OPENSEQ.org - 1441792440 - GREMLIN Submission

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FIVCA

ID:	1441792440	Query Sequence PIQTVNGVPQYVALDPKMVSIFMEKAREGLGGEEVQLWFTAFSANLTPTDMATLIMAAPGCAADKEILDESLKQLTAEYDRTHPPDAPRPLPYFTAAEIMGIGLTQEQQAEARFAPARMQCRAWYLEALGKLAAIKAKSPRAVQLRQGAKEDYSSFIDRLFAQIDQEQNTAEVKLYLKQSLSIANANADCKKAMSHLKPESTLEEKLRACQEIGSPGYKMQL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	222 (220)
Sequences:	298 (96.2)
Seq/Len:	1.355
Nf(neff/√len):	6.5

HHblits Results: (2015_06)
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: 1.355).

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
42_F	149_A	2.213	0.99
147_Q	151_E	2.019	0.98
62_A	65_K	1.884	0.96
156_F	160_L	1.854	0.96
193_A	213_I	1.814	0.95
194_M	206_K	1.774	0.94
181_L	190_C	1.748	0.93
215_S	220_M	1.663	0.91
32_G	35_V	1.656	0.91
153_Y	160_L	1.636	0.90
141_R	172_E	1.604	0.89
59_P	72_L	1.599	0.89
30_L	153_Y	1.526	0.85
210_C	214_G	1.520	0.85
97_A	103_G	1.485	0.83
190_C	210_C	1.454	0.81
29_G	128_A	1.386	0.77
209_A	219_K	1.384	0.77
59_P	62_A	1.383	0.77
59_P	65_K	1.365	0.75
201_S	207_L	1.360	0.75
59_P	71_S	1.349	0.74
153_Y	182_S	1.347	0.74
60_G	71_S	1.342	0.74
1_P	6_N	1.302	0.70
189_D	217_G	1.296	0.70
62_A	66_E	1.287	0.69
52_A	58_A	1.287	0.69
196_H	206_K	1.283	0.69
21_I	160_L	1.279	0.68
206_K	209_A	1.275	0.68
181_L	194_M	1.272	0.68
100_M	108_Q	1.271	0.68
1_P	4_T	1.271	0.68
48_P	109_Q	1.268	0.67
186_A	190_C	1.265	0.67
79_Y	99_I	1.265	0.67
177_L	181_L	1.252	0.66
32_G	142_A	1.243	0.65
145_L	157_I	1.216	0.63
65_K	72_L	1.215	0.63
41_A	54_L	1.207	0.62
68_L	71_S	1.207	0.62
212_E	215_S	1.205	0.62
66_E	79_Y	1.202	0.61
36_Q	130_G	1.193	0.61
28_E	34_E	1.188	0.60
174_K	186_A	1.183	0.60
18_M	32_G	1.182	0.59
128_A	156_F	1.181	0.59
14_L	130_G	1.180	0.59
70_E	76_T	1.170	0.58
38_W	54_L	1.167	0.58
206_K	212_E	1.152	0.57
56_M	66_E	1.149	0.56
210_C	213_I	1.145	0.56
134_A	154_S	1.141	0.55
201_S	213_I	1.139	0.55
203_L	206_K	1.133	0.55
66_E	72_L	1.130	0.54
188_A	212_E	1.129	0.54
79_Y	120_Q	1.121	0.53
181_L	187_N	1.117	0.53
99_I	181_L	1.115	0.53
141_R	170_T	1.114	0.53
33_E	205_E	1.113	0.53
51_M	125_Y	1.110	0.52
3_Q	18_M	1.108	0.52
102_I	202_T	1.103	0.52
47_T	106_Q	1.102	0.52
116_P	125_Y	1.101	0.51
18_M	38_W	1.098	0.51
83_H	183_I	1.093	0.51
57_A	71_S	1.093	0.51
38_W	46_L	1.088	0.50
82_T	119_M	1.081	0.49
153_Y	157_I	1.079	0.49
20_S	99_I	1.079	0.49
9_P	126_L	1.077	0.49
50_D	54_L	1.076	0.49
65_K	68_L	1.076	0.49
109_Q	147_Q	1.067	0.48
40_T	122_R	1.064	0.48
148_G	151_E	1.061	0.47
125_Y	137_A	1.060	0.47
107_E	135_I	1.059	0.47
205_E	208_R	1.054	0.47
6_N	58_A	1.053	0.47
5_V	155_S	1.046	0.46
143_V	153_Y	1.043	0.46
96_A	100_M	1.034	0.45
78_E	82_T	1.034	0.45
21_I	25_K	1.033	0.45
1_P	33_E	1.029	0.44
63_A	69_D	1.029	0.44
144_Q	153_Y	1.026	0.44
117_A	120_Q	1.025	0.44
57_A	63_A	1.021	0.43
56_M	62_A	1.016	0.43
3_Q	19_V	1.012	0.43
128_A	160_L	1.011	0.42
22_F	25_K	1.010	0.42
5_V	8_V	1.009	0.42
33_E	196_H	1.009	0.42
66_E	73_K	1.008	0.42
6_N	12_V	1.008	0.42
34_E	193_A	1.006	0.42
42_F	58_A	1.006	0.42
46_L	90_P	1.005	0.42
53_T	138_K	1.004	0.42
17_K	194_M	1.003	0.42
181_L	186_A	1.002	0.42
203_L	214_G	1.001	0.41

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

See coupling matrix (for protein design or mutagenesis)
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
4u0cA	1	0.8964	100	0.11	Contact Map
3gv2A	6	0.9369	100	0.164	Contact Map
1d1dA	1	0.9054	100	0.203	Contact Map
1eiaA	1	0.8964	100	0.204	Contact Map
3tirA	1	0.9369	100	0.249	Contact Map
4ph0A	6	0	100	0.31	Contact Map
1qrjA	1	0.9144	100	0.316	Contact Map
1l6nA	1	0.6577	100	0.443	Contact Map
2wlvA	1	0.6036	100	0.463	Contact Map
2xgvA	1	0.5901	100	0.487	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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