OPENSEQ.org - 1400605154 - GREMLIN Submission

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T0786

ID:	1400605154	Query Sequence MDTQQLYFLNDIGKQKPESIRNRSAACPFCDRENLTDILATEGSIIWLKNKFPTLKDTFQTVLIETDNCEDHIATYTEEHMRSLIRFSIKHWLNLQKNEEFTSVILYKNHGPFSGGSLHHAHMQIIGMKYVNYLDNVEQDNFQGVIVQKNEHIELNISDRPIIGFTEFNIIIEDIGCIDELANYIQQTVRYILTDFHKGCSSYNLFFYYLNEKIICKVVPRFVVSPLYVGYKIPQVSTKIEDVKIQLAAYFTKQNDAIIHKKIE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	264 (241)
Sequences:	907 (707.6)
Seq/Len:	3.763
Nf(neff/√len):	45.6

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: 3.763).

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
27_C	69_C	3.107	1.00
204_N	207_F	2.685	1.00
152_H	175_I	2.623	1.00
27_C	30_C	2.606	1.00
63_L	125_I	2.520	1.00
61_T	91_H	2.485	1.00
241_E	244_K	2.477	1.00
191_Y	195_D	2.423	1.00
190_R	194_T	2.349	1.00
43_G	46_I	2.321	1.00
30_C	69_C	2.268	1.00
82_R	86_R	2.153	1.00
245_I	249_A	2.145	1.00
68_N	71_D	2.020	1.00
138_E	213_K	1.995	1.00
208_Y	211_N	1.924	1.00
241_E	247_L	1.921	1.00
77_T	80_H	1.882	1.00
160_R	164_G	1.847	1.00
146_I	150_N	1.835	1.00
139_Q	145_V	1.751	0.99
186_Q	197_H	1.741	0.99
244_K	247_L	1.708	0.99
170_I	192_I	1.686	0.99
96_Q	104_V	1.683	0.99
128_M	231_Y	1.650	0.99
47_W	87_F	1.647	0.99
203_Y	207_F	1.596	0.98
158_S	192_I	1.582	0.98
231_Y	235_Q	1.551	0.98
65_E	108_K	1.542	0.98
73_I	81_M	1.540	0.98
146_I	149_K	1.520	0.98
23_R	32_R	1.501	0.97
91_H	125_I	1.495	0.97
145_V	148_Q	1.476	0.97
185_I	197_H	1.469	0.97
146_I	151_E	1.468	0.97
203_Y	206_F	1.468	0.97
202_S	205_L	1.417	0.96
140_D	146_I	1.409	0.96
179_D	183_N	1.407	0.96
192_I	196_F	1.387	0.95
240_I	248_A	1.373	0.95
185_I	202_S	1.372	0.95
152_H	155_L	1.354	0.94
201_S	205_L	1.349	0.94
88_S	123_M	1.335	0.94
196_F	200_C	1.325	0.93
47_W	61_T	1.321	0.93
156_N	172_I	1.315	0.93
197_H	204_N	1.310	0.93
139_Q	143_Q	1.309	0.93
198_K	201_S	1.306	0.93
185_I	207_F	1.302	0.92
158_S	170_I	1.297	0.92
92_W	106_L	1.290	0.92
33_E	36_T	1.289	0.92
229_V	232_K	1.288	0.92
48_L	64_I	1.284	0.92
196_F	202_S	1.284	0.92
81_M	190_R	1.283	0.92
185_I	204_N	1.278	0.92
44_S	83_S	1.258	0.91
201_S	204_N	1.258	0.91
198_K	202_S	1.256	0.91
197_H	200_C	1.256	0.91
180_E	183_N	1.254	0.91
193_L	205_L	1.252	0.90
196_F	199_G	1.246	0.90
76_Y	84_L	1.242	0.90
244_K	248_A	1.239	0.90
193_L	197_H	1.237	0.90
178_I	184_Y	1.237	0.90
22_N	68_N	1.237	0.90
196_F	204_N	1.233	0.90
197_H	205_L	1.231	0.89
239_K	246_Q	1.228	0.89
239_K	242_D	1.216	0.89
242_D	246_Q	1.177	0.86
49_K	59_F	1.175	0.86
139_Q	142_F	1.166	0.86
201_S	207_F	1.165	0.86
196_F	201_S	1.161	0.85
185_I	193_L	1.153	0.85
85_I	88_S	1.152	0.85
140_D	144_G	1.152	0.85
89_I	181_L	1.142	0.84
199_G	205_L	1.138	0.84
108_K	121_A	1.137	0.84
185_I	188_T	1.134	0.84
240_I	244_K	1.122	0.83
185_I	205_L	1.118	0.82
138_E	142_F	1.114	0.82
186_Q	204_N	1.087	0.80
200_C	203_Y	1.087	0.80
157_I	175_I	1.087	0.80
242_D	245_I	1.082	0.79
47_W	91_H	1.082	0.79
65_E	123_M	1.081	0.79
147_V	157_I	1.074	0.79
27_C	66_T	1.072	0.78
78_E	190_R	1.068	0.78
66_T	121_A	1.059	0.77
103_S	132_N	1.058	0.77
239_K	248_A	1.056	0.77
22_N	70_E	1.046	0.76
197_H	202_S	1.040	0.76
199_G	204_N	1.038	0.75
229_V	233_I	1.034	0.75
185_I	190_R	1.028	0.74
194_T	198_K	1.021	0.74
60_Q	114_S	1.016	0.73
29_F	64_I	1.012	0.73
110_H	116_G	1.012	0.73
63_L	123_M	1.010	0.72
108_K	123_M	1.007	0.72
187_Q	190_R	1.004	0.72

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: (10May14)
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
1gupA	4	0.9773	100	0.381	Contact Map
1z84A	2	0.928	100	0.401	Contact Map
4i5tA	2	0.9053	99.9	0.73	Contact Map
4njyA	1	0.3106	99.2	0.85	Contact Map
3o0mA	2	0.5038	99.2	0.852	Contact Map
3lb5A	4	0.4205	99	0.86	Contact Map
2eo4A	1	0.553	99	0.861	Contact Map
3o1cA	1	0.4129	99	0.862	Contact Map
3ksvA	1	0.4659	98.9	0.864	Contact Map
4incA	2	0.4015	98.9	0.865	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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