OPENSEQ.org - 1401993600 - GREMLIN Submission

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T0806

ID:	1401993600	Query Sequence MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINAARFHDWQPDFTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRFIIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	258 (256)
Sequences:	1178 (858.9)
Seq/Len:	4.602
Nf(neff/√len):	53.7

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: 4.602).

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
30_N	150_I	4.159	1.00
52_I	56_L	3.571	1.00
142_D	145_Q	2.845	1.00
17_L	77_R	2.824	1.00
60_N	63_R	2.739	1.00
100_D	223_R	2.733	1.00
47_S	54_D	2.579	1.00
241_D	244_S	2.565	1.00
81_L	101_F	2.466	1.00
4_L	167_V	2.449	1.00
168_I	219_I	2.448	1.00
92_Q	95_T	2.387	1.00
100_D	221_E	2.384	1.00
149_D	153_N	2.364	1.00
241_D	253_K	2.158	1.00
104_A	220_I	2.101	1.00
187_E	248_G	2.082	1.00
10_T	84_K	2.080	1.00
228_E	231_T	2.060	1.00
3_I	219_I	2.032	1.00
151_I	178_S	2.032	1.00
217_R	221_E	1.960	1.00
96_F	217_R	1.935	1.00
226_K	229_Q	1.911	1.00
244_S	253_K	1.900	1.00
13_Y	82_A	1.868	1.00
109_R	158_A	1.835	1.00
59_I	63_R	1.826	1.00
61_A	65_H	1.818	1.00
137_N	140_G	1.798	1.00
194_L	253_K	1.794	1.00
15_S	77_R	1.756	1.00
246_S	249_E	1.716	0.99
38_A	64_F	1.708	0.99
96_F	101_F	1.693	0.99
168_I	230_L	1.653	0.99
31_S	67_W	1.632	0.99
196_E	255_Y	1.630	0.99
96_F	104_A	1.623	0.99
231_T	250_L	1.619	0.99
18_T	81_L	1.615	0.99
5_I	108_L	1.608	0.99
5_I	216_S	1.595	0.99
192_V	249_E	1.560	0.99
219_I	230_L	1.558	0.99
141_K	145_Q	1.553	0.99
151_I	179_V	1.545	0.99
5_I	87_V	1.538	0.99
26_E	154_K	1.533	0.98
227_P	250_L	1.532	0.98
58_G	62_A	1.523	0.98
214_L	236_E	1.514	0.98
219_I	224_L	1.510	0.98
46_I	52_I	1.502	0.98
103_F	107_H	1.502	0.98
105_Q	121_L	1.500	0.98
168_I	191_P	1.491	0.98
8_A	11_L	1.482	0.98
97_S	100_D	1.479	0.98
37_E	135_L	1.472	0.98
26_E	158_A	1.470	0.98
52_I	57_A	1.466	0.98
224_L	229_Q	1.459	0.98
100_D	220_I	1.449	0.98
76_A	123_L	1.446	0.98
31_S	146_F	1.435	0.97
34_L	137_N	1.411	0.97
81_L	96_F	1.399	0.97
104_A	216_S	1.390	0.97
191_P	250_L	1.370	0.96
80_I	91_L	1.361	0.96
103_F	220_I	1.337	0.96
96_F	100_D	1.335	0.96
195_D	205_S	1.333	0.96
96_F	221_E	1.330	0.95
221_E	235_S	1.328	0.95
47_S	52_I	1.328	0.95
4_L	155_L	1.323	0.95
47_S	57_A	1.295	0.95
240_F	250_L	1.294	0.95
86_D	206_F	1.284	0.94
216_S	220_I	1.272	0.94
75_N	125_Q	1.249	0.93
99_D	223_R	1.246	0.93
84_K	94_E	1.246	0.93
35_I	114_L	1.234	0.92
166_V	187_E	1.233	0.92
166_V	227_P	1.229	0.92
27_L	154_K	1.227	0.92
207_Y	254_R	1.221	0.92
62_A	66_D	1.221	0.92
35_I	46_I	1.216	0.92
13_Y	124_M	1.195	0.91
229_Q	232_G	1.193	0.91
31_S	35_I	1.184	0.90
37_E	41_L	1.175	0.90
30_N	139_R	1.172	0.90
43_P	61_A	1.169	0.90
93_A	96_F	1.168	0.90
192_V	203_I	1.158	0.89
103_F	224_L	1.153	0.89
201_F	253_K	1.139	0.88
38_A	41_L	1.134	0.88
148_G	180_K	1.120	0.87
225_T	229_Q	1.109	0.86
28_L	70_D	1.092	0.85
159_L	186_A	1.091	0.85
71_F	75_N	1.088	0.85
144_Y	177_K	1.087	0.84
12_D	84_K	1.084	0.84
190_K	249_E	1.069	0.83
72_T	75_N	1.064	0.83
93_A	217_R	1.062	0.83
195_D	254_R	1.053	0.82
239_F	255_Y	1.050	0.82
154_K	157_E	1.049	0.81
149_D	180_K	1.048	0.81
10_T	89_T	1.043	0.81
117_V	154_K	1.038	0.81
2_L	165_N	1.029	0.80
153_N	183_K	1.014	0.78
37_E	137_N	1.011	0.78

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: (29May14)
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
4a1qA	2	0.2597	10.1	0.973	Contact Map
3eyiA	2	0.2403	9.9	0.973	Contact Map
2kyaA	1	0.1318	5.8	0.975	Contact Map
2vqeB	1	0.4729	5.6	0.976	Contact Map
1wrdA	1	0.2636	5.3	0.976	Contact Map
3bbnB	1	0.4922	5.2	0.976	Contact Map
2ddhA	1	0.4147	4.8	0.976	Contact Map
4kiyB	1	0.4574	4.6	0.977	Contact Map
1wy3A	1	0.1318	4.6	0.977	Contact Map
3arcU	2	0.3527	4.3	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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