D-I-TASSER Q08AF3

D-I-TASSER results for Q08AF3

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

Summary of the Protein

Uniprot ID: Q08AF3
Protein Name: Schlafen family member 5
Gene Name: SLFN5

Input Sequence in FASTA format

>Q08AF3 (891 residues)
MSLRIDVDTNFPECVVDAGKVTLGTQQRQEMDPRLREKQNEIILRAVCALLNSGGGIIKA
EIENKGYNYERHGVGLDVPPIFRSHLDKMQKENHFLIFVKSWNTEAGVPLATLCSNLYHR
ERTSTDVMDSQEALAFLKCRTQTPTNINVSNSLGPQAAQGSVQYEGNINVSAAALFDRKR
LQYLEKLNLPESTHVEFVMFSTDVSHCVKDRLPKCVSAFANTEGGYVFFGVHDETCQVIG
CEKEKIDLTSLRASIDGCIKKLPVHHFCTQRPEIKYVLNFLEVHDKGALRGYVCAIKVEK
FCCAVFAKVPSSWQVKDNRVRQLPTREWTAWMMEADPDLSRCPEMVLQLSLSSATPRSKP
VCIHKNSECLKEQQKRYFPVFSDRVVYTPESLYKELFSQHKGLRDLINTEMRPFSQGILI
FSQSWAVDLGLQEKQGVICDALLISQNNTPILYTIFSKWDAGCKGYSMIVAYSLKQKLVN
KGGYTGRLCITPLVCVLNSDRKAQSVYSSYLQIYPESYNFMTPQHMEALLQSLVIVLLGF
KSFLSEELGSEVLNLLTNKQYELLSKNLRKTRELFVHGLPGSGKTILALRIMEKIRNVFH
CEPANILYICENQPLKKLVSFSKKNICQPVTRKTFMKNNFEHIQHIIIDDAQNFRTEDGD
WYGKAKFITQTARDGPGVLWIFLDYFQTYHLSCSGLPPPSDQYPREEINRVVRNAGPIAN
YLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIEDLNLEEILIYVANKCRFL
LRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEESDLLLQIGDASDVLTDHI
VLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKRHLYILKASV

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	Q08AF3-D1	1-340	340		MSLRIDVDTNFPECVVDAGKVTLGTQQRQEMDPRLREKQNEIILRAVCALLNSGGGIIKAEIENKGYNYERHGVGLDVPPIFRSHLDKMQKENHFLIFVKSWNTEAGVPLATLCSNLYHRERTSTDVMDSQEALAFLKCRTQTPTNINVSNSLGPQAAQGSVQYEGNINVSAAALFDRKRLQYLEKLNLPESTHVEFVMFSTDVSHCVKDRLPKCVSAFANTEGGYVFFGVHDETCQVIGCEKEKIDLTSLRASIDGCIKKLPVHHFCTQRPEIKYVLNFLEVHDKGALRGYVCAIKVEKFCCAVFAKVPSSWQVKDNRVRQLPTREWTAWMMEADPDLS
2	Q08AF3-D2	341-571	231		RCPEMVLQLSLSSATPRSKPVCIHKNSECLKEQQKRYFPVFSDRVVYTPESLYKELFSQHKGLRDLINTEMRPFSQGILIFSQSWAVDLGLQEKQGVICDALLISQNNTPILYTIFSKWDAGCKGYSMIVAYSLKQKLVNKGGYTGRLCITPLVCVLNSDRKAQSVYSSYLQIYPESYNFMTPQHMEALLQSLVIVLLGFKSFLSEELGSEVLNLLTNKQYELLSKNLRKT
3	Q08AF3-D3	572-702	131		RELFVHGLPGSGKTILALRIMEKIRNVFHCEPANILYICENQPLKKLVSFSKKNICQPVTRKTFMKNNFEHIQHIIIDDAQNFRTEDGDWYGKAKFITQTARDGPGVLWIFLDYFQTYHLSCSGLPPPSDQ
4	Q08AF3-D4	703-891	189		YPREEINRVVRNAGPIANYLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIEDLNLEEILIYVANKCRFLLRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEESDLLLQIGDASDVLTDHIVLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKRHLYILKASV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.49

(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	7cpxA	0.36	8.48	0.044	0.551	model1_7cpxA.pdb.gz
2	7lrdA	0.35	2.66	0.362	0.370	model1_7lrdA.pdb.gz
3	6rr9A	0.35	0.50	1.000	0.349	model1_6rr9A.pdb.gz
4	7ky5A	0.35	8.40	0.030	0.533	model1_7ky5A.pdb.gz
5	5xjcQ	0.34	8.45	0.054	0.533	model1_5xjcQ.pdb.gz
6	5kf6A	0.33	8.94	0.045	0.535	model1_5kf6A.pdb.gz
7	6vr4A	0.33	9.32	0.056	0.550	model1_6vr4A.pdb.gz
8	6lcpA	0.33	8.65	0.045	0.522	model1_6lcpA.pdb.gz
9	6r9tA	0.33	8.52	0.028	0.518	model1_6r9tA.pdb.gz
10	5yd0A	0.32	2.45	0.374	0.341	model1_5yd0A.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:0003824	0.71	catalytic activity
GO:0016787	0.65	hydrolase activity
GO:0016788	0.57	hydrolase activity, acting on ester bonds
GO:0044877	0.56	macromolecular complex binding
GO:0004519	0.56	endonuclease activity
GO:0043022	0.55	ribosome binding
GO:0004521	0.55	endoribonuclease activity
GO:1901363	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound 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	0.85	cellular process
GO:0050896	0.73	response to stimulus
GO:0065007	0.71	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0008152	0.69	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0044238	0.66	primary metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0043170	0.63	macromolecule metabolic process
GO:0044699	0.62	single-organism process
GO:0044260	0.62	cellular macromolecule metabolic process
GO:0006807	0.62	nitrogen compound metabolic process
GO:0006139	0.61	nucleobase-containing compound metabolic process
GO:0090304	0.59	nucleic acid metabolic process
GO:0051716	0.55	cellular response to stimulus
GO:0044763	0.53	single-organism cellular process
GO:0048519	0.52	negative regulation of biological process
GO:0044767	0.51	single-organism developmental process
GO:0048523	0.50	negative regulation of cellular 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	1.00	cell part
GO:0044424	0.94	intracellular part
GO:0043226	0.83	organelle
GO:0043227	0.81	membrane-bounded organelle
GO:0043229	0.80	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0005634	0.77	nucleus
GO:0005622	0.73	intracellular
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	0.060	2vz8B	0.304	8.56	0.043	0.469	2.3.1.85	NA
2	0.060	1bxrA	0.288	8.99	0.032	0.470	6.3.5.5	NA
3	0.060	1ob2A	0.185	7.41	0.057	0.267	3.6.1.48	NA
4	0.060	1hn0A	0.287	8.85	0.040	0.455	4.2.2.20	NA
5	0.060	2uv8G	0.271	9.05	0.034	0.438	2.3.1.86	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	1ofdB	0.308	8.69	0.041	0.484	0.24	F3S	complex1.pdb.gz	228,229,230,231,232,236
2	0.01	2c3uA	0.300	8.64	0.040	0.474	0.24	SF4	complex2.pdb.gz	229,233,237,241
3	0.01	1llwA	0.322	9.10	0.053	0.524	0.12	FMN	complex3.pdb.gz	199,200,201,202,231,240,242
4	0.01	1ofeA	0.311	9.15	0.045	0.511	0.15	ONL	complex4.pdb.gz	196,197,238,239
5	0.01	2uzaB	0.298	8.91	0.030	0.480	0.14	SF4	complex5.pdb.gz	232,233,294
6	0.01	1lm1A	0.323	9.21	0.051	0.530	0.39	F3S	complex6.pdb.gz	198,201,239
7	0.01	1b0pA	0.297	8.92	0.036	0.478	0.20	SF4	complex7.pdb.gz	197,198,294
8	0.01	2c3oB	0.293	8.93	0.044	0.475	0.25	SF4	complex8.pdb.gz	196,228,230
9	0.01	2c3oB	0.293	8.93	0.044	0.475	0.26	SF4	complex9.pdb.gz	228,229,240,241,283

	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.