OPENSEQ.org - 1436453504 - GREMLIN Submission

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p31_cmd2 60-274

ID:	1436453504	Query Sequence FPGPVSQEGCCQFTCELLKHIMYQRQQLPLPYEQLKHFYRKPSPQAEEMLKKKPRATTEVSSRKCQQALAELESVLSHLEDFFARTLVPRVLILLGGNALSPKEFYELDLSLLAPYSVDQSLSTAACLRRLFRAIFMADAFSELQAPPLMGTVVMAQGHRNCGEDWFRPKLNYRVPSRGHKLTVTLSCGRPSIRTTAWEDYIWFQAPVTFKGFRE	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	215 (212)
Sequences:	216 (161.9)
Seq/Len:	1.019
Nf(neff/√len):	11.1

Jackhmmer Results: (2015_01_07)
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: 1.019).

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 > 50% 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
205_Q	211_K	2.297	0.99
21_I	95_L	2.059	0.96
203_W	212_G	1.971	0.95
25_R	104_E	1.937	0.95
35_L	53_K	1.766	0.90
23_Y	29_P	1.686	0.87
11_C	23_Y	1.673	0.87
5_V	12_Q	1.609	0.84
26_Q	33_E	1.488	0.76
16_E	19_K	1.476	0.76
100_L	133_R	1.467	0.75
23_Y	71_E	1.439	0.73
117_S	122_L	1.427	0.72
22_M	29_P	1.408	0.71
27_Q	96_G	1.392	0.69
77_S	134_A	1.386	0.69
20_H	31_P	1.374	0.68
27_Q	212_G	1.366	0.67
84_A	97_G	1.351	0.66
19_K	32_Y	1.326	0.64
93_I	99_A	1.323	0.64
113_L	154_V	1.320	0.63
18_L	63_R	1.303	0.62
108_L	117_S	1.300	0.62
123_S	133_R	1.298	0.61
14_T	23_Y	1.294	0.61
82_F	153_V	1.293	0.61
131_L	213_F	1.292	0.61
22_M	27_Q	1.284	0.60
29_P	96_G	1.278	0.60
33_E	173_Y	1.278	0.60
96_G	203_W	1.277	0.60
98_N	108_L	1.273	0.59
96_G	102_P	1.266	0.59
90_R	157_Q	1.263	0.58
16_E	28_L	1.263	0.58
90_R	107_E	1.240	0.56
22_M	131_L	1.232	0.55
42_P	45_Q	1.223	0.55
90_R	109_D	1.217	0.54
106_Y	142_S	1.214	0.54
29_P	212_G	1.211	0.54
21_I	36_K	1.199	0.52
67_Q	173_Y	1.198	0.52
20_H	129_R	1.174	0.50
149_L	152_T	1.173	0.50
72_L	139_D	1.170	0.50
13_F	31_P	1.168	0.50
23_Y	27_Q	1.166	0.49
33_E	78_H	1.165	0.49
98_N	103_K	1.160	0.49
69_L	93_I	1.158	0.49
167_F	170_K	1.157	0.49
189_G	195_T	1.157	0.49
156_A	177_S	1.156	0.48
88_V	108_L	1.147	0.48
99_A	168_R	1.146	0.48
14_T	184_V	1.143	0.47
19_K	25_R	1.142	0.47
152_T	189_G	1.141	0.47
109_D	126_A	1.127	0.46
25_R	68_A	1.127	0.46
64_K	154_V	1.125	0.46
21_I	106_Y	1.124	0.45
20_H	101_S	1.120	0.45
21_I	29_P	1.112	0.44
147_P	151_G	1.111	0.44
147_P	150_M	1.108	0.44
9_G	54_P	1.102	0.43
116_Y	121_S	1.101	0.43
14_T	91_V	1.095	0.43
60_V	65_C	1.093	0.43
19_K	33_E	1.089	0.42
189_G	196_T	1.086	0.42
16_E	35_L	1.078	0.41
30_L	39_Y	1.077	0.41
46_A	51_K	1.076	0.41
21_I	28_L	1.076	0.41
79_L	160_R	1.074	0.41
35_L	92_L	1.072	0.41
18_L	91_V	1.069	0.40
110_L	146_A	1.067	0.40
153_V	168_R	1.066	0.40
6_S	210_F	1.062	0.40
130_R	133_R	1.062	0.40
160_R	169_P	1.059	0.40
44_P	48_E	1.057	0.39
9_G	35_L	1.055	0.39
134_A	210_F	1.055	0.39
21_I	39_Y	1.054	0.39
101_S	141_F	1.053	0.39
205_Q	212_G	1.053	0.39
83_F	94_L	1.035	0.37
141_F	144_L	1.034	0.37
116_Y	119_D	1.031	0.37
137_M	145_Q	1.030	0.37
100_L	170_K	1.030	0.37
49_M	56_A	1.027	0.37
176_P	179_G	1.024	0.36
154_V	165_D	1.023	0.36
6_S	10_C	1.022	0.36
32_Y	66_Q	1.018	0.36
16_E	26_Q	1.017	0.36
108_L	210_F	1.017	0.36
162_C	200_D	1.013	0.36
74_S	110_L	1.010	0.35
86_T	148_P	1.005	0.35
6_S	13_F	1.005	0.35
154_V	194_R	1.003	0.35
3_G	16_E	1.001	0.35

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
2qyfB	2	0.8791	100	0.053	Contact Map
3abdA	2	0.7488	95.2	0.894	Contact Map
4trkA	1	0.8465	93.3	0.903	Contact Map
2vfxA	12	0.786	93.2	0.903	Contact Map
4tzmA	2	0.8698	91.6	0.908	Contact Map
4aezB	3	0.8279	91.2	0.909	Contact Map
3cxlA	1	0.5488	46.7	0.938	Contact Map
2xs6A	1	0.4977	31.4	0.944	Contact Map
1f7cA	1	0.5349	17.2	0.95	Contact Map
3byiA	4	0.5907	17.2	0.95	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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