D-I-TASSER O00548-D7

D-I-TASSER results for O00548-D7

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

Input Sequence in FASTA format

>O00548 (201 residues)
LPPGPAVVDLTEKLEGQGGPFPWVAVCAGVILVLMLLLGCAAVVVCVRLRLQKHRPPADP
CRGETETMNNLANCQREKDISVSIIGATQIKNTNKKADFHGDHSADKNGFKARYPAVDYN
LVQDLKGDDTAVRDAHSKRDTKCQPQGSSGEEKGTPTTLRGGEASERKRPDSGCSTSKDT
KYQSVYVISEEKDECVIATEV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LPPGPAVVDLTEKLEGQGGPFPWVAVCAGVILVLMLLLGCAAVVVCVRLRLQKHRPPADPCRGETETMNNLANCQREKDISVSIIGATQIKNTNKKADFHGDHSADKNGFKARYPAVDYNLVQDLKGDDTAVRDAHSKRDTKCQPQGSSGEEKGTPTTLRGGEASERKRPDSGCSTSKDTKYQSVYVISEEKDECVIATEV
Prediction	CCCCCCCCCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCCCCCCCCSSSSCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCSSSSSCC
Confidence	999887766753345778999765202567999999999999999999875211478764433112221322242222330223135543335652145404788767753358865543342224443321011223000256678741013565445567887433667777887776403689851566521665139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LPPGPAVVDLTEKLEGQGGPFPWVAVCAGVILVLMLLLGCAAVVVCVRLRLQKHRPPADPCRGETETMNNLANCQREKDISVSIIGATQIKNTNKKADFHGDHSADKNGFKARYPAVDYNLVQDLKGDDTAVRDAHSKRDTKCQPQGSSGEEKGTPTTLRGGEASERKRPDSGCSTSKDTKYQSVYVISEEKDECVIATEV
Prediction	636443426136437667250100001311321232333112010012033254555655344435314324515464533231132341443445241435455544324463331313105624566344645554455414546556456534451545754653436541534542313201003644621120258
	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

CCCCCCCCCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCCCCCCCCSSSSCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCSSSSSCC
LPPGPAVVDLTEKLEGQGGPFPWVAVCAGVILVLMLLLGCAAVVVCVRLRLQKHRPPADPCRGETETMNNLANCQREKDISVSIIGATQIKNTNKKADFHGDHSADKNGFKARYPAVDYNLVQDLKGDDTAVRDAHSKRDTKCQPQGSSGEEKGTPTTLRGGEASERKRPDSGCSTSKDTKYQSVYVISEEKDECVIATEV

2mouA

0.06

0.05

2.18

0.44

CEthreader

--------------------------------MDFKAIAQQTAQEVLGYNRDTSGWKVVKTSKKITVSSKASRKFHGNLYRVEGIIPESPAKLSDYQTGDRITWDKSLQVYNMVHRIDSDTFICHTITQSFAVGSISPRDFIDLVYIKRYEGNMNIISSKSVDFPEYPPSSNYIRGYNHPCGFVCSPMEENPAYSKLVMFV

4owdA

0.05

2.29

0.52

EigenThreader

GKRIMVLKGSSHAEQLAELKKQYLMNEVNAFLDQAKKEGLLQRLKDRYYGHVDVLGYVGAYTFAQHLQQRLPRYESHFKQSGKQLDTDWRLLAAIGYQESLWQPGAGLMMLDPKQSIQGGSKYFVQIRSELALAAYNIGGAHLEDARKMAEKEGLNPKTRYGYARGGETVHFVQNVRRYYDILTW-----VTQPQ------

2kluA

0.16

0.05

1.65

0.35

FFAS-3D

VPRGSM-----------------ALIVLGGVAGLLLFIG---LGIFFSVRSRHRRRQAERMSQIKRLLSEKKTSQSPHRFQ------------------------------------------------------------------------------------------------------------------------

5njtD

0.06

0.05

2.15

0.94

SPARKS-K

TGKELEKRPYAPHGPGQRKKLSEYGLQLQEKQKLRHM--------FRTLFDKAGKLAGKHLDSRLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVD-IPSYLVKPGQTIGVRE-------KSRNLSIIKESVEVN------NFVPEYLTFDAEKLEGTFTRLPERSELAPEINEALIVEFYSR----------------

4u8yA

0.16

0.04

1.33

0.65

CNFpred

--------------------FSINTLTMFGMVLAIGLLVDNAIVVVENVERVMAEEGLPPKEATRKSMGQI----------------------------------------------------------------------------------------------------------------------------------

4mz0A

0.07

0.05

2.04

0.83

DEthreader

----------------------LKQEQEKEQSLSALQRALIALKDARSKLEKYETSKEPI-AI--IG-MSCRLLLESVIATGSPNLAVSGGVNL---DGRCKTFDASANGYVRG----T---QDGGLTVP-NGPSQVAVIRKALSNGGVDPASVSYIIVFHPLIVGTAKTNI---G-----LEV---------T-------

1vt4I3

0.06

2.61

1.05

MapAlign

RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIPKYERLVNAILDFLPKGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

5tgzA

0.10

0.09

3.54

0.59

MUSTER

VLP-LLGWNCEKLQSVCSDIFPYLMFWIGVVSVLLLFIVYAYMYILWKAHSHAVAKALIVYGSTTGNTEYTAETIARELADAGYVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSWEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAIPD--ARMDI

2pffB

0.17

0.15

5.08

0.90

HHsearch

FTQGLNILEWLENSNTPDKDYL-LSIPISCPLIGVIQLAHYVVTAFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFSSHLPAGKQVSLVNGAKNLVVSGPP-QSL---------YGLNLTLRKAKLDQRIPFSERKLKFSNRFL------PVASPFHSHASDLINKDLNVSFNAKDIQIPVYSISERIVDCIIRLPV

1vt4I3

0.08

3.28

0.41

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

(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	0.4061

(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	4fyeA2	0.45	5.29	0.035	0.741	model1_4fyeA2.pdb.gz
2	3jd8A	0.45	5.00	0.058	0.682	model1_3jd8A.pdb.gz
3	6wu0B	0.44	4.98	0.050	0.682	model1_6wu0B.pdb.gz
4	6d4hA1	0.44	5.13	0.038	0.702	model1_6d4hA1.pdb.gz
5	2q5tA	0.44	5.61	0.040	0.776	model1_2q5tA.pdb.gz
6	3d0cA	0.31	5.91	0.036	0.547	model1_3d0cA.pdb.gz
7	3gkhA	0.31	5.71	0.035	0.547	model1_3gkhA.pdb.gz
8	2ipiA	0.31	6.15	0.046	0.592	model1_2ipiA.pdb.gz
9	1aerA	0.31	5.97	0.075	0.542	model1_1aerA.pdb.gz
10	2iufA	0.31	6.16	0.028	0.587	model1_2iufA.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	0.82	receptor binding
GO:0005112	0.80	Notch binding

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	1.00	regulation of cellular process
GO:0044767	1.00	single-organism developmental process
GO:0007389	1.00	pattern specification process
GO:0048646	0.93	anatomical structure formation involved in morphogenesis
GO:0009987	0.92	cellular process
GO:0044763	0.90	single-organism cellular process
GO:0048869	0.89	cellular developmental process
GO:0030154	0.88	cell differentiation
GO:0048523	0.84	negative regulation of cellular process
GO:2000026	0.83	regulation of multicellular organismal development
GO:0051241	0.83	negative regulation of multicellular organismal process
GO:0009653	0.81	anatomical structure morphogenesis
GO:0009966	0.80	regulation of signal transduction
GO:0048856	0.78	anatomical structure development
GO:0045765	0.71	regulation of angiogenesis
GO:0032879	0.71	regulation of localization
GO:0051093	0.70	negative regulation of developmental process
GO:0007165	0.69	signal transduction
GO:0007166	0.68	cell surface receptor signaling pathway
GO:0035239	0.67	tube morphogenesis
GO:0007219	0.67	Notch signaling pathway
GO:0001756	0.67	somitogenesis
GO:0048518	0.65	positive regulation of biological process
GO:0008593	0.65	regulation of Notch signaling pathway
GO:0060284	0.64	regulation of cell development
GO:0051960	0.64	regulation of nervous system development
GO:0050767	0.63	regulation of neurogenesis
GO:0048522	0.63	positive regulation of cellular process
GO:0009888	0.63	tissue development
GO:0009967	0.59	positive regulation of signal transduction
GO:0002376	0.59	immune system process
GO:0090287	0.58	regulation of cellular response to growth factor stimulus
GO:0045747	0.58	positive regulation of Notch signaling pathway
GO:0030098	0.58	lymphocyte differentiation
GO:0008285	0.58	negative regulation of cell proliferation
GO:0008284	0.58	positive regulation of cell proliferation
GO:1903670	0.57	regulation of sprouting angiogenesis
GO:0045665	0.57	negative regulation of neuron differentiation
GO:0002009	0.57	morphogenesis of an epithelium
GO:0046331	0.55	lateral inhibition
GO:0048513	0.54	animal organ development
GO:0048468	0.53	cell development
GO:0007368	0.53	determination of left/right symmetry
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0031323	0.52	regulation of cellular metabolic process
GO:0080090	0.51	regulation of primary metabolic process
GO:0009893	0.50	positive regulation of metabolic process

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:0005886	1.00	plasma membrane
GO:0044424	0.79	intracellular part
GO:0044425	0.63	membrane part
GO:0044459	0.60	plasma membrane part
GO:0044444	0.59	cytoplasmic part
GO:0098589	0.53	membrane region
GO:0030054	0.53	cell junction
GO:0045121	0.52	membrane raft
GO:0043226	0.52	organelle
GO:0016324	0.52	apical plasma membrane
GO:0005912	0.52	adherens junction
GO:0043227	0.51	membrane-bounded organelle

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	2pnrF	0.393	6.04	0.067	0.741	2.7.11.2	169
2	0.060	1fohC	0.411	6.16	0.079	0.761	1.14.13.7	NA
3	0.060	1clcA	0.414	5.40	0.016	0.677	3.2.1.4	NA
4	0.060	1m56A	0.414	5.24	0.043	0.642	1.9.3.1	NA
5	0.060	1h2rL	0.424	5.33	0.074	0.682	1.12.2.1	100

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	2z8yD	0.428	5.36	0.071	0.707	0.60	SF4	complex1.pdb.gz	80,81,86,88
	2	0.01	1e3dB	0.427	5.37	0.081	0.687	0.43	H2S	complex2.pdb.gz	102,107,109,110

	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.