D-I-TASSER A6NI56-D2

D-I-TASSER results for A6NI56-D2

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

Input Sequence in FASTA format

>A6NI56 (72 residues)
ALQKNQEDSSRRVDLEVARMQAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKAS
ESSRLKLEGSLR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| ALQKNQEDSSRRVDLEVARMQAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGSLR
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	811328898876648999999999998158889999999999999999999999998774778999861479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| ALQKNQEDSSRRVDLEVARMQAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGSLR
Prediction	835565754444253524514441362356131411444251143145213314541544753434456648
	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

                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
ALQKNQEDSSRRVDLEVARMQAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGSLR

3tnuA

0.12

4.38

1.67

DEthreader

SELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKILLV

1t1mC2

0.10

3.62

0.39

CEthreader

RPTTEQREKWVKKAKEIVEEGKIAIRNIRREILKKIKEDQKEGLIPEDDAKRLENEIQKLTDEFIEKLDEVF

2bvlA

0.11

4.00

0.42

EigenThreader

EIDELNTYIEESLNKITQNLYEQELVELAAASDILRISALKEIGCSNLIVKQIENRYKILNNSLNPAISEDN

6rwbA1

0.18

5.86

0.66

FFAS-3D

-LRNSADKVIRSIAKSIGSINNSMDDIDSTISIRNMYKALKLVSNLEKSKIQLEGKKKEEEIKLEQAKDNIQ

6w2rA2

0.12

0.11

3.94

0.74

SPARKS-K

EDAKKAVKLVQEAYKAAQRAIEAAKRTGTPDVIKLAIKLAKLAARAALEVIKSEEVNEALKKIVKAIQ----

4d1eA

0.18

5.88

0.47

CNFpred

ELNELDYHDAVNVNDRCQKICDQWDRLGTLTQREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ

3k5bA

0.03

1.75

1.67

DEthreader

EVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEE

6h7dA1

0.06

2.49

0.79

MapAlign

FDNQMLQLFTSSLYLAALVASFMASVISMFIGGLAFLIGALFNLIIGRLLLGVGVGFANQSTPVYLSEMAP-

6qajA

0.19

6.25

0.56

MUSTER

KSTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQE

1vt4I

0.18

5.86

0.64

HHsearch

ILSKEEIDHI-IMSSGTLRLFWTLLSKQEEMVQKFVEEVLRINKFLMSPQPSMMTRMYIEQRDRLYNDNQVF

(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	0.6419

(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	6fkfb	0.80	1.63	0.071	0.972	model1_6fkfb.pdb.gz
2	7d6dA2	0.79	1.64	0.100	0.972	model1_7d6dA2.pdb.gz
3	5nenA	0.77	2.05	0.029	0.972	model1_5nenA.pdb.gz
4	6rw9A	0.77	2.20	0.070	0.986	model1_6rw9A.pdb.gz
5	3tnuA	0.77	1.78	0.100	0.972	model1_3tnuA.pdb.gz
6	6zpjA	0.77	1.82	0.071	0.972	model1_6zpjA.pdb.gz
7	6ltjI	0.76	2.16	0.099	0.986	model1_6ltjI.pdb.gz
8	6u0uA	0.76	1.89	0.042	0.986	model1_6u0uA.pdb.gz
9	6ewyA	0.76	1.98	0.042	0.986	model1_6ewyA.pdb.gz
10	4tqlA	0.76	1.79	0.100	0.972	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	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0003677	0.61	DNA binding
GO:0001071	0.61	nucleic acid binding transcription factor activity
GO:0098811	0.59	transcriptional repressor activity, RNA polymerase II activating transcription factor binding
GO:0001134	0.59	transcription factor activity, transcription factor recruiting
GO:0001083	0.59	transcription factor activity, RNA polymerase II basal transcription factor binding
GO:0000987	0.59	core promoter proximal region sequence-specific DNA binding
GO:0000977	0.59	RNA polymerase II regulatory 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:0009987	0.81	cellular process
GO:0044699	0.76	single-organism process
GO:0050794	0.73	regulation of cellular process
GO:0044763	0.73	single-organism cellular process
GO:0008152	0.71	metabolic process
GO:0071704	0.69	organic substance metabolic process
GO:0044238	0.69	primary metabolic process
GO:0044237	0.69	cellular metabolic process
GO:0044710	0.66	single-organism metabolic process
GO:0044281	0.64	small molecule metabolic process
GO:0006807	0.64	nitrogen compound metabolic process
GO:0048523	0.63	negative regulation of cellular process
GO:1901576	0.61	organic substance biosynthetic process
GO:1901564	0.61	organonitrogen compound metabolic process
GO:0080090	0.61	regulation of primary metabolic process
GO:0048583	0.61	regulation of response to stimulus
GO:0044249	0.61	cellular biosynthetic process
GO:0031324	0.61	negative regulation of cellular metabolic process
GO:0010646	0.61	regulation of cell communication
GO:0010605	0.61	negative regulation of macromolecule metabolic process
GO:1903832	0.59	regulation of cellular response to amino acid starvation
GO:1901566	0.59	organonitrogen compound biosynthetic process
GO:0090294	0.59	nitrogen catabolite activation of transcription
GO:0060261	0.59	positive regulation of transcription initiation from RNA polymerase II promoter
GO:0046394	0.59	carboxylic acid biosynthetic process
GO:0045898	0.59	regulation of RNA polymerase II transcriptional preinitiation complex assembly
GO:0032109	0.59	positive regulation of response to nutrient levels
GO:0010688	0.59	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter
GO:0010647	0.59	positive regulation of cell communication
GO:0006520	0.59	cellular amino acid metabolic process
GO:0001079	0.59	nitrogen catabolite 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	0.94	intracellular part
GO:0043227	0.86	membrane-bounded organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0016020	0.80	membrane
GO:0044446	0.74	intracellular organelle part
GO:0044444	0.74	cytoplasmic part
GO:0005829	0.60	cytosol
GO:0005634	0.58	nucleus
GO:0005737	0.53	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	0.136	2h8nA	0.684	2.00	0.090	0.931	3.5.1.98	NA
2	0.089	1wt6B	0.636	2.50	0.061	0.917	2.7.11.1	NA
3	0.068	1qleD	0.472	2.05	0.048	0.556	1.9.3.1	NA
4	0.067	3brvC	0.454	1.82	0.050	0.556	2.7.11.10	NA
5	0.066	3e7kH	0.539	2.49	0.036	0.764	2.7.11.1	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.05	1zv8C	0.504	2.35	0.156	0.625	1.12	III	complex1.pdb.gz	18,21,24,25,28,31,32,35,36,41,42,45,48,49,52,56,60
2	0.04	1zv8A	0.509	2.00	0.133	0.625	1.11	III	complex2.pdb.gz	30,33,34,37,39,40,43,44,46,47,50,51,54,57,58
3	0.04	1gd20	0.656	2.38	0.063	0.861	1.14	III	complex3.pdb.gz	27,31,32,34,35,37,40,41,44,47,48,51,52,55,58,59,61,62
4	0.03	1w7i0	0.501	3.05	0.108	0.736	0.89	III	complex4.pdb.gz	28,31,33,35,36,37,41,42,43,44,46,47,50,53
5	0.02	1t2k1	0.659	1.63	0.052	0.806	1.05	III	complex5.pdb.gz	20,27,28,30,31,34,35,37,40,41,47,48,50,54

	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.