D-I-TASSER P49279

D-I-TASSER results for P49279

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

Summary of the Protein

Uniprot ID: P49279
Protein Name: Natural resistance-associated macrophage protein 1
Gene Name: SLC11A1

Input Sequence in FASTA format

>P49279 (550 residues)
MTGDKGPQRLSGSSYGSISSPTSPTSPGPQQAPPRETYLSEKIPIPDTKPGTFSLRKLWA
FTGPGFLMSIAFLDPGNIESDLQAGAVAGFKLLWVLLWATVLGLLCQRLAARLGVVTGKD
LGEVCHLYYPKVPRTVLWLTIELAIVGSDMQEVIGTAIAFNLLSAGRIPLWGGVLITIVD
TFFFLFLDNYGLRKLEAFFGLLITIMALTFGYEYVVARPEQGALLRGLFLPSCPGCGHPE
LLQAVGIVGAIIMPHNIYLHSALVKSREIDRARRADIREANMYFLIEATIALSVSFIINL
FVMAVFGQAFYQKTNQAAFNICANSSLHDYAKIFPMNNATVAVDIYQGGVILGCLFGPAA
LYIWAIGLLAAGQSSTMTGTYAGQFVMEGFLRLRWSRFARVLLTRSCAILPTVLVAVFRD
LRDLSGLNDLLNVLQSLLLPFAVLPILTFTSMPTLMQEFANGLLNKVVTSSIMVLVCAIN
LYFVVSYLPSLPHPAYFGLAALLAAAYLGLSTYLVWTCCLAHGATFLAHSSHHHFLYGLL
EEDQKGETSG

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	P49279-D1	1-422	422		MTGDKGPQRLSGSSYGSISSPTSPTSPGPQQAPPRETYLSEKIPIPDTKPGTFSLRKLWAFTGPGFLMSIAFLDPGNIESDLQAGAVAGFKLLWVLLWATVLGLLCQRLAARLGVVTGKDLGEVCHLYYPKVPRTVLWLTIELAIVGSDMQEVIGTAIAFNLLSAGRIPLWGGVLITIVDTFFFLFLDNYGLRKLEAFFGLLITIMALTFGYEYVVARPEQGALLRGLFLPSCPGCGHPELLQAVGIVGAIIMPHNIYLHSALVKSREIDRARRADIREANMYFLIEATIALSVSFIINLFVMAVFGQAFYQKTNQAAFNICANSSLHDYAKIFPMNNATVAVDIYQGGVILGCLFGPAALYIWAIGLLAAGQSSTMTGTYAGQFVMEGFLRLRWSRFARVLLTRSCAILPTVLVAVFRDLR
2	P49279-D2	423-550	128		DLSGLNDLLNVLQSLLLPFAVLPILTFTSMPTLMQEFANGLLNKVVTSSIMVLVCAINLYFVVSYLPSLPHPAYFGLAALLAAAYLGLSTYLVWTCCLAHGATFLAHSSHHHFLYGLLEEDQKGETSG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.79

(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	5m87A	0.80	2.53	0.292	0.856	model1_5m87A.pdb.gz
2	6m17A	0.66	4.32	0.104	0.802	model1_6m17A.pdb.gz
3	5i6xA	0.65	4.40	0.107	0.793	model1_5i6xA.pdb.gz
4	4m48A	0.64	4.43	0.106	0.789	model1_4m48A.pdb.gz
5	6c3iA	0.64	2.88	0.309	0.700	model1_6c3iA.pdb.gz
6	4wgvA	0.63	3.16	0.316	0.696	model1_4wgvA.pdb.gz
7	2q6hA	0.63	4.18	0.110	0.760	model1_2q6hA.pdb.gz
8	6zbvA	0.63	4.51	0.077	0.767	model1_6zbvA.pdb.gz
9	3gi9C	0.61	3.83	0.089	0.709	model1_3gi9C.pdb.gz
10	5oqtA	0.60	4.33	0.109	0.729	model1_5oqtA.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:0005215	0.99	transporter activity
GO:0008324	0.98	cation transmembrane transporter activity
GO:0022890	0.97	inorganic cation transmembrane transporter activity
GO:0046873	0.93	metal ion transmembrane transporter activity
GO:0046915	0.92	transition metal ion transmembrane transporter activity
GO:0005381	0.53	iron ion transmembrane transporter activity
GO:0005384	0.52	manganese ion transmembrane transporter 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:0051179	0.83	localization
GO:0006810	0.82	transport
GO:0044699	0.80	single-organism process
GO:0065007	0.79	biological regulation
GO:0009987	0.78	cellular process
GO:0006811	0.78	ion transport
GO:0030001	0.77	metal ion transport
GO:0000041	0.75	transition metal ion transport
GO:0050896	0.71	response to stimulus
GO:0065008	0.65	regulation of biological quality
GO:0042221	0.64	response to chemical
GO:0055076	0.63	transition metal ion homeostasis
GO:0044763	0.62	single-organism cellular process
GO:0072511	0.52	divalent inorganic cation transport
GO:0050789	0.51	regulation of biological process
GO:0008152	0.51	metabolic process
GO:0070838	0.50	divalent metal ion transport

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	0.98	cell part
GO:0016020	0.92	membrane
GO:0044424	0.89	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0044446	0.73	intracellular organelle part
GO:0044425	0.65	membrane part
GO:0043226	0.64	organelle
GO:0043229	0.63	intracellular organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0031090	0.59	organelle membrane
GO:0098588	0.55	bounding membrane of organelle
GO:0098805	0.54	whole membrane
GO:0005774	0.53	vacuolar membrane
GO:0016021	0.52	integral component of membrane
GO:0005886	0.52	plasma membrane

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	1w6jA	0.318	6.83	0.058	0.473	5.4.99.7	173
2	0.060	1llwA	0.336	7.83	0.059	0.554	1.4.7.1	NA
3	0.060	1g8kE	0.345	7.72	0.028	0.571	1.20.98.1	108,113,268
4	0.060	1ogyI	0.320	7.67	0.037	0.533	1.7.99.4	NA
5	0.060	1w07B	0.326	7.49	0.065	0.513	1.3.3.6	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	0.04	2q6hA	0.626	4.18	0.110	0.760	0.44	CXX	complex1.pdb.gz	64,67,106,107,110,281
2	0.03	3f3aA	0.615	4.23	0.106	0.744	0.43	TRP	complex2.pdb.gz	68,71,72,103
3	0.03	3qs5A	0.621	4.16	0.110	0.747	0.57	TRP	complex3.pdb.gz	71,72,75,76,77,150,255,375,378,379
4	0.02	2q72A	0.625	4.24	0.117	0.760	0.59	IXX	complex4.pdb.gz	64,67,114
5	0.02	3l1lA	0.588	4.23	0.079	0.707	0.43	ARG	complex5.pdb.gz	65,66,103,104,107,108,111,288
6	0.02	3ob6A	0.598	4.03	0.080	0.709	0.73	ARG	complex6.pdb.gz	72,144,148,152,249,434
7	0.01	2wsxC	0.560	4.35	0.068	0.687	0.44	NM2	complex7.pdb.gz	62,66,202
8	0.01	1n38A	0.359	7.53	0.034	0.576	0.57	CH1	complex8.pdb.gz	107,108,112,113

	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.