D-I-TASSER A4D1F6-D1

D-I-TASSER results for A4D1F6-D1

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

Input Sequence in FASTA format

>A4D1F6 (140 residues)
MSEKEGMSEVLEDTISQFRKESRSQSMKEPGFIKETSNLINEASDYLEGKSSNQIYETHP
RQNTLESTSSSGRKSKRNEEQKKNLQFSETSTRTGTSQSLSSLTGRTAEYQALVNFLSHE
TVGEVSPQVSEENQKQLGLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSEKEGMSEVLEDTISQFRKESRSQSMKEPGFIKETSNLINEASDYLEGKSSNQIYETHPRQNTLESTSSSGRKSKRNEEQKKNLQFSETSTRTGTSQSLSSLTGRTAEYQALVNFLSHETVGEVSPQVSEENQKQLGLG
Prediction	CCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCSCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCC
Confidence	97545886453456776511332222246522223321443210101588866422468776765555677777665766634677310235777655763112224555665336875221323677661011013689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSEKEGMSEVLEDTISQFRKESRSQSMKEPGFIKETSNLINEASDYLEGKSSNQIYETHPRQNTLESTSSSGRKSKRNEEQKKNLQFSETSTRTGTSQSLSSLTGRTAEYQALVNFLSHETVGEVSPQVSEENQKQLGLG
Prediction	86667645542552254146644443164451366245325532543675434412544467543644544554466455554725144344565344445534643552442162244742552355147634643748
	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 DeepPotential. 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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCSCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCC
MSEKEGMSEVLEDTISQFRKESRSQSMKEPGFIKETSNLINEASDYLEGKSSNQIYETHPRQNTLESTSSSGRKSKRNEEQKKNLQFSETSTRTGTSQSLSSLTGRTAEYQALVNFLSHETVGEVSPQVSEENQKQLGLG

4uosA

0.10

0.09

3.42

1.00

DEthreader

EVMLEKMIEEIKKMLEKAIKKVKEMEKMMAKILKMVIELAEKILKKAKAEILKKMLKMEEIKKMLEAIKKV-EM-EKM-KE--KM--E--N--GEDKILKAKMAEKILKMVIELAEKILKKAKEMAEKILK-KVKELGVG

5cwmA

0.11

4.09

0.49

CEthreader

QAEKEGDPEVALRAVELVVRVAEEALERALRVAEEAARLAKRVLELAEKQGDPEVALRAVELVVRVAELLLGSEEALERALRVAEEAARLAKRVLELAEKQGDPEVARRAVELVKRVAELLERIARESGSEEAKERAERV

5wj5A

0.10

3.70

0.53

EigenThreader

SFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFSDVLTISGTIMKIGIEAKNLLLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLING

6w1sE

0.08

0.07

2.88

0.39

FFAS-3D

----EASLDALLNQVADLKNENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKTQVIIPLVEDLMRQTEGPDKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKEKISKEERESESGGLRPNKQTFNPGDTNAL---

3rj1C

0.12

4.26

0.97

SPARKS-K

ALDAVRRLAQLTHSLRRIRDESKAELPQWYTLQSQLNVTLSQLVSVTSTLQHF--QETLDSTVVYPLPKFPTTKNIPEDEWKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDPFNVDDVLKFTFTG

7jh5A

0.13

0.09

2.98

0.47

CNFpred

LTDPKRIRDEIKEVKDKSKEIIRRAEKEIDDAAKESEKILEEAREAISGSGS-------ELAKLLLKAIAETQDL-------------------------------LRAAKAFLEAAA---------KLQELNIRAVELL

1l8wD

0.06

2.47

1.00

DEthreader

GNGFLDVFTSF-GGLVA--EAFGFKPKKDVKTYFTTVAAKLEKTKT-DLNSTVEGAIKEELLDKLVAVEIVLLSAIVTAAAAQGKPEEAKGGAEF-IAIALAVRKVLGAITGLIGDAVSSGLRKVGDSVKAASKE-----

5z3aA

0.08

3.11

0.92

MapAlign

-HVEHRHVSTLGAIHGGLVAVGLRSAPWSAATLQVAARIRSLVSVKWLGSSAVDGSLPACVVPFGLVPPDDDVAAMTRAAVAKDLDVDGGVHRFAADVFYGGGQWILLSALLGWNLAAAGDTAGALRHLYLILADELGLL

3rj1C

0.11

4.09

0.59

MUSTER

GQALDAVLAQLTHSLRRIRDESKAELPQWYTLQSQLNVTLSQLVSVTSFQETLDSTVVYPLPKFPTTSHESLKNIPEVDEWKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDPFNVDDVLKFTFTG

2pffB

0.18

5.81

0.64

HHsearch

IAEYPNTPSILED-SLENNEGVPSPMLSISNTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGP-PQSLYGLNLTLRKRIPFSERFSNRFASPFHSLLVDLINKNNVSFNAKVYDTLRVLSGSISERIVHILDFG

(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	0.5244

(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 DeepPotential, 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	4whjA2	0.68	3.50	0.051	0.957	model1_4whjA2.pdb.gz
2	3ljbA	0.68	3.39	0.037	0.950	model1_3ljbA.pdb.gz
3	3szrA	0.67	3.67	0.079	0.979	model1_3szrA.pdb.gz
4	5owvC2	0.67	3.82	0.066	0.943	model1_5owvC2.pdb.gz
5	5uot0	0.66	3.57	0.059	0.950	model1_5uot0.pdb.gz
6	4uosA	0.64	4.00	0.118	0.971	model1_4uosA.pdb.gz
7	3g9gA	0.51	4.10	0.022	0.750	model1_3g9gA.pdb.gz
8	2q13A1	0.44	4.56	0.059	0.736	model1_2q13A1.pdb.gz
9	3drwA	0.39	3.80	0.043	0.571	model1_3drwA.pdb.gz
10	4tqlA	0.38	4.46	0.074	0.657	model1_4tqlA.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:1901363	0.67	heterocyclic compound binding
GO:0097159	0.67	organic cyclic compound binding
GO:0032555	0.60	purine ribonucleotide binding
GO:0032550	0.59	purine ribonucleoside binding
GO:0035639	0.58	purine ribonucleoside triphosphate 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:0065007	0.76	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0009987	0.66	cellular process
GO:0007165	0.63	signal transduction
GO:0050896	0.53	response to stimulus
GO:0051716	0.51	cellular response to stimulus
GO:0051704	0.51	multi-organism process
GO:0010033	0.51	response to organic substance
GO:0009605	0.51	response to external stimulus
GO:0007166	0.51	cell surface receptor signaling pathway
GO:0006950	0.51	response to stress
GO:0002376	0.51	immune system process
GO:0098542	0.50	defense response to other organism
GO:0071357	0.50	cellular response to type I interferon
GO:0019221	0.50	cytokine-mediated signaling pathway
GO:0002252	0.50	immune effector process

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:0005737	1.00	cytoplasm
GO:0044444	0.96	cytoplasmic part
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0044446	0.90	intracellular organelle part
GO:0016020	0.73	membrane
GO:0044425	0.67	membrane part
GO:0005829	0.62	cytosol
GO:0044430	0.61	cytoskeletal part
GO:0043232	0.61	intracellular non-membrane-bounded organelle
GO:0031982	0.60	vesicle
GO:0005856	0.60	cytoskeleton
GO:0005874	0.59	microtubule
GO:0097458	0.54	neuron part
GO:0045202	0.53	synapse
GO:0044456	0.53	synapse part
GO:0005794	0.53	Golgi apparatus

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	0.066	3gm1B	0.569	3.65	0.089	0.814	2.7.10.2	NA
2	0.066	3eziA	0.461	3.76	0.031	0.679	2.7.13.3	NA
3	0.066	1c17M	0.551	3.65	0.026	0.814	3.6.3.14	NA
4	0.060	2np0A	0.540	3.60	0.059	0.786	3.4.24.69	NA
5	0.060	3ixzA	0.539	3.57	0.044	0.764	3.6.3.10	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	0.01	2j0n0	0.463	4.77	0.063	0.807	0.27	III	complex1.pdb.gz	96,102,103,104,106,107,109,110,111,114,117,118,121,124,125,128,129
2	0.01	1kwoA	0.523	4.38	0.063	0.821	0.20	AGS	complex2.pdb.gz	24,25,104,105,112
3	0.01	1kqmA	0.524	4.40	0.055	0.821	0.14	ANP	complex3.pdb.gz	2,3,4,5,128,129
4	0.01	2j68A	0.585	4.27	0.044	0.957	0.24	GDP	complex4.pdb.gz	108,109,110

	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.