OPENSEQ.org - 1434135897 - GREMLIN Submission

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KNL1

ID:	1434135897	Query Sequence EPPGVDNKWQSDVVLPTQDYTLREFIDEVGVGFLDTKLIDDLDKKVNFPLNSLNLMEIQRIDNVLSAYYIDIPILEVEAFRCKELWRSINESKNKFKDFETQIDRSHPPLLLQEYFSSSEKMKQLMKDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	164 (154)
Sequences:	238 (161.8)
Seq/Len:	1.545
Nf(neff/√len):	13.0

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: 1.545).

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	2.103	0.99
101_T	156_L	1.698	0.94
31_V	73_P	1.596	0.91
107_H	152_Q	1.541	0.89
136_Y	147_E	1.513	0.87
84_E	87_R	1.488	0.86
84_E	160_L	1.484	0.86
88_S	92_S	1.465	0.85
111_L	142_A	1.459	0.85
78_E	153_L	1.418	0.82
92_S	152_Q	1.402	0.81
55_L	59_Q	1.381	0.80
89_I	95_K	1.370	0.79
18_Q	29_V	1.342	0.77
20_Y	28_E	1.331	0.76
21_T	104_D	1.330	0.76
71_D	96_F	1.320	0.76
53_L	57_E	1.307	0.75
75_L	141_A	1.302	0.74
18_Q	24_E	1.297	0.74
114_E	126_M	1.292	0.73
53_L	154_N	1.276	0.72
82_C	107_H	1.270	0.72
84_E	148_W	1.261	0.71
82_C	91_E	1.254	0.70
141_A	144_E	1.245	0.69
78_E	130_L	1.236	0.69
74_I	140_E	1.229	0.68
83_K	130_L	1.225	0.68
108_P	112_L	1.218	0.67
20_Y	129_Q	1.216	0.67
42_L	142_A	1.216	0.67
39_I	79_A	1.210	0.66
115_Y	123_K	1.196	0.65
126_M	129_Q	1.190	0.64
151_K	155_G	1.187	0.64
91_E	158_L	1.181	0.63
51_N	94_N	1.179	0.63
101_T	117_S	1.174	0.63
108_P	145_W	1.167	0.62
70_I	130_L	1.159	0.61
16_P	55_L	1.159	0.61
41_D	44_K	1.156	0.61
8_K	12_D	1.147	0.60
14_V	53_L	1.140	0.59
121_K	160_L	1.138	0.59
115_Y	118_S	1.134	0.59
139_L	149_R	1.129	0.58
94_N	125_L	1.128	0.58
20_Y	131_Q	1.122	0.58
73_P	76_E	1.122	0.58
118_S	136_Y	1.118	0.57
33_F	114_E	1.115	0.57
60_R	63_N	1.104	0.56
99_F	107_H	1.099	0.55
156_L	159_I	1.094	0.55
92_S	155_G	1.092	0.54
19_D	86_W	1.088	0.54
109_P	141_A	1.087	0.54
49_P	157_E	1.083	0.54
73_P	111_L	1.080	0.53
8_K	11_S	1.078	0.53
86_W	129_Q	1.075	0.53
142_A	152_Q	1.069	0.52
75_L	82_C	1.068	0.52
10_Q	14_V	1.067	0.52
46_V	120_E	1.063	0.51
84_E	149_R	1.062	0.51
83_K	155_G	1.058	0.51
60_R	78_E	1.048	0.50
80_F	115_Y	1.047	0.50
85_L	134_K	1.046	0.50
29_V	41_D	1.038	0.49
106_S	149_R	1.037	0.49
9_W	13_V	1.032	0.48
77_V	145_W	1.030	0.48
26_I	127_K	1.029	0.48
26_I	130_L	1.023	0.47
21_T	153_L	1.018	0.47
134_K	146_Y	1.015	0.46
22_L	137_S	1.013	0.46
81_R	107_H	1.012	0.46
51_N	55_L	1.011	0.46
32_G	96_F	1.003	0.45
40_D	44_K	1.001	0.45

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
2ykoA	3	0.4268	8.8	0.94	Contact Map
1o5hA	2	0.811	8.3	0.941	Contact Map
4j2cA	2	0.5732	6.3	0.944	Contact Map
2msvA	1	0.6402	4.4	0.948	Contact Map
4p72C	2	0.0305	4.2	0.949	Contact Map
2w6aA	2	0.3537	4.1	0.949	Contact Map
3b1fA	1	0.8049	3.9	0.949	Contact Map
3pm8A	2	0.6037	3.8	0.95	Contact Map
2rigA	1	0.4878	3.8	0.95	Contact Map
4d1eA	1	0.6037	3.7	0.95	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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