OPENSEQ.org - 1412126327 - GREMLIN Submission

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4DUR_A 540-791

ID:	1412126327	Query Sequence QCAAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	252 (244)
Sequences:	14123 (9880)
Seq/Len:	57.881
Nf(neff/√len):	632.5

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: 57.881).

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
141_C	208_C	5.610	1.00
51_G	59_V	3.482	1.00
39_S	47_H	3.265	1.00
58_W	110_L	3.165	1.00
37_Q	144_T	2.965	1.00
33_S	160_E	2.944	1.00
28_V	159_K	2.779	1.00
49_C	65_C	2.756	1.00
97_S	112_K	2.730	1.00
53_L	117_A	2.712	1.00
64_H	202_S	2.617	1.00
34_W	160_E	2.601	1.00
79_L	117_A	2.581	1.00
60_L	216_L	2.580	1.00
66_L	109_A	2.511	1.00
198_C	226_C	2.416	1.00
106_K	241_F	2.396	1.00
52_T	216_L	2.356	1.00
95_E	114_S	2.308	1.00
103_P	248_V	2.236	1.00
196_D	233_G	2.224	1.00
58_W	112_K	2.163	1.00
161_A	195_T	2.146	1.00
98_R	112_K	2.050	1.00
57_E	116_P	2.046	1.00
96_V	111_L	2.041	1.00
57_E	112_K	1.978	1.00
38_V	79_L	1.977	1.00
171_C	187_C	1.971	1.00
41_R	47_H	1.950	1.00
38_V	51_G	1.944	1.00
113_L	117_A	1.943	1.00
222_W	234_V	1.936	1.00
105_R	184_T	1.911	1.00
144_T	207_V	1.848	1.00
34_W	144_T	1.840	1.00
119_I	125_P	1.811	1.00
100_F	248_V	1.779	1.00
143_I	161_A	1.759	1.00
78_I	93_E	1.746	1.00
52_T	126_A	1.734	1.00
143_I	197_S	1.725	1.00
108_I	241_F	1.712	1.00
94_I	117_A	1.686	1.00
184_T	240_R	1.677	1.00
186_L	206_L	1.674	1.00
164_P	189_G	1.671	1.00
52_T	219_V	1.663	1.00
141_C	165_V	1.647	1.00
56_P	116_P	1.627	1.00
94_I	114_S	1.618	1.00
28_V	157_L	1.606	1.00
55_S	58_W	1.600	1.00
126_A	216_L	1.596	1.00
155_A	159_K	1.574	1.00
242_V	246_E	1.571	1.00
81_A	91_V	1.569	1.00
97_S	114_S	1.529	1.00
61_T	66_L	1.512	1.00
9_C	127_C	1.501	1.00
126_A	207_V	1.466	1.00
38_V	59_V	1.462	1.00
28_V	82_H	1.453	1.00
36_W	127_C	1.436	1.00
29_A	34_W	1.426	1.00
32_H	82_H	1.416	1.00
197_S	220_T	1.416	1.00
220_T	223_G	1.411	1.00
105_R	182_Q	1.401	0.99
37_Q	158_L	1.387	0.99
168_N	237_R	1.360	0.99
23_V	26_G	1.359	0.99
236_V	241_F	1.350	0.99
10_G	127_C	1.336	0.99
83_Q	156_G	1.332	0.99
167_E	170_V	1.329	0.99
53_L	79_L	1.298	0.99
85_V	156_G	1.296	0.99
143_I	163_L	1.295	0.99
141_C	217_Q	1.290	0.99
196_D	235_Y	1.284	0.99
143_I	220_T	1.279	0.99
79_L	123_V	1.267	0.99
102_E	106_K	1.253	0.99
185_E	222_W	1.248	0.99
106_K	184_T	1.235	0.98
36_W	207_V	1.235	0.98
141_C	206_L	1.229	0.98
172_N	179_G	1.228	0.98
129_P	242_V	1.212	0.98
137_D	167_E	1.211	0.98
36_W	214_Y	1.205	0.98
237_R	240_R	1.202	0.98
40_L	77_V	1.192	0.98
208_C	217_Q	1.190	0.98
78_I	81_A	1.185	0.98
108_I	236_V	1.174	0.98
76_K	93_E	1.170	0.97
29_A	160_E	1.162	0.97
37_Q	50_G	1.154	0.97
164_P	190_H	1.130	0.97
184_T	241_F	1.128	0.97
128_L	242_V	1.128	0.97
32_H	122_K	1.122	0.97
92_Q	123_V	1.120	0.96
94_I	115_S	1.118	0.96
31_P	82_H	1.111	0.96
66_L	101_L	1.107	0.96
188_A	206_L	1.107	0.96
53_L	113_L	1.099	0.96
149_T	159_K	1.098	0.96
140_E	162_Q	1.098	0.96
206_L	235_Y	1.095	0.96
59_V	77_V	1.083	0.96
52_T	60_L	1.071	0.95
53_L	119_I	1.065	0.95
83_Q	157_L	1.063	0.95
166_I	232_P	1.058	0.95
62_A	219_V	1.054	0.95
34_W	214_Y	1.032	0.94
168_N	181_V	1.029	0.94
38_V	77_V	1.023	0.93
64_H	107_D	1.022	0.93
58_W	100_F	1.019	0.93
142_F	162_Q	1.011	0.93

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: (06Sep14)
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
4durA	2	0.9881	100	0.034	Contact Map
1ddjA	4	0.9802	100	0.094	Contact Map
4igdA	1	0.9563	100	0.108	Contact Map
3nxpA	1	0.9841	100	0.108	Contact Map
2f83A	1	0.881	100	0.109	Contact Map
4nzqA	1	0.9921	100	0.111	Contact Map
4kkdA	2	0.9921	100	0.114	Contact Map
4f4oC	4	0.9127	100	0.124	Contact Map
2xxlA	2	0.9603	100	0.124	Contact Map
2b9lA	1	0.9841	100	0.128	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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