OPENSEQ.org - 1399347233 - GREMLIN Submission

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4m5b

ID:	1399347233	Query Sequence MHIPEGYLSPQTCAVMGAAMVPVLTVAAKKVNKSFDKKDVPAMAIGSAFAFTIMMFNVPIPGGTTAHAIGATLLATTLGPWAASISLTLALFIQALLFGDGGILALGANSFNMAFIAPFVGYGIYRLMLSLKLNKVLSSAIGGYVGINAAALATAIELGLQPLLFHTANGTPLYFPYGLNVAIPAMMFAHLTVAGIVEAVITGLVVYYLLEHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	217 (208)
Sequences:	705 (498.6)
Seq/Len:	3.389
Nf(neff/√len):	34.6

HHblits Results: (2013_03)
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: 3.389).

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
140_A	199_A	3.913	1.00
112_N	157_E	3.300	1.00
20_M	111_F	2.975	1.00
88_T	110_S	2.624	1.00
139_S	203_G	2.066	1.00
24_L	88_T	1.951	1.00
116_I	153_A	1.897	1.00
74_L	83_A	1.846	0.99
20_M	24_L	1.812	0.99
16_M	111_F	1.798	0.99
120_V	149_A	1.766	0.99
50_A	74_L	1.714	0.99
24_L	110_S	1.701	0.99
196_I	200_V	1.689	0.99
47_S	86_S	1.687	0.99
31_V	85_I	1.647	0.98
87_L	114_A	1.591	0.98
75_A	123_G	1.586	0.98
10_P	14_A	1.563	0.98
13_C	17_G	1.554	0.97
14_A	18_A	1.534	0.97
29_K	33_K	1.473	0.96
57_N	100_D	1.470	0.96
20_M	121_G	1.469	0.96
188_F	192_T	1.460	0.96
20_M	28_A	1.451	0.96
73_L	205_V	1.446	0.96
147_I	158_L	1.434	0.95
81_W	119_F	1.410	0.95
64_T	185_A	1.407	0.95
15_V	18_A	1.379	0.94
17_G	103_I	1.349	0.93
53_I	68_A	1.347	0.93
66_A	190_H	1.335	0.92
16_M	108_A	1.321	0.92
20_M	110_S	1.321	0.92
66_A	193_V	1.318	0.92
66_A	150_A	1.309	0.91
69_I	117_A	1.304	0.91
21_V	24_L	1.303	0.91
48_A	200_V	1.301	0.91
152_L	156_I	1.281	0.90
9_S	12_T	1.244	0.88
28_A	45_I	1.243	0.88
197_V	201_I	1.221	0.87
129_L	137_L	1.204	0.86
28_A	96_L	1.200	0.86
146_G	205_V	1.196	0.86
60_I	98_F	1.194	0.85
17_G	114_A	1.189	0.85
92_F	106_L	1.188	0.85
17_G	21_V	1.176	0.84
114_A	118_P	1.174	0.84
123_G	127_L	1.158	0.83
126_R	129_L	1.152	0.82
71_A	121_G	1.151	0.82
14_A	120_V	1.145	0.82
46_G	77_T	1.144	0.82
144_Y	191_L	1.140	0.82
50_A	83_A	1.136	0.81
26_V	30_K	1.127	0.81
66_A	105_A	1.127	0.81
148_N	187_M	1.116	0.80
111_F	116_I	1.110	0.79
189_A	193_V	1.109	0.79
116_I	149_A	1.108	0.79
122_Y	125_Y	1.104	0.79
57_N	190_H	1.096	0.78
54_M	100_D	1.094	0.78
72_T	140_A	1.082	0.77
63_G	70_G	1.081	0.77
180_N	184_P	1.078	0.76
7_Y	64_T	1.077	0.76
140_A	203_G	1.063	0.75
82_A	119_F	1.062	0.75
76_T	125_Y	1.061	0.75
190_H	195_G	1.060	0.75
146_G	150_A	1.060	0.75
155_A	158_L	1.055	0.74
184_P	187_M	1.050	0.74
100_D	186_M	1.041	0.73
106_L	110_S	1.040	0.73
46_G	74_L	1.039	0.72
14_A	58_V	1.039	0.72
23_V	115_F	1.038	0.72
83_A	118_P	1.034	0.72
200_V	204_L	1.031	0.72
50_A	71_A	1.027	0.71
5_E	113_M	1.026	0.71
26_V	81_W	1.026	0.71
11_Q	14_A	1.026	0.71
32_N	36_D	1.024	0.71
154_T	158_L	1.024	0.71
4_P	7_Y	1.022	0.71
76_T	122_Y	1.018	0.70
108_A	121_G	1.010	0.69
161_Q	164_L	1.001	0.68

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: (01May14)
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
4m5bA	1	0.9862	100	0.166	Contact Map
4hzuS	1	0.7281	98.2	0.85	Contact Map
4huqS	1	0.7327	98.2	0.851	Contact Map
3p5nA	2	0.7465	97.3	0.877	Contact Map
3rlbA	2	0.7604	97.1	0.882	Contact Map
4dveA	3	0.7972	97	0.882	Contact Map
1u7gA	1	0.5115	19.8	0.952	Contact Map
1pi7A	1	0.0876	4.4	0.965	Contact Map
3jroA	1	0.2673	3.2	0.967	Contact Map
2ifoA	1	0.1567	2.9	0.968	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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