OPENSEQ.org - 1435841046 - GREMLIN Submission

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1MM4

ID:	1435841046	Query Sequence MNADEWMTTFRENIAQTWQQPEHYDLYIPAITWHARFAYDKEKTDRYNERPWGGGFGLSRWDEKGNWHGLYAMAFKDSWNKWEPIAGYGWESTWRPLADENFHLGLGFTAGVTARDNWNYIPLPVLLPLASVGYGPVTFQMTYIPGTYNNGNVYFAWMRFQFLEHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	170 (159)
Sequences:	178 (103.8)
Seq/Len:	1.119
Nf(neff/√len):	8.2

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: 1.119).

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
85_I	125_V	2.115	0.98
71_Y	109_T	2.035	0.97
66_N	90_W	1.973	0.96
25_D	59_S	1.823	0.93
101_N	135_G	1.812	0.93
17_T	60_R	1.775	0.92
17_T	106_L	1.726	0.90
24_Y	56_F	1.646	0.87
32_T	51_P	1.638	0.87
36_R	49_E	1.599	0.85
35_A	38_A	1.567	0.83
16_Q	20_Q	1.564	0.83
27_Y	57_G	1.559	0.83
79_W	117_N	1.547	0.82
111_G	125_V	1.506	0.80
54_G	144_I	1.494	0.79
29_P	155_F	1.459	0.77
26_L	162_F	1.452	0.76
9_T	13_N	1.446	0.76
62_D	83_E	1.428	0.75
132_V	139_F	1.416	0.74
29_P	51_P	1.387	0.72
106_L	130_A	1.382	0.71
41_K	44_T	1.382	0.71
39_Y	150_N	1.364	0.70
146_G	152_N	1.342	0.68
112_V	123_L	1.330	0.67
127_L	153_V	1.319	0.66
66_N	137_V	1.268	0.62
76_K	82_W	1.265	0.61
133_G	138_T	1.263	0.61
11_R	125_V	1.250	0.60
109_T	155_F	1.245	0.60
13_N	68_H	1.230	0.58
87_G	105_G	1.203	0.56
21_P	31_I	1.200	0.55
84_P	113_T	1.195	0.55
127_L	159_R	1.193	0.55
62_D	84_P	1.173	0.53
43_K	123_L	1.170	0.53
79_W	97_L	1.154	0.51
8_T	37_F	1.154	0.51
119_N	126_L	1.152	0.51
70_L	106_L	1.149	0.51
76_K	91_E	1.148	0.50
109_T	149_N	1.139	0.50
41_K	45_D	1.130	0.49
135_G	141_M	1.129	0.49
31_I	156_A	1.119	0.48
118_W	125_V	1.111	0.47
86_A	112_V	1.105	0.46
141_M	156_A	1.098	0.46
6_W	15_A	1.095	0.45
93_T	111_G	1.090	0.45
47_Y	146_G	1.089	0.45
56_F	63_E	1.088	0.45
30_A	118_W	1.087	0.45
71_Y	87_G	1.086	0.45
141_M	154_Y	1.083	0.44
86_A	123_L	1.077	0.44
6_W	137_V	1.075	0.43
143_Y	154_Y	1.072	0.43
105_G	153_V	1.070	0.43
72_A	86_A	1.060	0.42
120_Y	157_W	1.058	0.42
62_D	68_H	1.054	0.42
9_T	56_F	1.054	0.42
110_A	132_V	1.045	0.41
10_F	98_A	1.043	0.40
7_M	11_R	1.040	0.40
111_G	123_L	1.034	0.40
102_F	139_F	1.032	0.39
92_S	103_H	1.020	0.38
137_V	160_F	1.019	0.38
28_I	106_L	1.014	0.38
13_N	125_V	1.011	0.38
56_F	106_L	1.008	0.37
74_A	112_V	1.004	0.37
80_N	147_T	1.004	0.37
91_E	131_S	1.001	0.37

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
3gp6A	1	0.9118	100	-0.033	Contact Map
2fipA	6	0.2353	6	0.962	Contact Map
2ve3A	2	0.3059	2.7	0.968	Contact Map
4q8hA	1	0.3471	2.5	0.969	Contact Map
4txvB	2	0.5	2.3	0.969	Contact Map
2gr7A	6	0.4882	2.1	0.97	Contact Map
3emoC	3	0.5118	2	0.97	Contact Map
4p4hI	8	0.2059	2	0.97	Contact Map
1cyxA	1	0.4529	1.8	0.971	Contact Map
2gr8A	6	0.3824	1.8	0.971	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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