OPENSEQ.org - 1400294488 - GREMLIN Submission

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1LM7_A

ID:	1400294488	Query Sequence SFQGIRQPVTVTELVDSGILRPSTVNELESGQISYDEVGERIKDFLQGSSCIAGIYNETTKQKLGIYEAMKIGLVRPGTALELLEAQAATGFIVDPVSNLRLPVEEAYKRGLVGIEFKEKLLSAERAVTGYNDPETGNIISLFQAMNKELIEKGHGIRLLEAQIATGGIIDPKESHRLPVDIAYKRGYFNEELSEILSDPSDDTKGFFDPNTEENLTYLQLKERCIKDEETGLCLLPLKEKKKQVQTS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	248 (244)
Sequences:	622 (301.8)
Seq/Len:	2.549
Nf(neff/√len):	19.3

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: 2.549).

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
62_Q	72_I	2.316	1.00
108_Y	113_V	2.238	1.00
67_Y	114_G	2.121	1.00
214_E	224_R	2.099	1.00
78_G	208_F	1.947	0.99
21_R	24_T	1.869	0.99
100_L	110_R	1.801	0.99
66_I	217_T	1.751	0.98
88_A	124_A	1.748	0.98
17_S	21_R	1.644	0.97
2_F	11_V	1.606	0.96
105_E	118_K	1.602	0.96
25_V	115_I	1.588	0.96
19_I	42_I	1.556	0.95
4_G	156_G	1.535	0.95
184_Y	194_S	1.524	0.95
2_F	38_V	1.509	0.94
146_M	156_G	1.509	0.94
4_G	9_V	1.496	0.94
36_D	40_E	1.496	0.94
115_I	118_K	1.488	0.94
156_G	197_L	1.473	0.93
2_F	35_Y	1.460	0.93
22_P	26_N	1.459	0.93
73_G	156_G	1.452	0.93
208_F	217_T	1.445	0.92
60_T	177_R	1.434	0.92
189_F	215_N	1.433	0.92
190_N	197_L	1.400	0.91
189_F	194_S	1.399	0.91
28_L	38_V	1.398	0.91
53_A	224_R	1.366	0.89
133_D	137_G	1.362	0.89
13_E	17_S	1.355	0.89
24_T	38_V	1.333	0.88
138_N	198_S	1.310	0.87
133_D	148_K	1.308	0.87
189_F	219_L	1.304	0.86
13_E	16_D	1.298	0.86
70_M	80_A	1.294	0.86
66_I	140_I	1.275	0.85
3_Q	47_Q	1.273	0.84
141_S	188_Y	1.264	0.84
65_G	103_P	1.258	0.83
204_T	215_N	1.250	0.83
108_Y	118_K	1.249	0.83
199_D	205_K	1.236	0.82
5_I	10_T	1.235	0.82
15_V	25_V	1.226	0.81
18_G	185_K	1.224	0.81
227_K	234_C	1.222	0.81
61_K	71_K	1.217	0.81
2_F	28_L	1.216	0.81
169_I	175_S	1.205	0.80
165_A	221_L	1.196	0.79
37_E	169_I	1.189	0.78
158_R	186_R	1.183	0.78
110_R	173_K	1.176	0.77
204_T	216_L	1.173	0.77
164_I	203_D	1.169	0.77
42_I	55_I	1.167	0.77
56_Y	61_K	1.167	0.77
64_L	185_K	1.160	0.76
180_V	184_Y	1.151	0.75
15_V	42_I	1.144	0.75
100_L	119_E	1.139	0.74
56_Y	139_I	1.136	0.74
7_Q	175_S	1.131	0.73
189_F	204_T	1.130	0.73
222_K	226_I	1.127	0.73
191_E	197_L	1.124	0.73
26_N	30_S	1.123	0.73
175_S	205_K	1.117	0.72
125_E	137_G	1.114	0.72
135_E	214_E	1.114	0.72
189_F	202_D	1.110	0.71
18_G	182_I	1.107	0.71
116_E	228_D	1.106	0.71
33_I	37_E	1.106	0.71
155_H	164_I	1.096	0.70
93_I	112_L	1.096	0.70
19_I	102_L	1.095	0.70
58_E	61_K	1.090	0.69
25_V	51_C	1.087	0.69
203_D	208_F	1.085	0.69
65_G	112_L	1.085	0.69
10_T	13_E	1.085	0.69
68_E	71_K	1.083	0.69
7_Q	10_T	1.083	0.69
189_F	196_I	1.078	0.68
222_K	235_L	1.077	0.68
10_T	16_D	1.066	0.67
86_A	89_A	1.066	0.67
76_R	213_E	1.060	0.66
109_K	115_I	1.055	0.66
165_A	216_L	1.054	0.66
184_Y	189_F	1.049	0.65
79_T	155_H	1.045	0.65
60_T	235_L	1.044	0.65
157_I	217_T	1.039	0.64
67_Y	214_E	1.038	0.64
77_P	197_L	1.037	0.64
161_E	219_L	1.035	0.64
133_D	238_L	1.033	0.63
21_R	29_E	1.014	0.61
131_Y	159_L	1.013	0.61
80_A	101_R	1.010	0.61
164_I	180_V	1.010	0.61
27_E	220_Q	1.008	0.61
115_I	132_N	1.006	0.60
90_T	147_N	1.004	0.60

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: (10May14)
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
1lm7A	2	0.9597	100	0.215	Contact Map
1lm5A	2	0.7903	100	0.349	Contact Map
2yvqA	1	0.504	12.4	0.973	Contact Map
1mrzA	2	0.3105	5.4	0.977	Contact Map
3lyvA	6	0.2339	5.4	0.977	Contact Map
3ka5A	2	0.2298	4.8	0.978	Contact Map
4gn2A	1	0.496	4.7	0.978	Contact Map
1ij5A	1	0.7661	4.6	0.978	Contact Map
3k2tA	1	0.2056	4.5	0.978	Contact Map
3ne8A	1	0.2419	4.1	0.978	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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