OPENSEQ.org - 1480991021 - GREMLIN Submission

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Rpn5 Paranoid8 50 to 261 -force run

ID:	1480991021	Query Sequence SDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLKSSKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (212)
Sequences:	210 (150.7)
Seq/Len:	0.991
Nf(neff/√len):	10.4

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: 0.991).

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
103_K	106_E	3.077	1.00
204_D	207_K	2.598	0.99
125_S	166_S	2.582	0.99
49_Q	86_E	2.264	0.98
133_E	136_E	2.037	0.96
30_L	76_V	2.016	0.96
89_R	126_E	1.988	0.95
201_I	207_K	1.945	0.94
2_D	5_S	1.848	0.92
115_Q	122_M	1.678	0.86
186_L	193_Q	1.644	0.85
81_I	122_M	1.643	0.85
179_S	191_Y	1.631	0.84
89_R	122_M	1.629	0.84
23_W	83_V	1.597	0.82
112_C	146_Q	1.549	0.80
50_K	53_E	1.545	0.79
5_S	8_E	1.523	0.78
48_I	181_H	1.496	0.76
30_L	78_E	1.485	0.75
37_H	146_Q	1.459	0.74
174_L	195_I	1.437	0.72
99_K	136_E	1.417	0.71
74_R	91_T	1.405	0.70
144_Y	151_S	1.399	0.69
10_L	14_V	1.385	0.68
140_L	177_K	1.369	0.67
135_M	147_A	1.365	0.66
6_S	36_K	1.357	0.66
52_M	82_F	1.355	0.66
74_R	114_L	1.340	0.64
5_S	114_L	1.328	0.63
6_S	39_Q	1.320	0.63
95_V	111_L	1.299	0.61
131_I	152_R	1.298	0.61
22_K	25_D	1.289	0.60
78_E	169_L	1.281	0.59
87_R	132_L	1.269	0.58
8_E	71_E	1.266	0.58
62_D	212_L	1.256	0.57
99_K	175_L	1.238	0.55
151_S	185_Y	1.229	0.54
114_L	179_S	1.227	0.54
90_V	146_Q	1.223	0.54
26_L	82_F	1.219	0.53
36_K	180_L	1.211	0.53
189_A	193_Q	1.211	0.53
95_V	113_E	1.190	0.51
73_I	79_N	1.182	0.50
67_I	98_K	1.177	0.50
69_V	140_L	1.167	0.49
149_V	152_R	1.163	0.48
114_L	191_Y	1.162	0.48
184_E	187_E	1.160	0.48
89_R	167_L	1.150	0.47
79_N	136_E	1.145	0.47
56_K	176_V	1.144	0.47
104_I	108_A	1.142	0.46
130_F	174_L	1.139	0.46
86_E	144_Y	1.134	0.46
83_V	138_S	1.129	0.45
3_L	37_H	1.128	0.45
125_S	163_K	1.122	0.44
90_V	139_I	1.118	0.44
36_K	139_I	1.116	0.44
19_S	155_L	1.104	0.43
17_L	20_R	1.102	0.43
144_Y	163_K	1.098	0.42
37_H	99_K	1.095	0.42
136_E	175_L	1.087	0.41
159_F	167_L	1.085	0.41
91_T	179_S	1.084	0.41
91_T	113_E	1.081	0.41
151_S	154_I	1.080	0.41
113_E	172_Y	1.072	0.40
110_I	187_E	1.071	0.40
86_E	143_D	1.070	0.40
71_E	85_V	1.069	0.40
27_N	69_V	1.068	0.40
69_V	136_E	1.059	0.39
24_D	119_Y	1.050	0.38
10_L	13_I	1.046	0.38
4_A	64_N	1.046	0.38
102_G	195_I	1.043	0.37
99_K	146_Q	1.042	0.37
6_S	67_I	1.040	0.37
88_A	153_K	1.040	0.37
17_L	130_F	1.039	0.37
5_S	77_T	1.038	0.37
25_D	75_V	1.037	0.37
26_L	34_S	1.037	0.37
36_K	185_Y	1.033	0.37
47_M	154_I	1.020	0.35
34_S	72_T	1.019	0.35
42_L	138_S	1.014	0.35
15_D	50_K	1.012	0.35
98_K	106_E	1.010	0.35
130_F	186_L	1.007	0.34
62_D	211_V	1.004	0.34
76_V	122_M	1.002	0.34
122_M	168_K	1.001	0.34

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
4cr2P	1	1	100	0.471	Contact Map
4d0pA	1	0.934	100	0.633	Contact Map
3txnA	1	0.9623	100	0.635	Contact Map
4d10D	2	0.934	100	0.642	Contact Map
4cr2Q	1	0.9623	100	0.648	Contact Map
4cr2R	1	0.9481	99.6	0.793	Contact Map
4d10B	2	0.9104	99.1	0.838	Contact Map
4d10A	2	0.9434	99.1	0.838	Contact Map
4d10C	2	0.9575	98.2	0.881	Contact Map
4lctA	4	0.934	97.9	0.89	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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