OPENSEQ.org - 1496311030 - GREMLIN Submission

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3C_nash_HHbilts

ID:	1496311030	Query Sequence GPGFDFAQAIMKKNTVVARTEKGEFTMLGVYDRVAVIPTHASVGETIYINDVETKVLDACALRDLTDTNLEITIVKLDRNQKFRDIRHFLPKYEDDYNDAVLSVHTSKFPNMYIPVGQVTNYGFLNLGGTPTHRILMYNFPTRAGQCGGVVTTTGKVIGIHVGGNGAQGFAAMLLHSYFTDTQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	183 (183)
Sequences:	199 (114.5)
Seq/Len:	1.087
Nf(neff/√len):	8.5

HHblits Results: (2016_02)
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: 1.087).

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
159_G	171_A	2.997	1.00
135_I	162_V	2.262	0.99
27_M	35_A	2.241	0.98
31_Y	87_R	2.172	0.98
152_T	171_A	1.991	0.96
6_F	89_F	1.988	0.96
18_A	27_M	1.773	0.91
31_Y	85_D	1.744	0.90
39_T	72_I	1.725	0.90
36_V	160_I	1.599	0.84
5_D	151_V	1.595	0.84
85_D	142_T	1.571	0.83
115_P	156_K	1.555	0.82
29_G	83_F	1.514	0.80
28_L	150_V	1.488	0.78
48_Y	53_E	1.482	0.78
26_T	104_V	1.441	0.75
32_D	82_K	1.429	0.74
69_N	113_Y	1.337	0.67
33_R	82_K	1.330	0.66
40_H	161_H	1.330	0.66
112_M	115_P	1.323	0.66
40_H	145_G	1.308	0.64
3_G	153_T	1.296	0.63
136_L	157_V	1.294	0.63
92_K	176_H	1.288	0.63
47_I	57_L	1.281	0.62
33_R	100_A	1.280	0.62
77_L	83_F	1.278	0.62
140_F	163_G	1.276	0.62
145_G	161_H	1.272	0.61
1_G	142_T	1.263	0.60
99_D	115_P	1.262	0.60
5_D	128_G	1.260	0.60
57_L	78_D	1.257	0.60
122_Y	175_L	1.255	0.60
161_H	164_G	1.245	0.59
46_T	55_K	1.228	0.57
11_M	103_S	1.225	0.57
55_K	65_L	1.225	0.57
4_F	112_M	1.224	0.57
111_N	170_F	1.219	0.56
84_R	141_P	1.215	0.56
25_F	29_G	1.214	0.56
40_H	138_Y	1.214	0.56
18_A	35_A	1.213	0.56
40_H	148_G	1.210	0.55
30_V	52_V	1.204	0.55
71_E	87_R	1.202	0.55
33_R	76_K	1.182	0.53
33_R	78_D	1.179	0.53
138_Y	161_H	1.178	0.52
148_G	161_H	1.174	0.52
134_R	165_N	1.174	0.52
100_A	153_T	1.160	0.51
138_Y	145_G	1.155	0.50
106_T	111_N	1.154	0.50
145_G	148_G	1.151	0.50
47_I	56_V	1.133	0.48
47_I	172_A	1.129	0.48
56_V	62_L	1.128	0.48
30_V	176_H	1.116	0.47
49_I	92_K	1.114	0.46
25_F	38_P	1.114	0.46
127_L	166_G	1.103	0.45
142_T	146_Q	1.100	0.45
151_V	171_A	1.096	0.45
72_I	133_H	1.095	0.45
54_T	80_N	1.093	0.44
75_V	92_K	1.088	0.44
148_G	159_G	1.066	0.42
122_Y	133_H	1.059	0.41
138_Y	148_G	1.050	0.40
64_D	67_D	1.047	0.40
49_I	108_K	1.041	0.40
101_V	115_P	1.037	0.39
38_P	162_V	1.035	0.39
41_A	175_L	1.035	0.39
89_F	128_G	1.031	0.39
89_F	121_N	1.031	0.39
8_Q	63_R	1.030	0.39
14_N	160_I	1.028	0.38
3_G	63_R	1.028	0.38
47_I	62_L	1.027	0.38
36_V	174_L	1.026	0.38
66_T	98_N	1.017	0.37
122_Y	125_L	1.015	0.37
123_G	127_L	1.012	0.37
136_L	175_L	1.007	0.37
90_L	178_Y	1.004	0.36
123_G	172_A	1.003	0.36
11_M	115_P	1.001	0.36
63_R	115_P	1.001	0.36

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
3q3yA	2	0.9836	100	0.119	Contact Map
3qzrA	2	0.9836	100	0.144	Contact Map
1cqqA	1	0.9836	100	0.144	Contact Map
2b0fA	1	0.9945	100	0.163	Contact Map
3zveA	1	1	100	0.167	Contact Map
2ijd1	2	1	100	0.188	Contact Map
4dcdA	1	0.9836	100	0.217	Contact Map
2bhgA	2	0.9454	100	0.277	Contact Map
2halA	1	0.9617	100	0.364	Contact Map
1lvmA	2	0.9344	99.3	0.742	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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