OPENSEQ.org - 1492620897 - GREMLIN Submission

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Chmp7_CTD

ID:	1492620897	Query Sequence AKVSPVNDVDVGVYQLMQSEQLLSRKVESLSQEAERCKEEARRACRAGKKQLALRSLKAKQRTEKRIEALHAKLDTVQGILDRIYASQTDQMVFNAYQAGVGALKLSMKDVTVEKAESLVDQIQELCDTQDEVSQTLAGGVTNGLDFDSEELEKELDILLQDTTKEPLDLPDNPRNRHFTNSVPNPRISDAELEAELEKLSLSEGGLVPSSKSPKRQLEPTLKPL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	225 (205)
Sequences:	422 (321.3)
Seq/Len:	2.059
Nf(neff/√len):	22.4

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: 2.059).

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
50_K	54_L	2.690	1.00
98_Q	115_K	2.521	1.00
163_T	166_E	2.312	1.00
126_L	129_T	2.116	0.99
20_E	74_L	2.110	0.99
27_V	71_H	1.989	0.99
41_A	53_A	1.835	0.98
116_A	138_A	1.777	0.97
131_D	134_S	1.766	0.97
26_K	70_L	1.746	0.97
84_I	103_A	1.676	0.96
64_E	87_S	1.641	0.95
156_L	160_L	1.573	0.94
105_K	177_R	1.552	0.93
90_D	160_L	1.514	0.92
152_L	156_L	1.490	0.91
6_V	10_D	1.487	0.91
77_V	81_L	1.452	0.90
65_K	69_A	1.433	0.89
38_K	60_K	1.431	0.89
7_N	10_D	1.428	0.89
128_D	161_Q	1.391	0.87
58_K	88_Q	1.384	0.86
153_E	159_L	1.365	0.85
44_A	49_K	1.363	0.85
94_F	119_L	1.361	0.85
97_Y	108_M	1.347	0.84
33_E	116_A	1.337	0.84
28_E	117_E	1.325	0.83
60_K	133_V	1.307	0.82
64_E	136_T	1.298	0.81
41_A	56_S	1.293	0.81
26_K	62_R	1.283	0.80
98_Q	151_E	1.272	0.79
18_Q	60_K	1.263	0.79
98_Q	102_G	1.251	0.78
164_T	167_P	1.250	0.78
199_K	204_E	1.240	0.77
188_I	198_E	1.239	0.77
38_K	42_R	1.220	0.75
23_L	101_V	1.215	0.75
41_A	78_Q	1.213	0.75
202_L	205_G	1.197	0.73
40_E	56_S	1.191	0.73
78_Q	112_T	1.189	0.73
154_K	157_D	1.187	0.72
70_L	73_K	1.174	0.71
125_E	133_V	1.174	0.71
23_L	77_V	1.171	0.71
58_K	152_L	1.169	0.71
43_R	47_A	1.160	0.70
30_L	153_E	1.157	0.70
137_L	177_R	1.144	0.68
102_G	115_K	1.139	0.68
50_K	142_T	1.135	0.68
5_P	33_E	1.124	0.66
96_A	100_G	1.120	0.66
7_N	151_E	1.104	0.64
30_L	106_L	1.101	0.64
8_D	35_E	1.096	0.64
15_Q	107_S	1.095	0.64
188_I	191_A	1.092	0.63
191_A	195_A	1.092	0.63
93_V	126_L	1.090	0.63
13_V	103_A	1.087	0.63
97_Y	130_Q	1.075	0.61
196_E	202_L	1.071	0.61
201_S	204_E	1.070	0.61
171_P	174_P	1.064	0.60
31_S	35_E	1.064	0.60
52_L	159_L	1.061	0.60
81_L	138_A	1.059	0.60
42_R	158_I	1.052	0.59
182_S	190_D	1.047	0.58
179_F	182_S	1.045	0.58
53_A	93_V	1.044	0.58
94_F	98_Q	1.043	0.58
61_Q	149_S	1.042	0.58
54_L	78_Q	1.036	0.57
72_A	87_S	1.035	0.57
35_E	68_E	1.034	0.57
20_E	77_V	1.028	0.56
193_L	200_L	1.028	0.56
108_M	111_V	1.028	0.56
121_D	141_V	1.025	0.56
35_E	78_Q	1.025	0.56
186_P	191_A	1.023	0.56
117_E	198_E	1.022	0.56
101_V	119_L	1.021	0.56
105_K	137_L	1.014	0.55
60_K	134_S	1.013	0.55
184_P	191_A	1.013	0.55
135_Q	145_L	1.011	0.54
130_Q	134_S	1.008	0.54
6_V	110_D	1.006	0.54
30_L	67_I	1.003	0.53
108_M	134_S	1.003	0.53
192_E	196_E	1.000	0.53

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	0.6	99.7	0.652	Contact Map
2gd5A	4	0.6889	99.7	0.653	Contact Map
4abmA	4	0.3511	99.1	0.755	Contact Map
3um3B	1	0.08	99	0.763	Contact Map
2luhB	1	0.2533	98.5	0.799	Contact Map
3htuB	4	0.16	96.1	0.869	Contact Map
4txrC	1	0.1778	95.9	0.872	Contact Map
4cgkA	2	0.8844	20	0.941	Contact Map
4b86A	6	0.1333	18.7	0.942	Contact Map
2dfsA	2	0.5867	18.6	0.942	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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