D-I-TASSER P55103-D1

D-I-TASSER results for P55103-D1

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

Input Sequence in FASTA format

>P55103 (195 residues)
MTSSLLLAFLLLAPTTVATPRAGGQCPACGGPTLELESQRELLLDLAKRSILDKLHLTQR
PTLNRPVSRAALRTALQHLHGDCQGGSRMCCRQEFFVDFREIGWHDWIIQPEGYAMNFCI
GQCPLHIAGMPGIAASFHTAVLNLLKANTAAGTTGGGSCCVPTARRPLSLLYYDRDSNIV
KTDIPDMVVEACGCS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTSSLLLAFLLLAPTTVATPRAGGQCPACGGPTLELESQRELLLDLAKRSILDKLHLTQRPTLNRPVSRAALRTALQHLHGDCQGGSRMCCRQEFFVDFREIGWHDWIIQPEGYAMNFCIGQCPLHIAGMPGIAASFHTAVLNLLKANTAAGTTGGGSCCVPTARRPLSLLYYDRDSNIVKTDIPDMVVEACGCS
Prediction	CCHHHHHHHHHHCCCCSSCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCCCSSCCCCCSCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSCSCC
Confidence	941466778753402122146765167888745574333313343311332344430016444567420110222113566667787870668899862125894404369852221102547887667888776520788887876156876689987677531336899996898599997289287212077
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTSSLLLAFLLLAPTTVATPRAGGQCPACGGPTLELESQRELLLDLAKRSILDKLHLTQRPTLNRPVSRAALRTALQHLHGDCQGGSRMCCRQEFFVDFREIGWHDWIIQPEGYAMNFCIGQCPLHIAGMPGIAASFHTAVLNLLKANTAAGTTGGGSCCVPTARRPLSLLYYDRDSNIVKTDIPDMVVEACGCS
Prediction	641433310122135304455342322324455352645363135235464365444544554645455554455455455547655540323413030441324411221541323203130423245345234420130242243443645631521333452430200011674413345165020641618
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCCSSCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCCCSSCCCCCSCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSCSCC
MTSSLLLAFLLLAPTTVATPRAGGQCPACGGPTLELESQRELLLDLAKRSILDKLHLTQRPTLNRPVSRAALRTALQHLHGDCQGGSRMCCRQEFFVDFREIGWHDWIIQPEGYAMNFCIGQCPLHIAGMPGIAASFHTAVLNLLKANTAAGTTGGGSCCVPTARRPLSLLYYDRDSNIVKTDIPDMVVEACGCS

2pjyA

0.32

0.17

5.10

0.67

DEthreader

-----------------------------------------------------------------------------DTNYCFRNLEENCCVRPLYIDFRDLGWK-WVHEPKGYYANFCSGPCP-YLR-----HSTVLGLYNTLNPE-A-----SASPCCVPQDLEPLTILYYVG-RTPKVEQLSNMVVKSCKCS

5ntuA1

0.34

0.25

7.53

2.64

SPARKS-K

------------------------------------QNTKSSRIEAIKIQILSKLRLETAPNISKLLPAPPLRELIDQYDLDCDEHSTECCRYPLTVDFEAFGWD-WIIAPKRYKANYCSGECEFVAAYPHTH------------LVHQANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

5ntuA

0.23

0.21

6.58

0.87

MapAlign

PKAPPLRELIDTPTTVFVQILRLIKPMKDGTRYTGIRSLWQSIDVKTVLQNWLAAPASNLGIEIKALTDTPKRSRRDFGLDCEHSTESRCCRYPLTVDFEAFGWD-WIIAPKRYKANYCSGECE-----------------FVFLAAYPHTHLVQANPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

2p6aA

0.50

0.30

8.63

0.84

CEthreader

-------------------------------------------------------------------------------GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS

5ntuA1

0.36

0.27

8.10

1.85

MUSTER

------------------------------------QNTKSSRIEAIKIQILSKLRLETAPNISLPKAPPLRELIDQYDGLDCDEHSTECCRYPLTVDFEAFGW-DWIIAPKRYKANYCSGECEFVFL-----AAYPHTHLVHQ-----ANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

3rjrA

0.25

0.23

6.98

3.25

HHsearch

V-TGVVRQWL-TRREAIEGFRLSAHCSCDSKDNTLHVEI--------N-GDLATIHGMNRPFLLLMATPLERA-QHALDTNYCFSTEKNCCVRQLYIDFRDLGW-KWIHEPKGYHANFCLGPCPYIWS-----LDTQYSKVLALYNQH--NPGASAAPCCVPQALEPLPIVYYVGRK-PKVEQLSNMIVRSCKCS

5ntuA1

0.32

0.25

7.41

1.81

FFAS-3D

------------------------------------QNTKSSRIEAIKIQILSKLRLETAPNISLPKAPPLRELIDQYDGLDCDEHESRCCRYPLTVDFEAFGW-DWIIAPKRYKANYCSGECEFVFLAAYPHTH----------LVHQANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

2k8pA

0.14

0.09

3.15

0.83

EigenThreader

TEII-------PELGEYPEPPPE----------LEN------------------NKTMNRAENGGRPPHH--------PFETKDVSEYSCRELHFTRYV----TDGPCRSAKPVTELVCSGQCGPARLLPNAIGPSG-----------------PDFRCIPDRYRAQRVQLLCPG-GEAPRARKV-RLVASCKCK

5ntuA

0.30

0.26

7.78

3.22

CNFpred

DVKTVLQNWLAAP---ASNLGIEIKALDENGHDLAVT-------------FPGPGEDGLNPFLEVKV-TDTPKRSRRDFGLDCDSTESRCCRYPLTVDFEAFGW-DWIIAPKRYKANYCSGECEFVF-----LAAYPHTHLVHQ-----ANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

1urjB

0.07

0.06

2.35

0.67

DEthreader

VAVYLLFEAVVGPAAVALRSTFTAF---GGF-QRLSTEVPGTAEHAMLSFSPALLAKMLFYLERCDGTLMRLRARHPK-----RG-----AIGVFGTLTLDPYAC-PCPLQLLGSN-VKSRVLFAYQKPDKNFINLAPEYYMANQILRYCDHS--FINTLTAIIAGS-------------G-W-SPMVVCLLIRK

(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	0.6029

(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 AttentionPotential, 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	5ntuA	0.56	3.48	0.297	0.682	model1_5ntuA.pdb.gz
2	2b0uA	0.48	2.55	0.500	0.559	model1_2b0uA.pdb.gz
3	4n1dA	0.47	1.79	0.380	0.513	model1_4n1dA.pdb.gz
4	2qcqB	0.47	2.40	0.311	0.533	model1_2qcqB.pdb.gz
5	1m4uL	0.46	2.42	0.364	0.533	model1_1m4uL.pdb.gz
6	2pjyA	0.46	2.75	0.306	0.538	model1_2pjyA.pdb.gz
7	3bmpA	0.46	2.25	0.362	0.518	model1_3bmpA.pdb.gz
8	1waqA	0.45	2.27	0.359	0.508	model1_1waqA.pdb.gz
9	3hh2A	0.45	2.49	0.404	0.518	model1_3hh2A.pdb.gz
10	3rjrA	0.44	3.07	0.182	0.518	model1_3rjrA.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:0005102	0.98	receptor binding
GO:0005160	0.97	transforming growth factor beta receptor binding
GO:0005125	0.89	cytokine activity
GO:0046983	0.56	protein dimerization activity
GO:0033612	0.56	receptor serine/threonine kinase binding
GO:0070696	0.55	transmembrane receptor protein serine/threonine kinase binding
GO:0042802	0.53	identical protein binding
GO:0046982	0.51	protein heterodimerization activity
GO:0008083	0.51	growth factor 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:0050794	0.98	regulation of cellular process
GO:0044699	0.96	single-organism process
GO:0080090	0.93	regulation of primary metabolic process
GO:0060255	0.93	regulation of macromolecule metabolic process
GO:0048522	0.93	positive regulation of cellular process
GO:0031323	0.93	regulation of cellular metabolic process
GO:0048583	0.92	regulation of response to stimulus
GO:0044767	0.92	single-organism developmental process
GO:0044763	0.92	single-organism cellular process
GO:0031325	0.92	positive regulation of cellular metabolic process
GO:0010604	0.92	positive regulation of macromolecule metabolic process
GO:0007165	0.92	signal transduction
GO:0023051	0.91	regulation of signaling
GO:0010646	0.91	regulation of cell communication
GO:0051246	0.90	regulation of protein metabolic process
GO:0009967	0.90	positive regulation of signal transduction
GO:0048869	0.89	cellular developmental process
GO:0001934	0.89	positive regulation of protein phosphorylation
GO:0010862	0.87	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0048856	0.86	anatomical structure development
GO:0042981	0.85	regulation of apoptotic process
GO:0060395	0.84	SMAD protein signal transduction
GO:0043408	0.82	regulation of MAPK cascade
GO:0010556	0.78	regulation of macromolecule biosynthetic process
GO:0007178	0.78	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0031326	0.75	regulation of cellular biosynthetic process
GO:0048519	0.72	negative regulation of biological process
GO:0048523	0.71	negative regulation of cellular process
GO:0051239	0.68	regulation of multicellular organismal process
GO:2000026	0.66	regulation of multicellular organismal development
GO:0042127	0.66	regulation of cell proliferation
GO:0048468	0.65	cell development
GO:0045595	0.65	regulation of cell differentiation
GO:0051241	0.64	negative regulation of multicellular organismal process
GO:0008285	0.64	negative regulation of cell proliferation
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0051240	0.60	positive regulation of multicellular organismal process
GO:0006357	0.59	regulation of transcription from RNA polymerase II promoter
GO:0051094	0.58	positive regulation of developmental process
GO:0044707	0.58	single-multicellular organism process
GO:0031324	0.58	negative regulation of cellular metabolic process
GO:0051093	0.57	negative regulation of developmental process
GO:0045597	0.57	positive regulation of cell differentiation
GO:0042221	0.57	response to chemical
GO:0051128	0.56	regulation of cellular component organization
GO:0045596	0.56	negative regulation of cell differentiation
GO:0030154	0.56	cell differentiation
GO:0010033	0.56	response to organic substance
GO:0009719	0.56	response to endogenous stimulus
GO:1901700	0.55	response to oxygen-containing compound
GO:0031327	0.55	negative regulation of cellular biosynthetic process
GO:0010558	0.55	negative regulation of macromolecule biosynthetic process
GO:0009725	0.55	response to hormone
GO:0002682	0.55	regulation of immune system process
GO:0051049	0.54	regulation of transport
GO:0033993	0.54	response to lipid
GO:0014070	0.54	response to organic cyclic compound
GO:0008152	0.54	metabolic process
GO:0002683	0.54	negative regulation of immune system process
GO:0001818	0.54	negative regulation of cytokine production
GO:0045786	0.53	negative regulation of cell cycle
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0040008	0.53	regulation of growth
GO:0071702	0.52	organic substance transport
GO:0051050	0.52	positive regulation of transport
GO:0044765	0.52	single-organism transport
GO:0030308	0.52	negative regulation of cell growth
GO:0007050	0.52	cell cycle arrest
GO:0065008	0.51	regulation of biological quality
GO:0048513	0.51	animal organ development
GO:0045936	0.51	negative regulation of phosphate metabolic process
GO:0030509	0.51	BMP signaling pathway
GO:1903530	0.50	regulation of secretion by cell

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:0044421	1.00	extracellular region part
GO:0005576	1.00	extracellular region
GO:0005615	0.97	extracellular space
GO:0044464	0.54	cell part

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	0.342	1lx5A	0.472	1.58	0.394	0.508	2.7.11.30	90,119,121,123,160,162,189,192
2	0.060	1wnbA	0.399	5.44	0.054	0.692	1.2.1.19 1.2.1.8	NA
3	0.060	1dgjA	0.397	5.66	0.039	0.687	1.2.-.-	NA
4	0.060	3kvnX	0.403	5.76	0.088	0.713	3.1.1.1	12,168
5	0.060	2esdA	0.412	5.19	0.056	0.687	1.2.1.9	44,46

	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	0.27	1nys3	0.406	1.54	0.576	0.436	0.89	III	complex1.pdb.gz	109,111,169,170,171,173,179,181,183
2	0.25	1nys0	0.406	1.54	0.576	0.436	1.31	III	complex2.pdb.gz	158,159,161,195
3	0.23	1s4y4	0.436	2.91	0.491	0.518	0.92	III	complex3.pdb.gz	164,166,167,169,170,190
4	0.06	2h625	0.467	1.85	0.400	0.513	1.57	III	complex4.pdb.gz	100,101,102,104,170,182,184
5	0.06	2h620	0.467	1.85	0.400	0.513	1.29	III	complex5.pdb.gz	95,104,116,117,118,141,142,144,153,159,161,162,165,185,186,187,189,195

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.