OPENSEQ.org - 1488241886 - GREMLIN Submission

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COMMD1

ID:	1488241886	Query Sequence MAAGELEGGKPLSGLLNALAQDTFHGYPGITEELLRSQLYPEVPPEEFRPFLAKMRGILKSIASADMDFNQLEAFLTAQTKKQGGITSDQAAVISKFWKSHKTKIRESLMNQSRWNSGLRGLSWRVDGKSQSRHSAQIHTPVAIIELELGKYGQESEFLCLEFDEVKVNQILKTLSEVEESISTLISQPN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	190 (177)
Sequences:	646 (480.4)
Seq/Len:	3.650
Nf(neff/√len):	36.1

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: 3.650).

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
161_L	164_D	1.809	0.99
143_A	168_V	1.739	0.99
164_D	167_K	1.674	0.99
163_F	168_V	1.669	0.99
12_L	90_Q	1.660	0.99
11_P	14_G	1.627	0.98
151_K	157_E	1.611	0.98
163_F	171_I	1.574	0.98
94_I	148_E	1.561	0.98
75_F	84_G	1.549	0.98
164_D	168_V	1.516	0.97
179_E	183_S	1.491	0.97
168_V	172_L	1.491	0.97
123_S	146_E	1.489	0.97
8_G	12_L	1.484	0.97
37_S	41_P	1.476	0.97
161_L	183_S	1.460	0.96
178_V	183_S	1.438	0.96
125_R	141_P	1.408	0.95
174_T	178_V	1.382	0.95
47_E	72_L	1.366	0.94
15_L	158_F	1.354	0.94
126_V	144_I	1.337	0.93
15_L	62_I	1.333	0.93
126_V	143_A	1.330	0.93
131_Q	162_E	1.321	0.93
176_S	183_S	1.319	0.93
121_G	148_E	1.312	0.92
68_D	71_Q	1.310	0.92
72_L	94_I	1.304	0.92
39_L	42_E	1.294	0.92
44_P	154_Q	1.280	0.91
124_W	141_P	1.279	0.91
168_V	171_I	1.272	0.91
37_S	145_I	1.268	0.91
20_A	97_F	1.264	0.91
67_M	75_F	1.257	0.90
172_L	179_E	1.230	0.89
163_F	174_T	1.229	0.89
135_S	138_I	1.224	0.89
130_S	143_A	1.223	0.89
105_I	109_L	1.219	0.88
175_L	178_V	1.217	0.88
165_E	168_V	1.213	0.88
15_L	119_L	1.213	0.88
172_L	175_L	1.212	0.88
66_D	106_R	1.204	0.87
129_K	133_R	1.201	0.87
63_A	94_I	1.187	0.86
127_D	141_P	1.182	0.86
168_V	182_I	1.179	0.86
140_T	153_G	1.168	0.85
77_T	88_S	1.167	0.85
164_D	173_K	1.165	0.85
19_L	33_E	1.164	0.85
171_I	175_L	1.162	0.85
51_F	166_V	1.161	0.85
72_L	76_L	1.158	0.85
44_P	47_E	1.158	0.85
132_S	182_I	1.157	0.84
98_W	119_L	1.146	0.84
174_T	177_E	1.133	0.83
14_G	18_A	1.128	0.82
179_E	182_I	1.123	0.82
53_A	176_S	1.117	0.82
162_E	168_V	1.113	0.81
48_F	94_I	1.113	0.81
145_I	161_L	1.106	0.81
168_V	181_S	1.105	0.81
119_L	146_E	1.105	0.81
168_V	175_L	1.103	0.80
19_L	25_H	1.103	0.80
87_T	90_Q	1.100	0.80
118_G	151_K	1.099	0.80
164_D	178_V	1.091	0.79
126_V	168_V	1.085	0.79
171_I	176_S	1.083	0.79
63_A	109_L	1.083	0.79
165_E	169_N	1.082	0.79
121_G	153_G	1.081	0.79
32_E	59_L	1.080	0.78
167_K	170_Q	1.080	0.78
172_L	182_I	1.068	0.77
76_L	119_L	1.067	0.77
18_A	30_I	1.065	0.77
28_P	34_L	1.061	0.77
26_G	133_R	1.057	0.76
66_D	102_K	1.052	0.76
173_K	177_E	1.036	0.74
32_E	36_R	1.036	0.74
129_K	168_V	1.035	0.74
49_R	64_S	1.027	0.73
128_G	147_L	1.026	0.73
38_Q	42_E	1.011	0.72
62_I	92_A	1.008	0.71
125_R	140_T	1.006	0.71
177_E	184_T	1.006	0.71
131_Q	169_N	1.003	0.71

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
2h2mA	1	0.5684	99.3	0.629	Contact Map
4oe9A	2	0.5421	91.8	0.852	Contact Map
2ymyA	2	0.2105	8.1	0.932	Contact Map
1ecaA	1	0.5632	7.2	0.933	Contact Map
3hy0A	2	0.5789	6.9	0.934	Contact Map
4wv4B	1	0.4842	5.1	0.938	Contact Map
1ho8A	1	0.8579	4.5	0.939	Contact Map
3c1dA	2	0.6947	4.1	0.94	Contact Map
2c0kA	2	0.5842	4.1	0.94	Contact Map
2i4kA	1	0.3579	4	0.941	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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