D-I-TASSER P05107-D1

D-I-TASSER results for P05107-D1

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

Input Sequence in FASTA format

>P05107 (213 residues)
MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSI
RCDTRPQLLMRGCAADDIMDCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQ
TQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERY
NGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER
Prediction	CCCCCCCSSSSSCCCCCCCCCCCSSCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCSSCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSCCCCCSCCCCCCCC
Confidence	986456413453334786689875558997434887678999756877240688877787798498631797565575443388988887877548995780892193998316988788888767766777768899987899945839927966898888754448987788767888996478999627529957929996138998869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER
Prediction	644230300000023033123424336373131441243246154265240314243652404142410343030423441404044454444403530304224041474240740314364434663444046674444033404042340304236344440304201133240553514403253304044442415744517436278
	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

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSSCCCCCCCCCCCSSCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCSCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCSSCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCSSSCCCCCSCCCCCCCC
MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

4cvuA

0.05

0.04

1.92

0.83

DEthreader

------DNASLDF---SVIIYSGK---LEG--VT---QSDMTV-TG-SVTID---AHKPKLYITVSVSSPILV--SQR-RVGFRTILFSSGIQ-ITNNWHFEIEFAWSSANN----IYGDT---DFYNYDTVSFMLAERYYLFADMKSEIQFYRVSRTE-VIASAFWNY-NLILTWVDPIANNAGMTK---ITAN-IQSD----L-KIPD---

3k6sB

0.67

0.66

18.73

4.56

SPARKS-K

IKNAYNKLSSRVFLDHNALPDTSFCSN----GVTHRNQPRGDCDGVVPITFQVKVTATECSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

4g1eB

0.30

0.25

7.70

1.16

MapAlign

-----LQLIVDAYGKI----RSKVELEVRDLPFNATCLNNEVIEKEKSFTIKPVGFKDSLIVQVTFD------------CDCACQAQAEPNSHRCNGNGTFECGVCRCGPGWLGSQCECSE-----EDYQDECSPREGQPVCSQRGECLCGQCVCHSSDF--GKITGKYCECDDFSCVRYKGEMCSG--HGQCSCGDCLCDSDWTGYYCNCTT

3k6sB3

0.98

0.87

24.47

0.97

CEthreader

----------------------QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGC-AADDIMCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

3k6sB3

0.98

0.87

24.47

3.58

MUSTER

----------------------QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCA-ADDIMCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

3k6sB

0.72

0.67

18.92

4.10

HHsearch

RVFLDPDTL-KVTYDSNGNQPRGDCDGVQIN---------------VPITFQVKVTATEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

3k6sB

0.70

0.63

18.02

1.14

FFAS-3D

------------------DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCE-

3k6sB

0.51

0.48

14.00

1.30

EigenThreader

FDYPSVGQLAHKLAENNIQPIVQLIKNAYNKLSSRVFLDHNRGDCDGVVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHG-KGFLECGCDIGK---NCEQGRSSQELEG-----SCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCET--INCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

5es4B

0.78

0.64

18.06

5.14

CNFpred

-----------------------DCDGVQI---------------NVPITFQVKVTA-EQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCER

1hn0A

0.06

0.05

2.20

0.67

DEthreader

------------KRSIMSFWLYLTIFKV-KL-DFT--------G-WRAVGVDLEN-DAYQWSDQ----TLNGGTKHLQFLVTTHHREFKSS---SADSSD----LDYFSILGLAWRHESAFGNLKAMVSAWIYSN----P-EVGLLAPLFGGFTKSSNRYGRYQSHGVAQIVNRMEGATTIHL-NLINFTAKKSVIFIGSNI-KDASYEYVKD

(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	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5469

(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)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3k6sB	0.73	3.73	0.678	0.906	model1_3k6sB.pdb.gz
2	4g1eB	0.65	3.97	0.294	0.869	model1_4g1eB.pdb.gz
3	2e26A2	0.28	6.08	0.026	0.516	model1_2e26A2.pdb.gz
4	2ygqA	0.28	5.46	0.050	0.469	model1_2ygqA.pdb.gz
5	2dduA	0.28	5.72	0.090	0.488	model1_2dduA.pdb.gz
6	1pu6A	0.27	5.88	0.047	0.484	model1_1pu6A.pdb.gz
7	3ho4B	0.27	6.20	0.062	0.502	model1_3ho4B.pdb.gz
8	1gvzA	0.25	6.21	0.053	0.474	model1_1gvzA.pdb.gz
9	1rp3A	0.25	6.15	0.018	0.460	model1_1rp3A.pdb.gz
10	3vi3B	0.24	6.22	0.029	0.451	model1_3vi3B.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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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	Cscore^GO	Name
GO:0050839	0.61	cell adhesion molecule binding
GO:0046983	0.55	protein dimerization activity
GO:0046982	0.54	protein heterodimerization activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO 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 Cscore^GO:

[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	Cscore^GO	Name
GO:0044699	0.94	single-organism process
GO:0044763	0.91	single-organism cellular process
GO:0065007	0.78	biological regulation
GO:0050789	0.77	regulation of biological process
GO:0050794	0.75	regulation of cellular process
GO:0016043	0.67	cellular component organization
GO:0007155	0.62	cell adhesion
GO:0050896	0.61	response to stimulus
GO:0032502	0.61	developmental process
GO:0044767	0.58	single-organism developmental process
GO:0007165	0.58	signal transduction
GO:0048518	0.57	positive regulation of biological process
GO:0007166	0.57	cell surface receptor signaling pathway
GO:0098609	0.56	cell-cell adhesion
GO:0051179	0.56	localization
GO:0006928	0.56	movement of cell or subcellular component
GO:1902578	0.54	single-organism localization
GO:0098602	0.54	single organism cell adhesion
GO:0042221	0.54	response to chemical
GO:0008152	0.54	metabolic process
GO:0006810	0.54	transport
GO:0071704	0.53	organic substance metabolic process
GO:0051716	0.53	cellular response to stimulus
GO:0051128	0.53	regulation of cellular component organization
GO:0048522	0.53	positive regulation of cellular process
GO:0044765	0.53	single-organism transport
GO:0044237	0.53	cellular metabolic process
GO:0031589	0.53	cell-substrate adhesion
GO:0016337	0.53	single organismal cell-cell adhesion
GO:0016192	0.53	vesicle-mediated transport
GO:0010033	0.53	response to organic substance
GO:0007229	0.53	integrin-mediated signaling pathway
GO:0071495	0.52	cellular response to endogenous stimulus
GO:0071310	0.52	cellular response to organic substance
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0051239	0.52	regulation of multicellular organismal process
GO:0048870	0.52	cell motility
GO:0044710	0.52	single-organism metabolic process
GO:0043170	0.52	macromolecule metabolic process
GO:0007160	0.52	cell-matrix adhesion
GO:0006897	0.52	endocytosis
GO:0044260	0.51	cellular macromolecule metabolic process
GO:0016477	0.51	cell migration
GO:0006898	0.51	receptor-mediated endocytosis
GO:0071404	0.50	cellular response to low-density lipoprotein particle stimulus
GO:0048869	0.50	cellular developmental process
GO:0032879	0.50	regulation of localization
GO:0031623	0.50	receptor internalization

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO 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 Cscore^GO:

[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	Cscore^GO	Name
GO:0044464	0.87	cell part
GO:0016020	0.82	membrane
GO:0044425	0.72	membrane part
GO:0044459	0.71	plasma membrane part
GO:0005886	0.68	plasma membrane
GO:0044421	0.58	extracellular region part
GO:0044424	0.56	intracellular part
GO:0043226	0.56	organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0009986	0.52	cell surface
GO:0043234	0.50	protein complex

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO 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 Cscore^GO:

[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

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1bxrA	0.411	5.90	0.041	0.737	6.3.5.5	NA
2	0.060	2ebsB	0.426	5.84	0.056	0.756	3.2.1.150	NA
3	0.060	1v5eA	0.363	6.69	0.030	0.723	1.2.3.3	NA
4	0.060	1x74A	0.403	5.52	0.065	0.681	5.1.99.4	NA
5	0.060	2eabA	0.420	5.88	0.046	0.737	3.2.1.63	23

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC 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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.02	1u8cB	0.325	4.37	0.223	0.465	0.45	UUU	complex1.pdb.gz	96,98,102,106
2	0.01	2vdoB	0.246	5.34	0.089	0.394	0.52	III	complex2.pdb.gz	200,201,203,205
3	0.01	1l5gB	0.290	6.54	0.050	0.563	0.51	UUU	complex3.pdb.gz	186,187,190,202,204,206,210
4	0.01	3n75A	0.375	6.35	0.060	0.709	0.46	G4P	complex4.pdb.gz	190,192,196
5	0.01	1l5gB	0.290	6.54	0.050	0.563	0.43	III	complex5.pdb.gz	199,200,201,203,205
6	0.01	1jv2B	0.283	6.23	0.054	0.535	0.65	UUU	complex6.pdb.gz	185,186,187,190,202,206

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB 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)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a 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.