D-I-TASSER Q14894

D-I-TASSER results for Q14894

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

Summary of the Protein

Uniprot ID: Q14894
Protein Name: Ketimine reductase mu-crystallin
Gene Name: CRYM

Input Sequence in FASTA format

>Q14894 (314 residues)
MSRVPAFLSAAEVEEHLRSSSLLIPPLETALANFSSGPEGGVMQPVRTVVPVTKHRGYLG
VMPAYSAAEDALTTKLVTFYEDRGITSVVPSHQATVLLFEPSNGTLLAVMDGNVITAKRT
AAVSAIATKFLKPPSSEVLCILGAGVQAYSHYEIFTEQFSFKEVRIWNRTKENAEKFADT
VQGEVRVCSSVQEAVAGADVIITVTLATEPILFGEWVKPGAHINAVGASRPDWRELDDEL
MKEAVLYVDSQEAALKESGDVLLSGAEIFAELGEVIKGVKPAHCEKTTVFKSLGMAVEDT
VAAKLIYDSWSSGK

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 AttentionPotential. 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	Q14894-D1	1-314	314		MSRVPAFLSAAEVEEHLRSSSLLIPPLETALANFSSGPEGGVMQPVRTVVPVTKHRGYLGVMPAYSAAEDALTTKLVTFYEDRGITSVVPSHQATVLLFEPSNGTLLAVMDGNVITAKRTAAVSAIATKFLKPPSSEVLCILGAGVQAYSHYEIFTEQFSFKEVRIWNRTKENAEKFADTVQGEVRVCSSVQEAVAGADVIITVTLATEPILFGEWVKPGAHINAVGASRPDWRELDDELMKEAVLYVDSQEAALKESGDVLLSGAEIFAELGEVIKGVKPAHCEKTTVFKSLGMAVEDTVAAKLIYDSWSSGK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9363

(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 AttentionPotential, 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	2i99A	0.99	0.52	1.000	0.994	model1_2i99A.pdb.gz
2	6t3eA	0.94	1.36	0.367	0.971	model1_6t3eA.pdb.gz
3	5gziB	0.90	2.23	0.276	0.981	model1_5gziB.pdb.gz
4	1vllA	0.89	1.98	0.313	0.955	model1_1vllA.pdb.gz
5	6rqaA	0.89	2.16	0.246	0.965	model1_6rqaA.pdb.gz
6	1u7hA	0.88	1.72	0.222	0.933	model1_1u7hA.pdb.gz
7	4mp3A	0.87	2.22	0.212	0.946	model1_4mp3A.pdb.gz
8	3hdjA	0.86	2.13	0.265	0.927	model1_3hdjA.pdb.gz
9	2haeA	0.52	4.43	0.142	0.672	model1_2haeA.pdb.gz
10	2hk7A	0.50	4.16	0.163	0.624	model1_2hk7A.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	0.72	catalytic activity
GO:1901363	0.66	heterocyclic compound binding
GO:0097159	0.66	organic cyclic compound binding
GO:0000166	0.64	nucleotide binding
GO:0046983	0.61	protein dimerization activity
GO:0042803	0.60	protein homodimerization activity
GO:0000989	0.60	transcription factor activity, transcription factor binding
GO:0048037	0.59	cofactor binding
GO:0003714	0.59	transcription corepressor activity
GO:0050662	0.58	coenzyme binding
GO:0070324	0.50	thyroid hormone binding
GO:0050661	0.50	NADP 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:0044699	0.82	single-organism process
GO:0009987	0.82	cellular process
GO:0008152	0.76	metabolic process
GO:0006810	0.76	transport
GO:0071704	0.74	organic substance metabolic process
GO:0044237	0.73	cellular metabolic process
GO:1901564	0.70	organonitrogen compound metabolic process
GO:0065007	0.70	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0080090	0.61	regulation of primary metabolic process
GO:0048523	0.61	negative regulation of cellular process
GO:0044763	0.60	single-organism cellular process
GO:0006355	0.60	regulation of transcription, DNA-templated
GO:0000122	0.59	negative regulation of transcription from RNA polymerase II promoter
GO:0044765	0.55	single-organism transport
GO:0044710	0.54	single-organism metabolic process
GO:0044281	0.52	small molecule metabolic process
GO:0032501	0.52	multicellular organismal process
GO:0065008	0.51	regulation of biological quality
GO:0007600	0.51	sensory perception
GO:0071705	0.50	nitrogen compound transport
GO:0071702	0.50	organic substance transport
GO:0010817	0.50	regulation of hormone levels

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:0044424	1.00	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0005737	0.69	cytoplasm
GO:0043226	0.67	organelle
GO:0043227	0.66	membrane-bounded organelle
GO:0044421	0.54	extracellular region part
GO:0070062	0.53	extracellular exosome

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	0.066	2hk7A	0.499	4.16	0.163	0.624	1.1.1.25	NA
2	0.066	2be9A	0.532	4.44	0.107	0.707	2.1.3.2	NA
3	0.066	1ml4A	0.547	4.84	0.061	0.742	2.1.3.2	NA
4	0.066	1wxdA	0.484	4.16	0.176	0.608	1.1.1.25	NA
5	0.066	2ef0A	0.522	4.57	0.089	0.694	2.1.3.3	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	0.74	2i99A	0.988	0.52	1.000	0.994	1.78	NDP	complex1.pdb.gz	82,91,92,116,119,120,143,144,145,146,147,168,169,170,173,204,205,206,207,226,227,228,292,293,294
2	0.52	2i990	0.988	0.52	1.000	0.994	1.99	III	complex2.pdb.gz	5,7,43,45,48,50,51,52,54,55,59,61,63,65,70,72,74,76,78,80,97,99,101,102,103,104,106,109
3	0.34	1omoB	0.906	1.77	0.313	0.955	1.00	NAD	complex3.pdb.gz	120,145,146,147,167,168,204,205,206,207,226,227,229,233,292,293,294
4	0.05	1x7dA	0.904	1.65	0.221	0.952	0.86	NA	complex4.pdb.gz	225,226,227,228,291,292

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.