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# D-I-TASSER results for Q9NRA0-D1

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

Input Sequence in FASTA format

>Q9NRA0 (284 residues) MNGHLEAEEQQDQRPDQELTGSWGHGPRSTLVRAKAMALAGAVNQHGGFEPALGLDLLLN CSLLLCRGGGHPLDLLSVTLASGSRCFSFLSVAWGFVSDVDIQSERFRALGSARFTLGTV LGLATLHTYRGRLSYLPATVSTCGPPDHLLPPLGTPLPPDWVTLEGDFVLMLAISPSHLG ADLVAAPHARFDDGLVHLCWVRSGISRAALLRLFLAMERGSHFSLGCPQLGYAAARAFRL EPLTPRGVLTVDGEQVEYGPLQAQMHPGIGTLLTGPPGCPGREP

Predicted Secondary Structure

Sequence

20 40 60 80 100 120 140 160 180 200 220 240 260 280
| | | | | | | | | | | | | |
MNGHLEAEEQQDQRPDQELTGSWGHGPRSTLVRAKAMALAGAVNQHGGFEPALGLDLLLNCSLLLCRGGGHPLDLLSVTLASGSRCFSFLSVAWGFVSDVDIQSERFRALGSARFTLGTVLGLATLHTYRGRLSYLPATVSTCGPPDHLLPPLGTPLPPDWVTLEGDFVLMLAISPSHLGADLVAAPHARFDDGLVHLCWVRSGISRAALLRLFLAMERGSHFSLGCPQLGYAAARAFRLEPLTPRGVLTVDGEQVEYGPLQAQMHPGIGTLLTGPPGCPGREP
Prediction
CCCCSCCCCCCCCCSCHH S HCCCCCCCSSSSCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCSSCSSSSSSCCCCCSSSSSSSSSSCSSSSSCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCSSSSSSSCCCCCCCCCCSCCCCCCCCCSSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCCCCSSSSSSSSSSSSSSCCCCCSSSSCCCCCCCCCSSSSSSCCSSSSSSCCCCCCCCCC
Confidence 98640021138996203001212589749954887699998747667766555877699999999809642221789985899679999876642456402455011125732456999999986065230699973343235544444433345557898899622899999646743899632888838899489999869999899999999974597544579829999999999997799974881686158854799998465689728977887899
H:Helix; S:Strand; C:Coil
Predicted Solvent Accessibility

Sequence | 20 40 60 80 100 120 140 160 180 200 220 240 260 280 | | | | | | | | | | | | | | MNGHLEAEEQQDQRPDQELTGSWGHGPRSTLVRAKAMALAGAVNQHGGFEPALGLDLLLNCSLLLCRGGGHPLDLLSVTLASGSRCFSFLSVAWGFVSDVDIQSERFRALGSARFTLGTVLGLATLHTYRGRLSYLPATVSTCGPPDHLLPPLGTPLPPDWVTLEGDFVLMLAISPSHLGADLVAAPHARFDDGLVHLCWVRSGISRAALLRLFLAMERGSHFSLGCPQLGYAAARAFRLEPLTPRGVLTVDGEQVEYGPLQAQMHPGIGTLLTGPPGCPGREP
Prediction | 73010314637432132213231642100000000000001000222434311427202300200044443402002022464321000000011120211341531323233211100021014334141202022332432332332222233335453431423000000011121124020013042320100000023713214003003204524114173440321304303020325511000001315424010200230020003367156668
| 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 80 100 120 140 160 180 200 220 240 260 280 | | | | | | | | | | | | | |
| SS Seq | CCCCSCCCCCCCCCSCHH S HCCCCCCCSSSSCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCSSCSSSSSSCCCCCSSSSSSSSSSCSSSSSCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCSSSSSSSCCCCCCCCCCSCCCCCCCCCSSSSSSSCCCCCHHHHHHHHHHHHCCCCCCCCCCSSSSSSSSSSSSSSCCCCCSSSSCCCCCCCCCSSSSSSCCSSSSSSCCCCCCCCCC MNGHLEAEEQQDQRPDQELTGSWGHGPRSTLVRAKAMALAGAVNQHGGFEPALGLDLLLNCSLLLCRGGGHPLDLLSVTLASGSRCFSFLSVAWGFVSDVDIQSERFRALGSARFTLGTVLGLATLHTYRGRLSYLPATVSTCGPPDHLLPPLGTPLPPDWVTLEGDFVLMLAISPSHLGADLVAAPHARFDDGLVHLCWVRSGISRAALLRLFLAMERGSHFSLGCPQLGYAAARAFRLEPLTPRGVLTVDGEQVEYGPLQAQMHPGIGTLLTGPPGCPGREP
1 | 3vzdA | 0.42 | 0.39 | 11.58 | 1.33 | DEthreader |  | HAVMEVVNGLMERP-W---ET-AIQKPLCSLPAGSGNA L AASLNHYEQVTNEDLLTNCTLLLCR---RLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVGRVGS--VDAHLVP LEEPVPSHWTVVDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVS------G---
2 | 3vzdA | 0.47 | 0.45 | 13.13 | 2.73 | SPARKS-K |  | DGLMHEVVNGLMER---PDWETAIQKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVRVGSQG PVDAHLVP LEEPVPSHWTVVDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
3 | 3vzdA | 0.45 | 0.43 | 12.65 | 2.18 | MapAlign |  | ---DGLMHEVVNGLMERPDWETAIQKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVGRVGSQGPVDAHVP LEEPVPSHWTVVDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
4 | 3vzdA | 0.45 | 0.43 | 12.65 | 1.75 | CEthreader |  | DGLMHEVVNGLMER P DWETA---IQKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVGRVGSQGPVDAHLVPLEEPVHWTVVPDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
5 | 3vzdA | 0.48 | 0.46 | 13.31 | 1.67 | MUSTER |  | --LMHEVVNGLMER P DWETA---IQKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVGRVGQG PVDAHLVP LEEPVPSHWTVVDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
6 | 3vzdA | 0.48 | 0.46 | 13.32 | 3.99 | HHsearch |  | DGLMHEVVNGLMER P DWETA---IQKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVGRVGSG PVDAHLVP LEEPVPSHWTVVDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
7 | 3vzdA2 | 0.50 | 0.36 | 10.41 | 2.12 | FFAS-3D |  | -----------------------------------------------------------------------PMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PVVGSQGPVDAH LVPLEEPVPSHWTVVPDED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVS----------
8 | 3vzdA | 0.32 | 0.29 | 8.81 | 1.87 | EigenThreader |  | DGLMHEVVNGLMER P DWETAI---QKPLCSLSGNALAASLNHYAGYEQVTNEDLLTNCTLLLCRR---LLSPMNL L SLHTA S GLRLF SVL SLA W GIADVDLESEKYRRLGEMRFTLGTFLRLAA---LRTYRGRLAYLRVGSQG PVDAHLVP LEEPVPSHWTVVPDEDFLVL ALLHSGS----EMA PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVHY---FWMVSG--------
9 | 4l02A | 0.48 | 0.46 | 13.41 | 2.73 | CNFpred |  | DGLMHEVVNGLMER P DWETAI---QKPLCSLPAGSGNA L AASLNHYAGYEQVTNED L LTN CTL L L C RRLLSPMNL L SLHTA S GLRLF SVL SLA W G FIAD V DLES EKYRRL GEMR F T L G TFLRL AALRT Y R G R LAY L PV-VVQQG PVDAHLVP LEEPVPSHWTVVPED F V LVL ALLHS H L GSEMFA A PMGRCAAGVMH LFYV RAGVS R AML L R L F L A M EKGRHMEYEC PYLVYVPVVA F R L E PKDGKG VFAV D G ELMVSEAVQGQVH PNYFWMVSG---------
10 | 7cgpB | 0.12 | 0.10 | 3.58 | 1.17 | DEthreader |  | TAVLEVVTGVLRRT-E--ATF--SKIPIGFIPLGETSSLSHTLFAE-SGNKVQHITDATLAIVK---GETVP L DVLQIKGEKEQPVFAMTGLRW GSFRDAGVKVSKYWYL GPLKIKAAHFFSTLEPQTHQASIS YTGP--------------------V-WKDVQLSTIELSITTRN----------NQLDPEDFLNICIEPDTI SKGDFITIGSRKRNPKLH--VEG-TECLQASQCTLLIP-E--SFSIDSEEYEAMPVEVKLLPRKLQFFCDP--RKREQ-
(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 | 0.8704
(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 | 3vzdA | 0.94 | 0.88 | 0.471 | 0.954 | model1_3vzdA.pdb.gz
| 2 | 7cgpB | 0.70 | 3.27 | 0.139 | 0.831 | model1_7cgpB.pdb.gz
| 3 | 2qv7A | 0.65 | 2.91 | 0.141 | 0.743 | model1_2qv7A.pdb.gz
| 4 | 2p1rA | 0.65 | 3.26 | 0.175 | 0.761 | model1_2p1rA.pdb.gz
| 5 | 4werA | 0.64 | 2.81 | 0.174 | 0.729 | model1_4werA.pdb.gz
| 6 | 3s40A | 0.63 | 2.55 | 0.134 | 0.711 | model1_3s40A.pdb.gz
| 7 | 1nmpA | 0.29 | 6.51 | 0.035 | 0.486 | model1_1nmpA.pdb.gz
| 8 | 5fa0A | 0.26 | 6.95 | 0.036 | 0.472 | model1_5fa0A.pdb.gz
| 9 | 1l7nB | 0.25 | 5.58 | 0.063 | 0.377 | model1_1l7nB.pdb.gz
| 10 | 2v1uA1 | 0.25 | 5.76 | 0.019 | 0.394 | model1_2v1uA1.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:0016301 | 0.99 | kinase activity
GO:0017050 | 0.71 | D-erythro-sphingosine kinase activity
GO:0016773 | 0.69 | phosphotransferase activity, alcohol group as acceptor
GO:0001727 | 0.58 | lipid kinase activity
GO:0000287 | 0.52 | magnesium ion binding
GO:0008481 | 0.50 | sphinganine kinase 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:0044699 | 0.94 | single-organism process
GO:0009987 | 0.94 | cellular process
GO:0044763 | 0.92 | single-organism cellular process
GO:0044237 | 0.84 | cellular metabolic process
GO:0071704 | 0.82 | organic substance metabolic process
GO:0044255 | 0.81 | cellular lipid metabolic process
GO:0006643 | 0.71 | membrane lipid metabolic process
GO:0006665 | 0.70 | sphingolipid metabolic process
GO:0065007 | 0.67 | biological regulation
GO:0050789 | 0.67 | regulation of biological process
GO:0050794 | 0.64 | regulation of cellular process
GO:0048519 | 0.53 | negative regulation of biological process
GO:0006796 | 0.53 | phosphate-containing compound metabolic process
GO:1901576 | 0.52 | organic substance biosynthetic process
GO:0048523 | 0.50 | negative regulation of cellular process
GO:0046519 | 0.50 | sphingoid metabolic process
GO:0043067 | 0.50 | regulation of programmed cell death
GO:0034311 | 0.50 | diol 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:0016020 | 0.82 | membrane
GO:0044444 | 0.74 | cytoplasmic part
GO:0005737 | 0.70 | cytoplasm
GO:0005886 | 0.50 | plasma membrane

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 | 0.078 | 2qv7A | 0.647 | 2.91 | 0.141 | 0.743 | 2.7.1.107 | 176
| 2 | 0.060 | 2azdB | 0.367 | 6.40 | 0.031 | 0.627 | 2.4.1.1 | NA
| 3 | 0.060 | 1ofdA | 0.312 | 6.93 | 0.038 | 0.581 | 1.4.7.1 | NA
| 4 | 0.060 | 2q5fA | 0.508 | 4.10 | 0.069 | 0.644 | 2.7.1.23 | NA
| 5 | 0.060 | 2z1qB | 0.364 | 6.51 | 0.066 | 0.637 | 1.3.99.3 | 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 | 0.02 | 1suwA | 0.494 | 4.15 | 0.071 | 0.644 | 0.63 | NAP | complex1.pdb.gz | 195,234,236
| 2 | 0.01 | 2ih9A | 0.374 | 6.32 | 0.041 | 0.630 | 0.45 | UUU | complex2.pdb.gz | 178,180,221
| 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.