OPENSEQ.org - 1507040272 - GREMLIN Submission

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KNL1 C-term -force run

ID:	1507040272	Query Sequence QAVFTFVYDTIQLTITFEESVVGFPFLDKRYRKIVDVNFQSLLDEDQAPPSSLLVHKLIFQYVEEKESWKKTCTTQHQLPKMLEEFSLVVHHCRLLGEEIEYLKRWGPNYNLMNIDINNNELRLLFSSSAAFAKFEITLFLSAYYPSVPL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	150 (149)
Sequences:	130 (84.3)
Seq/Len:	0.872
Nf(neff/√len):	6.9

Jackhmmer Results: (2016_04)
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: 0.872).

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 > 50% 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
126_F	135_F	1.918	0.92
10_T	109_N	1.662	0.83
73_C	82_M	1.659	0.83
53_L	76_Q	1.596	0.79
110_Y	115_I	1.588	0.79
126_F	131_A	1.500	0.73
86_F	147_S	1.467	0.71
4_F	87_S	1.439	0.68
62_Y	71_K	1.405	0.66
37_V	149_P	1.404	0.66
11_I	45_E	1.403	0.66
137_I	140_F	1.401	0.65
108_P	114_N	1.389	0.64
62_Y	109_N	1.378	0.64
15_I	79_L	1.368	0.63
55_V	97_G	1.349	0.61
11_I	41_S	1.343	0.61
128_S	131_A	1.332	0.60
30_R	71_K	1.318	0.58
88_L	98_E	1.276	0.55
48_A	86_F	1.267	0.54
122_L	133_A	1.257	0.53
29_K	68_S	1.250	0.52
108_P	121_E	1.238	0.51
47_Q	66_K	1.225	0.50
34_I	100_I	1.222	0.50
10_T	60_F	1.206	0.49
88_L	92_H	1.203	0.48
73_C	101_E	1.197	0.48
108_P	113_M	1.190	0.47
79_L	115_I	1.185	0.47
4_F	26_F	1.185	0.47
82_M	94_R	1.183	0.46
71_K	74_T	1.180	0.46
82_M	112_L	1.178	0.46
39_F	44_D	1.173	0.46
85_E	119_N	1.164	0.45
48_A	52_S	1.157	0.44
38_N	118_N	1.151	0.44
109_N	122_L	1.147	0.43
59_I	67_E	1.142	0.43
58_L	63_V	1.118	0.41
93_C	97_G	1.111	0.40
127_S	136_E	1.108	0.40
88_L	97_G	1.103	0.39
5_T	15_I	1.101	0.39
15_I	86_F	1.089	0.38
112_L	143_A	1.088	0.38
125_L	136_E	1.087	0.38
101_E	112_L	1.083	0.38
31_Y	117_I	1.083	0.38
24_F	47_Q	1.082	0.38
2_A	12_Q	1.079	0.37
84_E	119_N	1.079	0.37
36_D	45_E	1.073	0.37
78_Q	140_F	1.070	0.37
5_T	53_L	1.069	0.37
13_L	17_F	1.068	0.37
67_E	75_T	1.065	0.36
78_Q	149_P	1.064	0.36
51_S	99_E	1.062	0.36
109_N	113_M	1.061	0.36
34_I	63_V	1.060	0.36
15_I	21_V	1.057	0.36
126_F	132_F	1.055	0.35
27_L	34_I	1.052	0.35
6_F	13_L	1.048	0.35
93_C	98_E	1.046	0.35
24_F	27_L	1.042	0.34
127_S	137_I	1.037	0.34
124_L	132_F	1.036	0.34
64_E	69_W	1.033	0.34
11_I	40_Q	1.028	0.33
106_W	126_F	1.027	0.33
3_V	90_V	1.025	0.33
57_K	64_E	1.021	0.33
39_F	43_L	1.020	0.33
36_D	70_K	1.017	0.32
76_Q	121_E	1.017	0.32
17_F	139_L	1.011	0.32
48_A	57_K	1.004	0.31

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
4nfaA	1	0.98	100	-0.012	Contact Map
4ccgA	2	0.42	42.5	0.936	Contact Map
1fxtA	1	0.3867	37.9	0.937	Contact Map
1jatA	1	0.4	33.5	0.939	Contact Map
1yh2A	1	0.4067	32.8	0.94	Contact Map
1jatB	1	0.3933	32.4	0.94	Contact Map
2r0jA	1	0.38	31.5	0.94	Contact Map
1tteA	1	0.3933	28.3	0.941	Contact Map
4y1lC	1	0	27.4	0.942	Contact Map
1wzvA	2	0.38	27.1	0.942	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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