D-I-TASSER Q9Y2H6

D-I-TASSER results for Q9Y2H6

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

Summary of the Protein

Uniprot ID: Q9Y2H6
Protein Name: Fibronectin type-III domain-containing protein 3A
Gene Name: FNDC3A

Input Sequence in FASTA format

>Q9Y2H6 (1198 residues)
MAEHPPLLDTTQILSSDISLLSAPIVSADGTQQVILVQVNPGEAFTIRREDGQFQCITGP
AQVPMMSPNGSVPPIYVPPGYAPQVIEDNGVRRVVVVPQAPEFHPGSHTVLHRSPHPPLP
GFIPVPTMMPPPPRHMYSPVTGAGDMTTQYMPQYQSSQVYGDVDAHSTHGRSNFRDERSS
KTYERLQKKLKDRQGTQKDKMSSPPSSPQKCPSPINEHNGLIKGQIAGGINTGSAKIKSG
KGKGGTQVDTEIEEKDEETKAFEALLSNIVKPVASDIQARTVVLTWSPPSSLINGETDES
SVPELYGYEVLISSTGKDGKYKSVYVGEETNITLNDLKPAMDYHAKVQAEYNSIKGTPSE
AEIFTTLSCEPDIPNPPRIANRTKNSLTLQWKAPSDNGSKIQNFVLEWDEGKGNGEFCQC
YMGSQKQFKITKLSPAMGCKFRLSARNDYGTSGFSEEVLYYTSGCAPSMPASPVLTKAGI
TWLSLQWSKPSGTPSDEGISYILEMEEETSGYGFKPKYDGEDLAYTVKNLRRSTKYKFKV
IAYNSEGKSNPSEVVEFTTCPDKPGIPVKPSVKGKIHSHSFKITWDPPKDNGGATINKYV
VEMAEGSNGNKWEMIYSGATREHLCDRLNPGCFYRLRVYCISDGGQSAVSESLLVQTPAV
PPGPCLPPRLQGRPKAKEIQLRWGPPLVDGGSPISCYSVEMSPIEKDEPREVYQGSEVEC
TVSSLLPGKTYSFRLRAANKMGFGPFSEKCDITTAPGPPDQCKPPQVTCRSATCAQVNWE
VPLSNGTDVTEYRLEWGGVEGSMQICYCGPGLSYEIKGLSPATTYYCRVQALSVVGAGPF
SEVVACVTPPSVPGIVTCLQEISDDEIENPHYSPSTCLAISWEKPCDHGSEILAYSIDFG
DKQSLTVGKVTSYIINNLQPDTTYRIRIQALNSLGAGPFSHMIKLKTKPLPPDPPRLECV
AFSHQNLKLKWGEGTPKTLSTDSIQYHLQMEDKNGRFVSLYRGPCHTYKVQRLNESTSYK
FCIQACNEAGEGPLSQEYIFTTPKSVPAALKAPKIEKVNDHICEITWECLQPMKGDPVIY
SLQVMLGKDSEFKQIYKGPDSSFRYSSLQLNCEYRFRVCAIRQCQDSLGHQDLVGPYSTT
VLFISQRTEPPASTNRDTVESTRTRRALSDEQCAAVILVLFAFFSILIAFIIQYFVIK

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9Y2H6-D1	1-183,563-755	376		MAEHPPLLDTTQILSSDISLLSAPIVSADGTQQVILVQVNPGEAFTIRREDGQFQCITGPAQVPMMSPNGSVPPIYVPPGYAPQVIEDNGVRRVVVVPQAPEFHPGSHTVLHRSPHPPLPGFIPVPTMMPPPPRHMYSPVTGAGDMTTQYMPQYQSSQVYGDVDAHSTHGRSNFRDERSSKTYKPGIPVKPSVKGKIHSHSFKITWDPPKDNGGATINKYVVEMAEGSNGNKWEMIYSGATREHLCDRLNPGCFYRLRVYCISDGGQSAVSESLLVQTPAVPPGPCLPPRLQGRPKAKEIQLRWGPPLVDGGSPISCYSVEMSPIEKDEPREVYQGSEVECTVSSLLPGKTYSFRLRAANKMGFGPFSEKCDITTA
2	Q9Y2H6-D2	184-463	280		ERLQKKLKDRQGTQKDKMSSPPSSPQKCPSPINEHNGLIKGQIAGGINTGSAKIKSGKGKGGTQVDTEIEEKDEETKAFEALLSNIVKPVASDIQARTVVLTWSPPSSLINGETDESSVPELYGYEVLISSTGKDGKYKSVYVGEETNITLNDLKPAMDYHAKVQAEYNSIKGTPSEAEIFTTLSCEPDIPNPPRIANRTKNSLTLQWKAPSDNGSKIQNFVLEWDEGKGNGEFCQCYMGSQKQFKITKLSPAMGCKFRLSARNDYGTSGFSEEVLYYTS
3	Q9Y2H6-D3	464-562	99		GCAPSMPASPVLTKAGITWLSLQWSKPSGTPSDEGISYILEMEEETSGYGFKPKYDGEDLAYTVKNLRRSTKYKFKVIAYNSEGKSNPSEVVEFTTCPD
4	Q9Y2H6-D4	756-851	96		PGPPDQCKPPQVTCRSATCAQVNWEVPLSNGTDVTEYRLEWGGVEGSMQICYCGPGLSYEIKGLSPATTYYCRVQALSVVGAGPFSEVVACVTPPS
5	Q9Y2H6-D5	852-949	98		VPGIVTCLQEISDDEIENPHYSPSTCLAISWEKPCDHGSEILAYSIDFGDKQSLTVGKVTSYIINNLQPDTTYRIRIQALNSLGAGPFSHMIKLKTKP
6	Q9Y2H6-D6	950-1045	96		LPPDPPRLECVAFSHQNLKLKWGEGTPKTLSTDSIQYHLQMEDKNGRFVSLYRGPCHTYKVQRLNESTSYKFCIQACNEAGEGPLSQEYIFTTPKS
7	Q9Y2H6-D7	1046-1198	153		VPAALKAPKIEKVNDHICEITWECLQPMKGDPVIYSLQVMLGKDSEFKQIYKGPDSSFRYSSLQLNCEYRFRVCAIRQCQDSLGHQDLVGPYSTTVLFISQRTEPPASTNRDTVESTRTRRALSDEQCAAVILVLFAFFSILIAFIIQYFVIK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.53

(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	0.27	9.44	0.022	0.418	model1_6fb3A.pdb.gz
2	6tpwA	0.27	3.52	0.149	0.290	model1_6tpwA.pdb.gz
3	7lhtA	0.27	9.96	0.043	0.432	model1_7lhtA.pdb.gz
4	3lxuX	0.26	8.89	0.036	0.388	model1_3lxuX.pdb.gz
5	7jptA	0.26	9.89	0.040	0.410	model1_7jptA.pdb.gz
6	4u48A	0.26	9.34	0.032	0.397	model1_4u48A.pdb.gz
7	6um1A	0.26	10.07	0.039	0.421	model1_6um1A.pdb.gz
8	6sytA	0.26	9.55	0.033	0.395	model1_6sytA.pdb.gz
9	7b54X	0.25	9.89	0.029	0.407	model1_7b54X.pdb.gz
10	5xjcA	0.25	10.37	0.036	0.427	model1_5xjcA.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:0004872	0.47	receptor activity
GO:0004871	0.47	signal transducer activity
GO:0038023	0.46	signaling receptor activity
GO:0004888	0.45	transmembrane signaling receptor activity
GO:0042802	0.41	identical protein binding
GO:0046983	0.34	protein dimerization activity
GO:0042803	0.32	protein homodimerization activity
GO:0008046	0.30	axon guidance receptor activity
GO:0003824	0.30	catalytic activity

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:0044699	0.91	single-organism process
GO:0009987	0.90	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0065007	0.74	biological regulation
GO:0032502	0.74	developmental process
GO:0050789	0.71	regulation of biological process
GO:0044767	0.67	single-organism developmental process
GO:0050794	0.66	regulation of cellular process
GO:0048856	0.59	anatomical structure development
GO:0048869	0.51	cellular developmental process

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	0.96	cell part
GO:0044424	0.69	intracellular part
GO:0044444	0.48	cytoplasmic part
GO:0044425	0.48	membrane part
GO:0044459	0.43	plasma membrane part
GO:0031224	0.42	intrinsic component of membrane
GO:0016021	0.41	integral component of membrane
GO:0016020	0.41	membrane
GO:0043226	0.38	organelle
GO:0031226	0.38	intrinsic component of plasma membrane
GO:0097458	0.37	neuron part
GO:0005887	0.37	integral component of plasma membrane
GO:0042995	0.36	cell projection
GO:0044422	0.35	organelle part
GO:0043227	0.35	membrane-bounded organelle
GO:0043005	0.33	neuron projection
GO:0043229	0.31	intracellular organelle
GO:0030424	0.31	axon
GO:0043025	0.30	neuronal cell body

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	2ckjA	0.219	10.12	0.036	0.356	1.17.1.4 1.17.3.2	NA
2	0.060	2vdcA	0.251	10.08	0.024	0.406	1.4.1.13	NA
3	0.060	1k32A	0.224	9.45	0.025	0.348	3.4.21.-	NA
4	0.060	1t3tA	0.231	10.23	0.040	0.383	6.3.5.3	NA
5	0.060	3eqlD	0.254	9.48	0.040	0.394	2.7.7.6	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	1lm1A	0.245	9.95	0.035	0.392	0.29	F3S	complex1.pdb.gz	235,236,237,238
2	0.01	2vdcB	0.246	10.09	0.032	0.399	0.11	FMN	complex2.pdb.gz	239,240,241,242
3	0.01	2x2iB	0.241	9.09	0.024	0.363	0.20	QPS	complex3.pdb.gz	234,235,236,239,243,244
4	0.01	3ir5A	0.241	10.21	0.036	0.397	0.24	SF4	complex4.pdb.gz	223,237,245
5	0.01	3pt6B	0.240	9.05	0.041	0.364	0.14	SAH	complex5.pdb.gz	222,223,224,237,238,240
6	0.01	1ea0B	0.247	10.16	0.022	0.403	0.11	FMN	complex6.pdb.gz	239,240,241,242
7	0.01	3pt9A	0.231	8.91	0.047	0.348	0.16	SAH	complex7.pdb.gz	220,221,222,224,230,236
8	0.01	1ofdA	0.244	9.85	0.027	0.389	0.17	F3S	complex8.pdb.gz	237,239,246
9	0.01	3av6A	0.240	9.93	0.053	0.390	0.10	SAM	complex9.pdb.gz	200,209,234,235,244

	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.