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# D-I-TASSER results for Q8WUU5

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

Summary of the Protein

Uniprot ID: Q8WUU5
Protein Name: GATA zinc finger domain-containing protein 1
Gene Name: GATAD1

Input Sequence in FASTA format

>Q8WUU5 (269 residues) MPLGLKPTCSVCKTTSSSMWKKGAQGEILCHHCTGRGGAGSGGAGSGAAGGTGGSGGGGF GAATFASTSATPPQSNGGGGGKQSKQEIHRRSARLRNTKYKSAPAAEKKVSTKGKGRRHI FKLKNPIKAPESVSTIITAESIFYKGVYYQIGDVVSVIDEQDGKPYYAQIRGFIQDQYCE KSAALTWLIPTLSSPRDQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTV PTRPEKGYIWTHVGPTPAITIKESVANHL

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 | Q8WUU5-D1 | 1-269 | 269 |  | MPLGLKPTCSVCKTTSSSMWKKGAQGEILCHHCTGRGGAGSGGAGSGAAGGTGGSGGGGFGAATFASTSATPPQSNGGGGGKQSKQEIHRRSARLRNTKYKSAPAAEKKVSTKGKGRRHIFKLKNPIKAPESVSTIITAESIFYKGVYYQIGDVVSVIDEQDGKPYYAQIRGFIQDQYCEKSAALTWLIPTLSSPRDQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPEKGYIWTHVGPTPAITIKESVANHL

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.5001
(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 | 3pt6A | 0.66 | 4.16 | 0.087 | 0.859 | model1_3pt6A.pdb.gz
| 2 | 4wxxA | 0.66 | 4.42 | 0.062 | 0.874 | model1_4wxxA.pdb.gz
| 3 | 1hn0A | 0.44 | 6.15 | 0.077 | 0.751 | model1_1hn0A.pdb.gz
| 4 | 4m5dA | 0.43 | 6.23 | 0.069 | 0.747 | model1_4m5dA.pdb.gz
| 5 | 7bqxS | 0.42 | 5.88 | 0.046 | 0.703 | model1_7bqxS.pdb.gz
| 6 | 6w2jA | 0.41 | 6.08 | 0.031 | 0.699 | model1_6w2jA.pdb.gz
| 7 | 5kf6A | 0.41 | 6.09 | 0.054 | 0.684 | model1_5kf6A.pdb.gz
| 8 | 1j0nA | 0.41 | 6.33 | 0.037 | 0.710 | model1_1j0nA.pdb.gz
| 9 | 5fjsA | 0.41 | 6.40 | 0.029 | 0.706 | model1_5fjsA.pdb.gz
| 10 | 1i8qA | 0.39 | 6.15 | 0.027 | 0.658 | model1_1i8qA.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:1901363 | 0.95 | heterocyclic compound binding
GO:0097159 | 0.95 | organic cyclic compound binding
GO:0003676 | 0.94 | nucleic acid binding
GO:0003677 | 0.93 | DNA binding
GO:0043565 | 0.92 | sequence-specific DNA binding
GO:0003682 | 0.88 | chromatin binding
GO:0003700 | 0.84 | transcription factor activity, sequence-specific DNA binding
GO:0044212 | 0.83 | transcription regulatory region DNA binding
GO:0000981 | 0.83 | RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000976 | 0.82 | transcription regulatory region sequence-specific DNA binding
GO:0001228 | 0.81 | transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001085 | 0.81 | RNA polymerase II transcription factor binding
GO:0000977 | 0.81 | RNA polymerase II regulatory region sequence-specific DNA binding
GO:0046872 | 0.60 | metal ion binding
GO:0000166 | 0.60 | nucleotide binding
GO:0046914 | 0.58 | transition metal ion binding
GO:0019899 | 0.54 | enzyme binding
GO:0035258 | 0.53 | steroid hormone receptor binding
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:0009987 | 0.98 | cellular process
GO:0044699 | 0.94 | single-organism process
GO:0044763 | 0.93 | single-organism cellular process
GO:0048869 | 0.92 | cellular developmental process
GO:0030154 | 0.81 | cell differentiation
GO:0008152 | 0.71 | metabolic process
GO:0071704 | 0.70 | organic substance metabolic process
GO:0065007 | 0.70 | biological regulation
GO:0050789 | 0.70 | regulation of biological process
GO:0044237 | 0.70 | cellular metabolic process
GO:0050794 | 0.69 | regulation of cellular process
GO:0048856 | 0.69 | anatomical structure development
GO:0044767 | 0.69 | single-organism developmental process
GO:0044238 | 0.69 | primary metabolic process
GO:0048513 | 0.67 | animal organ development
GO:0080090 | 0.66 | regulation of primary metabolic process
GO:0060255 | 0.66 | regulation of macromolecule metabolic process
GO:0031323 | 0.66 | regulation of cellular metabolic process
GO:0051171 | 0.65 | regulation of nitrogen compound metabolic process
GO:1901360 | 0.64 | organic cyclic compound metabolic process
GO:0006807 | 0.64 | nitrogen compound metabolic process
GO:0006725 | 0.64 | cellular aromatic compound metabolic process
GO:0006355 | 0.64 | regulation of transcription, DNA-templated
GO:0048522 | 0.63 | positive regulation of cellular process
GO:0006139 | 0.63 | nucleobase-containing compound metabolic process
GO:0045935 | 0.61 | positive regulation of nucleobase-containing compound metabolic process
GO:0010604 | 0.61 | positive regulation of macromolecule metabolic process
GO:0006357 | 0.60 | regulation of transcription from RNA polymerase II promoter
GO:0048519 | 0.59 | negative regulation of biological process
GO:0048523 | 0.58 | negative regulation of cellular process
GO:0010605 | 0.58 | negative regulation of macromolecule metabolic process
GO:0050896 | 0.57 | response to stimulus
GO:0031324 | 0.57 | negative regulation of cellular metabolic process
GO:0051716 | 0.56 | cellular response to stimulus
GO:0007165 | 0.56 | signal transduction
GO:0044710 | 0.55 | single-organism metabolic process
GO:0035556 | 0.55 | intracellular signal transduction
GO:0031399 | 0.55 | regulation of protein modification process
GO:0010033 | 0.55 | response to organic substance
GO:0006950 | 0.55 | response to stress
GO:1901564 | 0.54 | organonitrogen compound metabolic process
GO:1901135 | 0.54 | carbohydrate derivative metabolic process
GO:0071310 | 0.54 | cellular response to organic substance
GO:0051128 | 0.54 | regulation of cellular component organization
GO:0044281 | 0.54 | small molecule metabolic process
GO:0043170 | 0.54 | macromolecule metabolic process
GO:0033993 | 0.54 | response to lipid
GO:0031401 | 0.54 | positive regulation of protein modification process
GO:0031400 | 0.54 | negative regulation of protein modification process
GO:0009719 | 0.54 | response to endogenous stimulus
GO:0009628 | 0.54 | response to abiotic stimulus
GO:0009605 | 0.54 | response to external stimulus
GO:0007264 | 0.54 | small GTPase mediated signal transduction
GO:1990089 | 0.53 | response to nerve growth factor
GO:1901701 | 0.53 | cellular response to oxygen-containing compound
GO:1901654 | 0.53 | response to ketone
GO:1901605 | 0.53 | alpha-amino acid metabolic process
GO:0097305 | 0.53 | response to alcohol
GO:0090308 | 0.53 | regulation of methylation-dependent chromatin silencing
GO:0071559 | 0.53 | response to transforming growth factor beta
GO:0071417 | 0.53 | cellular response to organonitrogen compound
GO:0071363 | 0.53 | cellular response to growth factor stimulus
GO:0071248 | 0.53 | cellular response to metal ion
GO:0071229 | 0.53 | cellular response to acid chemical
GO:0060322 | 0.53 | head development
GO:0051570 | 0.53 | regulation of histone H3-K9 methylation
GO:0051569 | 0.53 | regulation of histone H3-K4 methylation
GO:0051054 | 0.53 | positive regulation of DNA metabolic process
GO:0048699 | 0.53 | generation of neurons
GO:0046128 | 0.53 | purine ribonucleoside metabolic process
GO:0044260 | 0.53 | cellular macromolecule metabolic process
GO:0044030 | 0.53 | regulation of DNA methylation
GO:0043279 | 0.53 | response to alkaloid
GO:0043200 | 0.53 | response to amino acid
GO:0042493 | 0.53 | response to drug
GO:0036119 | 0.53 | response to platelet-derived growth factor
GO:0033273 | 0.53 | response to vitamin
GO:0031937 | 0.53 | positive regulation of chromatin silencing
GO:0031062 | 0.53 | positive regulation of histone methylation
GO:0031061 | 0.53 | negative regulation of histone methylation
GO:0014074 | 0.53 | response to purine-containing compound
GO:0010288 | 0.53 | response to lead ion
GO:0009314 | 0.53 | response to radiation
GO:0009266 | 0.53 | response to temperature stimulus
GO:0008283 | 0.53 | cell proliferation
GO:0007417 | 0.53 | central nervous system development
GO:0006790 | 0.53 | sulfur compound metabolic process
GO:0006732 | 0.53 | coenzyme metabolic process
GO:0002237 | 0.53 | response to molecule of bacterial origin

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:0005634 | 1.00 | nucleus

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 | 2vdcA | 0.373 | 6.72 | 0.038 | 0.688 | 1.4.1.13 | NA
| 2 | 0.060 | 1eusA | 0.273 | 6.11 | 0.036 | 0.461 | 3.2.1.18 | NA
| 3 | 0.060 | 1ikpA | 0.387 | 6.46 | 0.065 | 0.688 | 2.4.2.- | NA
| 4 | 0.060 | 2vncB | 0.388 | 6.85 | 0.029 | 0.736 | 3.2.1.- | NA
| 5 | 0.060 | 1llwA | 0.400 | 5.86 | 0.021 | 0.662 | 1.4.7.1 | 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 | 0.01 | 1llzA | 0.400 | 5.89 | 0.021 | 0.665 | 0.51 | F3S | complex1.pdb.gz | 36,39,46,47,48,51
| 2 | 0.01 | 3fahA | 0.404 | 6.47 | 0.049 | 0.725 | 0.70 | GOL | complex2.pdb.gz | 36,56,57,58,60
| 3 | 0.01 | 3ptaA | 0.383 | 3.84 | 0.064 | 0.472 | 0.62 | ZN | complex3.pdb.gz | 12,35,62
| 4 | 0.01 | 1sijA | 0.406 | 6.53 | 0.057 | 0.732 | 0.67 | FES | complex4.pdb.gz | 39,40,45,46,47,51,53
| 5 | 0.01 | 1dgjA | 0.398 | 6.75 | 0.045 | 0.736 | 0.72 | FES | complex5.pdb.gz | 39,43,45,46,47,49,53
| 6 | 0.01 | 1sijA | 0.406 | 6.53 | 0.057 | 0.732 | 0.52 | FES | complex6.pdb.gz | 40,41,42,56
| 7 | 0.01 | 1dgjA | 0.398 | 6.75 | 0.045 | 0.736 | 0.51 | FES | complex7.pdb.gz | 40,41,42,43,54,55,56
| 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.