OPENSEQ.org - 1492173081 - GREMLIN Submission

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1-240x788

ID:	1492173081	Query Sequence SIVQIPLVLKSKDLKQAFYQHFPNPVLEGKTEELKLQLSGRKKETDKNFLDKLASPLLKWVDKTFYVSSKLAYALDLSKYDFWFEGDQFYADVLLDARTTMQLRNEAKILNENIRLNGDLNCPMQVRVVLNGKIELTKEASINILLNDDDAKIKFQKVCSSKAIQNIDFPELLRPIVEPVKRRISKTINKIITQQLQRLLNHDQTGSYLSFKEKIDAAAWQLGKPYELTQGIWLVPKVEQVFVSPVYGVGLGVENRLEFCIGVKAKPVVTLAEKAPNVVIPK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	282 (234)
Sequences:	421 (308.3)
Seq/Len:	1.799
Nf(neff/√len):	20.2

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: 1.799).

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
8_V	256_R	2.338	1.00
240_Q	264_K	2.286	1.00
155_F	159_C	2.215	0.99
228_L	234_L	2.147	0.99
25_P	51_D	1.917	0.98
24_N	52_K	1.831	0.97
237_K	268_V	1.814	0.97
227_E	230_Q	1.768	0.96
137_T	141_S	1.718	0.96
70_K	155_F	1.669	0.95
235_V	268_V	1.665	0.95
65_F	128_V	1.662	0.94
22_F	170_P	1.623	0.94
19_Y	225_P	1.603	0.93
136_L	211_F	1.585	0.92
35_K	38_L	1.488	0.89
3_V	192_I	1.470	0.88
49_F	267_P	1.469	0.88
73_Y	79_K	1.464	0.88
132_G	189_N	1.459	0.88
146_L	189_N	1.440	0.87
224_K	275_A	1.438	0.87
34_L	39_S	1.432	0.86
38_L	41_R	1.424	0.86
48_N	76_D	1.421	0.86
50_L	155_F	1.377	0.83
10_K	13_D	1.371	0.83
15_K	19_Y	1.368	0.83
34_L	41_R	1.358	0.82
164_I	269_V	1.355	0.82
50_L	269_V	1.346	0.81
80_Y	140_A	1.326	0.80
131_N	178_E	1.323	0.80
8_V	258_E	1.317	0.79
161_S	169_F	1.301	0.78
26_V	177_V	1.297	0.78
35_K	40_G	1.291	0.77
186_K	190_K	1.264	0.75
144_I	189_N	1.256	0.75
30_K	186_K	1.255	0.75
19_Y	24_N	1.251	0.74
159_C	233_W	1.244	0.74
51_D	72_A	1.241	0.73
184_I	188_I	1.239	0.73
77_L	153_I	1.235	0.73
5_I	68_S	1.231	0.73
56_P	269_V	1.220	0.72
70_K	140_A	1.212	0.71
49_F	73_Y	1.212	0.71
4_Q	177_V	1.210	0.71
58_L	239_E	1.197	0.69
21_H	209_L	1.197	0.69
31_T	48_N	1.196	0.69
273_E	277_N	1.195	0.69
26_V	257_L	1.195	0.69
70_K	159_C	1.188	0.69
140_A	164_I	1.188	0.69
275_A	278_V	1.187	0.69
159_C	267_P	1.187	0.69
26_V	169_F	1.172	0.67
32_E	48_N	1.166	0.67
132_G	144_I	1.151	0.65
137_T	143_N	1.146	0.65
7_L	55_S	1.145	0.64
34_L	38_L	1.139	0.64
50_L	71_L	1.137	0.64
23_P	52_K	1.133	0.63
218_A	221_Q	1.130	0.63
83_W	241_V	1.128	0.63
3_V	21_H	1.128	0.63
4_Q	69_S	1.126	0.63
35_K	39_S	1.125	0.62
88_Q	91_A	1.124	0.62
61_V	217_A	1.121	0.62
9_L	14_L	1.120	0.62
34_L	40_G	1.118	0.62
64_T	145_L	1.114	0.61
5_I	273_E	1.112	0.61
140_A	155_F	1.111	0.61
72_A	96_D	1.104	0.60
58_L	62_D	1.103	0.60
57_L	263_V	1.102	0.60
26_V	54_A	1.102	0.60
137_T	147_N	1.098	0.60
20_Q	263_V	1.096	0.59
56_P	140_A	1.095	0.59
59_K	68_S	1.091	0.59
140_A	269_V	1.085	0.58
16_Q	20_Q	1.085	0.58
229_T	233_W	1.085	0.58
163_A	282_K	1.084	0.58
135_E	194_Q	1.075	0.57
142_I	188_I	1.074	0.57
11_S	239_E	1.070	0.57
7_L	261_I	1.064	0.56
14_L	221_Q	1.064	0.56
30_K	46_D	1.053	0.55
138_K	160_S	1.050	0.55
79_K	88_Q	1.047	0.54
163_A	176_I	1.045	0.54
23_P	177_V	1.043	0.54
71_L	236_P	1.043	0.54
158_V	173_L	1.041	0.54
213_E	262_G	1.041	0.54
26_V	209_L	1.040	0.54
133_K	145_L	1.039	0.53
153_I	159_C	1.035	0.53
47_K	50_L	1.034	0.53
54_A	70_K	1.032	0.53
3_V	215_I	1.032	0.53
259_F	262_G	1.027	0.52
167_I	238_V	1.025	0.52
222_L	248_G	1.021	0.51
4_Q	22_F	1.017	0.51
159_C	174_R	1.014	0.51
59_K	129_V	1.013	0.51
219_A	265_A	1.010	0.50
59_K	135_E	1.009	0.50
249_V	254_E	1.006	0.50
19_Y	27_L	1.005	0.50

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
1ewfA	1	0.7447	5.4	0.965	Contact Map
4m4dA	2	0.773	4.2	0.967	Contact Map
3h4zA	3	0.6064	3.5	0.968	Contact Map
1l4zB	1	0.2553	3	0.969	Contact Map
1l4dB	1	0.2518	3	0.969	Contact Map
1yycA	1	0.2234	2.7	0.97	Contact Map
1cxzB	1	0.305	2.4	0.971	Contact Map
4kegA	1	0.5106	2.3	0.971	Contact Map
1mp9A	2	0.2872	2.2	0.971	Contact Map
1bgvA	1	0.3121	2.2	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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