OPENSEQ.org - 1417707592 - GREMLIN Submission

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KNL1

ID:	1417707592	Query Sequence EPPGVDNKWQSDVVLPTQDYTLREFIDEVGVGFLDTKLIDDLDKKVNFPLNSLNLMEIQRIDNVLSAYYIDIPILEVEAFRCKELWRSINESKNKFKDFETQIDRSHPPLLLQEYFSSSEKMKQLMKDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	164 (154)
Sequences:	182 (136.8)
Seq/Len:	1.182
Nf(neff/√len):	11.0

Jackhmmer Results: (2014_04_16)
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: 1.182).

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
145_W	148_W	2.334	0.99
101_T	156_L	1.966	0.96
107_H	152_Q	1.826	0.94
41_D	44_K	1.661	0.89
84_E	87_R	1.521	0.82
82_C	91_E	1.514	0.82
92_S	152_Q	1.506	0.81
31_V	73_P	1.492	0.80
141_A	144_E	1.453	0.78
111_L	142_A	1.450	0.78
78_E	130_L	1.442	0.77
88_S	99_F	1.382	0.73
136_Y	147_E	1.382	0.73
78_E	153_L	1.373	0.72
89_I	95_K	1.366	0.72
26_I	149_R	1.352	0.71
139_L	149_R	1.331	0.69
73_P	76_E	1.330	0.69
96_F	131_Q	1.325	0.68
84_E	92_S	1.283	0.65
84_E	148_W	1.272	0.64
26_I	130_L	1.269	0.63
39_I	79_A	1.249	0.62
19_D	86_W	1.247	0.61
81_R	107_H	1.223	0.59
151_K	155_G	1.222	0.59
83_K	155_G	1.216	0.59
8_K	11_S	1.208	0.58
88_S	92_S	1.203	0.57
114_E	126_M	1.198	0.57
26_I	111_L	1.196	0.57
115_Y	146_Y	1.193	0.56
82_C	111_L	1.191	0.56
92_S	130_L	1.187	0.56
71_D	96_F	1.184	0.55
101_T	117_S	1.175	0.55
75_L	141_A	1.174	0.55
35_D	61_I	1.168	0.54
21_T	104_D	1.167	0.54
22_L	137_S	1.165	0.54
111_L	160_L	1.163	0.53
126_M	129_Q	1.158	0.53
19_D	23_R	1.158	0.53
16_P	55_L	1.153	0.52
20_Y	131_Q	1.151	0.52
82_C	107_H	1.146	0.52
18_Q	30_G	1.140	0.51
122_M	155_G	1.139	0.51
20_Y	28_E	1.125	0.50
91_E	158_L	1.123	0.50
40_D	82_C	1.114	0.49
90_N	156_L	1.106	0.48
118_S	136_Y	1.099	0.47
22_L	71_D	1.084	0.46
22_L	92_S	1.061	0.44
15_L	53_L	1.060	0.44
71_D	160_L	1.060	0.44
24_E	119_S	1.057	0.43
74_I	140_E	1.056	0.43
113_Q	131_Q	1.046	0.42
69_Y	123_K	1.041	0.42
78_E	156_L	1.040	0.42
78_E	118_S	1.040	0.42
88_S	152_Q	1.038	0.41
56_M	101_T	1.036	0.41
139_L	152_Q	1.033	0.41
114_E	155_G	1.033	0.41
147_E	155_G	1.029	0.41
115_Y	123_K	1.024	0.40
143_M	147_E	1.021	0.40
32_G	134_K	1.016	0.39
114_E	133_V	1.014	0.39
74_I	153_L	1.013	0.39
51_N	56_M	1.013	0.39
43_D	46_V	1.012	0.39
63_N	143_M	1.009	0.39
61_I	64_V	1.005	0.38
84_E	152_Q	1.002	0.38
93_K	133_V	1.001	0.38

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: (06Sep14)
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
4bt9A	2	0.5976	17.1	0.933	Contact Map
2e0aA	2	0.7073	4.8	0.948	Contact Map
1qjtA	1	0.3476	4.7	0.948	Contact Map
2q13A	1	0.6037	4.2	0.949	Contact Map
3b5oA	1	0.4634	4.1	0.95	Contact Map
2ve7C	2	0.878	3.8	0.95	Contact Map
4btfA	1	0.5305	3.2	0.952	Contact Map
3ci9A	2	0.2866	3.2	0.952	Contact Map
2bezF	1	0.2256	3.1	0.953	Contact Map
4j2cA	2	0.5732	3.1	0.953	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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