D-I-TASSER Q86W25-D2

D-I-TASSER results for Q86W25-D2

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

Input Sequence in FASTA format

>Q86W25 (200 residues)
PMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQWRALC
SLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQEFFA
AMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIARELEDTL
HCKISPRVMEELLKWGEELG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| PMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQWRALCSLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQEFFAAMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIARELEDTLHCKISPRVMEELLKWGEELG
Prediction	CSSSHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCSSSCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCSSSSSCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Confidence	91213439999999961787666888789999999999806677788861138999999999999999787555399999959998899887542122145788845998504899999999999954655666531246899999998614476158999999963480899999998289889999999999999719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| PMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQWRALCSLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQEFFAAMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIARELEDTLHCKISPRVMEELLKWGEELG
Prediction	33000000000241156475155433110100130012104455563567423510320030004003643110336204614043630331031200443573642000001010000000010022466345442334203400441364653202211100000035621530372062512561144004006738
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCSSSCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCSSSSSCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
PMVCWTVCSCLKQPKVRYYDLQSITQTTTSLYAYFFSNLFSTAEVDLADDSWPGQWRALCSLAIEGLWSMNFTFNKEDTEIEGLEVPFIDSLYEFNILQKINDCGGCTTFTHLSFQEFFAAMSFVLEEPREFPPHSTKPQEMKMLLQHVLLDKEAYWTPVVLFFFGLLNKNIARELEDTLHCKISPRVMEELLKWGEELG

5irlA

0.19

0.17

5.47

1.17

DEthreader

PVFSWMVSKCHQEL-LLQDGG--SPKTTTDMYLLILQHFL-RHASL-QG--RLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDI-SLG---FLVQ-----APLEFLHITFQCFLAAFYLVLST---D---V-PTASLRYLFNALQKTEPHNLQITAAFLAGLLSREHRDLLAA-CQASELLRRRACARWCLARSH

5irlA

0.18

0.16

5.21

1.64

SPARKS-K

PVFSWMVSKCHQELLLQDGG---SPKTTTDMYLLILQHFLRH---ASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISL----GFLVQAP-----LEFLHITFQCFLAAFYLVLS-------TDVPTASLRYLFALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQSERSLLRRRACARWCLARSL

5irlA

0.18

0.16

5.20

1.37

MapAlign

--FSWMVSKCHQELLL---QDGGSPKTTTDMYLLILQHFLRHASL---LQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDI----SLGFLV-----QAPLEFLHITFQCFLAAFYLVLSTD-------VPTASLRYLFALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASEL-LRRRACARWCLARSL

5irlA

0.16

0.15

4.97

1.25

CEthreader

PVFSWMVSKCHQELLLQDGG---SPKTTTDMYLLILQHF---LRHASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLGFL---------VQAPLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFN-CSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERLLRRRACARWCLARSL

5irlA

0.17

0.16

5.24

1.42

MUSTER

PVFSWMVSKCHQELLLQDG---GSPKTTTDMYLLILQHFL---RHASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISL----GFLVQAP-----LEFLHITFQCFLAAFYLVLSTDVPTASLRYLFN-CSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLRRRACARWCLARSL

5irlA

0.17

0.15

5.11

3.60

HHsearch

PVFSWMVSKCHQELLLQDG---GSPKTTTDMYLLILQHF---LRHASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDIS----LGFLVQA-----PLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFN-CSTVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLLRRACARWCLARSL

5irlA4

0.18

0.14

4.55

1.72

FFAS-3D

-------------------------KTTTDMYLLILQHFLRHAS---LLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLGFL---------VQAPLEFLHITFQCFLAAFYLVLSTDVPT-------ASLRYVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLLRRRACARWCLA--

5irlA

0.13

0.12

4.01

1.05

EigenThreader

LPVFSWMVSKCHQELLLQDGG--SPKTTTDMYLLILQHFLRH---ASLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLG-----FLV-QAP----LEFLHITFQCFLAAFYLVLSTDV---PTASLRYLFNVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERSLLRRRACARWCLARS

5irmA

0.16

0.15

5.16

1.31

CNFpred

PVFSWMVSKCHQELLLQ---DGGSPKTTTDMYLLILQHFLRHA-GPSLLQGRLPTLLRLGQLALWGLGMCCYVFSAQQLQAAQVDPDDISLGFLVQAQGVVPGSTAPLEFLHITFQCFLAAFYLVLSTDVPTASLRYLFNC-STVAALLQKTEPHNLQITAAFLAGLLSREHRDLLAACQASERLLRRRACARWCLARSL

6npyA

0.28

0.24

7.34

1.17

DEthreader

PLVCWIVCTGLKQMSGKSL-A-QTSKTTTAVYVFFLSSLLQP--R---G-GLCAHLWGLCSLAADGIWNQKILFESDLRNH-GLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLE-------------NVPGSRLKLP-S-R---ENYGKFEKGYLI-FVVRFLLVNQERTAKKKLQIQPSQLELCRA

(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	0.7733

(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	5irlA	0.79	2.30	0.186	0.885	model1_5irlA.pdb.gz
2	6npyA3	0.72	2.54	0.271	0.850	model1_6npyA3.pdb.gz
3	4kxfK	0.69	3.28	0.157	0.855	model1_4kxfK.pdb.gz
4	6b5bA	0.66	3.47	0.145	0.865	model1_6b5bA.pdb.gz
5	1uz4A	0.51	4.66	0.080	0.770	model1_1uz4A.pdb.gz
6	4a01A	0.50	4.85	0.064	0.785	model1_4a01A.pdb.gz
7	3zizA	0.45	4.75	0.038	0.685	model1_3zizA.pdb.gz
8	3wflA	0.44	4.84	0.058	0.695	model1_3wflA.pdb.gz
9	1qnqA	0.44	4.77	0.053	0.680	model1_1qnqA.pdb.gz
10	3k46A2	0.42	4.85	0.070	0.650	model1_3k46A2.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	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0097367	0.64	carbohydrate derivative binding
GO:0030554	0.59	adenyl nucleotide binding
GO:0035639	0.58	purine ribonucleoside triphosphate binding
GO:0032559	0.58	adenyl ribonucleotide binding
GO:0032550	0.58	purine ribonucleoside 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	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0009987	0.77	cellular process
GO:0048518	0.76	positive regulation of biological process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0050896	0.72	response to stimulus
GO:0044699	0.72	single-organism process
GO:0080090	0.71	regulation of primary metabolic process
GO:0031323	0.71	regulation of cellular metabolic process
GO:0048522	0.70	positive regulation of cellular process
GO:0044763	0.67	single-organism cellular process
GO:0009893	0.67	positive regulation of metabolic process
GO:0048583	0.66	regulation of response to stimulus
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0006950	0.64	response to stress
GO:0065009	0.63	regulation of molecular function
GO:0031325	0.63	positive regulation of cellular metabolic process
GO:0006952	0.63	defense response
GO:0032268	0.61	regulation of cellular protein metabolic process
GO:0050790	0.59	regulation of catalytic activity
GO:0010941	0.59	regulation of cell death
GO:0042981	0.58	regulation of apoptotic process
GO:0043281	0.57	regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0051239	0.56	regulation of multicellular organismal process
GO:0044093	0.56	positive regulation of molecular function
GO:0043207	0.56	response to external biotic stimulus
GO:0010468	0.55	regulation of gene expression
GO:0043085	0.54	positive regulation of catalytic activity
GO:0032270	0.54	positive regulation of cellular protein metabolic process
GO:0031347	0.54	regulation of defense response
GO:0010942	0.54	positive regulation of cell death
GO:0051707	0.53	response to other organism
GO:0001817	0.53	regulation of cytokine production
GO:0048584	0.52	positive regulation of response to stimulus
GO:0043280	0.52	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:2000112	0.51	regulation of cellular macromolecule biosynthetic process
GO:0098542	0.51	defense response to other organism
GO:0051171	0.51	regulation of nitrogen compound metabolic process
GO:0050776	0.51	regulation of immune response
GO:0048519	0.51	negative regulation of biological process
GO:0002376	0.51	immune system process
GO:0009617	0.50	response to bacterium

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0043227	0.85	membrane-bounded organelle
GO:0044444	0.82	cytoplasmic part
GO:0043229	0.79	intracellular organelle
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0005737	0.69	cytoplasm
GO:0032991	0.64	macromolecular complex
GO:0005634	0.64	nucleus
GO:0043234	0.63	protein complex
GO:0005829	0.55	cytosol

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	0.060	2oykB	0.473	4.59	0.059	0.720	3.2.1.123	65,117
2	0.060	2gtqA	0.434	5.37	0.080	0.730	3.4.11.2	NA
3	0.060	3hz3A	0.450	5.02	0.042	0.725	2.4.1.5	NA
4	0.060	1nbwA	0.448	5.49	0.043	0.750	4.2.1.30	117,121
5	0.060	1qoxM	0.473	4.72	0.023	0.730	3.2.1.21	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:

Click to view	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	1n38A	0.434	5.60	0.043	0.765	0.56	CH1	complex1.pdb.gz	66,67,74,75,79,80
	2	0.01	3ro5A	0.461	4.96	0.059	0.735	0.51	LGH	complex2.pdb.gz	65,78,81,83

	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.