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# D-I-TASSER results for A6NLU0

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

Summary of the Protein

Uniprot ID: A6NLU0
Protein Name: Ret finger protein-like 4A
Gene Name: RFPL4A

Input Sequence in FASTA format

>A6NLU0 (287 residues) MAEHFKQIIRCPVCLKDLEEAVQLKCGYACCLQCLNSLQKEPDGEGLLCRFCSVVSQKDD IKPKYKLRALVSIIKELEPKLKSVLTMNPRMRKFQVDMTFDVDTANNYLIISEDLRSFRS GDLSQNRKEQAERFDTALCVLGTPRFTSGRHYWEVDVGTSQVWDVGVCKESVNRQGKIVL SSEHGFLTVGCREGKVFAASTVPMTPLWVSPQLHRVGIFLDVGMRSIAFYNVSDGCHIYT FIEIPVCEPWRPFFAHKRGSQDDQSILSICSVINPSAASAPVSSEGK

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 | A6NLU0-D1 | 1-87 | 87 |  | MAEHFKQIIRCPVCLKDLEEAVQLKCGYACCLQCLNSLQKEPDGEGLLCRFCSVVSQKDDIKPKYKLRALVSIIKELEPKLKSVLTM
2 | A6NLU0-D2 | 88-287 | 200 |  | NPRMRKFQVDMTFDVDTANNYLIISEDLRSFRSGDLSQNRKEQAERFDTALCVLGTPRFTSGRHYWEVDVGTSQVWDVGVCKESVNRQGKIVLSSEHGFLTVGCREGKVFAASTVPMTPLWVSPQLHRVGIFLDVGMRSIAFYNVSDGCHIYTFIEIPVCEPWRPFFAHKRGSQDDQSILSICSVINPSAASAPVSSEGK

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.81
(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)
Click to view | Rank | PDB Hit | TM-score | RMSDa | IDENa | Cov. | Download Alignment
--- | --- | --- | --- | --- | --- | --- | ---
| 1 | 2fbeC | 0.65 | 1.57 | 0.944 | 0.683 | model1_2fbeC.pdb.gz
| 2 | 4cg4A | 0.64 | 1.73 | 0.286 | 0.669 | model1_4cg4A.pdb.gz
| 3 | 2wl1A | 0.63 | 1.21 | 0.374 | 0.652 | model1_2wl1A.pdb.gz
| 4 | 4n7iA | 0.62 | 1.48 | 0.368 | 0.645 | model1_4n7iA.pdb.gz
| 5 | 3kb5A | 0.61 | 1.76 | 0.270 | 0.645 | model1_3kb5A.pdb.gz
| 6 | 2iwgB | 0.61 | 1.05 | 0.430 | 0.624 | model1_2iwgB.pdb.gz
| 7 | 4b8eA | 0.59 | 1.71 | 0.246 | 0.624 | model1_4b8eA.pdb.gz
| 8 | 4wvmA3 | 0.57 | 2.20 | 0.245 | 0.624 | model1_4wvmA3.pdb.gz
| 9 | 2lm3A | 0.56 | 2.09 | 0.269 | 0.603 | model1_2lm3A.pdb.gz
| 10 | 4qolA | 0.30 | 5.96 | 0.014 | 0.498 | model1_4qolA.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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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 | CscoreGO | Name
GO:0046872 | 0.81 | metal ion binding
GO:0008270 | 0.80 | zinc ion binding
GO:0003824 | 0.75 | catalytic activity
GO:0016740 | 0.73 | transferase activity
GO:0004842 | 0.72 | ubiquitin-protein transferase activity
GO:0004871 | 0.62 | signal transducer activity
GO:0004872 | 0.61 | receptor activity
GO:0038023 | 0.60 | signaling receptor activity
GO:0038187 | 0.58 | pattern recognition receptor activity
GO:0042802 | 0.55 | identical protein binding
GO:0019899 | 0.53 | enzyme binding
GO:0008092 | 0.53 | cytoskeletal protein binding
GO:0046983 | 0.50 | protein dimerization activity
Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | Name
GO:0065007 | 0.92 | biological regulation
GO:0050789 | 0.92 | regulation of biological process
GO:0009987 | 0.91 | cellular process
GO:0050794 | 0.88 | regulation of cellular process
GO:0071704 | 0.83 | organic substance metabolic process
GO:0044238 | 0.83 | primary metabolic process
GO:0048518 | 0.82 | positive regulation of biological process
GO:0044237 | 0.82 | cellular metabolic process
GO:0019222 | 0.82 | regulation of metabolic process
GO:0043170 | 0.81 | macromolecule metabolic process
GO:0031323 | 0.81 | regulation of cellular metabolic process
GO:0080090 | 0.80 | regulation of primary metabolic process
GO:0060255 | 0.80 | regulation of macromolecule metabolic process
GO:0044260 | 0.80 | cellular macromolecule metabolic process
GO:0048522 | 0.78 | positive regulation of cellular process
GO:0048583 | 0.77 | regulation of response to stimulus
GO:0019538 | 0.76 | protein metabolic process
GO:0006464 | 0.74 | cellular protein modification process
GO:0050896 | 0.73 | response to stimulus
GO:0010468 | 0.73 | regulation of gene expression
GO:2001141 | 0.72 | regulation of RNA biosynthetic process
GO:0048519 | 0.72 | negative regulation of biological process
GO:0048523 | 0.71 | negative regulation of cellular process
GO:0016567 | 0.71 | protein ubiquitination
GO:0006355 | 0.71 | regulation of transcription, DNA-templated
GO:0065009 | 0.69 | regulation of molecular function
GO:0032268 | 0.69 | regulation of cellular protein metabolic process
GO:0044093 | 0.68 | positive regulation of molecular function
GO:0009966 | 0.68 | regulation of signal transduction
GO:0002376 | 0.68 | immune system process
GO:0043900 | 0.67 | regulation of multi-organism process
GO:0010604 | 0.67 | positive regulation of macromolecule metabolic process
GO:0048584 | 0.66 | positive regulation of response to stimulus
GO:0031325 | 0.66 | positive regulation of cellular metabolic process
GO:0080134 | 0.65 | regulation of response to stress
GO:0044699 | 0.65 | single-organism process
GO:0031399 | 0.65 | regulation of protein modification process
GO:0051090 | 0.64 | regulation of sequence-specific DNA binding transcription factor activity
GO:0006950 | 0.64 | response to stress
GO:0002682 | 0.64 | regulation of immune system process
GO:1902531 | 0.63 | regulation of intracellular signal transduction
GO:0051247 | 0.63 | positive regulation of protein metabolic process
GO:0031347 | 0.63 | regulation of defense response
GO:0031324 | 0.63 | negative regulation of cellular metabolic process
GO:0009967 | 0.63 | positive regulation of signal transduction
GO:0000209 | 0.63 | protein polyubiquitination
GO:0050776 | 0.62 | regulation of immune response
GO:0032270 | 0.62 | positive regulation of cellular protein metabolic process
GO:0051239 | 0.61 | regulation of multicellular organismal process
GO:0032101 | 0.61 | regulation of response to external stimulus
GO:0010605 | 0.61 | negative regulation of macromolecule metabolic process
GO:1902533 | 0.60 | positive regulation of intracellular signal transduction
GO:0001817 | 0.60 | regulation of cytokine production
GO:0050792 | 0.59 | regulation of viral process
GO:0043122 | 0.59 | regulation of I-kappaB kinase/NF-kappaB signaling
GO:1903900 | 0.58 | regulation of viral life cycle
GO:0045088 | 0.58 | regulation of innate immune response
GO:0031401 | 0.58 | positive regulation of protein modification process
GO:0010033 | 0.58 | response to organic substance
GO:0006952 | 0.58 | defense response
GO:0001932 | 0.58 | regulation of protein phosphorylation
GO:0051128 | 0.57 | regulation of cellular component organization
GO:0044763 | 0.57 | single-organism cellular process
GO:0031327 | 0.57 | negative regulation of cellular biosynthetic process
GO:0002684 | 0.57 | positive regulation of immune system process
GO:0051241 | 0.56 | negative regulation of multicellular organismal process
GO:0050778 | 0.56 | positive regulation of immune response
GO:0002831 | 0.56 | regulation of response to biotic stimulus
GO:1903901 | 0.55 | negative regulation of viral life cycle
GO:0048585 | 0.55 | negative regulation of response to stimulus
GO:0045089 | 0.55 | positive regulation of innate immune response
GO:0043408 | 0.55 | regulation of MAPK cascade
GO:0002253 | 0.55 | activation of immune response
GO:0001934 | 0.55 | positive regulation of protein phosphorylation
GO:0001818 | 0.55 | negative regulation of cytokine production
GO:1902679 | 0.54 | negative regulation of RNA biosynthetic process
GO:0051129 | 0.54 | negative regulation of cellular component organization
GO:0032879 | 0.54 | regulation of localization
GO:0030162 | 0.54 | regulation of proteolysis
GO:0010629 | 0.54 | negative regulation of gene expression
GO:0010506 | 0.54 | regulation of autophagy
GO:0007165 | 0.54 | signal transduction
GO:0002218 | 0.54 | activation of innate immune response
GO:1902186 | 0.53 | regulation of viral release from host cell
GO:0046782 | 0.53 | regulation of viral transcription
GO:0034097 | 0.53 | response to cytokine
GO:0050790 | 0.52 | regulation of catalytic activity
GO:0046596 | 0.52 | regulation of viral entry into host cell
GO:0043254 | 0.52 | regulation of protein complex assembly
GO:1900225 | 0.51 | regulation of NLRP3 inflammasome complex assembly
GO:0032651 | 0.51 | regulation of interleukin-1 beta production
GO:0032102 | 0.51 | negative regulation of response to external stimulus
GO:0031348 | 0.51 | negative regulation of defense response
GO:0031333 | 0.51 | negative regulation of protein complex assembly
GO:0007166 | 0.51 | cell surface receptor signaling pathway
GO:2000116 | 0.50 | regulation of cysteine-type endopeptidase activity
GO:1900015 | 0.50 | regulation of cytokine production involved in inflammatory response
GO:0071640 | 0.50 | regulation of macrophage inflammatory protein 1 alpha production
GO:0032692 | 0.50 | negative regulation of interleukin-1 production
GO:0032682 | 0.50 | negative regulation of chemokine production
GO:0032655 | 0.50 | regulation of interleukin-12 production
GO:0016043 | 0.50 | cellular component organization
GO:0010950 | 0.50 | positive regulation of endopeptidase activity

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | Name
GO:0044464 | 1.00 | cell part
GO:0044424 | 0.99 | intracellular part
GO:0043226 | 0.87 | organelle
GO:0043229 | 0.81 | intracellular organelle
GO:0044444 | 0.76 | cytoplasmic part
GO:0043227 | 0.75 | membrane-bounded organelle
GO:0043231 | 0.66 | intracellular membrane-bounded organelle
GO:0005737 | 0.66 | cytoplasm
GO:0032991 | 0.58 | macromolecular complex
GO:0005634 | 0.58 | nucleus
GO:0044422 | 0.56 | organelle part
GO:0044446 | 0.55 | intracellular organelle part
GO:0043232 | 0.51 | intracellular non-membrane-bounded organelle

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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
Click to view | Rank | CscoreEC | PDB Hit | TM-score | RMSDa | IDENa | Cov. | EC Number | Predicted Active Site Residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.060 | 2ayhA | 0.425 | 3.65 | 0.065 | 0.537 | 3.2.1.73 | 154,230
| 2 | 0.060 | 1o4zB | 0.455 | 4.11 | 0.066 | 0.589 | 3.2.1.81 | 235
| 3 | 0.060 | 1wd4A | 0.410 | 4.83 | 0.074 | 0.596 | 3.2.1.55 | NA
| 4 | 0.060 | 1uaiA | 0.418 | 3.84 | 0.083 | 0.540 | 4.2.2.11 | 116
| 5 | 0.060 | 3b9jJ | 0.229 | 6.46 | 0.028 | 0.387 | 1.17.1.4 1.17.3.2 | NA
| Click on the radio buttons to visualize predicted active site residues.
(a) | CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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:
Click to view | Rank | CscoreLB | PDB Hit | TM-score | RMSDa | IDENa | Cov. | BS-score | Lig. Name | Download Complex | Predicted binding site residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.07 | 2vol2 | 0.605 | 1.07 | 0.421 | 0.620 | 0.96 | III | complex1.pdb.gz | 108,120,138,139,164,190
| 2 | 0.01 | 1lu1A | 0.461 | 3.93 | 0.066 | 0.599 | 0.63 | ADE | complex2.pdb.gz | 142,167,169,186
| 3 | 0.01 | 1sbfA | 0.448 | 3.95 | 0.071 | 0.582 | 0.48 | UUU | complex3.pdb.gz | 169,186,251
| Click on the radio buttons to visualize predicted binding site and residues.
(a) | CscoreLB is the confidence score of predicted binding site. CscoreLB 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) | RMSDa the RMSD between residues that are structurally aligned by TM-align.
(e) | IDENa 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.