OPENSEQ.org - 1435359153 - GREMLIN Submission

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2KSY

ID:	1435359153	Query Sequence MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYAVMALGVGWVPVAERTVFVPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGESLAGVDTDTPAVADLEHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	247 (218)
Sequences:	361 (289.5)
Seq/Len:	1.656
Nf(neff/√len):	19.6

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: 1.656).

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
46_I	78_L	4.438	1.00
14_G	202_L	2.553	1.00
75_D	205_K	2.324	1.00
9_W	55_A	2.254	0.99
80_T	105_N	2.132	0.99
22_F	209_G	1.989	0.98
79_T	82_L	1.906	0.98
53_V	126_L	1.756	0.96
50_A	54_M	1.734	0.95
19_T	44_S	1.733	0.95
75_D	79_T	1.640	0.93
47_A	75_D	1.579	0.91
47_A	83_I	1.554	0.90
111_A	204_T	1.522	0.89
76_W	174_Y	1.487	0.87
105_N	108_V	1.486	0.87
80_T	205_K	1.459	0.86
60_W	69_F	1.449	0.86
79_T	205_K	1.427	0.84
79_T	112_G	1.416	0.84
108_V	112_G	1.396	0.83
50_A	116_A	1.396	0.83
183_P	193_D	1.391	0.82
107_V	133_A	1.390	0.82
73_Y	81_P	1.389	0.82
18_G	206_V	1.389	0.82
112_G	205_K	1.365	0.81
171_W	205_K	1.361	0.80
178_W	200_L	1.347	0.79
16_L	48_A	1.344	0.79
40_L	209_G	1.339	0.79
17_V	202_L	1.297	0.76
20_L	23_A	1.290	0.75
40_L	86_F	1.289	0.75
153_S	157_K	1.263	0.73
18_G	210_F	1.257	0.72
43_I	50_A	1.255	0.72
47_A	205_K	1.253	0.72
105_N	109_M	1.252	0.72
11_G	106_T	1.238	0.71
51_Y	82_L	1.236	0.71
11_G	15_M	1.234	0.70
178_W	184_G	1.234	0.70
76_W	81_P	1.231	0.70
77_I	106_T	1.230	0.70
12_A	52_A	1.222	0.69
20_L	45_G	1.215	0.69
37_Y	94_D	1.206	0.68
75_D	80_T	1.197	0.67
61_V	117_M	1.192	0.67
84_V	128_G	1.187	0.66
80_T	108_V	1.176	0.65
109_M	205_K	1.172	0.65
39_T	75_D	1.171	0.65
47_A	82_L	1.169	0.64
112_G	208_F	1.168	0.64
11_G	206_V	1.167	0.64
23_A	41_V	1.164	0.64
16_L	45_G	1.161	0.64
79_T	204_T	1.158	0.63
178_W	193_D	1.158	0.63
87_L	146_T	1.154	0.63
67_T	190_P	1.151	0.63
47_A	80_T	1.144	0.62
45_G	49_V	1.144	0.62
75_D	82_L	1.143	0.62
70_V	74_I	1.132	0.61
43_I	178_W	1.120	0.59
54_M	72_R	1.120	0.59
188_L	195_A	1.118	0.59
43_I	79_T	1.117	0.59
42_G	132_V	1.115	0.59
76_W	112_G	1.113	0.59
43_I	82_L	1.113	0.59
75_D	204_T	1.112	0.59
60_W	67_T	1.112	0.59
40_L	156_I	1.110	0.58
47_A	171_W	1.107	0.58
43_I	208_F	1.101	0.57
14_G	206_V	1.097	0.57
28_D	147_E	1.087	0.56
48_A	52_A	1.075	0.55
188_L	192_V	1.072	0.54
179_L	185_V	1.072	0.54
115_G	178_W	1.068	0.54
44_S	209_G	1.066	0.54
80_T	170_L	1.060	0.53
43_I	204_T	1.058	0.53
130_G	133_A	1.055	0.53
111_A	129_M	1.054	0.53
39_T	82_L	1.053	0.52
8_F	135_I	1.052	0.52
20_L	36_Y	1.052	0.52
47_A	54_M	1.051	0.52
68_V	137_L	1.049	0.52
80_T	200_L	1.047	0.52
47_A	108_V	1.041	0.51
135_I	176_F	1.039	0.51
123_R	184_G	1.038	0.51
22_F	44_S	1.036	0.51
44_S	206_V	1.035	0.51
88_G	94_D	1.030	0.50
82_L	112_G	1.029	0.50
87_L	163_L	1.029	0.50
47_A	105_N	1.028	0.50
122_E	186_A	1.027	0.50
40_L	137_L	1.023	0.49
165_N	169_V	1.021	0.49
47_A	141_L	1.021	0.49
102_I	173_I	1.017	0.49
80_T	112_G	1.016	0.49
107_V	129_M	1.011	0.48
56_L	67_T	1.006	0.47
142_V	168_V	1.004	0.47

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: (31Jan15)
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
3qapA	1	0.8866	100	0.12	Contact Map
1xioA	1	0.8583	100	0.155	Contact Map
4l35A	1	0.9271	100	0.182	Contact Map
3wqjA	1	0.8826	100	0.183	Contact Map
4fbzA	1	0.919	100	0.188	Contact Map
1m0kA	1	0.8664	100	0.188	Contact Map
3qbgA	3	0.9109	100	0.242	Contact Map
2jafA	1	0.9069	100	0.242	Contact Map
3am6A	4	0.8785	100	0.245	Contact Map
3ddlA	2	0.9069	100	0.25	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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