OPENSEQ.org - 1492553574 - GREMLIN Submission

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iqgap1 CHD

ID:	1492553574	Query Sequence MSAADEVDGLGVARPHYGSVLDNERLTAEEMDERRRQNVAYEYLCHLEEAKRWMEACLGEDLPPTTELEEGLRNGVYLAKLGNFFSPKVVSLKKIYDREQTRYKATGLHFRHTDNVIQWLNAMDEIGLPKIFYPETTDIYDRKNMPRCIYCIHALSLYLFKLGLAPQIQDLYGKVDFTEEEINNMKTELEKYGIQMPAFSKIGGILANELSVDEAALH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	218 (197)
Sequences:	237 (134.7)
Seq/Len:	1.203
Nf(neff/√len):	9.6

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: 1.203).

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
41_Y	45_C	2.175	0.98
32_D	35_R	2.084	0.98
108_L	112_H	2.035	0.97
60_E	80_K	1.994	0.97
64_P	68_L	1.967	0.96
111_R	114_D	1.746	0.92
143_K	153_H	1.663	0.89
51_K	109_H	1.641	0.88
139_I	148_C	1.630	0.88
72_L	149_I	1.625	0.88
124_D	133_Y	1.579	0.86
132_F	154_A	1.498	0.81
152_I	159_L	1.494	0.81
85_F	90_V	1.481	0.80
46_H	49_E	1.471	0.80
134_P	139_I	1.440	0.78
120_L	136_T	1.418	0.76
114_D	128_L	1.406	0.75
173_G	197_P	1.402	0.75
46_H	68_L	1.386	0.74
178_T	181_E	1.384	0.74
215_A	218_H	1.374	0.73
137_T	156_S	1.361	0.72
72_L	95_I	1.359	0.72
40_A	163_G	1.348	0.71
74_N	123_M	1.329	0.69
152_I	196_M	1.316	0.68
70_E	142_R	1.311	0.68
138_D	144_N	1.306	0.67
137_T	141_D	1.301	0.67
119_W	213_D	1.300	0.67
74_N	166_P	1.297	0.66
202_I	207_A	1.288	0.66
55_E	143_K	1.275	0.64
71_G	76_V	1.259	0.63
68_L	181_E	1.256	0.63
143_K	150_Y	1.248	0.62
45_C	197_P	1.238	0.61
178_T	183_N	1.236	0.61
57_C	85_F	1.231	0.60
96_Y	109_H	1.221	0.60
168_I	189_L	1.216	0.59
144_N	151_C	1.215	0.59
85_F	123_M	1.198	0.57
52_R	62_L	1.189	0.57
116_V	139_I	1.185	0.56
23_N	28_A	1.169	0.55
63_P	76_V	1.162	0.54
79_A	95_I	1.161	0.54
129_P	197_P	1.160	0.54
76_V	95_I	1.158	0.54
120_L	148_C	1.158	0.54
41_Y	199_F	1.146	0.52
110_F	115_N	1.141	0.52
80_K	137_T	1.131	0.51
32_D	50_A	1.125	0.50
170_D	173_G	1.122	0.50
144_N	155_L	1.120	0.50
61_D	168_I	1.120	0.50
207_A	210_L	1.118	0.50
119_W	123_M	1.118	0.50
182_I	196_M	1.117	0.50
54_M	62_L	1.113	0.49
153_H	156_S	1.103	0.48
81_L	85_F	1.098	0.48
137_T	180_E	1.094	0.47
48_E	52_R	1.093	0.47
43_Y	49_E	1.093	0.47
65_T	170_D	1.092	0.47
48_E	152_I	1.092	0.47
54_M	145_M	1.090	0.47
137_T	143_K	1.090	0.47
31_M	35_R	1.085	0.46
57_C	81_L	1.083	0.46
100_Q	119_W	1.081	0.46
93_K	181_E	1.078	0.46
46_H	172_Y	1.077	0.46
124_D	130_K	1.075	0.45
121_N	124_D	1.074	0.45
112_H	154_A	1.069	0.45
142_R	168_I	1.068	0.45
71_G	211_S	1.067	0.45
180_E	183_N	1.064	0.44
38_N	186_K	1.062	0.44
55_E	171_L	1.056	0.44
66_T	88_K	1.053	0.43
58_L	120_L	1.053	0.43
74_N	97_D	1.052	0.43
154_A	199_F	1.051	0.43
211_S	214_E	1.048	0.43
47_L	141_D	1.037	0.42
53_W	78_L	1.036	0.42
140_Y	146_P	1.034	0.42
109_H	136_T	1.031	0.41
57_C	189_L	1.030	0.41
150_Y	154_A	1.027	0.41
44_L	49_E	1.024	0.41
104_K	119_W	1.023	0.40
136_T	144_N	1.021	0.40
77_Y	86_S	1.020	0.40
64_P	181_E	1.018	0.40
54_M	77_Y	1.017	0.40
82_G	86_S	1.015	0.40
98_R	119_W	1.014	0.40
62_L	77_Y	1.011	0.39
41_Y	44_L	1.009	0.39
27_T	36_R	1.002	0.39

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
2rr8A	1	0.8716	100	0.421	Contact Map
3i6xA	4	0.7523	100	0.428	Contact Map
1p5sA	1	0.7294	100	0.458	Contact Map
1p2xA	1	0.7294	100	0.468	Contact Map
1wymA	1	0.6514	100	0.623	Contact Map
1wynA	1	0.6422	100	0.628	Contact Map
1wypA	1	0.6239	100	0.629	Contact Map
1ujoA	1	0.6193	100	0.658	Contact Map
2l3gA	1	0.5459	100	0.679	Contact Map
3ky9A	2	0.6789	100	0.682	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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