D-I-TASSER P61978-D2

D-I-TASSER results for P61978-D2

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

Input Sequence in FASTA format

>P61978 (163 residues)
QPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDD
MSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSAD
ETWDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| QPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGG
Prediction	CCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9978653222245787135640588877888898888888899888888899877777778998899999999898998887778889999998887767787789877778745666887654455678876556776788877765456788777554689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| QPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGG
Prediction	8545462244327332011213446444463445444444444745544444554553473554644444464654544545554746544444456444456554454344334434455324443444444545444445435445334423434255468
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
QPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGG

2fkjA1

0.05

2.23

0.67

CEthreader

TVDKLELKGTSDKNNGSGVLEGVKADKSKVKLTISDDLGQTTLEVFKEDGKTLVSKKV--TSKDKSSTEEKFNEKGELSEK---------KITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSE-----

5wlzC

0.03

1.77

0.50

EigenThreader

GSLVSEPSITKTLKSGFVITLTDG--HSAWTGTVSESKISQEAATMAMNKGKYVGELRKALLSGAGPAKESRNLKDVSFENPAEVIRELIDYALDRNNLLQAELEELRAVVEQTERSRKLAEQELIETSERVQLLHSQN-------TSLINQKKKMDADLSQL

2xd8A3

0.12

4.15

0.43

FFAS-3D

KLFSGEMFQHETIARDLVTKRTLKNGKSLQFIYTGRMTSSFHTPGTPILGNADKAPPVAEMDDLLISSASATNFVEPGGTQIRVGSGTNESDAFTASALVMDEKGPFLGKYGVKYGGTTGETSPGNLGSHIGNATGGVNNDYGTNAELGAKSCGLIFQKEAAG

7jjvA

0.18

0.13

4.39

1.18

SPARKS-K

QCDGLDGADGTSN-GQ-----AGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNDVAAGGAGAAGGAAGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPGQTTVL-----------------------------------

2axnA

0.31

0.07

2.04

0.13

CNFpred

---------------------------------------------------------------------------------------------------------------------------YEEIRDTYPEEYALREQ----DKYYYRYPTG-ESYQDLVQ

5amqA

0.05

0.04

1.98

0.83

DEthreader

------D--LMARHYFGLCKSL------NIEYRNDDNDYKIIISRFKLYPTIVV--DINF-NQFFDLKQLEFGDAPCKGFNAYRWNTVREYKKDSEHIKSTN-------------NLKILIHSLCKNLLDTAERCKLEMIEGDGKLVLKHSMSVYKILKILVN

4g1eA

0.03

1.83

0.84

MapAlign

WFGASVRSKQDKILACAPYHWRTEMKQEREPVGTCFLQAPCRIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNF

6d4hA

0.11

3.96

0.72

MUSTER

SRVHVYMYNRQWKLEH----LCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGG

6mabA1

0.17

0.09

2.81

0.52

HHsearch

QATDSSLDLVSISKEQFCDVFLRDDICPPHLLL-------------------------------------------RP-----PLNLDPL--PYGEN-------------FVSFC-IGNTEMWGYIHRILTYEEKSIIF---ASLWR----------------

1xi0A

0.11

0.07

2.65

0.64

CEthreader

VWHFANGGTTQGGSGTSGVLRFLSTKGERITVAVGVHNYKRWCDVVTGLKPDETALV---------INPQYYNNGGRDYVREKQLAEYSVTSAIGTKVEVVYTVAEGNNLEANVIFS----------------------------------------------

(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	0.487

(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	6fb3A	0.40	5.02	0.031	0.644	model1_6fb3A.pdb.gz
2	4o9xA	0.37	4.49	0.031	0.583	model1_4o9xA.pdb.gz
3	3cmmC	0.37	4.83	0.057	0.607	model1_3cmmC.pdb.gz
4	1t3tA	0.36	5.21	0.034	0.632	model1_1t3tA.pdb.gz
5	7kbtA	0.36	5.27	0.037	0.632	model1_7kbtA.pdb.gz
6	7naqc	0.36	4.99	0.013	0.595	model1_7naqc.pdb.gz
7	4bxsV	0.36	5.24	0.040	0.632	model1_4bxsV.pdb.gz
8	5ganA	0.36	5.00	0.025	0.607	model1_5ganA.pdb.gz
9	7evnA	0.36	5.03	0.039	0.595	model1_7evnA.pdb.gz
10	6uebA	0.36	5.91	0.046	0.699	model1_6uebA.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	0.89	heterocyclic compound binding
GO:0097159	0.89	organic cyclic compound binding
GO:0003676	0.85	nucleic acid binding
GO:0003723	0.83	RNA binding
GO:0044822	0.78	poly(A) RNA binding
GO:0003677	0.77	DNA binding
GO:0003690	0.75	double-stranded DNA binding
GO:0001159	0.75	core promoter proximal region DNA binding
GO:0003700	0.51	transcription factor activity, sequence-specific DNA binding
GO:0003697	0.51	single-stranded DNA binding
GO:0001077	0.50	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000978	0.50	RNA polymerase II core promoter proximal region 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:0051254	1.00	positive regulation of RNA metabolic process
GO:0051239	1.00	regulation of multicellular organismal process
GO:0051130	1.00	positive regulation of cellular component organization
GO:0043066	1.00	negative regulation of apoptotic process
GO:0032879	1.00	regulation of localization
GO:0010628	1.00	positive regulation of gene expression
GO:0006357	1.00	regulation of transcription from RNA polymerase II promoter
GO:0009987	0.87	cellular process
GO:0051246	0.68	regulation of protein metabolic process
GO:0031328	0.68	positive regulation of cellular biosynthetic process
GO:0031324	0.68	negative regulation of cellular metabolic process
GO:0010605	0.68	negative regulation of macromolecule metabolic process
GO:0010557	0.68	positive regulation of macromolecule biosynthetic process
GO:0072369	0.67	regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter
GO:0051253	0.67	negative regulation of RNA metabolic process
GO:0048260	0.67	positive regulation of receptor-mediated endocytosis
GO:0045716	0.67	positive regulation of low-density lipoprotein particle receptor biosynthetic process
GO:0043484	0.67	regulation of RNA splicing
GO:0023051	0.67	regulation of signaling
GO:0010988	0.67	regulation of low-density lipoprotein particle clearance
GO:0010646	0.67	regulation of cell communication
GO:0010629	0.67	negative regulation of gene expression
GO:0008152	0.65	metabolic process
GO:0071704	0.64	organic substance metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0044238	0.62	primary metabolic process
GO:0043170	0.62	macromolecule metabolic process
GO:0044260	0.61	cellular macromolecule metabolic process
GO:0034641	0.59	cellular nitrogen compound metabolic process
GO:0090304	0.58	nucleic acid metabolic process
GO:0016070	0.57	RNA metabolic process
GO:0006396	0.50	RNA processing

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:0043227	1.00	membrane-bounded organelle
GO:0032991	1.00	macromolecular complex
GO:0044446	0.80	intracellular organelle part
GO:0044428	0.77	nuclear part
GO:0043229	0.76	intracellular organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0030529	0.74	intracellular ribonucleoprotein complex
GO:0005634	0.73	nucleus
GO:0005681	0.72	spliceosomal complex
GO:0016020	0.69	membrane
GO:0071013	0.68	catalytic step 2 spliceosome
GO:0044421	0.68	extracellular region part
GO:0070062	0.67	extracellular exosome
GO:0005925	0.67	focal adhesion
GO:0005737	0.67	cytoplasm
GO:0000790	0.67	nuclear chromatin

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	1a47A	0.232	5.02	0.021	0.399	2.4.1.19	NA
2	0.060	1q16A	0.229	5.86	0.025	0.472	1.7.99.4	NA
3	0.060	3ffzA	0.328	5.51	0.027	0.632	3.4.24.69	NA
4	0.060	1b0pA	0.238	6.44	0.041	0.503	1.2.7.1	NA
5	0.060	3ecqB	0.289	6.39	0.012	0.595	3.2.1.97	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	3e4aA	0.277	5.92	0.028	0.546	0.32	III	complex1.pdb.gz	35,37,39
2	0.01	2g49A	0.277	5.75	0.049	0.546	0.11	III	complex2.pdb.gz	71,73,75
3	0.01	3p7oA	0.290	5.89	0.037	0.583	0.20	III	complex3.pdb.gz	74,76,78
4	0.01	1siwA	0.242	5.40	0.074	0.429	0.30	SF4	complex4.pdb.gz	35,36,37,39
5	0.01	3ofiB	0.286	6.02	0.043	0.577	0.13	III	complex5.pdb.gz	73,74,75,77
6	0.01	3tuvA	0.307	5.57	0.032	0.577	0.37	ATP	complex6.pdb.gz	109,110,111,112,113
7	0.01	3h44B	0.314	5.54	0.038	0.571	0.23	III	complex7.pdb.gz	76,77,78,80,81
8	0.01	2jbuB	0.254	6.18	0.027	0.528	0.26	III	complex8.pdb.gz	77,78,79,81
9	0.01	3n57A	0.312	5.65	0.025	0.583	0.11	III	complex9.pdb.gz	74,75,76,79
10	0.01	3cwwA	0.311	5.69	0.025	0.577	0.15	III	complex10.pdb.gz	45,46,47,48,49

	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.