
89_I	129_S	1.049	0.77
94_Q	146_M	1.048	0.77
120_M	124_Q	1.047	0.77
192_S	216_N	1.047	0.77
16_E	23_R	1.046	0.77
59_V	63_K	1.044	0.76
171_V	174_E	1.042	0.76
71_R	88_A	1.037	0.76
53_S	62_A	1.036	0.76
42_Q	72_T	1.030	0.75
136_S	167_I	1.028	0.75
6_W	10_K	1.027	0.75
188_Q	198_E	1.025	0.75
179_L	223_A	1.024	0.74
35_E	50_I	1.023	0.74
36_K	76_I	1.020	0.74
70_V	167_I	1.018	0.74
184_Q	187_P	1.013	0.73
82_M	102_M	1.010	0.73
199_T	215_G	1.010	0.73
4_F	11_N	1.001	0.72
7_V	10_K	1.000	0.72

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)).

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
3frtA	2	0.6121	100	0.291	Contact Map
2gd5A	4	0.6983	100	0.362	Contact Map
3eabG	6	0.181	98.7	0.819	Contact Map
2v6xB	1	0.1767	96	0.891	Contact Map
3frrA	1	0.7629	95.5	0.895	Contact Map
3um3B	1	0.0776	91.8	0.91	Contact Map
3ggyA	2	0.7198	91.1	0.911	Contact Map
2xzeQ	2	0.0991	61.1	0.934	Contact Map
2luhB	1	0.2543	32.9	0.945	Contact Map
4abmA	4	0.3405	28.5	0.947	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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