OPENSEQ.org - 1436223774 - GREMLIN Submission

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brca1_pfam300-500 40-210

ID:	1436223774	Query Sequence VDLNADPLCERKEWNKQKLPCSENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKRKRRPTS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	171 (171)
Sequences:	276 (131.7)
Seq/Len:	1.614
Nf(neff/√len):	10.1

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: 1.614).

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
118_E	127_R	3.557	1.00
23_E	28_T	3.239	1.00
23_E	68_A	1.970	0.98
32_P	71_A	1.907	0.98
68_A	74_L	1.850	0.97
58_D	63_E	1.748	0.95
83_Y	168_R	1.695	0.94
93_L	109_H	1.589	0.91
22_S	51_D	1.586	0.91
52_E	56_S	1.552	0.90
52_E	55_G	1.532	0.89
36_L	50_S	1.525	0.89
94_A	116_N	1.513	0.88
102_I	136_S	1.512	0.88
68_A	104_K	1.493	0.87
91_D	94_A	1.432	0.84
112_S	162_K	1.430	0.84
23_E	74_L	1.414	0.83
50_S	91_D	1.408	0.83
105_S	114_E	1.384	0.81
78_N	113_V	1.362	0.80
68_A	87_S	1.348	0.79
100_A	124_K	1.344	0.78
25_P	64_S	1.341	0.78
133_P	158_P	1.298	0.75
65_E	158_P	1.293	0.75
70_V	134_N	1.292	0.75
36_L	63_E	1.287	0.74
75_D	118_E	1.278	0.73
2_D	23_E	1.260	0.72
112_S	139_T	1.260	0.72
101_L	116_N	1.254	0.71
66_S	86_S	1.250	0.71
79_E	83_Y	1.236	0.70
4_N	9_C	1.231	0.69
2_D	28_T	1.228	0.69
141_N	155_Q	1.207	0.67
127_R	130_A	1.195	0.66
104_K	138_V	1.182	0.65
104_K	147_F	1.175	0.64
144_I	150_E	1.174	0.64
49_R	67_N	1.171	0.64
45_E	148_V	1.170	0.64
157_R	169_P	1.156	0.62
107_R	114_E	1.147	0.61
34_I	37_N	1.137	0.60
87_S	96_D	1.133	0.60
44_N	47_F	1.131	0.60
51_D	60_H	1.125	0.59
47_F	66_S	1.113	0.58
36_L	91_D	1.108	0.57
50_S	58_D	1.105	0.57
153_I	156_E	1.100	0.57
36_L	87_S	1.097	0.56
47_F	154_I	1.097	0.56
157_R	161_N	1.075	0.54
107_R	124_K	1.074	0.54
91_D	135_L	1.062	0.53
14_W	93_L	1.061	0.53
49_R	89_K	1.060	0.52
29_E	37_N	1.060	0.52
54_L	57_D	1.057	0.52
99_E	143_I	1.057	0.52
13_E	25_P	1.056	0.52
47_F	61_D	1.056	0.52
9_C	36_L	1.056	0.52
63_E	91_D	1.049	0.51
156_E	161_N	1.043	0.51
14_W	56_S	1.043	0.51
124_K	164_K	1.043	0.51
138_V	156_E	1.039	0.50
93_L	121_I	1.034	0.50
12_K	24_N	1.028	0.49
41_Q	114_E	1.024	0.49
28_T	118_E	1.023	0.49
28_T	68_A	1.023	0.49
28_T	149_T	1.019	0.48
111_K	165_R	1.015	0.48
11_R	86_S	1.014	0.48
25_P	54_L	1.012	0.47
24_N	99_E	1.012	0.47
28_T	147_F	1.011	0.47
10_E	109_H	1.010	0.47
77_L	102_I	1.005	0.47
23_E	36_L	1.004	0.47
20_P	146_A	1.004	0.47

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
1xdtR	1	0	4.5	0.971	Contact Map
3cmqA	1	0.3041	3.1	0.973	Contact Map
3kpeB	1	0.2047	2.8	0.974	Contact Map
4nf9C	2	0	2.5	0.974	Contact Map
2eqgA	1	0.1345	2.4	0.974	Contact Map
3j7aV	1	0.3216	2.4	0.975	Contact Map
4af3D	1	0.2398	2	0.975	Contact Map
2mblA	1	0.345	1.9	0.976	Contact Map
3j80L	1	0.386	1.7	0.976	Contact Map
4bg7A	2	0.3041	1.6	0.977	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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