D-I-TASSER O00165-D1

D-I-TASSER results for O00165-D1

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

Input Sequence in FASTA format

>O00165 (279 residues)
MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEE
FGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLR
EGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPR
TREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTV
TRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEEFGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLREGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPRTREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTVTRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR
Prediction	CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC
Confidence	968898887528999999889877876667788764112477777778777777897221576656799876434662578999999998763236666777777889987789888877788875222589877787667888766678889888767788888655798676789830135566533345567765557887656665312466469985255777765999748999873589876789999999876761799999997652269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEEFGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLREGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPRTREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTVTRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR
Prediction	452242021001133745452322433344564446655644433644552542324574241324132643342444420440053035104521432326444725434555556446654412141043254444444544356744554554456154522245156214443565544455146504773145214233443364243430444714354443343474444230225354744565674444642623321044004411478
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC
MSLFDLFRGFFGFPGPRSHRDPFFGGMTRDEDDDEEEEEEGGSWGRGNPRFHSPQHPPEEFGFGFSFSPGGGIRFHDNFGFDDLVRDFNSIFSDMGAWTLPSHPPELPGPESETPGERLREGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPQPAPDWGSQRPFHRFDDVWPMDPHPRTREDNDLDSQVSQEGLGPVLQPQPKSYFKSISVTKITKPDGIVEERRTVVDSEGRTETTVTRHEADSSPRGDPESPRPPALDDAFSILDLFLGRWFRSR

4fl2A

0.04

2.16

0.54

CEthreader

ERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPGSKTNGKFLIRARDNNGSYALCLLLHYRIDKDKTKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKIGTQREALPMDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKD

1no3A

0.05

0.04

2.10

0.58

EigenThreader

TPAPLVKYREEELHDGTGERKEWERIYDNDLGDPD---KGENHARPVLGGNDTFPYPRRGRTGRKPTRKDPNSESRSNDVY---------------LPRDEAFGHLKSSDFLTYGLKSVSQNVLPLLQSAFDLNFTPREFDSFDEVHGLYSGGIKLPRTDGEQALKFPPPKVIQVSKSAWMTSKLDSQVYGDHTSQITKEHLEPNLEGLTRLFLLDHHTKAYATRTILFLKNDGTLRPLAIELSLPHPQGDQSGLVNDGGDWVFTDQALPADLIKRGMA

6xp5a

0.13

0.11

3.86

0.44

FFAS-3D

-DVYESLARLH-----AWELQKLREDPSLAGKDDEYLENLGLALDYEAEVASWIADNERTWSILIGCAPLRDLSINPVR----------------ISDKWIGPNVKTSLPDGLHTGEPIIDWLDPEPTFIPATDQQQQQPNADTTTSKPTPNAKASHKKLDDFEAFSSHSGPISNMTPSQHQPSSDLSIDVTLRPKLQIVFPLHATSKEEVK-GKIAHEEGQMEGVKTEGDEDGEEKKR--------------RRPQPGDLARALEVLEDV-GKWAE--

4btgA

0.10

0.09

3.21

1.04

SPARKS-K

YEDWQFAKEITAFTPVKLANNSNQRFLDVEPGISDRMSATLAPIGNTFAAVSQRGTVNSNGAEMTLGFPSVVERDYALRASNDLKRSMFNYYAAVMHYAVAHNPEVVVSEH----QGVAAEQGSL---YLVWNVRTELRIPVGYNAI---EGGSIRTPEPLEAIAYNKPIQPEVLQAKV-----LDLANHTTSIHIWPWHEASTEFAYEDAYSVTIR-----------------NKRYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWFVED

4r7kA

0.08

0.02

0.72

0.40

CNFpred

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRLAWRGWNE-YLEVYHAWLVEKLNDRVRILTQESQSGVPAKALAKSVPNAM----LNGHQAWLDGLVAYS

6fijA

0.06

0.04

1.76

0.67

DEthreader

VIAQLGLFIRHYPSCITGVGATAALPI-HSFSIALDRMAV-SIANH----A--L-KDSVLPSPI-A-L---SFSD-------KS-PS--GAEQQPMAKSPLTGLTDISVCYILDLAARNTHIVWPRP-KRRVL--LN--N--------FSAAGGNT-CL-V-LEDA----------NTNMIRLQEQL-RR----------------------EEVPPGEA-YEFSCR----------EQRNVLGGTVAPMAGQVDCRSSVNMDALQSAVLDKKVGTTMQ

5kisB

0.07

2.91

0.87

MapAlign

VYAGNGAEKTLNLAGTVLTTTDAKGNIQRVRYDRTEQVIVKSLTYSAAGQKQREDHGNGVVITYTYEAETQRLTGIRTERANVGQQGSRLPSATVPFPTDSSAYTSYTRTYTYDEASNLTQIRHSPVDALFTAGGQQTQLQPGLGLVWTARNELLKVTPVDDSENYRYDGGSQRILKVSVQKTSAQTQRALYLPGLELRSAKNGDTETESLQVITVGEASRAQVRMLHWESGDGITDDKVRYSYDNYKTVRYSGKERDATGLYYYGYRYYDGR------

3txaA1

0.11

3.89

0.61

MUSTER

EKLIDKITTYASTIFDGTEATVSKGVADQNGKALNDSVSWDYHKTTFTATTHNYSNDANEVNILKSRIPKEAEHINGDRTTQKALMKANEILETQSSNARKKLVPTMSYAINFNPYISTSYQNQFNSFLNKIPDRSGILQEDFIINGDDYQIVKGDGESFKLFSDRKVPVTGGTTQAAYRVPQNQ--LSVMSNEGYAINSGYIYLYWRDYNWVYPFDPKTKKVSATKQIKTPKGYDIFTVGIGVNGDPGATPLEAESKTENDDTNKIYDELNKYF-EEK

2jorA

0.23

0.06

2.02

0.74

HHsearch

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MIDNEKVTSGH----TTTTRRSCSKVITKTVT-NADGRTETTKEVVKSEGSDCGDA--DFDWHHTFPSRGN-----LDDFFHRDK---DDFFT--

4zzpA

0.07

2.94

0.52

CEthreader

ADDGSCKTMNGEIVIDANWRWVHSEQGTNCYTGNTWNPTLCPDDKTCAENCYLDGANYESVYGITTEDDSVRLNFITQSQGKNIGSRTFLMANSTNYQMFYVLGQEFSDSDGGIARFPSNEAGAQYGTDLKFISGSANVEGWIPSSNNPNTGYGNHGSCCAEMDLWEANNMATALTPHPCDTSSQTVCESDSCGGATSSNRYGGTTFFGPGQTVDTKSVMTVVTQFITNDGTTTGTLKSIKRLYVQNVISQSESTVPGVAGNEITEDFCHNQKQVFGDK

(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	0.4064

(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	3gwjA	0.42	6.25	0.054	0.728	model1_3gwjA.pdb.gz
2	4l37A	0.41	6.27	0.057	0.724	model1_4l37A.pdb.gz
3	3hhsB	0.41	6.51	0.051	0.735	model1_3hhsB.pdb.gz
4	1qhbA	0.41	6.60	0.065	0.731	model1_1qhbA.pdb.gz
5	1wqlA	0.40	6.31	0.033	0.692	model1_1wqlA.pdb.gz
6	1hcyA2	0.35	6.19	0.056	0.599	model1_1hcyA2.pdb.gz
7	3ixvM2	0.30	6.45	0.028	0.523	model1_3ixvM2.pdb.gz
8	2p3xA	0.29	6.56	0.037	0.516	model1_2p3xA.pdb.gz
9	3wecA	0.29	6.81	0.071	0.527	model1_3wecA.pdb.gz
10	3ba1A	0.28	6.63	0.073	0.512	model1_3ba1A.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:0047485	0.63	protein N-terminus binding
GO:0019966	0.63	interleukin-1 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:0009987	1.00	cellular process
GO:0065007	0.92	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0044699	0.91	single-organism process
GO:0044763	0.90	single-organism cellular process
GO:0080090	0.89	regulation of primary metabolic process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0050896	0.89	response to stimulus
GO:0048518	0.89	positive regulation of biological process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0065008	0.88	regulation of biological quality
GO:0051716	0.88	cellular response to stimulus
GO:0051247	0.88	positive regulation of protein metabolic process
GO:0051240	0.88	positive regulation of multicellular organismal process
GO:0048584	0.88	positive regulation of response to stimulus
GO:0048523	0.88	negative regulation of cellular process
GO:0045595	0.88	regulation of cell differentiation
GO:0042981	0.88	regulation of apoptotic process
GO:0031399	0.88	regulation of protein modification process
GO:0031325	0.88	positive regulation of cellular metabolic process
GO:0019220	0.88	regulation of phosphate metabolic process
GO:0016043	0.88	cellular component organization
GO:0009966	0.88	regulation of signal transduction
GO:0006355	0.88	regulation of transcription, DNA-templated
GO:0002684	0.88	positive regulation of immune system process
GO:2000251	0.87	positive regulation of actin cytoskeleton reorganization
GO:0071345	0.87	cellular response to cytokine stimulus
GO:0051897	0.87	positive regulation of protein kinase B signaling
GO:0050731	0.87	positive regulation of peptidyl-tyrosine phosphorylation
GO:0045944	0.87	positive regulation of transcription from RNA polymerase II promoter
GO:0043066	0.87	negative regulation of apoptotic process
GO:0033138	0.87	positive regulation of peptidyl-serine phosphorylation
GO:0030854	0.87	positive regulation of granulocyte differentiation
GO:0030833	0.87	regulation of actin filament polymerization
GO:0014068	0.87	positive regulation of phosphatidylinositol 3-kinase signaling
GO:0006996	0.50	organelle organization

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:0044444	1.00	cytoplasmic part
GO:0043229	0.93	intracellular organelle
GO:0043227	0.93	membrane-bounded organelle
GO:0016020	0.93	membrane
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0005783	0.91	endoplasmic reticulum
GO:0044422	0.80	organelle part
GO:0044446	0.79	intracellular organelle part
GO:0032991	0.75	macromolecular complex
GO:0043234	0.74	protein complex
GO:0031090	0.66	organelle membrane
GO:0098805	0.65	whole membrane
GO:0098588	0.65	bounding membrane of organelle
GO:0044429	0.65	mitochondrial part
GO:0031966	0.64	mitochondrial membrane
GO:0005758	0.64	mitochondrial intermembrane space
GO:0070013	0.63	intracellular organelle lumen
GO:0030027	0.63	lamellipodium
GO:0015629	0.63	actin cytoskeleton
GO:0005741	0.63	mitochondrial outer membrane
GO:0005739	0.63	mitochondrion
GO:0005667	0.63	transcription factor complex
GO:0016529	0.57	sarcoplasmic reticulum

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	1izjA	0.373	5.81	0.042	0.595	3.2.1.135 3.2.1.1	NA
2	0.060	3fedA	0.372	6.41	0.024	0.645	3.4.17.21	NA
3	0.060	2zoxA	0.360	6.42	0.051	0.634	3.2.1.21	70
4	0.060	3nqbA	0.390	6.36	0.055	0.681	3.5.4.2	NA
5	0.060	2dgaA	0.373	6.19	0.065	0.638	3.2.1.21	NA

	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	2xshG	0.393	6.02	0.040	0.674	0.55	FES	complex1.pdb.gz	208,230,232,233,234
	2	0.01	2gbwC	0.397	6.33	0.042	0.685	0.70	FES	complex2.pdb.gz	230,232,233

	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.