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# D-I-TASSER results for Q99828-D1

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

Input Sequence in FASTA format

>Q99828 (95 residues) MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILS LPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL

Predicted Secondary Structure

Sequence

20 40 60 80
| | | |
MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL
Prediction
CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSCHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCSSCHHHHHHHC
Confidence 99876628999999999972999999999999999968777776444752544899974165778884899999985057999925399998629
H:Helix; S:Strand; C:Coil
Predicted Solvent Accessibility

Sequence | 20 40 60 80 | | | | MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL
Prediction | 86554251456205313723603461033004203712576455466436140326303614714443025200500263677440305302736
| Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map | Distance Map | Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank | PDB hit | ID1 | ID2 | Cov | Norm. Zscore | Downloadalignment |  | 20 40 60 80 | | | |
| SS Seq | CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCSSSCHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCSSCHHHHHHHC MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLL
1 | 3cs1A | 0.11 | 0.09 | 3.43 | 1.00 | DEthreader |  | ---GKKTSRVRDITKRAFDKSCYIYDFFELTVMFDEIDA-S-------GNMLVDEEEFKRAPKLEKVEDPAALFKELDKNG-TGSVTFDEFAAWA
2 | 1y1aA1 | 1.00 | 0.92 | 25.64 | 1.68 | SPARKS-K |  | --------S K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
3 | 1y1aA | 1.00 | 0.91 | 25.35 | 0.66 | MapAlign |  | ---------K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
4 | 1y1aA | 1.00 | 0.92 | 25.64 | 0.46 | CEthreader |  | --------S K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
5 | 1y1aA1 | 1.00 | 0.92 | 25.64 | 1.60 | MUSTER |  | --------S K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
6 | 1tuzA | 0.13 | 0.13 | 4.35 | 0.83 | HHsearch |  | MAKERGLISPSDFAQLQKYMEYSTKKVSDVLKLFED-GEMA----KYVQGDAIGYEGFQQFLKLVPRHLSLALFQSFET-GTK DVVCLNDVSCYF
7 | 1y1aA1 | 1.00 | 0.92 | 25.64 | 1.41 | FFAS-3D |  | --------S K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
8 | 1y1aA1 | 0.99 | 0.91 | 25.36 | 0.88 | EigenThreader |  | -------S-K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
9 | 2l4hA | 1.00 | 0.93 | 25.94 | 1.00 | CNFpred |  | -------L S K E L L A E Y Q D L T F L T K Q E I L L A H R R F C E L L P Q E Q R S V E S S L R A Q V P F E Q I L S L P E L K A N P F K E R I C R V F S T S P A K D S L S F E D F L D L L
10 | 2lvvA | 0.10 | 0.09 | 3.46 | 1.00 | DEthreader |  | DGKTEFTTHLPDIVQRAFKALCYIYDIFELTVMFDTMDKD--G-----S-LLLELQEFKEAPKL KDITDATTVFNEIDTNGS-GVVTFDEFSCWA
(a) | ID1 is the number of template residues identical to query divided by number of aligned residues.
(b) | ID2 is the number of template residues identical to query divided by query sequence length.
(c) | Cov is equal the number of aligned template residues divided by query sequence length.
(d) | Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e) | Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f) | Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.615
(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 | 7uswC | 0.82 | 1.85 | 0.416 | 0.937 | model1_7uswC.pdb.gz
| 2 | 6wu5A1 | 0.81 | 2.00 | 0.378 | 0.947 | model1_6wu5A1.pdb.gz
| 3 | 1y1aA1 | 0.79 | 1.58 | 0.977 | 0.916 | model1_1y1aA1.pdb.gz
| 4 | 1ij5A | 0.69 | 2.63 | 0.141 | 0.874 | model1_1ij5A.pdb.gz
| 5 | 1y1xA | 0.65 | 3.01 | 0.116 | 0.863 | model1_1y1xA.pdb.gz
| 6 | 7eebI | 0.65 | 2.58 | 0.100 | 0.832 | model1_7eebI.pdb.gz
| 7 | 1uhnA | 0.64 | 2.21 | 0.187 | 0.789 | model1_1uhnA.pdb.gz
| 8 | 1v1gA1 | 0.63 | 2.33 | 0.175 | 0.800 | model1_1v1gA1.pdb.gz
| 9 | 6sl2A | 0.63 | 2.86 | 0.085 | 0.842 | model1_6sl2A.pdb.gz
| 10 | 6tz8B1 | 0.63 | 2.41 | 0.185 | 0.821 | model1_6tz8B1.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 | 0.95 | metal ion binding
GO:0005509 | 0.94 | calcium ion binding
GO:0000287 | 0.52 | magnesium ion 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:0065007 | 0.96 | biological regulation
GO:0009987 | 0.93 | cellular process
GO:0044699 | 0.91 | single-organism process
GO:0050896 | 0.90 | response to stimulus
GO:0044763 | 0.85 | single-organism cellular process
GO:0071310 | 0.83 | cellular response to organic substance
GO:0071495 | 0.79 | cellular response to endogenous stimulus
GO:0050789 | 0.79 | regulation of biological process
GO:0050794 | 0.78 | regulation of cellular process
GO:0031323 | 0.68 | regulation of cellular metabolic process
GO:0080090 | 0.67 | regulation of primary metabolic process
GO:0060255 | 0.67 | regulation of macromolecule metabolic process
GO:0048518 | 0.67 | positive regulation of biological process
GO:0044767 | 0.67 | single-organism developmental process
GO:0048856 | 0.66 | anatomical structure development
GO:0048522 | 0.66 | positive regulation of cellular process
GO:0006355 | 0.66 | regulation of transcription, DNA-templated
GO:0048523 | 0.65 | negative regulation of cellular process
GO:0031325 | 0.65 | positive regulation of cellular metabolic process
GO:0010604 | 0.65 | positive regulation of macromolecule metabolic process
GO:0007165 | 0.65 | signal transduction
GO:2000026 | 0.64 | regulation of multicellular organismal development
GO:0051240 | 0.64 | positive regulation of multicellular organismal process
GO:0051094 | 0.64 | positive regulation of developmental process
GO:0045597 | 0.64 | positive regulation of cell differentiation
GO:0030155 | 0.64 | regulation of cell adhesion
GO:0002682 | 0.64 | regulation of immune system process
GO:0045652 | 0.63 | regulation of megakaryocyte differentiation
GO:0033628 | 0.63 | regulation of cell adhesion mediated by integrin
GO:0008285 | 0.63 | negative regulation of cell proliferation
GO:0016043 | 0.61 | cellular component organization
GO:0044093 | 0.60 | positive regulation of molecular function
GO:0032879 | 0.60 | regulation of localization
GO:0030154 | 0.60 | cell differentiation
GO:0051050 | 0.59 | positive regulation of transport
GO:0048468 | 0.59 | cell development
GO:0044702 | 0.59 | single organism reproductive process
GO:0030099 | 0.59 | myeloid cell differentiation
GO:0003006 | 0.59 | developmental process involved in reproduction
GO:0048583 | 0.57 | regulation of response to stimulus
GO:0051128 | 0.56 | regulation of cellular component organization
GO:0050790 | 0.56 | regulation of catalytic activity
GO:0048584 | 0.56 | positive regulation of response to stimulus
GO:0031324 | 0.56 | negative regulation of cellular metabolic process
GO:0010605 | 0.56 | negative regulation of macromolecule metabolic process
GO:0009966 | 0.56 | regulation of signal transduction
GO:0006996 | 0.56 | organelle organization
GO:0001932 | 0.56 | regulation of protein phosphorylation
GO:2000256 | 0.55 | positive regulation of male germ cell proliferation
GO:1990090 | 0.55 | cellular response to nerve growth factor stimulus
GO:1900026 | 0.55 | positive regulation of substrate adhesion-dependent cell spreading
GO:0090314 | 0.55 | positive regulation of protein targeting to membrane
GO:0090050 | 0.55 | positive regulation of cell migration involved in sprouting angiogenesis
GO:0071902 | 0.55 | positive regulation of protein serine/threonine kinase activity
GO:0071356 | 0.55 | cellular response to tumor necrosis factor
GO:0070374 | 0.55 | positive regulation of ERK1 and ERK2 cascade
GO:0051898 | 0.55 | negative regulation of protein kinase B signaling
GO:0051302 | 0.55 | regulation of cell division
GO:0051092 | 0.55 | positive regulation of NF-kappaB transcription factor activity
GO:0045653 | 0.55 | negative regulation of megakaryocyte differentiation
GO:0043066 | 0.55 | negative regulation of apoptotic process
GO:0038163 | 0.55 | thrombopoietin-mediated signaling pathway
GO:0033630 | 0.55 | positive regulation of cell adhesion mediated by integrin
GO:0031122 | 0.55 | cytoplasmic microtubule organization
GO:0030307 | 0.55 | positive regulation of cell growth
GO:0030220 | 0.55 | platelet formation
GO:0010977 | 0.55 | negative regulation of neuron projection development
GO:0008152 | 0.55 | metabolic process
GO:0007286 | 0.55 | spermatid development
GO:0007113 | 0.55 | endomitotic cell cycle
GO:0007026 | 0.55 | negative regulation of microtubule depolymerization
GO:0002931 | 0.55 | response to ischemia
GO:0001954 | 0.55 | positive regulation of cell-matrix adhesion
GO:0001933 | 0.55 | negative regulation of protein phosphorylation
GO:0071704 | 0.54 | organic substance metabolic process
GO:0044238 | 0.54 | primary metabolic process
GO:0043170 | 0.53 | macromolecule metabolic process
GO:0044237 | 0.51 | cellular metabolic process
GO:0044260 | 0.50 | cellular macromolecule metabolic process

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:0044424 | 1.00 | intracellular part
GO:0043226 | 0.97 | organelle
GO:0042995 | 0.89 | cell projection
GO:0043229 | 0.86 | intracellular organelle
GO:0043227 | 0.85 | membrane-bounded organelle
GO:0005737 | 0.85 | cytoplasm
GO:0043231 | 0.84 | intracellular membrane-bounded organelle
GO:0044422 | 0.83 | organelle part
GO:0005634 | 0.81 | nucleus
GO:0097458 | 0.80 | neuron part
GO:0016020 | 0.74 | membrane
GO:0005886 | 0.72 | plasma membrane
GO:0044444 | 0.68 | cytoplasmic part
GO:0030027 | 0.65 | lamellipodium
GO:0044446 | 0.62 | intracellular organelle part
GO:0044430 | 0.58 | cytoskeletal part
GO:0043232 | 0.57 | intracellular non-membrane-bounded organelle
GO:0071944 | 0.56 | cell periphery
GO:0048471 | 0.56 | perinuclear region of cytoplasm
GO:0043025 | 0.56 | neuronal cell body
GO:0043005 | 0.56 | neuron projection
GO:0032433 | 0.56 | filopodium tip
GO:0030426 | 0.56 | growth cone
GO:0005813 | 0.56 | centrosome

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 | 2i94A | 0.524 | 3.03 | 0.164 | 0.768 | 2.7.11.14 | NA
| 2 | 0.060 | 2aaoA | 0.546 | 2.53 | 0.122 | 0.705 | 2.7.11.1 | 28
| 3 | 0.060 | 1qxpB | 0.605 | 2.79 | 0.082 | 0.789 | 3.4.22.53 3.4.22.52 | NA
| 4 | 0.060 | 3fycA | 0.500 | 3.65 | 0.039 | 0.800 | 2.1.1.- | NA
| 5 | 0.060 | 2weiA | 0.360 | 5.16 | 0.063 | 0.779 | 2.7.1.17 | 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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
No Binding sites was predicted
| 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.