OPENSEQ.org - 1452700939 - GREMLIN Submission

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1wdn

ID:	1452700939	Query Sequence ADKKLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	226 (223)
Sequences:	23058 (16139.7)
Seq/Len:	103.399
Nf(neff/√len):	1080.8

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: 103.399).

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
113_A	151_A	4.283	1.00
8_A	62_V	3.934	1.00
4_K	44_E	3.358	1.00
38_E	206_T	2.667	1.00
136_F	145_E	2.551	1.00
71_I	76_K	2.355	1.00
56_A	62_V	2.350	1.00
6_V	44_E	2.320	1.00
142_A	154_V	2.277	1.00
4_K	42_D	2.190	1.00
83_D	205_K	2.175	1.00
121_V	135_Q	2.083	1.00
34_A	37_K	2.074	1.00
58_Q	78_A	2.014	1.00
103_S	106_D	2.005	1.00
6_V	46_K	2.002	1.00
30_D	219_K	1.999	1.00
138_N	141_N	1.997	1.00
34_A	212_T	1.996	1.00
56_A	61_N	1.972	1.00
121_V	125_K	1.961	1.00
82_S	201_N	1.958	1.00
73_D	76_K	1.940	1.00
71_I	186_G	1.935	1.00
156_H	161_I	1.932	1.00
79_I	188_A	1.923	1.00
197_R	201_N	1.915	1.00
36_A	43_Y	1.906	1.00
214_N	218_K	1.888	1.00
83_D	201_N	1.861	1.00
212_T	215_E	1.856	1.00
80_D	197_R	1.830	1.00
95_K	149_N	1.814	1.00
189_F	200_V	1.785	1.00
205_K	209_E	1.782	1.00
189_F	197_R	1.781	1.00
34_A	207_L	1.735	1.00
30_D	220_W	1.721	1.00
145_E	150_R	1.711	1.00
93_M	161_I	1.691	1.00
7_V	32_W	1.630	1.00
111_V	134_R	1.610	1.00
38_E	203_A	1.569	1.00
53_I	65_A	1.558	1.00
102_K	106_D	1.548	1.00
198_D	202_G	1.548	1.00
7_V	64_L	1.545	1.00
29_V	33_A	1.538	1.00
48_M	56_A	1.531	1.00
194_D	198_D	1.519	1.00
55_P	59_T	1.511	1.00
35_I	203_A	1.491	1.00
110_K	152_D	1.469	1.00
18_F	25_V	1.461	1.00
203_A	207_L	1.447	1.00
136_F	142_A	1.443	1.00
66_L	187_I	1.432	1.00
34_A	38_E	1.428	1.00
145_E	151_A	1.425	1.00
89_G	158_T	1.415	1.00
111_V	152_D	1.412	1.00
92_V	153_A	1.412	1.00
112_V	153_A	1.411	1.00
38_E	210_N	1.406	0.99
91_L	158_T	1.405	0.99
28_D	85_Y	1.405	0.99
146_L	154_V	1.403	0.99
144_M	148_T	1.402	0.99
49_D	52_G	1.384	0.99
116_S	137_P	1.379	0.99
199_K	203_A	1.379	0.99
95_K	98_N	1.374	0.99
199_K	202_G	1.373	0.99
94_V	153_A	1.371	0.99
54_I	79_I	1.364	0.99
113_A	142_A	1.361	0.99
64_L	189_F	1.349	0.99
55_P	58_Q	1.344	0.99
190_P	193_S	1.338	0.99
158_T	162_L	1.329	0.99
87_K	184_Q	1.317	0.99
203_A	206_T	1.282	0.99
111_V	132_D	1.245	0.98
39_L	203_A	1.234	0.98
19_K	47_P	1.225	0.98
94_V	176_V	1.215	0.98
20_Q	25_V	1.210	0.98
144_M	147_G	1.205	0.98
3_K	41_L	1.198	0.98
208_R	213_Y	1.196	0.98
206_T	210_N	1.187	0.98
33_A	45_L	1.177	0.98
80_D	192_G	1.163	0.97
97_N	174_K	1.159	0.97
90_L	120_S	1.155	0.97
33_A	37_K	1.154	0.97
27_F	216_I	1.150	0.97
137_P	141_N	1.127	0.97
52_G	56_A	1.110	0.96
60_K	190_P	1.104	0.96
202_G	206_T	1.102	0.96
134_R	145_E	1.089	0.96
94_V	174_K	1.074	0.95
141_N	144_M	1.063	0.95
69_I	188_A	1.060	0.95
96_A	174_K	1.041	0.94
27_F	217_Y	1.030	0.94
116_S	135_Q	1.029	0.94
125_K	135_Q	1.029	0.94
81_F	188_A	1.020	0.93
32_W	66_L	1.020	0.93
25_V	30_D	1.018	0.93
31_L	213_Y	1.015	0.93
80_D	194_D	1.014	0.93
201_N	205_K	1.009	0.93
72_T	75_R	1.006	0.93
27_F	221_F	1.002	0.92

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
1wdnA	1	0.9867	100	0.011	Contact Map
4powA	2	0.9912	100	0.022	Contact Map
3k4uA	6	1	100	0.034	Contact Map
3kzgA	4	0.969	100	0.035	Contact Map
4ohnA	1	0.9956	100	0.036	Contact Map
3h7mA	1	0.9956	100	0.039	Contact Map
3hv1A	2	0.9956	100	0.041	Contact Map
3kbrA	1	0.9602	100	0.043	Contact Map
4c0rA	2	0.9956	100	0.043	Contact Map
2ylnA	1	0.9867	100	0.047	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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