D-I-TASSER P42224-D2

D-I-TASSER results for P42224-D2

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

Input Sequence in FASTA format

>P42224 (189 residues)
NIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVA
KSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACI
GGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSL
FQQLIQSSF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	987405468999999999999999999999999999999999999999986777750332278999999999999999999999999999999999999999999999999999999626899611089999999999999999999999999645505789985155668999999999999998529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| NIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF
Prediction	846545346425504530550353044126305503631440333034244355545544574344434314411540453145105414510530450144103740550454043223422355315401500320040023024104405603651516775156425403630350043005528
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC
NIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF

1y1uA

0.25

0.24

7.39

1.50

DEthreader

-------SQKHLQINQRFEELRLITQDTENELKKLQQTQEYFIIQYQESLRIQAQFLETLQQKQVSLETWLQREAQTLQQYRVELAEKHQKTLQLLRKQQTIILDDELIQWKRRQQLAGNGGPPEGSLDVLQSWCEKLAEIIWQNRQQIRRAEHLCQQLPI-PGPVEEMLAEVNATITDIISALVTSTI

1bg1A1

0.44

0.41

11.93

1.94

SPARKS-K

-----VVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDSVTR-------QKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKS--

1bg1A

0.44

0.41

11.93

1.24

MapAlign

------VTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQ-------GDSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSLV

1bg1A

0.45

0.42

12.22

1.00

CEthreader

-----VVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQG-------DSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSAF

1yvlB

0.96

0.92

25.81

1.32

MUSTER

NAQRFNMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHDQK--------QEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF

1bg1A1

0.44

0.40

11.78

3.84

HHsearch

-----VVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDS--------VTRQKQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKS--

1bg1A1

0.43

0.40

11.78

2.43

FFAS-3D

-----VVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDSVTRQ-------KMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKS--

1bg1A1

0.43

0.40

11.64

1.13

EigenThreader

-VVT----EKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQG--DSVTRQ-----KMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKS--

1yvlA

1.00

0.95

26.52

1.33

CNFpred

----TVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNRE------AKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF

1bg1A

0.43

0.40

11.79

1.50

DEthreader

---V--VTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGD-S----V-TR-QKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSAV

(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	0.8449

(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	1y1uA	0.91	1.24	0.249	0.958	model1_1y1uA.pdb.gz
2	1bg1A	0.90	1.25	0.435	0.936	model1_1bg1A.pdb.gz
3	1yvlB	0.88	1.48	0.934	0.931	model1_1yvlB.pdb.gz
4	1uusA	0.49	2.38	0.142	0.550	model1_1uusA.pdb.gz
5	4qkwA	0.33	1.60	0.069	0.349	model1_4qkwA.pdb.gz
6	2blmA	0.33	5.01	0.057	0.529	model1_2blmA.pdb.gz
7	1g8pA1	0.30	5.13	0.104	0.503	model1_1g8pA1.pdb.gz
8	2h5gB1	0.24	5.03	0.040	0.381	model1_2h5gB1.pdb.gz
9	4erhA	0.23	4.59	0.037	0.354	model1_4erhA.pdb.gz
10	2ptkA1	0.23	5.49	0.057	0.402	model1_2ptkA1.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:0003700	0.72	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.55	heterocyclic compound binding
GO:0097159	0.55	organic cyclic compound binding
GO:0000981	0.55	RNA polymerase II transcription factor activity, sequence-specific DNA 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	0.95	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.94	cellular process
GO:0048518	0.89	positive regulation of biological process
GO:0044699	0.84	single-organism process
GO:0007165	0.82	signal transduction
GO:0048522	0.81	positive regulation of cellular process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0050896	0.78	response to stimulus
GO:0035556	0.78	intracellular signal transduction
GO:0007259	0.77	JAK-STAT cascade
GO:0006355	0.75	regulation of transcription, DNA-templated
GO:0044763	0.74	single-organism cellular process
GO:0010033	0.74	response to organic substance
GO:0071310	0.72	cellular response to organic substance
GO:0048869	0.68	cellular developmental process
GO:0042127	0.67	regulation of cell proliferation
GO:0034097	0.67	response to cytokine
GO:0032501	0.67	multicellular organismal process
GO:0008284	0.66	positive regulation of cell proliferation
GO:0050793	0.65	regulation of developmental process
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0051239	0.64	regulation of multicellular organismal process
GO:0045893	0.64	positive regulation of transcription, DNA-templated
GO:0009719	0.63	response to endogenous stimulus
GO:0030154	0.62	cell differentiation
GO:0019221	0.61	cytokine-mediated signaling pathway
GO:0009725	0.61	response to hormone
GO:2000026	0.60	regulation of multicellular organismal development
GO:1901700	0.60	response to oxygen-containing compound
GO:0048583	0.59	regulation of response to stimulus
GO:0045595	0.59	regulation of cell differentiation
GO:0014070	0.59	response to organic cyclic compound
GO:0048519	0.57	negative regulation of biological process
GO:0071495	0.56	cellular response to endogenous stimulus
GO:0048523	0.56	negative regulation of cellular process
GO:0043434	0.56	response to peptide hormone
GO:0009605	0.55	response to external stimulus
GO:0048661	0.54	positive regulation of smooth muscle cell proliferation
GO:0032870	0.54	cellular response to hormone stimulus
GO:0003008	0.54	system process
GO:0065009	0.53	regulation of molecular function
GO:0051591	0.53	response to cAMP
GO:0051246	0.53	regulation of protein metabolic process
GO:0023051	0.53	regulation of signaling
GO:0010941	0.53	regulation of cell death
GO:0010646	0.53	regulation of cell communication
GO:0008015	0.53	blood circulation
GO:0044093	0.52	positive regulation of molecular function
GO:0009966	0.52	regulation of signal transduction
GO:0051241	0.51	negative regulation of multicellular organismal process
GO:0051093	0.51	negative regulation of developmental process
GO:0042981	0.51	regulation of apoptotic process
GO:1901701	0.50	cellular response to oxygen-containing compound
GO:0045596	0.50	negative regulation of cell differentiation

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:0044424	1.00	intracellular part
GO:0043229	0.95	intracellular organelle
GO:0005737	0.95	cytoplasm
GO:0005634	0.92	nucleus
GO:0044446	0.65	intracellular organelle part
GO:0044428	0.61	nuclear part

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	1k7wD	0.478	3.65	0.066	0.640	4.3.2.1	NA
2	0.060	2a06C	0.400	4.12	0.070	0.550	1.10.2.2	NA
3	0.060	1k62B	0.486	3.94	0.011	0.661	4.3.2.1	NA
4	0.060	2e9fB	0.483	3.85	0.067	0.645	4.3.2.1	NA
5	0.060	2b5uA	0.522	3.08	0.037	0.640	3.1.-.-	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:

No Binding sites was predicted

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

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.