D-I-TASSER O00408-D3

D-I-TASSER results for O00408-D3

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>O00408 (189 residues)
KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDG
GVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPI
KNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLA
NEMMMYHMK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK
Prediction	CHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCSSSSSSSSCCCSSSSSSSCCCCCCCCSSSSCCCCCCHHHHHHHHCCSSSSCCCCCCCCCCCCHHHHCCCCSCSSSSSSSSCCCCCSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	758999999999999998132399999999999999969977999999899239999974788542113412699867899994098299678122975345314434981135999925728994999999997699999999999999999999999999999999999999999999999998709
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK
Prediction	745531530150044015305405533634042026105022001032377311010012334664255040336310012005343003042035144235424743624120030000214743000000001345654036401410313041001003104126404644444520441243248
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCSSSSSSSSCCCSSSSSSSCCCCCCCCSSSSCCCCCCHHHHHHHHCCSSSSCCCCCCCCCCCCHHHHCCCCSCSSSSSSSSCCCCCSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK

4mcwA

0.33

0.32

9.53

1.33

DEthreader

DPERKLKILLDYSSKI-ANEKDLRNVLLFLTDLAKEIMEADRASIFLYDKKTLWTIVA-----HGV-DRIEIDADKGIAGYVFRTGEILNIPDAYKDPRFDRDIDKRTGYRTRTILAVPLFDRKQNIIGVFQVINKLTNSVFTEEDIELLRHISLYASSTIENAILYEKLKKAHEDVIYRLSHATKFKK

3trcA

0.18

0.16

5.16

1.72

SPARKS-K

-SNANLKILRQITQEVNAA-PNLEQALKLVVVRLCEALPADACSLFICDDVHGEYVLATQGLNSKQVGKLRLKFGEGLIGLVGEREEPINLADAPLHPA-YKHRPELGEEDYHGFLGIPIIEQ-GELLGILVIQQL-ESHHFAEEEEAFCVTLAIHLAAEIAHARAKGAL-------------------

3mmhA

0.20

0.16

5.10

0.71

MapAlign

KAALYREVLPQIESVVADETD-WVANLANTAAVLKEAFGWFWVGFYLVDSDELVLAPFQGPLA-----CTRIPFGRGVCGQAWAKGGTVVVGDVDAHPDHI------ACSLSRSEIVVPLFS-DGRCIGVLDADSEH-LAQFDETDALYLGELAKILEKRFEASRQA----------------------

3mmhA

0.19

0.16

5.11

0.51

CEthreader

KAALYREVLPQIESVVAD-ETDWVANLANTAAVLKEAFGWFWVGFYLVDTDELVLAPFQGPLA-----CTRIPFGRGVCGQAWAKGGTVVVGDVDAHPDHIA-----CSSLSRSEIVVPLFS-DGRCIGVLDADS-EHLAQFDETDALYLGELAKILEKRFEASRQAV---------------------

3ibjA

1.00

0.97

27.11

1.40

MUSTER

KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLF------STGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK

3ibjA

1.00

0.97

27.11

1.95

HHsearch

KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLF------STGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK

3ibjA2

1.00

0.86

24.15

2.13

FFAS-3D

-------------------LDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLF------STGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHM-

6x88A2

0.26

0.24

7.50

1.02

EigenThreader

IESRRSQMLLWSANKVFEELTDIERQFHKALYTIRMYLNCERYSVGLLDMVNFYKIIDYLHGKEEIKVIPTP-PADHLPTYVAENGFICNMMNAPAYFTFQKGPVDETGWVIKNVLSLPIVNKKEEIVGVATFYNRKDGKPFDEYDEQIIETLTQFLGWSVLNTDTYDKMNKLEN-------------R

3ibjA

1.00

0.97

27.11

1.60

CNFpred

KLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLF------STGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMK

3lfvA

0.33

9.84

1.33

DEthreader

--GDQSSRLLELVKDISS-HLDVTALCHKIFLHIHGLISADRYSLFLVCDKFLISRLFDVAESTESNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLFEE

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8935

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3lfvA	0.85	2.34	0.342	0.984	model1_3lfvA.pdb.gz
2	4mcwA	0.84	2.32	0.324	0.963	model1_4mcwA.pdb.gz
3	3ibjA	0.83	2.09	0.929	0.921	model1_3ibjA.pdb.gz
4	4o01A	0.81	2.44	0.083	0.936	model1_4o01A.pdb.gz
5	6x88A	0.78	3.21	0.229	0.963	model1_6x88A.pdb.gz
6	3trcA	0.78	1.84	0.193	0.852	model1_3trcA.pdb.gz
7	4ehoA	0.76	2.84	0.074	0.926	model1_4ehoA.pdb.gz
8	3ci6B	0.73	2.12	0.186	0.820	model1_3ci6B.pdb.gz
9	1vhmB	0.72	2.27	0.166	0.825	model1_1vhmB.pdb.gz
10	2oolA2	0.72	2.54	0.102	0.831	model1_2oolA2.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	1.00	catalytic activity
GO:0004114	0.99	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:1901363	0.87	heterocyclic compound binding
GO:0097159	0.87	organic cyclic compound binding
GO:0097367	0.84	carbohydrate derivative binding
GO:0000166	0.84	nucleotide binding
GO:0032555	0.83	purine ribonucleotide binding
GO:0030551	0.76	cyclic nucleotide binding
GO:0004118	0.73	cGMP-stimulated cyclic-nucleotide phosphodiesterase activity
GO:0032561	0.70	guanyl ribonucleotide binding
GO:0030553	0.65	cGMP binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.95	single-organism process
GO:0009987	0.95	cellular process
GO:0008152	0.92	metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044763	0.91	single-organism cellular process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0006139	0.90	nucleobase-containing compound metabolic process
GO:0055086	0.88	nucleobase-containing small molecule metabolic process
GO:0006796	0.88	phosphate-containing compound metabolic process
GO:0009150	0.87	purine ribonucleotide metabolic process
GO:0065007	0.83	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0046068	0.83	cGMP metabolic process
GO:0050794	0.81	regulation of cellular process
GO:0007165	0.73	signal transduction
GO:0032501	0.72	multicellular organismal process
GO:0050896	0.70	response to stimulus
GO:1901565	0.67	organonitrogen compound catabolic process
GO:0009261	0.67	ribonucleotide catabolic process
GO:0046069	0.66	cGMP catabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0048519	0.65	negative regulation of biological process
GO:0031323	0.65	regulation of cellular metabolic process
GO:0003008	0.65	system process
GO:0065008	0.64	regulation of biological quality
GO:0019219	0.64	regulation of nucleobase-containing compound metabolic process
GO:0048523	0.63	negative regulation of cellular process
GO:0046058	0.63	cAMP metabolic process
GO:0042221	0.63	response to chemical
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0010468	0.63	regulation of gene expression
GO:1901700	0.62	response to oxygen-containing compound
GO:0051716	0.62	cellular response to stimulus
GO:0035556	0.62	intracellular signal transduction
GO:0051051	0.61	negative regulation of transport
GO:0045934	0.61	negative regulation of nucleobase-containing compound metabolic process
GO:0031327	0.61	negative regulation of cellular biosynthetic process
GO:0006198	0.61	cAMP catabolic process
GO:0014070	0.60	response to organic cyclic compound
GO:0006355	0.60	regulation of transcription, DNA-templated
GO:0003018	0.60	vascular process in circulatory system
GO:0010605	0.59	negative regulation of macromolecule metabolic process
GO:0010243	0.59	response to organonitrogen compound
GO:0006357	0.59	regulation of transcription from RNA polymerase II promoter
GO:0097011	0.58	cellular response to granulocyte macrophage colony-stimulating factor stimulus
GO:0071321	0.58	cellular response to cGMP
GO:0043117	0.58	positive regulation of vascular permeability
GO:0043116	0.58	negative regulation of vascular permeability
GO:0036006	0.58	cellular response to macrophage colony-stimulating factor stimulus
GO:0035690	0.58	cellular response to drug
GO:0033159	0.58	negative regulation of protein import into nucleus, translocation
GO:0019934	0.58	cGMP-mediated signaling
GO:0019933	0.58	cAMP-mediated signaling
GO:0000122	0.58	negative regulation of transcription from RNA polymerase II promoter

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	0.97	cell part
GO:0044424	0.90	intracellular part
GO:0016020	0.89	membrane
GO:0044444	0.76	cytoplasmic part
GO:0043226	0.76	organelle
GO:0043229	0.74	intracellular organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005886	0.72	plasma membrane
GO:0005634	0.72	nucleus
GO:0048471	0.62	perinuclear region of cytoplasm

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.330	3ci6B	0.734	2.12	0.186	0.820	2.7.3.9	48,88,119,147,161
2	0.301	3dbaB	0.695	2.90	0.281	0.809	3.1.4.35	46,79,90,127,147
3	0.189	1f5mB	0.724	1.82	0.172	0.799	1.8.4.14	NA
4	0.060	2z8kC	0.320	4.66	0.061	0.497	2.3.2.2	39
5	0.060	2ix6A	0.455	4.90	0.049	0.714	1.3.3.6	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.69	2zmfA	0.705	3.16	0.417	0.884	1.37	CMP	complex1.pdb.gz	42,43,44,58,59,72,77,78,79,100,101,104,110,112,115,132,134
2	0.28	3mmhA	0.734	1.96	0.187	0.820	0.99	SME	complex2.pdb.gz	43,47,72,77,78,79,100,101,115,131,133
3	0.04	1f5m0	0.724	1.83	0.166	0.799	0.88	III	complex3.pdb.gz	16,20,22,24,25,28,29,32,33,36,54,55,56,57,58,59,60,70,102,105

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.