D-I-TASSER Q9NPC8-D3

D-I-TASSER results for Q9NPC8-D3

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

Input Sequence in FASTA format

>Q9NPC8 (86 residues)
KSVLGSSEDEKTPSGTPDHSSSSPALLLSPPPPGLPSLHSLGHPPGPSAVPVPVPGGGGA
DPLQHHHGLQDSILNPMSANLVDLGS

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| KSVLGSSEDEKTPSGTPDHSSSSPALLLSPPPPGLPSLHSLGHPPGPSAVPVPVPGGGGADPLQHHHGLQDSILNPMSANLVDLGS
Prediction	CCCCCCCCCCCCCCCCCCCCCCCHHHSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHCCC
Confidence	96445666667999998778998121107899999875557899998656556788888772565555543211233454432179
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| KSVLGSSEDEKTPSGTPDHSSSSPALLLSPPPPGLPSLHSLGHPPGPSAVPVPVPGGGGADPLQHHHGLQDSILNPMSANLVDLGS
Prediction	85336556566445544644444213124465443343452443444433424464464443354444345322442344236348
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCHHHSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHCCC
KSVLGSSEDEKTPSGTPDHSSSSPALLLSPPPPGLPSLHSLGHPPGPSAVPVPVPGGGGADPLQHHHGLQDSILNPMSANLVDLGS

5oqlO1

0.05

2.26

0.52

CEthreader

PSDLDQPIKQILIFGGWIVACALTRIEVWKAATLEHYTTIFPAASKKGDNELTGGAINFVGRKDGWVEIWNVSTGKLIYTLLPPSP

7nepP

0.06

2.57

0.60

EigenThreader

KLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEL

2ftcD1

0.09

0.08

3.10

0.30

FFAS-3D

---KNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRAGLKVALTVKL-----

3hgfC

0.02

1.59

1.23

SPARKS-K

ENIVTKIDKKKYIY---KKLLNEIAEIEKDKTSLEEVKNNMSYGKSLNKLFLEKIKKKSENMIKSMEKYIKDLDEIKEQSPKAEMN

5x4hA

0.11

0.02

0.84

0.44

CNFpred

--------------------------------------------------------------------IRDTLVGIAASMAINAGL

3b8cA2

0.07

2.84

1.00

DEthreader

LTTQEEDGREALDIIPASGHTFKAA-HLVDST-NQVG-HFQVSMAGHLSAIAVPG-LSVIISAVLTSRAIFQRMKNYTIYAVSITI

2bibA

0.07

2.86

0.89

MapAlign

MDSTGVMKTGEIEVAGQHYYLEDSGAMKQGWH--KKANDWYFYKTDGSRAVGWIKDKDKWYFLKENGQLLVNGKTPEGYTVDSSGA

5tx1R

0.15

5.07

0.64

MUSTER

QNVMGSTVDGR-PVLPANSSTMTYATVGNSSLDSTAAAAAAAAAMTATRLASSYMPSSGSSPSVPSSIIAEEKLLALLAELEALSR

2yy4A2

0.30

0.10

3.17

0.50

HHsearch

RTILGSTEDEFTPFDVVRQCSG---VTFQG---------KFK--------------------------------------------

3fssA2

0.09

0.08

3.10

0.51

CEthreader

QCHRGTKEGTLYFLPDHIIFGFKKPILLLDAS--DIESITYSSITRLTFNASLVTKDGEKYEFSIDQTEYAKIDDYVKRK------

(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	0.5672

(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	3umvA1	0.49	4.28	0.037	0.895	model1_3umvA1.pdb.gz
2	3qljA	0.48	3.40	0.045	0.767	model1_3qljA.pdb.gz
3	1uwkA	0.48	4.15	0.097	0.837	model1_1uwkA.pdb.gz
4	6k8sA	0.48	3.45	0.119	0.767	model1_6k8sA.pdb.gz
5	1qnfA1	0.47	4.19	0.048	0.849	model1_1qnfA1.pdb.gz
6	2fknB2	0.47	4.14	0.125	0.826	model1_2fknB2.pdb.gz
7	1iy8A	0.47	3.67	0.000	0.779	model1_1iy8A.pdb.gz
8	1hxhA	0.47	3.71	0.072	0.779	model1_1hxhA.pdb.gz
9	1h5qL	0.46	3.78	0.058	0.791	model1_1h5qL.pdb.gz
10	4u63A	0.46	4.05	0.063	0.814	model1_4u63A.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	1.00	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.86	heterocyclic compound binding
GO:0097159	0.86	organic cyclic compound binding
GO:0003676	0.85	nucleic acid binding
GO:0003677	0.84	DNA binding
GO:0043565	0.82	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:0048513	1.00	animal organ development
GO:0044767	1.00	single-organism developmental process
GO:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0009987	0.93	cellular process
GO:0001822	0.93	kidney development
GO:0050794	0.92	regulation of cellular process
GO:0044763	0.91	single-organism cellular process
GO:0048869	0.90	cellular developmental process
GO:0030154	0.89	cell differentiation
GO:0048522	0.85	positive regulation of cellular process
GO:0044707	0.84	single-multicellular organism process
GO:0009653	0.84	anatomical structure morphogenesis
GO:2000026	0.83	regulation of multicellular organismal development
GO:0048562	0.83	embryonic organ morphogenesis
GO:0022603	0.83	regulation of anatomical structure morphogenesis
GO:0016477	0.83	cell migration
GO:0007389	0.83	pattern specification process
GO:0090189	0.82	regulation of branching involved in ureteric bud morphogenesis
GO:0080090	0.72	regulation of primary metabolic process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0060255	0.71	regulation of macromolecule metabolic process
GO:0009893	0.71	positive regulation of metabolic process
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0006355	0.70	regulation of transcription, DNA-templated
GO:0045893	0.69	positive regulation of transcription, DNA-templated
GO:0048523	0.68	negative regulation of cellular process
GO:0006357	0.68	regulation of transcription from RNA polymerase II promoter
GO:0045944	0.67	positive regulation of transcription from RNA polymerase II promoter
GO:0048701	0.66	embryonic cranial skeleton morphogenesis
GO:0045595	0.66	regulation of cell differentiation
GO:0009888	0.57	tissue development
GO:0048839	0.56	inner ear development
GO:0007519	0.56	skeletal muscle tissue development
GO:0048729	0.51	tissue morphogenesis
GO:0035148	0.51	tube formation
GO:0090190	0.50	positive regulation of branching involved in ureteric bud morphogenesis
GO:0072172	0.50	mesonephric tubule formation
GO:0072107	0.50	positive regulation of ureteric bud formation
GO:0072095	0.50	regulation of branch elongation involved in ureteric bud branching
GO:0072075	0.50	metanephric mesenchyme development
GO:0051451	0.50	myoblast migration
GO:0048699	0.50	generation of neurons
GO:0048538	0.50	thymus development
GO:0045664	0.50	regulation of neuron differentiation
GO:0043524	0.50	negative regulation of neuron apoptotic process
GO:0042472	0.50	inner ear morphogenesis
GO:0030878	0.50	thyroid gland development
GO:0030855	0.50	epithelial cell differentiation
GO:0001759	0.50	organ induction
GO:0001658	0.50	branching involved in ureteric bud morphogenesis
GO:0001657	0.50	ureteric bud development

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:0005634	1.00	nucleus
GO:0032991	0.67	macromolecular complex
GO:0043234	0.66	protein complex
GO:0005667	0.64	transcription factor complex
GO:0044446	0.61	intracellular organelle part
GO:0044428	0.58	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	3dbmA	0.474	3.95	0.059	0.826	4.2.1.92	71
2	0.060	1iy8A	0.467	3.67	0.000	0.779	1.1.1.-	37
3	0.060	1so8A	0.402	4.02	0.087	0.721	1.1.1.35 1.1.1.178	NA
4	0.060	3dsiA	0.465	3.78	0.047	0.802	4.2.1.92	74
5	0.060	1u7tA	0.473	3.73	0.074	0.791	1.1.1.178 1.1.1.35	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	1so8A	0.402	4.02	0.087	0.721	0.62	NA	complex1.pdb.gz	46,67,68,70

	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.