OPENSEQ.org - 1412290735 - GREMLIN Submission

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1KN0_A -force run

ID:	1412290735	Query Sequence MSGTEEAILGGRDSHPAAGGGSVLCFGQCQYTAEEYQAIQKALRQRLGPEYISSRMAGGGQKVCYIEGHRVINLANEMFGYNGWAHSITQQNVDFVDLNNGKFYVGVCAFVRVQLKDGSYHEDVGYGVSEGLKSKALSLEKARKEAVTDGLKRALRSFGNALGNCILDKDYLRSLNKLPRQLPLEVDLTKAKRQDLEPSVEEARYNSCRPNM	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (196)
Sequences:	182 (120.6)
Seq/Len:	0.929
Nf(neff/√len):	8.6

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: 0.929).

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
109_A	147_V	2.714	1.00
82_N	117_D	2.556	0.99
106_G	126_Y	2.180	0.97
68_G	146_A	2.108	0.96
31_Y	35_E	1.991	0.95
68_G	148_T	1.964	0.94
109_A	146_A	1.879	0.92
141_K	145_E	1.835	0.91
77_E	97_D	1.824	0.91
39_I	157_S	1.632	0.83
156_R	167_L	1.622	0.82
57_A	63_V	1.591	0.80
72_I	151_L	1.569	0.79
148_T	165_C	1.524	0.76
124_V	139_L	1.496	0.74
40_Q	78_M	1.494	0.74
66_I	166_I	1.483	0.74
49_P	165_C	1.474	0.73
66_I	204_R	1.452	0.71
141_K	148_T	1.435	0.70
51_Y	114_Q	1.428	0.69
107_V	129_S	1.426	0.69
66_I	71_V	1.423	0.69
48_G	165_C	1.405	0.68
47_L	148_T	1.368	0.65
94_D	126_Y	1.359	0.64
129_S	132_L	1.358	0.64
104_Y	107_V	1.344	0.63
47_L	168_D	1.336	0.62
97_D	135_K	1.323	0.61
97_D	106_G	1.305	0.59
200_V	203_A	1.291	0.58
58_G	132_L	1.276	0.57
48_G	148_T	1.248	0.54
136_A	151_L	1.246	0.54
40_Q	62_K	1.237	0.53
141_K	165_C	1.237	0.53
141_K	171_Y	1.236	0.53
145_E	160_N	1.235	0.53
94_D	97_D	1.225	0.52
47_L	165_C	1.224	0.52
111_V	145_E	1.218	0.51
66_I	197_E	1.212	0.51
111_V	150_G	1.212	0.51
86_H	138_S	1.208	0.51
92_N	105_V	1.206	0.50
71_V	99_N	1.201	0.50
31_Y	93_V	1.199	0.50
94_D	106_G	1.173	0.47
73_N	156_R	1.171	0.47
107_V	132_L	1.149	0.45
113_V	187_D	1.145	0.45
106_G	162_L	1.145	0.45
170_D	173_R	1.144	0.45
102_K	140_E	1.141	0.44
129_S	142_A	1.136	0.44
72_I	154_A	1.122	0.43
49_P	148_T	1.121	0.43
87_S	178_L	1.116	0.42
90_Q	142_A	1.114	0.42
54_S	64_C	1.112	0.42
39_I	180_R	1.110	0.42
33_A	38_A	1.108	0.42
50_E	193_R	1.104	0.41
105_V	132_L	1.102	0.41
103_F	173_R	1.100	0.41
52_I	175_L	1.094	0.40
164_N	167_L	1.094	0.40
91_Q	109_A	1.088	0.40
64_C	142_A	1.086	0.40
103_F	134_S	1.081	0.39
178_L	188_L	1.078	0.39
75_A	155_L	1.076	0.39
81_Y	132_L	1.064	0.38
78_M	176_N	1.063	0.38
195_D	198_P	1.057	0.37
50_E	165_C	1.055	0.37
57_A	143_R	1.055	0.37
107_V	139_L	1.053	0.37
32_T	77_E	1.051	0.37
74_L	130_E	1.044	0.36
27_G	116_K	1.044	0.36
199_S	202_E	1.041	0.36
106_G	135_K	1.040	0.36
70_R	177_K	1.027	0.35
65_Y	153_R	1.025	0.34
123_D	168_D	1.023	0.34
33_A	36_Y	1.017	0.34
123_D	163_G	1.012	0.33
63_V	119_S	1.010	0.33
89_T	98_L	1.006	0.33
159_G	163_G	1.003	0.33

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
1h2iA	22	0.8774	100	0.234	Contact Map
3n3wA	2	0.2547	13.1	0.967	Contact Map
1di2A	2	0.3255	12.3	0.968	Contact Map
3w1eA	1	0.4057	9.4	0.969	Contact Map
2xexA	2	0.8491	8.7	0.97	Contact Map
3ddmA	4	0.4575	7.9	0.97	Contact Map
3otrA	6	0.5472	7	0.971	Contact Map
1x47A	1	0.434	5.5	0.972	Contact Map
4nzrM	1	0.4292	5.3	0.973	Contact Map
3adjA	1	0.3396	4.8	0.973	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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