OPENSEQ.org - 1515595952 - GREMLIN Submission

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India-Argentina

ID:	1515595952	Query Sequence MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	270 (228)
Sequences:	2951 (2042.2)
Seq/Len:	12.943
Nf(neff/√len):	135.2

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: 12.943).

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
118_V	129_M	4.425	1.00
181_K	199_D	3.647	1.00
234_R	263_A	3.583	1.00
89_V	119_T	3.309	1.00
202_D	244_S	3.039	1.00
143_A	170_E	3.021	1.00
91_T	116_A	2.826	1.00
169_V	194_I	2.737	1.00
53_Q	56_P	2.699	1.00
138_A	167_G	2.315	1.00
89_V	196_V	2.237	1.00
87_L	180_L	2.123	1.00
225_D	228_H	2.042	1.00
77_G	205_F	2.002	1.00
78_L	105_I	1.965	1.00
104_W	107_Q	1.945	1.00
83_G	177_F	1.935	1.00
53_Q	57_N	1.924	1.00
142_N	184_Y	1.921	1.00
115_L	138_A	1.886	1.00
125_K	208_C	1.884	1.00
86_V	109_I	1.878	1.00
237_G	260_T	1.876	1.00
90_D	120_H	1.804	1.00
115_L	140_Y	1.796	1.00
172_A	179_P	1.777	1.00
85_R	114_A	1.772	1.00
198_I	201_T	1.765	1.00
235_A	238_A	1.755	1.00
174_A	179_P	1.739	1.00
98_T	131_A	1.734	1.00
57_N	178_G	1.720	1.00
125_K	250_H	1.694	1.00
248_M	251_S	1.687	1.00
197_G	204_A	1.672	1.00
234_R	267_D	1.669	1.00
124_D	250_H	1.661	1.00
117_V	196_V	1.649	1.00
120_H	208_C	1.643	1.00
203_I	245_M	1.630	1.00
185_P	195_T	1.613	1.00
178_G	201_T	1.608	1.00
99_A	103_N	1.597	1.00
230_A	267_D	1.592	1.00
254_D	258_A	1.557	1.00
53_Q	59_W	1.557	1.00
172_A	181_K	1.538	1.00
140_Y	167_G	1.529	1.00
89_V	205_F	1.525	1.00
142_N	194_I	1.519	1.00
119_T	196_V	1.511	1.00
87_L	117_V	1.500	1.00
234_R	238_A	1.487	1.00
144_L	147_Q	1.483	1.00
126_M	149_A	1.442	1.00
182_V	194_I	1.436	1.00
233_A	259_I	1.415	1.00
122_H	125_K	1.414	1.00
120_H	125_K	1.413	1.00
179_P	200_G	1.411	1.00
95_D	99_A	1.391	0.99
57_N	201_T	1.382	0.99
133_H	166_N	1.374	0.99
237_G	263_A	1.360	0.99
204_A	246_I	1.357	0.99
55_A	201_T	1.349	0.99
197_G	202_D	1.345	0.99
179_P	199_D	1.344	0.99
102_L	106_K	1.329	0.99
174_A	177_F	1.308	0.99
182_V	196_V	1.304	0.99
85_R	115_L	1.290	0.99
78_L	86_V	1.284	0.99
116_A	132_L	1.280	0.99
145_S	192_D	1.279	0.99
188_G	232_S	1.275	0.99
86_V	105_I	1.267	0.99
115_L	167_G	1.264	0.99
146_N	150_P	1.233	0.98
143_A	168_W	1.229	0.98
185_P	232_S	1.215	0.98
117_V	182_V	1.206	0.98
193_N	207_G	1.180	0.98
102_L	132_L	1.179	0.98
87_L	175_P	1.167	0.97
76_N	92_A	1.165	0.97
178_G	200_G	1.165	0.97
178_G	198_I	1.162	0.97
102_L	131_A	1.159	0.97
183_F	239_A	1.157	0.97
116_A	129_M	1.152	0.97
90_D	208_C	1.141	0.97
90_D	125_K	1.140	0.97
58_V	198_I	1.138	0.97
181_K	197_G	1.133	0.97
119_T	125_K	1.132	0.97
195_T	204_A	1.128	0.97
189_H	208_C	1.126	0.97
198_I	203_I	1.119	0.96
87_L	115_L	1.110	0.96
91_T	129_M	1.105	0.96
124_D	208_C	1.085	0.96
84_G	114_A	1.079	0.95
197_G	243_A	1.075	0.95
195_T	236_F	1.069	0.95
83_G	111_L	1.068	0.95
141_A	145_S	1.040	0.94
120_H	189_H	1.031	0.94
208_C	250_H	1.014	0.93
119_T	207_G	1.013	0.93
98_T	132_L	1.011	0.93
103_N	107_Q	1.007	0.93
109_I	112_P	1.007	0.93
188_G	209_L	1.004	0.93
120_H	124_D	1.004	0.93
59_W	108_E	1.003	0.93

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
4eybA	2	0.8852	100	0.418	Contact Map
4d1tA	1	0.8481	100	0.444	Contact Map
4hl2A	2	0.8926	100	0.462	Contact Map
1a7tA	2	0.8222	100	0.479	Contact Map
2fhxA	2	0.8	100	0.484	Contact Map
4c1dA	2	0.8481	100	0.485	Contact Map
2yntA	2	0.8074	100	0.487	Contact Map
1m2xA	4	0.7963	100	0.491	Contact Map
2yheA	6	0.9481	100	0.491	Contact Map
3iogA	1	0.7852	100	0.494	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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