D-I-TASSER Q9NPJ1-D3

D-I-TASSER results for Q9NPJ1-D3

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

Input Sequence in FASTA format

>Q9NPJ1 (263 residues)
VDFSSTQILLCLVRSILTSKPACMLTRKETEHVSALILRAFLLTIPENAEGHIILGKSLI
VPLKGQRVIDSTVLPGILIEMSEVQLMRLLPIKKSTALKVALFCTTLSGDTSDTGEGTVV
VSYGVSLENAVLDQLLNLGRQLISDHVDLVLCQKVIHPSLKQFLNMHRIIAIDRIGVTLM
EPLTKMTGTQPIGSLGSICPNSYGSVKDVCTAKFGSKHFFHLIPNEATICSLLLCNRNDT
AWDELKLTCQTALHVLQLTLKEP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| VDFSSTQILLCLVRSILTSKPACMLTRKETEHVSALILRAFLLTIPENAEGHIILGKSLIVPLKGQRVIDSTVLPGILIEMSEVQLMRLLPIKKSTALKVALFCTTLSGDTSDTGEGTVVVSYGVSLENAVLDQLLNLGRQLISDHVDLVLCQKVIHPSLKQFLNMHRIIAIDRIGVTLMEPLTKMTGTQPIGSLGSICPNSYGSVKDVCTAKFGSKHFFHLIPNEATICSLLLCNRNDTAWDELKLTCQTALHVLQLTLKEP
Prediction	CCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSCCCCHHHCSSSSSSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCSSSSSCHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSCCCCCHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHCCSSSCCCCCCCHHHCSSSSSSSSSSSCCSSSSSSSCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	99764999999999997167863223455999999999999995254678986555468998039892224898449980754578899776556785799981788877641354499828089999999999999999999619969996688888999999990983998258789999999979977367112996367155279999988948999977999869999976988999999999999999999997486
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| VDFSSTQILLCLVRSILTSKPACMLTRKETEHVSALILRAFLLTIPENAEGHIILGKSLIVPLKGQRVIDSTVLPGILIEMSEVQLMRLLPIKKSTALKVALFCTTLSGDTSDTGEGTVVVSYGVSLENAVLDQLLNLGRQLISDHVDLVLCQKVIHPSLKQFLNMHRIIAIDRIGVTLMEPLTKMTGTQPIGSLGSICPNSYGSVKDVCTAKFGSKHFFHLIPNEATICSLLLCNRNDTAWDELKLTCQTALHVLQLTLKEP
Prediction	74473462023002000221333302451142005000400230046567651306204012254351510310410003233336735444540530000000020427356345333334543412530152025005401744030000333024102400462401002304562042003104030133165045721030430223514542001122773300000000115300520230041002002201658
	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                 200                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSSSSCCCCHHHCSSSSSSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCSSSSSCHHHHHHHHHHHHHHHHHHHHHHHCCCSSSSCCCCCHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHCCSSSCCCCCCCHHHCSSSSSSSSSSSCCSSSSSSSCCCCCSSSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHHCC
VDFSSTQILLCLVRSILTSKPACMLTRKETEHVSALILRAFLLTIPENAEGHIILGKSLIVPLKGQRVIDSTVLPGILIEMSEVQLMRLLPIKKSTALKVALFCTTLSGDTSDTGEGTVVVSYGVSLENAVLDQLLNLGRQLISDHVDLVLCQKVIHPSLKQFLNMHRIIAIDRIGVTLMEPLTKMTGTQPIGSLGSICPNSYGSVKDVCTAKFGSKHFFHLIPNEATICSLLLCNRNDTAWDELKLTCQTALHVLQLTLKEP

3ko1A

0.16

5.28

1.50

DEthreader

VSINDTDLLRKIAMTSLSSKAVA--G--AREYIADIVVKAVTQVAELRGKWYVDLDNIQIVKKAGGSINDTQLVYGIVVDKEV-VHP-GMPKR-LENAKIALIDASLEVEKPEL-DAEIRINTQQKFLDEEENLIKEKVDKILATGANVIICQKGIDEVAQSYLAKKGVLAVRRAKKSDLEKLARATGGRVVSNIDEISEQDLGYASLIEERKVGEDKMVFVEAKNPKSISILIRGGLERLVDETERALRDALGTVADVIKDG

1q3rA

0.19

0.18

5.89

2.26

SPARKS-K

VDPDDEETLLKIAATSITGKN----AESHKELLAKLAVEAVKQVAEKKDGKVVDLDNIKFEKKAGEGVEESELVRGVVIDKEVV--HPRMP-KRVENAKIALINEALEVKKTETDAKI---NITMSFLEQEEKMLKDMVDHIAQTGANVVFVQKGIDDLAQHYLAKYGIMAVRRVKKSDMEKLAKATGAKIVTNVKDLTPEDLGYAEVVEERKLAGENMIFVEGCNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDG

1a6eB

0.18

0.17

5.59

1.24

MapAlign

IGADEKALLLKMAQTSLNSKSAS----VAKDKLAEISYEAVKSVAERDGKYYVDFDNIQVVKKQGGAIDDTQLINGIIVDKEKV-HP-GM-PDVVKDAKIALLDAPLEIKKPEFDTLRIEDPSMIKFLAQEENMLREMVDKIKSVGANVVITQKGIDDMAQHYLSRAGIYAVRRVKKSDMDKLAKATGASIVSTIDEISSSDLGTAERVEQVKVGEDYMTFVTCKNPKAVSILVRGETEHVVDEMERSITDSLHVVASALEDG

1a6eB

0.18

0.17

5.70

0.70

CEthreader

IGADEKALLLKMAQTSLNSK----SASVAKDKLAEISYEAVKSVAELRGKYYVDFDNIQVVKKQGGAIDDTQLINGIIVDKEKV--HPGMP-DVVKDAKIALLDAPLEIKKPEFDTNLRDPSMIQKFLAQEENMLREMVDKIKSVGANVVITQKGIDDMAQHYLSRAGIYAVRRVKKSDMDKLAKATGASIVSTIDEISSSDLGTAERVEQVKVGEDYMTFVTGCNPKAVSILVRGETEHVVDEMERSITDSLHVVASALEDG

1q3rA

0.18

5.79

1.88

MUSTER

VDPDDEETLLKIAATSITGK----NAESHKELLAKLAVEAVKQVAEKKDGKVVDLDNIKFEKKAGEGVEESELVRGVVIDKEVVHPRM---PKRVENAKIALINEALEVKKTETDAKINI-DQLMSFLEQEEKMLKDMVDHIAQTGANVVFVQKGIDDLAQHYLAKYGIMAVRRVKKSDMEKLAKATGAKIVTNVKDLTPEDLGYAEVVEERKLAGENMIFVEGCNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDG

3p9dG2

0.17

0.16

5.26

1.95

HHsearch

--DITSELLERCARTAMSSKLIH--N--NADFFVKMCVDAVLSLDRN----DLDDKLIGIKKIPGGAMEESLFINGVAFKKTFS--YAGQP-KKFNNPKILSLNVELELKAEKD-NAEVRVEHDYAIVDAEWQLIFEKLRQVEETGANIVLSKLPIGDLATQFFADRNIFCAGRVSADDMNRVIQAVGGSIQSTTSDIKPEHLGTCALFEEMQIGSERYNLFQGCQAKTCTLLLRGGAEQVIAEVERSLHDAIMIVKRALQNK

3p9dG2

0.17

0.16

5.27

2.35

FFAS-3D

-DI-TSELLERCARTAMSSK----LIHNNADFFVKMCVDAVLSLDRNDLD----DKLIGIKKIPGGAMEESLFINGVAFKKTFSYAGFEQQPKKFNNPKILSLNVELELKAEKDNAEVRVEEDYQAIVDAEWQLIFEKLRQVEETGANIVLSKLPIGDLATQFFADRNIFCAGRVSADDMNRVIQAVGGSIQSTTSDIKPEHLGTCALFEEMQIGSERYNLFGCPQAKTCTLLLRGGAEQVIAEVERSLHDAIMIVKRALQN-

3p9dG2

0.17

0.16

5.15

1.57

EigenThreader

DITSEL--LERCARTAMSSKLI----HNNADFFVKMCVDAVLSL----DRNDLDDKLIGIKKIPGGAMEESLFINGVAFKKTFSYAGFEQQPKKFNNPKILSLNVELELKAEKDNAEV-----RVEHVDAEWQLIFEKLRQVEETGANIVLSKLPIGDLATQFFADRNIFCAGRVSADDMNRVIQAVGGSIQSTTSDIKPEHLGTCALFEEMQIGSERYNLFQGCPAKTCTLLLRGGAEQVIAEVERSLHDAIMIVKRALQNK

1a6dB

0.18

0.17

5.59

2.40

CNFpred

IGADEKALLLKMAQTSLNSKSASV----AKDKLAEISYEAVKSVAELRGKYYVDFDNIQVVKKQGGAIDDTQLINGIIVDKE--KVHPGMP-DVVKDAKIALLDAPLEIKKPEF-DTNLRIEDIQKFLAQEENMLREMVDKIKSVGANVVITQKGIDDMAQHYLSRAGIYAVRRVKKSDMDKLAKATGASIVSTIDEISSSDLGTAERVEQVKVGEDYMTFVTGCKPKAVSILVRGETEHVVDEMERSITDSLHVVASALEDG

1a6eA

0.19

0.18

5.89

1.50

DEthreader

KST-DDATLRKIALTALSGKNT--G-L-SNDFLADLVVKAVNAVAEVRGKTIVDTANIKVDKKNGGSVNDTQFISGIVIDKEK-VHS-KMPDV-VKNAKIALIDSALEIKKTEIEA-KVQISDKQDFLNQETNTFKQMVEKIKKSGANVVLCQKGIDDVAQHYLAKEGIYAVRRVKKSDMEKLAKATGAKIVTDLDDLTPSVLGEAETVEERKIGDDRMTFVMGKNPKAVSILIRGGTDHVVSEVERALNDAIRVVAITKEDG

(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	0.884

(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	1a6eB	0.95	1.13	0.180	0.973	model1_1a6eB.pdb.gz
2	1a6eA	0.95	0.97	0.184	0.970	model1_1a6eA.pdb.gz
3	3ko1A	0.92	1.79	0.168	0.973	model1_3ko1A.pdb.gz
4	3iygH	0.91	1.78	0.105	0.977	model1_3iygH.pdb.gz
5	7lumO	0.90	2.05	0.133	0.973	model1_7lumO.pdb.gz
6	1q3rA	0.89	1.88	0.176	0.973	model1_1q3rA.pdb.gz
7	3iygE	0.89	2.08	0.133	0.970	model1_3iygE.pdb.gz
8	7lumN	0.89	1.93	0.188	0.970	model1_7lumN.pdb.gz
9	3iygG	0.89	2.15	0.191	0.973	model1_3iygG.pdb.gz
10	7lumI	0.88	1.88	0.171	0.958	model1_7lumI.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:0001103	1.00	RNA polymerase II repressing transcription factor binding
GO:0051082	0.57	unfolded protein 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:0044707	1.00	single-multicellular organism process
GO:0042384	1.00	cilium assembly
GO:0009653	1.00	anatomical structure morphogenesis
GO:0048869	0.84	cellular developmental process
GO:0060271	0.83	cilium morphogenesis
GO:0065007	0.74	biological regulation
GO:0051179	0.74	localization
GO:0050789	0.74	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0044765	0.73	single-organism transport
GO:1902580	0.72	single-organism cellular localization
GO:0060562	0.72	epithelial tube morphogenesis
GO:0051650	0.72	establishment of vesicle localization
GO:0046907	0.72	intracellular transport
GO:0007389	0.72	pattern specification process
GO:0060027	0.71	convergent extension involved in gastrulation
GO:0051877	0.71	pigment granule aggregation in cell center
GO:0032402	0.71	melanosome transport
GO:0007368	0.71	determination of left/right symmetry
GO:0001947	0.71	heart looping
GO:0050896	0.69	response to stimulus
GO:0065008	0.68	regulation of biological quality
GO:0051704	0.68	multi-organism process
GO:0048583	0.68	regulation of response to stimulus
GO:0048519	0.68	negative regulation of biological process
GO:0022414	0.68	reproductive process
GO:0007165	0.68	signal transduction
GO:0060296	0.67	regulation of cilium beat frequency involved in ciliary motility
GO:0050910	0.67	detection of mechanical stimulus involved in sensory perception of sound
GO:0048854	0.67	brain morphogenesis
GO:0045494	0.67	photoreceptor cell maintenance
GO:0045444	0.67	fat cell differentiation
GO:0038108	0.67	negative regulation of appetite by leptin-mediated signaling pathway
GO:0035176	0.67	social behavior
GO:0021987	0.67	cerebral cortex development
GO:0021766	0.67	hippocampus development
GO:0021756	0.67	striatum development
GO:0007608	0.67	sensory perception of smell
GO:0007286	0.67	spermatid 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:0031514	1.00	motile cilium
GO:0005813	1.00	centrosome
GO:0005622	1.00	intracellular

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	1fa9A	0.382	5.77	0.056	0.616	2.4.1.1	NA
2	0.060	3a3iA	0.405	5.58	0.072	0.627	3.4.16.4	183
3	0.060	1c7sA	0.327	6.05	0.067	0.547	3.2.1.52	NA
4	0.060	1hp4A	0.391	5.88	0.043	0.635	3.2.1.52	NA
5	0.060	2vkzG	0.382	5.67	0.050	0.624	2.3.1.38 3.1.2.14	76,181

	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	0.10	3kfeB	0.791	2.26	0.197	0.890	0.14	UUU	complex1.pdb.gz	79,92,172
2	0.02	1aonC	0.578	4.12	0.093	0.783	0.15	ADP	complex2.pdb.gz	186,204,209
3	0.01	1pcqA	0.588	4.01	0.093	0.779	0.12	UUU	complex3.pdb.gz	76,77,187,188
4	0.01	3itoB	0.419	5.76	0.043	0.665	0.11	PSV	complex4.pdb.gz	185,189,225
5	0.01	1dkdD	0.419	1.99	0.125	0.456	0.16	III	complex5.pdb.gz	64,70,71
6	0.01	1sjp0	0.487	4.05	0.088	0.624	0.23	III	complex6.pdb.gz	76,97,208,223,224,228

	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.