D-I-TASSER Q9Y2C9-D3

D-I-TASSER results for Q9Y2C9-D3

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

Input Sequence in FASTA format

>Q9Y2C9 (234 residues)
GCLQLTNIKLNDDNCQVFIKFLSELTRGSTLLNFTLNHIETTWKCLVRVFQFLWPKPVEY
LNIYNLTIIESIREEDFTYSKTTLKALTIEHITNQVFLFSQTALYTVFSEMNIMMLTISD
TPFIHMLCPHAPSTFKFLNFTQNVFTDSIFEKCSTLVKLETLILQKNGLKDLFKVGLMTK
DMPSLEILDVSWNSLESGRHKENCTWVESIVVLNLSSNMLTDSVFRCLPPRIKV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| GCLQLTNIKLNDDNCQVFIKFLSELTRGSTLLNFTLNHIETTWKCLVRVFQFLWPKPVEYLNIYNLTIIESIREEDFTYSKTTLKALTIEHITNQVFLFSQTALYTVFSEMNIMMLTISDTPFIHMLCPHAPSTFKFLNFTQNVFTDSIFEKCSTLVKLETLILQKNGLKDLFKVGLMTKDMPSLEILDVSWNSLESGRHKENCTWVESIVVLNLSSNMLTDSVFRCLPPRIKV
Prediction	CCCCCCSSSCCCCCCCCCCCCCHHHCCCCCSSSSSSSCSSCCCCCHHHHHHHCCCCCCCSSSSSCCSSSCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCHHHHHCCCCCCSSSCSCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCHHHHCCCCCCSSSCCCCCCCCCCCCCHHHCCCCCCCSSSCCCCCCCCCCCCHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCCSC
Confidence	962045136058864346664400124773337881141146710234532213777557996583540527820114467711117872644654336886124443148725797518978788788779852189888897678786455125236846788997889888522215689988786868818898990676177889889787883778688657977519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| GCLQLTNIKLNDDNCQVFIKFLSELTRGSTLLNFTLNHIETTWKCLVRVFQFLWPKPVEYLNIYNLTIIESIREEDFTYSKTTLKALTIEHITNQVFLFSQTALYTVFSEMNIMMLTISDTPFIHMLCPHAPSTFKFLNFTQNVFTDSIFEKCSTLVKLETLILQKNGLKDLFKVGLMTKDMPSLEILDVSWNSLESGRHKENCTWVESIVVLNLSSNMLTDSVFRCLPPRIKV
Prediction	741503504144341442362245135344034020431504262034104323423043034240403140444314333320310204403243030434303310441404303035140322222743330220101324242500630350430330242424042324343334604424342203232634304520540644421120345541501631266168
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSSCCCCCCCCCCCCCHHHCCCCCSSSSSSSCSSCCCCCHHHHHHHCCCCCCCSSSSSCCSSSCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCHHHHHCCCCCCSSSCSCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCHHHHCCCCCCSSSCCCCCCCCCCCCCHHHCCCCCCCSSSCCCCCCCCCCCCHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCCSC
GCLQLTNIKLNDDNCQVFIKFLSELTRGSTLLNFTLNHIETTWKCLVRVFQFLWPKPVEYLNIYNLTIIESIREEDFTYSKTTLKALTIEHITNQVFLFSQTALYTVFSEMNIMMLTISDTPFIHMLCPHAPSTFKFLNFTQNVFTDSIFEKCSTLVKLETLILQKNGLKDLFKVGLMTKDMPSLEILDVSWNSLESGRHKENCTWVESIVVLNLSSNMLTDSVFRCLPPRIKV

2z7xB

0.39

11.61

1.33

DEthreader

KTVANLELSNIKCVCSYFLSILAKLQTNPKLSNLTLNNIETTWNSFIRILQLVWHTTVWYFSISNVKLQGQLDFR-DFDYSGTSLKALSIHQVVSDVFFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIFRCLPPRIVL

5a5cA1

0.16

0.15

4.96

1.92

SPARKS-K

CRCEKLLFYCDSQGFH---SVPNGLPS--QLLGLSLRHNQLQ-SLPNGVFDKL--TQLTWLHLDHNQLQSLPNGVFD-----KLTKLTELILSSNQL---QSLPNGTFDKLTLQNLDLSFNQLQSLGVFDKLTNLQTLHLRSNQLQSLPNGVFDKLTSLTFLDLSTNQLQSLP--NGVFDKLTNLRELHLEHNQLQS-LPNGVFDKLTSLTTLFLQWNQLQSLPNGVFLTNLEK

3a79B

0.69

19.58

0.47

MapAlign

NALGHLQLNIKLENCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLTGSVFRCLPPKVKV

3a79B

0.68

19.46

0.43

CEthreader

SVNALGHLQLSNIKLQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLTGSVFRCLPPKVKV

3a79B

0.73

20.62

1.65

MUSTER

GHLQLSNIKLNDENCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLTGSVFRCLPPKVKV

6g9lA

0.15

0.13

4.48

0.67

HHsearch

EELHLQKLSINNEGTKLVLNSLKKM---VNLTELELIRCDLE-----RIPHSIFSHNLQEIDLKDNNLKTIEE-IISF---QHLHRLTCLKLWYNHIA---YIPIQIGNLTNLERLYLNRNKIEKIPTQLYCRKLRYLDLSHNNLT-FLPADIGLLQNLQNLAVTANRIEALPP---ELFQCRKLRALHLGNNVLQSLP-SRVGE-LTNLTQIELRGNRLE-CLPVELGPLLKR

6qwnA

0.12

4.06

1.40

FFAS-3D

SVLVVAGIDLNHADIA--GYLPPELGLLTDVALFHVNSNRFCGVIPKSLSK---LTLMYEFDVSNNRFVGPFPT-----VALSWPSLKFLDIRYNDFEGKLPPIPETIGKSTASVVTFAHNKFSGCIPKTQMKNLNEIVFIGNNLSGCLPNEIGSLNNVTVFDASSNGFVGSLPS--TLSGLANVEQMDFSYNKFTG-FVTDNICKLPKLSNFTFSYNFFNGEAQSCSSQEKQF

1dfjI

0.11

4.00

0.73

EigenThreader

QLETLRLENCGL-TPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSSRLKTLWLWECDITASGCRDLCRVLQAKETKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSLTSLMLTQNKHLLELQLSSNKLGDSGIQELCQGTTLRVLCLGDCEVTGCSSLASLLLANRSLRELDLSNNCVGLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGS

3a79B

0.73

20.62

5.77

CNFpred

GHLQLSNIKLNDENCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLTGSVFRCLPPKVKV

3a79B

0.63

0.62

17.84

1.33

DEthreader

NALGHLQLSNIKLNCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITRIDREE-FTY-SETALKSLMIEHVKNQVFFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLTGSVFRCLPLALEL

(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	0.8381

(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	2z7xB	0.95	1.39	0.444	1.000	model1_2z7xB.pdb.gz
2	3a79B	0.95	1.37	0.688	1.000	model1_3a79B.pdb.gz
3	3a79A	0.82	3.04	0.189	0.974	model1_3a79A.pdb.gz
4	3v44A	0.79	3.05	0.139	0.953	model1_3v44A.pdb.gz
5	2a0zA	0.79	2.84	0.169	0.936	model1_2a0zA.pdb.gz
6	2id5B	0.78	2.89	0.181	0.919	model1_2id5B.pdb.gz
7	5gmfA	0.78	3.19	0.181	0.944	model1_5gmfA.pdb.gz
8	3w3gA2	0.78	3.26	0.158	0.949	model1_3w3gA2.pdb.gz
9	3wpbA	0.77	3.12	0.210	0.936	model1_3wpbA.pdb.gz
10	4kt1A	0.77	2.68	0.184	0.906	model1_4kt1A.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:0004872	1.00	receptor activity
GO:0038023	0.94	signaling receptor activity
GO:0004888	0.92	transmembrane signaling receptor activity
GO:0008289	0.66	lipid binding
GO:0071723	0.65	lipopeptide binding
GO:0005102	0.61	receptor binding
GO:0035325	0.59	Toll-like receptor binding
GO:0035663	0.57	Toll-like receptor 2 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:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048518	0.95	positive regulation of biological process
GO:0048583	0.92	regulation of response to stimulus
GO:0007165	0.92	signal transduction
GO:0002376	0.92	immune system process
GO:0002253	0.91	activation of immune response
GO:0002224	0.90	toll-like receptor signaling pathway
GO:0009987	0.77	cellular process
GO:0050896	0.76	response to stimulus
GO:0010033	0.73	response to organic substance
GO:0032493	0.72	response to bacterial lipoprotein
GO:0051716	0.63	cellular response to stimulus
GO:0071221	0.62	cellular response to bacterial lipopeptide
GO:0006950	0.58	response to stress
GO:0006952	0.57	defense response
GO:0051707	0.52	response to other organism
GO:0042742	0.51	defense response to bacterium

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	0.99	cell part
GO:0044425	0.97	membrane part
GO:0031224	0.87	intrinsic component of membrane
GO:0031226	0.82	intrinsic component of plasma membrane
GO:0016021	0.81	integral component of membrane
GO:0005887	0.75	integral component of plasma membrane
GO:0044424	0.71	intracellular part
GO:0032991	0.54	macromolecular complex
GO:0044444	0.52	cytoplasmic part
GO:0043234	0.52	protein complex
GO:0098796	0.50	membrane protein complex
GO:0043235	0.50	receptor 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	0.066	1pclA	0.627	4.66	0.090	0.927	4.2.2.2	NA
2	0.066	1gq8A	0.591	5.09	0.059	0.936	3.1.1.11	NA
3	0.060	1bn8A	0.609	5.00	0.063	0.927	4.2.2.2	NA
4	0.060	1idjA	0.591	4.96	0.052	0.902	4.2.2.10	NA
5	0.060	1bheA	0.605	4.55	0.087	0.885	3.2.1.15	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:

No Binding sites was predicted

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

	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.