OPENSEQ.org - 1517593014 - GREMLIN Submission

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RatApobecStart

ID:	1517593014	Query Sequence HEFEVFFDPRELRKETCLLYEINWGGRHSIWRHTSQNTNKHVEVNFIEKFTTERYFCPNTRCSITWFLSWSPCGECSRAITEFLSRYPHVTLFIYIARLYHHADPRNRQGLRDLISSGVTIQIMTEQESGYCWRNFVNYSPSNEAHWPRYPHLWVRLYVLELYCI	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	165 (149)
Sequences:	267 (150.1)
Seq/Len:	1.792
Nf(neff/√len):	12.3

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: 1.792).

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
3_F	7_F	2.618	1.00
3_F	9_P	2.383	1.00
144_E	147_W	2.317	1.00
90_V	97_A	1.853	0.97
69_S	84_L	1.794	0.97
3_F	37_N	1.731	0.96
66_W	69_S	1.534	0.91
97_A	129_S	1.531	0.91
19_L	22_I	1.463	0.88
83_F	132_C	1.443	0.87
7_F	37_N	1.431	0.86
47_I	69_S	1.382	0.83
64_I	77_S	1.374	0.83
145_A	148_P	1.363	0.82
47_I	67_F	1.331	0.80
47_I	119_V	1.329	0.80
40_K	48_E	1.324	0.80
73_C	98_R	1.309	0.79
19_L	144_E	1.301	0.78
66_W	92_L	1.298	0.78
73_C	76_C	1.293	0.77
17_C	93_F	1.273	0.76
3_F	6_F	1.273	0.76
16_T	20_Y	1.256	0.75
5_V	12_L	1.239	0.73
111_L	124_M	1.232	0.72
131_Y	135_N	1.229	0.72
144_E	149_R	1.229	0.72
111_L	114_L	1.226	0.72
13_R	98_R	1.225	0.72
21_E	128_E	1.221	0.72
70_W	100_Y	1.217	0.71
143_N	148_P	1.217	0.71
6_F	12_L	1.215	0.71
89_H	96_I	1.215	0.71
131_Y	141_P	1.204	0.70
87_Y	125_T	1.201	0.70
143_N	146_H	1.201	0.70
73_C	114_L	1.198	0.69
46_F	99_L	1.197	0.69
63_S	93_F	1.195	0.69
33_H	62_C	1.174	0.67
114_L	124_M	1.165	0.66
85_S	93_F	1.160	0.66
142_S	145_A	1.149	0.65
144_E	148_P	1.123	0.62
38_T	66_W	1.122	0.62
78_R	130_G	1.117	0.62
63_S	121_I	1.111	0.61
107_N	138_N	1.109	0.61
144_E	150_Y	1.108	0.61
22_I	84_L	1.106	0.60
129_S	146_H	1.101	0.60
47_I	65_T	1.101	0.60
18_L	137_V	1.100	0.60
73_C	124_M	1.098	0.60
18_L	22_I	1.097	0.59
68_L	96_I	1.093	0.59
5_V	8_D	1.089	0.59
20_Y	57_C	1.089	0.59
19_L	35_S	1.081	0.58
94_I	132_C	1.080	0.58
46_F	133_W	1.078	0.57
41_H	76_C	1.074	0.57
22_I	64_I	1.073	0.57
16_T	91_T	1.072	0.57
33_H	126_E	1.069	0.57
4_E	8_D	1.066	0.56
55_Y	97_A	1.065	0.56
17_C	51_T	1.058	0.55
66_W	94_I	1.051	0.55
48_E	66_W	1.045	0.54
16_T	19_L	1.043	0.54
142_S	146_H	1.040	0.53
142_S	148_P	1.034	0.53
52_T	68_L	1.033	0.53
64_I	71_S	1.033	0.53
66_W	80_I	1.032	0.53
23_N	88_P	1.025	0.52
70_W	83_F	1.021	0.51
66_W	105_P	1.020	0.51
12_L	15_E	1.017	0.51
80_I	97_A	1.005	0.50
23_N	28_H	1.002	0.49

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

See coupling matrix (for protein design or mutagenesis)
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
4j4jA	2	0.9879	100	0.157	Contact Map
3v4kA	2	0.9818	100	0.163	Contact Map
3vowA	2	0.9879	100	0.174	Contact Map
4xxoA	2	0	100	0.18	Contact Map
2mzzA	1	0	100	0.186	Contact Map
2nytA	4	0.9818	100	0.572	Contact Map
4p9cA	12	0.6242	97.9	0.874	Contact Map
2hvwA	3	0.703	97	0.893	Contact Map
1vq2A	1	0.7636	96.5	0.899	Contact Map
3g8qA	4	0.7636	95.2	0.909	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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