OPENSEQ.org - 1468575584 - GREMLIN Submission

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c-Src SH4-Unique_SH3

ID:	1468575584	Query Sequence MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	150 (150)
Sequences:	151 (100.7)
Seq/Len:	1.007
Nf(neff/√len):	8.2

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: 1.007).

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
119_G	122_W	1.831	0.92
110_R	143_S	1.809	0.91
119_G	124_A	1.753	0.90
90_V	112_Q	1.686	0.87
99_T	115_N	1.609	0.83
119_G	126_S	1.600	0.83
32_F	35_S	1.542	0.80
119_G	137_S	1.504	0.77
111_L	123_L	1.490	0.76
10_D	114_V	1.486	0.76
109_E	127_L	1.476	0.75
122_W	140_V	1.427	0.72
142_P	147_Q	1.424	0.72
109_E	126_S	1.416	0.71
89_F	99_T	1.392	0.69
3_S	101_T	1.367	0.67
140_V	149_E	1.339	0.65
134_Y	144_D	1.327	0.64
85_G	89_F	1.320	0.63
120_D	134_Y	1.312	0.62
86_V	89_F	1.311	0.62
41_P	44_A	1.306	0.62
53_A	56_P	1.286	0.60
49_G	52_A	1.283	0.60
95_Y	105_F	1.259	0.58
89_F	115_N	1.252	0.57
98_R	148_A	1.235	0.55
89_F	98_R	1.232	0.55
120_D	148_A	1.222	0.54
138_N	141_A	1.211	0.53
6_S	112_Q	1.200	0.52
122_W	126_S	1.190	0.51
96_E	144_D	1.185	0.51
83_A	109_E	1.183	0.51
87_T	113_I	1.182	0.51
122_W	129_T	1.176	0.50
141_A	145_S	1.174	0.50
142_P	146_I	1.167	0.49
118_E	123_L	1.161	0.49
142_P	148_A	1.160	0.48
6_S	90_V	1.158	0.48
141_A	149_E	1.155	0.48
87_T	142_P	1.151	0.48
45_D	48_R	1.148	0.47
45_D	49_G	1.137	0.46
87_T	99_T	1.133	0.46
82_L	114_V	1.131	0.46
42_A	45_D	1.129	0.46
138_N	149_E	1.123	0.45
32_F	36_Q	1.113	0.44
6_S	100_E	1.113	0.44
99_T	120_D	1.109	0.44
126_S	137_S	1.109	0.44
86_V	142_P	1.107	0.44
17_S	20_P	1.102	0.43
4_N	8_P	1.092	0.42
99_T	148_A	1.088	0.42
124_A	129_T	1.086	0.42
98_R	115_N	1.081	0.41
94_D	145_S	1.075	0.41
126_S	129_T	1.075	0.41
124_A	140_V	1.068	0.40
122_W	141_A	1.065	0.40
120_D	146_I	1.058	0.39
118_E	145_S	1.056	0.39
139_Y	150_E	1.055	0.39
124_A	137_S	1.053	0.39
144_D	148_A	1.047	0.38
113_I	130_G	1.044	0.38
87_T	116_N	1.043	0.38
137_S	150_E	1.042	0.38
139_Y	148_A	1.040	0.38
7_K	97_S	1.036	0.37
42_A	49_G	1.035	0.37
118_E	130_G	1.028	0.37
63_L	97_S	1.027	0.36
140_V	145_S	1.018	0.36
23_N	28_G	1.012	0.35
130_G	144_D	1.008	0.35
99_T	147_Q	1.006	0.35
2_G	7_K	1.004	0.34
124_A	135_I	1.003	0.34
126_S	149_E	1.002	0.34
101_T	111_L	1.002	0.34
8_P	11_A	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
2h8hA	1	0.42	100	0.528	Contact Map
1fmkA	1	0.44	99.9	0.634	Contact Map
1qcfA	1	0.4467	99.9	0.638	Contact Map
1k9aA	6	0.4733	99.8	0.651	Contact Map
4xi2A	1	0.44	99.8	0.657	Contact Map
1opkA	1	0.4133	99.8	0.659	Contact Map
4u5wB	2	0.4267	99.8	0.66	Contact Map
4d8kA	1	0.42	99.8	0.669	Contact Map
4m4zA	1	0.3733	99.7	0.684	Contact Map
2yt6A	1	0.6067	99.7	0.684	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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