OPENSEQ.org - 1390017539 - GREMLIN Submission

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T0735

ID:	1390017539	Query Sequence MTNDHYVSKKKMFAVVFCVFAPNEVLLANDTAVGGEGSLPIPVSQPHIKMVSELIRISGKNLNEPQMNGSWHYNCNFTFKNTLNKEVTISMAFPFPINDGNSEIALPAGQQTNVGQALVYDFLVTVNDKQVSAQRGNIAPDQNKGLYYEDAYFWKTTFPPLATVNIHHDYSTGATYDVMGYHWVRYVLKTGALWQDSSIGHTRLEVIPNTPTRLCSEIDQKADYLNPTPSGMSISGSRADRKYIWDLRHFQPQADLSLCLFTGISYVRYKVIYPWLNSDDALSKLARLSNKELRFLRNTIYAQYGRQFQSPDLQEYFSKKWWYVPNPDYSDRMLNEEDKKLLSMINQAK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	349 (221)
Sequences:	620 (337.3)
Seq/Len:	2.805
Nf(neff/√len):	22.7

HHblits Results: (2013_03)
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: 2.805).

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
77_F	91_M	3.073	1.00
76_N	167_H	2.267	1.00
73_Y	184_V	2.200	1.00
159_P	162_A	2.151	1.00
147_Y	152_Y	2.012	1.00
73_Y	100_G	2.004	1.00
86_E	160_P	1.898	0.99
145_G	152_Y	1.890	0.99
72_H	120_Y	1.789	0.99
80_K	163_T	1.759	0.99
158_F	164_V	1.721	0.98
122_F	152_Y	1.701	0.98
123_L	130_Q	1.687	0.98
127_N	162_A	1.612	0.97
121_D	132_S	1.588	0.97
126_V	161_L	1.568	0.96
79_F	96_P	1.568	0.96
96_P	124_V	1.562	0.96
129_K	158_F	1.532	0.96
57_I	73_Y	1.525	0.96
125_T	130_Q	1.491	0.95
123_L	167_H	1.476	0.94
79_F	82_T	1.463	0.94
150_D	168_H	1.455	0.94
96_P	99_D	1.437	0.93
147_Y	150_D	1.422	0.93
79_F	86_E	1.416	0.93
125_T	167_H	1.399	0.92
146_L	152_Y	1.399	0.92
147_Y	156_T	1.396	0.92
51_V	163_T	1.381	0.92
51_V	80_K	1.370	0.91
59_G	184_V	1.350	0.90
61_N	129_K	1.320	0.89
36_E	40_P	1.320	0.89
127_N	170_Y	1.303	0.88
57_I	71_W	1.302	0.88
122_F	145_G	1.286	0.87
53_E	152_Y	1.276	0.87
53_E	57_I	1.263	0.86
59_G	166_I	1.244	0.85
69_G	96_P	1.242	0.85
93_F	142_Q	1.235	0.84
78_T	165_N	1.230	0.84
210_T	213_R	1.226	0.83
157_T	164_V	1.224	0.83
137_N	140_P	1.222	0.83
128_D	137_N	1.197	0.81
75_C	96_P	1.194	0.81
136_G	139_A	1.191	0.81
73_Y	158_F	1.180	0.80
152_Y	156_T	1.180	0.80
226_N	229_P	1.178	0.80
136_G	140_P	1.169	0.79
161_L	170_Y	1.167	0.79
89_I	158_F	1.155	0.78
54_L	60_K	1.154	0.78
123_L	161_L	1.153	0.78
51_V	170_Y	1.152	0.78
120_Y	124_V	1.150	0.78
74_N	97_I	1.149	0.78
123_L	132_S	1.148	0.78
72_H	169_D	1.141	0.77
127_N	145_G	1.141	0.77
37_G	45_Q	1.138	0.77
120_Y	168_H	1.137	0.77
185_R	189_K	1.137	0.77
171_S	175_T	1.125	0.76
121_D	169_D	1.120	0.75
199_I	202_T	1.118	0.75
93_F	170_Y	1.110	0.74
58_S	170_Y	1.099	0.73
60_K	122_F	1.096	0.73
98_N	126_V	1.094	0.73
80_K	130_Q	1.092	0.72
122_F	137_N	1.086	0.72
54_L	165_N	1.080	0.71
54_L	203_R	1.077	0.71
125_T	128_D	1.077	0.71
72_H	91_M	1.076	0.71
190_T	194_W	1.075	0.71
96_P	123_L	1.073	0.71
146_L	162_A	1.070	0.70
73_Y	170_Y	1.067	0.70
53_E	128_D	1.067	0.70
78_T	163_T	1.064	0.70
78_T	82_T	1.063	0.69
58_S	74_N	1.055	0.69
48_I	53_E	1.055	0.69
123_L	149_E	1.048	0.68
59_G	71_W	1.048	0.68
100_G	120_Y	1.047	0.68
84_N	121_D	1.043	0.67
92_A	170_Y	1.043	0.67
124_V	169_D	1.039	0.67
48_I	52_S	1.037	0.67
122_F	149_E	1.033	0.66
140_P	162_A	1.028	0.66
181_Y	186_Y	1.020	0.65
57_I	163_T	1.020	0.65
82_T	85_K	1.017	0.65
126_V	143_N	1.014	0.64
139_A	146_L	1.013	0.64
89_I	124_V	1.013	0.64
54_L	61_N	1.012	0.64
52_S	72_H	1.008	0.64
148_Y	158_F	1.005	0.63
241_R	256_L	1.003	0.63
75_C	91_M	1.001	0.63

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: (08Feb14)
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
4g2aA	1	0.9198	100	0.202	Contact Map
2x3cA	1	0.5215	89.3	0.948	Contact Map
2q1fA	2	0.6705	28.7	0.967	Contact Map
3isyA	1	0.3238	24.7	0.968	Contact Map
4jg9A	2	0.2607	17.6	0.97	Contact Map
1g0dA	1	0.3954	17.2	0.97	Contact Map
2e6jA	1	0.3152	15.1	0.971	Contact Map
3m7oA	4	0.3782	15.1	0.971	Contact Map
1yycA	1	0.4298	14.8	0.971	Contact Map
2llgA	1	0.404	13.9	0.972	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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