OPENSEQ.org - 1430333628 - GREMLIN Submission

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test Ecoli

ID:	1430333628	Query Sequence MKSLSYKRIYKSQEYLATLGTIEYRSLFGSYSLTVDDTVFAMVSDGELYLRACEQSAQYCVKHPPVWLTYKKCGRSVTLNYYRVDESLWRNQLKLVRLSKYSLDAALKEKSTRNTRERLKDLPNMSFHLEAILGEVGIKDVRALRILGAKMCWLRLRQQNSLVTEKILFMLEGAIIGIHEAALPVARRQELAEWADSLTPKQEFPAELE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	209 (200)
Sequences:	272 (199.1)
Seq/Len:	1.360
Nf(neff/√len):	14.1

Jackhmmer Results: (2015_01_07)
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: 1.360).

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
41_A	48_L	2.348	0.99
118_R	121_D	2.191	0.99
140_D	143_A	2.109	0.98
50_L	98_L	1.824	0.95
50_L	84_V	1.703	0.92
131_A	153_W	1.629	0.90
50_L	156_L	1.617	0.89
32_S	39_V	1.575	0.88
123_P	137_G	1.531	0.86
144_L	171_L	1.500	0.84
29_G	177_G	1.492	0.84
19_L	25_R	1.478	0.83
81_Y	179_H	1.449	0.81
138_I	152_C	1.439	0.81
19_L	73_C	1.433	0.80
12_S	48_L	1.422	0.79
125_M	129_L	1.386	0.77
30_S	81_Y	1.362	0.75
45_D	183_L	1.347	0.74
36_D	107_L	1.338	0.73
55_Q	141_V	1.334	0.73
131_A	135_E	1.334	0.73
40_F	49_Y	1.305	0.71
89_W	95_L	1.290	0.69
16_L	35_V	1.274	0.68
109_E	141_V	1.269	0.68
136_V	156_L	1.269	0.68
151_M	165_E	1.269	0.68
149_A	172_E	1.268	0.68
33_L	126_S	1.268	0.68
25_R	163_V	1.253	0.66
156_L	163_V	1.247	0.66
33_L	95_L	1.246	0.66
157_R	193_E	1.244	0.65
4_L	199_T	1.229	0.64
21_T	97_R	1.228	0.64
32_S	68_L	1.218	0.63
54_E	99_S	1.216	0.63
133_L	171_L	1.215	0.63
18_T	41_A	1.214	0.63
43_V	179_H	1.200	0.61
60_C	64_P	1.196	0.61
138_I	158_Q	1.192	0.61
39_V	153_W	1.192	0.61
74_G	95_L	1.191	0.60
74_G	170_M	1.190	0.60
29_G	179_H	1.187	0.60
116_R	188_R	1.181	0.59
149_A	175_I	1.178	0.59
11_K	14_E	1.167	0.58
141_V	163_V	1.156	0.57
61_V	157_R	1.153	0.57
104_D	108_K	1.149	0.56
84_V	95_L	1.146	0.56
144_L	191_L	1.142	0.56
7_K	131_A	1.142	0.56
144_L	182_A	1.141	0.56
150_K	154_L	1.137	0.55
109_E	163_V	1.130	0.54
39_V	59_Y	1.129	0.54
123_P	177_G	1.125	0.54
12_S	25_R	1.124	0.54
85_D	88_L	1.124	0.54
33_L	157_R	1.123	0.54
25_R	43_V	1.119	0.53
48_L	96_V	1.109	0.52
6_Y	10_Y	1.102	0.52
80_N	166_K	1.101	0.52
135_E	169_F	1.098	0.51
20_G	35_V	1.097	0.51
95_L	119_L	1.093	0.51
74_G	171_L	1.090	0.50
36_D	115_T	1.088	0.50
59_Y	153_W	1.087	0.50
18_T	107_L	1.081	0.50
25_R	29_G	1.076	0.49
27_L	126_S	1.072	0.49
32_S	64_P	1.069	0.48
172_E	183_L	1.064	0.48
89_W	171_L	1.064	0.48
82_Y	96_V	1.063	0.48
72_K	177_G	1.061	0.48
72_K	123_P	1.059	0.47
72_K	179_H	1.057	0.47
109_E	184_P	1.057	0.47
39_V	64_P	1.053	0.47
77_V	144_L	1.049	0.46
101_Y	104_D	1.048	0.46
32_S	56_S	1.048	0.46
37_D	158_Q	1.044	0.46
172_E	191_L	1.042	0.46
73_C	170_M	1.039	0.45
150_K	194_W	1.033	0.45
45_D	157_R	1.031	0.45
121_D	125_M	1.030	0.44
25_R	119_L	1.025	0.44
182_A	200_P	1.025	0.44
185_V	189_Q	1.023	0.44
91_N	97_R	1.016	0.43
152_C	175_I	1.014	0.43
8_R	11_K	1.011	0.43
50_L	82_Y	1.005	0.42
168_L	191_L	1.005	0.42
20_G	149_A	1.002	0.42
22_I	133_L	1.001	0.42

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: (31Jan15)
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
2od0A	2	0.4928	99.9	0.665	Contact Map
3mabA	2	0.4258	99.8	0.722	Contact Map
2fkiA	1	0.5215	81.4	0.938	Contact Map
2a1vA	1	0.5742	61.4	0.947	Contact Map
2z43A	3	0.4115	57.8	0.948	Contact Map
2kfpA	1	0.4928	47.2	0.951	Contact Map
1wcnA	1	0.3349	37.7	0.954	Contact Map
2i1qA	1	0.3971	24.7	0.958	Contact Map
3k4gA	8	0.3732	19.1	0.96	Contact Map
1u9lA	2	0.3349	16.6	0.961	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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