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# D-I-TASSER results for P05090-D1

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

Input Sequence in FASTA format

>P05090 (189 residues) MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGR CIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWI LATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVT DQVNCPKLS

Predicted Secondary Structure

Sequence

20 40 60 80 100 120 140 160 180
| | | | | | | | |
MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWILATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVTDQVNCPKLS
Prediction
CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHCCSSSSSSSSSCCCCSCCCSSSSSSSSCCCCCSSSSSSSSSCCCCSSSSSSSSSSCCCCCCCSSSSSSCCCCCCCCSSSSSCCCCCSSSSSSSSSSCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCHHH SSSCCCCCCCCCC
Confidence 917999999999999974234457789999875789895882914389998067523241579999994899489999999359957999999998689998189999536766655799961899589999985533788713999997699999999999999999929997884883699999999
H:Helix; S:Strand; C:Coil
Predicted Solvent Accessibility

Sequence | 20 40 60 80 100 120 140 160 180 | | | | | | | | | MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWILATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVTDQVNCPKLS
Prediction | 433210221321111110213234446146163267142740343021013244324434223130323662423022212345333430403031354754130313144233333120120445200000013333534423000000134514661153025206737043740441637615758
| 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 | | | | | | | | |
| SS Seq | CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHCCSSSSSSSSSCCCCSCCCSSSSSSSSCCCCCSSSSSSSSSCCCCSSSSSSSSSSCCCCCCCSSSSSSCCCCCCCCSSSSSCCCCCSSSSSSSSSSCCCCCCSSSSSSSCCCCCCHHHHHHHHHHHHHHCCCHHH SSSCCCCCCCCCC MVMLLLLLSALAGLFGAAEGQAFHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWILATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVTDQVNCPKLS
1 | 5ez2A | 0.40 | 0.35 | 10.31 | 1.33 | DEthreader |  | ----------------M--FIKP--GRC PKPAV Q EDF DAARY L GVW YDIQRLPNKFQKGECATATY S LSPGVGFSVFNRERLANG TIKSVIGSAIAEDPCE P A K LQFFHEN-AAPVP Y WVLST D YDN Y A L V Y S CINL-GASHAAYASIVSRQPTL PEE TIKKLQGTMSSFGVGVDTLLTTNQDYCSAMN
2 | 5ez2A | 0.39 | 0.34 | 10.17 | 2.53 | SPARKS-K |  | --------------------MFIKPGRC PKPAV Q EDF DAARY L GVW YDIQRLPNKFQKGECATATY S LSPGVGFSVFNRERLANG TIKSVIGSAIAEDPCE P A K LQFFHE-NAAPVP Y WVLST D YDN Y A L V Y S CINLGA-SHAAYASIVSRQPTL PEE TIKKLQGTMSSFGVGVDTLLTTNQDAAYCSA
3 | 1gkaB | 0.26 | 0.23 | 7.02 | 1.16 | MapAlign |  | ---------------------FVTAG K CASVANQDN F DLRRYAG R W YQTHIIENAYQVTR C IHSN YEYSNDYGFK VTTAGFNPNDEYLKIDFKVYPTKEFPAAHMLIDAP-SVFAA P YEVIET D Y ETYSCV Y S CITT-DNYKSEF AFVFSRTPQTSGPAVEKTAAVFNKNGVEFSKFVPVSHTECVYR-
4 | 1gkaB | 0.26 | 0.23 | 7.19 | 0.87 | CEthreader |  | ----------------DGIPSFVTAG K CASVANQDN F DLRRYAG R W YQTHIIENAYQPVR C IHSN YEYSTNYGFK VTTAGFNPNDEYLKIDFKVYPTKEFPAAHMLIDAPS-VFAA P YEVIET D Y ETYSCV Y S CITT-DNYKSEF AFVFSRTPQTSGPAVEKTAAVFNKNGVEFSKFVPVSHTECVYRA
5 | 2hzqA | 0.93 | 0.80 | 22.58 | 2.06 | MUSTER |  | ----------------------F H L G K C P N P P V Q E N F D V N K YPG R W Y E I E K I P T T F E N G R C I Q A N Y S L-E N G K I K V L N Q E L R A D G T V N Q I E G E A T P V N L T E P A K L E V K F S W F-P S A P YHI L A T D Y E N Y A L V Y S C TSISQSF H V D F A W I L A R NVAL P P E T V D S L K N I L T S N N I D V K KTVTD-Q V N C P K L-
6 | 5ez2A | 0.40 | 0.35 | 10.31 | 1.99 | HHsearch |  | --------------------MFIKPGRC PKPAV Q EDF DAARY L GVW YDIQRLPNKFQKGECATATY S LSPGVGFSVFNRERLANG TIKSVIGSAIAEDPCE P A K LQ-FFHENAAPVP Y WVLST D YDN Y A L V Y S CINL-GASHAAYASIVSRQPTL PEE TIKKLQGTMSSFGVGVDTLLTTNQDAAYCSA
7 | 5ez2A | 0.40 | 0.35 | 10.31 | 2.28 | FFAS-3D |  | ---------------------FIKPGRC PKPAV Q EDF DAARY L GVW YDIQRLPNKFQKGECATATY S LSPGVGFSVFNRERLANG TIKSVIGSAIAEDPCE P A K LQFFH-ENAAPVP Y WVLST D YDN Y A L V Y S CINL-GASHAAYASIVSRQPTL PEE TIKKLQGTMSSFGVGVDTLLTTNQDACSAMN
8 | 5ez2A | 0.40 | 0.35 | 10.30 | 1.42 | EigenThreader |  | ----------------------MFIGRC PKPAV Q EDF DAARY L GVW YDIQRLPNKFQKGECATATY S LSPGVGFSVFNRERLANG TIKSVIGSAIAEDPCE P A K LQFFHEN-AAPVP Y WVLST D YDN Y A L V Y S CINLG-ASHAAYASIVSRQPTL PEE TIKKLQGTMSSFGVGVDTLLTT DAAYCSAMN
9 | 2hzqA | 0.96 | 0.84 | 23.59 | 2.69 | CNFpred |  | ----------------------F H L G K C P N P P V Q E N F D V N K YPG R W Y E I E K I P T T F E N G R C I Q A N Y S L M E N G K I K V L N Q E L R A D G T V N Q I E G E A T P V N L T E P A K L E V K F S W F M P S A P YHI L A T D Y E N Y A L V Y S C TSISQSF H V D F A W I L A R NVAL P P E T V D S L K N I L T S N N I D V K K M T V T D Q V N C P K L-
10 | 2hzqA | 0.93 | 0.80 | 22.43 | 1.33 | DEthreader |  | -------------------F--HL-G K C P N P P V Q E N F D V N K YPG R W Y E I E K I P T T F E N G R C I Q A N Y S L-E N G K I K V L N Q E L R A D G T V N Q I E G E A T P V N L T E P A K L E V K F S W F-P S A P YHI L A T D Y E N Y A L V Y S C TSISQSF H V D F A W I L A R NVAL P P E T V D S L K N I L T S N N I D V K K-T V T D Q V N C P-KL
(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 | 0.751
(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 | 5ez2A | 0.86 | 1.17 | 0.395 | 0.884 | model1_5ez2A.pdb.gz
| 2 | 1gkaB | 0.83 | 1.85 | 0.251 | 0.905 | model1_1gkaB.pdb.gz
| 3 | 1i4uA | 0.81 | 1.96 | 0.254 | 0.894 | model1_1i4uA.pdb.gz
| 4 | 2hzqA | 0.81 | 1.64 | 0.957 | 0.862 | model1_2hzqA.pdb.gz
| 5 | 1z24A | 0.78 | 2.29 | 0.305 | 0.878 | model1_1z24A.pdb.gz
| 6 | 2acoA | 0.74 | 1.98 | 0.285 | 0.799 | model1_2acoA.pdb.gz
| 7 | 1aqbA | 0.73 | 2.41 | 0.228 | 0.841 | model1_1aqbA.pdb.gz
| 8 | 1qabE | 0.72 | 2.71 | 0.211 | 0.852 | model1_1qabE.pdb.gz
| 9 | 3qkgA | 0.71 | 2.77 | 0.140 | 0.825 | model1_3qkgA.pdb.gz
| 10 | 1t0vA | 0.70 | 2.94 | 0.248 | 0.857 | model1_1t0vA.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:0043178 | 1.00 | alcohol binding
GO:0008289 | 1.00 | lipid binding
GO:0097159 | 0.94 | organic cyclic compound binding
GO:0015485 | 0.93 | cholesterol 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:0044699 | 0.96 | single-organism process
GO:0050896 | 0.95 | response to stimulus
GO:0065007 | 0.92 | biological regulation
GO:0042221 | 0.89 | response to chemical
GO:0009987 | 0.89 | cellular process
GO:0050789 | 0.87 | regulation of biological process
GO:0044763 | 0.87 | single-organism cellular process
GO:0006950 | 0.87 | response to stress
GO:0032502 | 0.86 | developmental process
GO:1901700 | 0.84 | response to oxygen-containing compound
GO:0050794 | 0.84 | regulation of cellular process
GO:0044767 | 0.84 | single-organism developmental process
GO:0008152 | 0.84 | metabolic process
GO:0006979 | 0.84 | response to oxidative stress
GO:0048856 | 0.83 | anatomical structure development
GO:0044710 | 0.83 | single-organism metabolic process
GO:0071704 | 0.82 | organic substance metabolic process
GO:0044281 | 0.82 | small molecule metabolic process
GO:0044238 | 0.81 | primary metabolic process
GO:0048519 | 0.80 | negative regulation of biological process
GO:0048513 | 0.80 | animal organ development
GO:0033554 | 0.80 | cellular response to stress
GO:0006629 | 0.80 | lipid metabolic process
GO:0048523 | 0.79 | negative regulation of cellular process
GO:0051239 | 0.78 | regulation of multicellular organismal process
GO:0051223 | 0.78 | regulation of protein transport
GO:0023051 | 0.78 | regulation of signaling
GO:0019222 | 0.78 | regulation of metabolic process
GO:0010646 | 0.78 | regulation of cell communication
GO:0006006 | 0.78 | glucose metabolic process
GO:0080090 | 0.77 | regulation of primary metabolic process
GO:0051241 | 0.77 | negative regulation of multicellular organismal process
GO:0048583 | 0.77 | regulation of response to stimulus
GO:0031323 | 0.77 | regulation of cellular metabolic process
GO:0009888 | 0.77 | tissue development
GO:0008285 | 0.77 | negative regulation of cell proliferation
GO:0002682 | 0.77 | regulation of immune system process
GO:0080134 | 0.76 | regulation of response to stress
GO:0060255 | 0.76 | regulation of macromolecule metabolic process
GO:0031324 | 0.76 | negative regulation of cellular metabolic process
GO:0016043 | 0.76 | cellular component organization
GO:0048589 | 0.75 | developmental growth
GO:0045833 | 0.75 | negative regulation of lipid metabolic process
GO:0010605 | 0.75 | negative regulation of macromolecule metabolic process
GO:2000405 | 0.74 | negative regulation of T cell migration
GO:2000098 | 0.74 | negative regulation of smooth muscle cell-matrix adhesion
GO:1900016 | 0.74 | negative regulation of cytokine production involved in inflammatory response
GO:0071638 | 0.74 | negative regulation of monocyte chemotactic protein-1 production
GO:0060588 | 0.74 | negative regulation of lipoprotein lipid oxidation
GO:0051895 | 0.74 | negative regulation of focal adhesion assembly
GO:0048662 | 0.74 | negative regulation of smooth muscle cell proliferation
GO:0042493 | 0.74 | response to drug
GO:0042308 | 0.74 | negative regulation of protein import into nucleus
GO:0042246 | 0.74 | tissue regeneration
GO:0014012 | 0.74 | peripheral nervous system axon regeneration
GO:0010642 | 0.74 | negative regulation of platelet-derived growth factor receptor signaling pathway
GO:0007568 | 0.74 | aging
GO:0007420 | 0.74 | brain development
GO:0000302 | 0.74 | response to reactive oxygen species

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:0044421 | 0.97 | extracellular region part
GO:0005615 | 0.96 | extracellular space
GO:0044464 | 0.93 | cell part
GO:0044424 | 0.91 | intracellular part
GO:0044444 | 0.89 | cytoplasmic part
GO:0043226 | 0.85 | organelle
GO:0043227 | 0.84 | membrane-bounded organelle
GO:0043231 | 0.81 | intracellular membrane-bounded organelle
GO:0032991 | 0.77 | macromolecular complex
GO:0005783 | 0.75 | endoplasmic reticulum
GO:0043232 | 0.74 | intracellular non-membrane-bounded organelle
GO:0043025 | 0.74 | neuronal cell body
GO:0030529 | 0.74 | intracellular ribonucleoprotein complex
GO:0048471 | 0.73 | perinuclear region of cytoplasm
GO:0030425 | 0.73 | dendrite
GO:0022626 | 0.73 | cytosolic ribosome

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 | 2zj7A | 0.405 | 4.92 | 0.052 | 0.645 | 3.1.1.3 | NA
| 2 | 0.060 | 1crkA | 0.433 | 4.54 | 0.053 | 0.651 | 2.7.3.2 | NA
| 3 | 0.060 | 2j2mA | 0.426 | 4.05 | 0.043 | 0.609 | 1.11.1.6 | NA
| 4 | 0.060 | 1cb7B | 0.419 | 5.30 | 0.042 | 0.693 | 5.4.99.1 | NA
| 5 | 0.060 | 1kdgB | 0.412 | 4.55 | 0.024 | 0.609 | 1.1.99.18 | 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 | 0.29 | 1n0sA | 0.747 | 2.46 | 0.274 | 0.857 | 0.95 | FLU | complex1.pdb.gz | 42,48,66,78,90,107,116,118,147
| 2 | 0.26 | 1bbpA | 0.762 | 2.36 | 0.297 | 0.868 | 0.88 | BLV | complex2.pdb.gz | 48,55,56,63,64,78,79,80,90,118,133,145,147,149
| 3 | 0.24 | 2wq9A | 0.726 | 2.45 | 0.230 | 0.836 | 0.83 | OLA | complex3.pdb.gz | 56,57,66,76,78,90,91,92,107,109,118,131,147,149
| 4 | 0.18 | 1epbA | 0.661 | 2.79 | 0.208 | 0.778 | 0.90 | REA | complex4.pdb.gz | 39,42,46,77,116,118,120,129,131,133,147,149
| 5 | 0.05 | 1gkaA | 0.804 | 1.96 | 0.256 | 0.889 | 0.96 | AXT | complex5.pdb.gz | 23,56,57,64,79,107,109,116,133,141,145,147,149
| 6 | 0.05 | 1obq0 | 0.810 | 1.99 | 0.254 | 0.894 | 0.84 | III | complex6.pdb.gz | 54,55,56,57,91,92,93,108,109,110,111,112,113,115,117,135
| 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.