D-I-TASSER Q8TCY9-D4

D-I-TASSER results for Q8TCY9-D4

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

Input Sequence in FASTA format

>Q8TCY9 (273 residues)
PLELIDGSTLSMPVRWVTGLLKELHVRLERRSRLVVLSTVGVPGTGKSTLLNTMFGLRFA
TGKSCGPRGAFMQLITVAEGFSQDLGCDHILVIDSGGLIGGALTSAGDRFELEASLATLL
MGLSNVTVISLAETKDIPAAILHAFLRLEKTGHMPNYQFVYQNLHDVSVPGPRPRDKRQL
LDPPGDLSRAAAQMEKQGDGFRALAGLAFCDPEKQHIWHIPGLWHGAPPMAAVSLAYSEA
IFELKRCLLENIRNGLSNQNKNIQQLIELVRRL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| PLELIDGSTLSMPVRWVTGLLKELHVRLERRSRLVVLSTVGVPGTGKSTLLNTMFGLRFATGKSCGPRGAFMQLITVAEGFSQDLGCDHILVIDSGGLIGGALTSAGDRFELEASLATLLMGLSNVTVISLAETKDIPAAILHAFLRLEKTGHMPNYQFVYQNLHDVSVPGPRPRDKRQLLDPPGDLSRAAAQMEKQGDGFRALAGLAFCDPEKQHIWHIPGLWHGAPPMAAVSLAYSEAIFELKRCLLENIRNGLSNQNKNIQQLIELVRRL
Prediction	CCSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHSSSSSHHHHCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCSSSSCCCCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC
Confidence	953663764557768999999999998557874899998626887646899998699642157765672788741124432233589727999849999732356553067899999999997310376303213379999999999984487664499995576665433587899999999999999865332145665343114542266686464254357999988898167899999999999999952233345689999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| PLELIDGSTLSMPVRWVTGLLKELHVRLERRSRLVVLSTVGVPGTGKSTLLNTMFGLRFATGKSCGPRGAFMQLITVAEGFSQDLGCDHILVIDSGGLIGGALTSAGDRFELEASLATLLMGLSNVTVISLAETKDIPAAILHAFLRLEKTGHMPNYQFVYQNLHDVSVPGPRPRDKRQLLDPPGDLSRAAAQMEKQGDGFRALAGLAFCDPEKQHIWHIPGLWHGAPPMAAVSLAYSEAIFELKRCLLENIRNGLSNQNKNIQQLIELVRRL
Prediction	740000130331224104400540264246523000000003344343200010141404224411020010121314562465350300000000004042346665435233200000111110000214424400310130022145364342010001024434464534632440253045015413635545742431220202326453121001016442353324551040024015200510464454445405402510575
	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

CCSSSCCCCCCCCHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHSSSSSHHHHCCHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCSSSSCCCCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC
PLELIDGSTLSMPVRWVTGLLKELHVRLERRSRLVVLSTVGVPGTGKSTLLNTMFGLRFATGKSCGPRGAFMQLITVAEGFSQDLGCDHILVIDSGGLIGGALTSAGDRFELEASLATLLMGLSNVTVISLAETKDIPAAILHAFLRLEKTGHMPNYQFVYQNLHDVSVPGPRPRDKRQLLDPPGDLSRAAAQMEKQGDGFRALAGLAFCDPEKQHIWHIPGLWHGAPPMAAVSLAYSEAIFELKRCLLENIRNGLSNQNKNIQQLIELVRRL

6sytC

0.12

4.12

1.23

FFAS-3D

SIKLVDDQ-----MNWCDSAIEYLL----DQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLI--NNYNLPHTYVEMQSLQIAAFLFTVCHVVIVVQDWFTSLYRFLQTAEMVKPSTEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPDFLDSEVNLFLVPFMDSLLPGYRGHPSFQSLVSKLRSQVMSMARPQLSHTILTEKNWFHYAARI

4huqA

0.18

0.15

4.76

1.12

SPARKS-K

IAFEHVTYTYQAGTPMAHTALTDVSLTVPDR---GYLAIIGHTGSGKSTLIQQLNALLKPTSPLRQHVGMVFQLETVRQDIAF--GPKNFGMAADEMLTTVGLDSYAERSPFEVAIAGVLAMQPKVLVLDEPTAPQGRQEMMRLFARLHQEQ-GLTIVLVTHQMEDVAQYAEKFGTPADVFSNREWLQDH----------------------------------QLDVP-------------QAAQFARRLRDRGLTFPKQPLDQLADYLAQQ

2b8wA

0.16

0.15

4.88

1.09

CNFpred

PMCLIENTNG--RLMANPEALKILSAI---TQPMVVVAIVGLYRTGKSYLMNKLAGFSLGSTVQSHTKGIWMWCVPHPKKP-----GHILVLLDTEGLGDV----EKGDNQNDSWIFALAVLLSSTFVYNSI-AMDQLYYVTELTHRIRSK-FFPDFVWTLRDFSDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFP----KKKCFVFDRPVHEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSIQVNGPRLESLVLTY

6gebA

0.09

0.08

3.09

0.38

CEthreader

TLRTIPTTPPKLSTMNLPDNIIEA-----IAPQEGIVFITGATGSGKSTLLASIIRELIETSDSNRKVLTYESPIEFVYDEIETISAVVSQSEIPR-----------HLPNFADGVRNALRRKPRLIMVGECRDAETISAALEAALTGH------PVYTTLHTSGVAETMRRLVTS--FSGEERLGRTIDILETIRLCIWQKLVPTVDERRVALREYLVFDEEVRDILLEGDPNEVTSATRKLVRQKGMTWDAKMKFEQGIISERVYKLIIAG

3dvlA

0.08

0.07

2.74

0.45

EigenThreader

AIAKMRTMIEG---------FDDIS----HGGLPITLVSGTSG-TGKTLFSIQFLYNGIIEFD--EPGVFVTFEETPQDIIKNARSFGFILDASPD-----PEGQEVVGGLIERINYAIQKYRARRVSIDSVVRRELFRLVARLKQIG------ATTVMTTERIEEYGPIARYGVEEFVSSSGVVRLDEMC-----GGGFFKLLVSRFVENACANLLKIVCAYPESA-----GLEDHLQIIKSEINDFKSALARGVSNNAFRQFVIGVTGYAK

5ca8A1

0.16

0.14

4.73

1.16

FFAS-3D

AIQIIDENKHFNTG--ILDYINKTSPA-DVGNNYHIISVFGSQSTGKSTLLNRLFNTNFDVMGIWLAYSPVVSTTL-----GHTTSKSNILVMDVEG--------TDEDQDFERKAALFALSTSEVLIINMGLLKTVFEVNLSLFGKSKLETHNVLLLIVIR---DHVGVTPVESLAKTFTLDLQNMWSSLAKPAEEHLQFADFFDV--------TFHAL-------NHKVLQPKEFGEGINRLGDRLVVSNEKPEYHHDVPIDGWTMYAERC

2q0hB

0.16

0.11

3.66

1.09

SPARKS-K

--LQMIDVHQLKKSFGSLEVLKGINVHIREG---EVVVVIGPSGSGKSTFLRCLNLLEDFDEKVREEVGMVFQLMTVLNNITLAPMWPREKAEAMELLDKVGLKDKAHAYPDSVAIARALAMEPKIMLFDEPTSPEMVGEVLSVMKQLANE--GMTMVVVTHEMGFAREVGDREGKPEDLFDRPERTKAFLSKVF------------------------------------------------------------------------------

5ca8A

0.18

0.16

5.11

1.05

CNFpred

AIQIIDENKH--FNTGILDYINKTSPAD--GNNYHIISVFGSQSTGKSTLLNRLFNTNFDV-------GIWLAYSPVVSTTLGHTTKSNILVMDVEGTD----------QDFERKAALFALSTSEVLIINIWELKTVFEVNLSLFGKSKLETHKVLLLIVIRDHVGV---TPVESLAKTFTLDLQNMWSSLAKPAELE--HLQFADFFDVT-----FHALNH-------KVLQPKEFGEGINRLGDRLVELFKPEYHH--VPIDGWTMYAERC

5ca8A1

0.06

0.05

2.03

0.83

DEthreader

D-AIQINTGIDYINKTSPADVG-NNY-H-----IISVF---TGKSTLLNLFNTFIWLAYSP-----LVMDVEGTDED---------------------------------Q-DFERKAALFLSTSEVLIINIANMGLLKTVFEVNLSLFGKSKHKVLLLIVIRDHV-GVTPV-ESLAKTFTLDLQNMWSSL--AK-P-AELEHL-QFADF----FDVTFHALNHKQPKEFGEGINRLGDRLVVSNELFKPEYH-H-----D---VPIDGWTME

1ubgA

0.12

0.11

3.85

0.55

MapAlign

AQIDKNFGKGSVISVIPTGSILDVALGIGGLPRGRVIEIYGPESSGKTTVALHAV---ANAQAAGGIAAFIDAEHALDPEYAKKLGVLLVSQPDT----------------GEQALEIADMLVLDIIVISVAALVLQARLMSQALRKMTGANSGTTAIFINQLREVMFGSPETTTGGKALSVRLDVRRIETLKDGTDAVGNRTRVKVVKNKVSPPFKREGSLISWFTYEGEQLGQGKENARKFLLDVANEI-----------EKKIKEKLG--

(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	0.6161

(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	5ca8A	0.50	5.29	0.075	0.744	model1_5ca8A.pdb.gz
2	3jb9B1	0.49	5.28	0.089	0.747	model1_3jb9B1.pdb.gz
3	5mqfB1	0.49	5.43	0.056	0.766	model1_5mqfB1.pdb.gz
4	7abir	0.48	5.49	0.064	0.755	model1_7abir.pdb.gz
5	1x6lA2	0.48	5.83	0.097	0.780	model1_1x6lA2.pdb.gz
6	3ez2B	0.48	5.65	0.085	0.755	model1_3ez2B.pdb.gz
7	5t5iA	0.48	5.51	0.043	0.747	model1_5t5iA.pdb.gz
8	4qlbA	0.48	6.16	0.090	0.802	model1_4qlbA.pdb.gz
9	5do7A1	0.48	5.25	0.098	0.700	model1_5do7A1.pdb.gz
10	3jc8Ba	0.47	5.46	0.079	0.722	model1_3jc8Ba.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:1901363	0.85	heterocyclic compound binding
GO:0097159	0.85	organic cyclic compound binding
GO:0003824	0.85	catalytic activity
GO:0032555	0.84	purine ribonucleotide binding
GO:0032550	0.84	purine ribonucleoside binding
GO:0016787	0.84	hydrolase activity
GO:0035639	0.83	purine ribonucleoside triphosphate binding
GO:0032561	0.83	guanyl ribonucleotide binding
GO:0003924	0.83	GTPase activity
GO:0005525	0.82	GTP binding
GO:0044877	0.70	macromolecular complex binding
GO:0003723	0.69	RNA binding
GO:0043024	0.68	ribosomal small subunit binding
GO:0019843	0.68	rRNA binding
GO:0008092	0.53	cytoskeletal protein binding
GO:0031072	0.52	heat shock protein 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	0.93	cellular process
GO:0016043	0.83	cellular component organization
GO:0065007	0.70	biological regulation
GO:0050794	0.69	regulation of cellular process
GO:0050896	0.67	response to stimulus
GO:0044699	0.66	single-organism process
GO:0044763	0.63	single-organism cellular process
GO:0051704	0.62	multi-organism process
GO:0010033	0.62	response to organic substance
GO:0022607	0.61	cellular component assembly
GO:0006950	0.61	response to stress
GO:0065003	0.60	macromolecular complex assembly
GO:0051716	0.60	cellular response to stimulus
GO:0098542	0.59	defense response to other organism
GO:0071346	0.59	cellular response to interferon-gamma
GO:0051179	0.59	localization
GO:0034622	0.58	cellular macromolecular complex assembly
GO:0007165	0.58	signal transduction
GO:0060255	0.57	regulation of macromolecule metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0002376	0.57	immune system process
GO:0000028	0.57	ribosomal small subunit assembly
GO:1902578	0.56	single-organism localization
GO:0080090	0.56	regulation of primary metabolic process
GO:0050776	0.56	regulation of immune response
GO:0032268	0.55	regulation of cellular protein metabolic process
GO:0008104	0.55	protein localization
GO:0051239	0.54	regulation of multicellular organismal process
GO:0051128	0.54	regulation of cellular component organization
GO:0048523	0.54	negative regulation of cellular process
GO:0035556	0.54	intracellular signal transduction
GO:0023051	0.54	regulation of signaling
GO:0019220	0.54	regulation of phosphate metabolic process
GO:0016032	0.54	viral process
GO:1902580	0.53	single-organism cellular localization
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0060341	0.53	regulation of cellular localization
GO:0051129	0.53	negative regulation of cellular component organization
GO:0051051	0.53	negative regulation of transport
GO:0034613	0.53	cellular protein localization
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:0001932	0.53	regulation of protein phosphorylation
GO:0001817	0.53	regulation of cytokine production
GO:1904376	0.52	negative regulation of protein localization to cell periphery
GO:1903729	0.52	regulation of plasma membrane organization
GO:1900040	0.52	regulation of interleukin-2 secretion
GO:1900024	0.52	regulation of substrate adhesion-dependent cell spreading
GO:0070372	0.52	regulation of ERK1 and ERK2 cascade
GO:0050858	0.52	negative regulation of antigen receptor-mediated signaling pathway
GO:0050856	0.52	regulation of T cell receptor signaling pathway
GO:0050710	0.52	negative regulation of cytokine secretion
GO:0044802	0.52	single-organism membrane organization
GO:0043409	0.52	negative regulation of MAPK cascade
GO:0032703	0.52	negative regulation of interleukin-2 production
GO:0019722	0.52	calcium-mediated signaling
GO:0019221	0.52	cytokine-mediated signaling pathway
GO:0010812	0.52	negative regulation of cell-substrate adhesion
GO:0010771	0.52	negative regulation of cell morphogenesis involved in differentiation
GO:0002252	0.52	immune effector process
GO:0072659	0.51	protein localization to plasma membrane
GO:0009615	0.51	response to virus

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	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0043226	0.83	organelle
GO:0044444	0.81	cytoplasmic part
GO:0043229	0.78	intracellular organelle
GO:0043227	0.77	membrane-bounded organelle
GO:0005737	0.77	cytoplasm
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0044422	0.54	organelle 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	0.060	1ll6A	0.458	5.72	0.066	0.736	3.2.1.14	NA
2	0.060	1k6wA	0.449	5.58	0.066	0.703	3.5.4.1	NA
3	0.060	2pffA	0.466	5.79	0.090	0.729	2.3.1.41 2.3.1.86	NA
4	0.060	1d2kA	0.455	5.72	0.081	0.747	3.2.1.14	NA
5	0.060	1zedA	0.459	6.03	0.030	0.769	3.1.3.1	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:

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	3defA	0.452	5.27	0.112	0.703	0.43	GDP	complex1.pdb.gz	44,45,46,47,48,49
2	0.01	3arxA	0.470	5.97	0.073	0.777	0.45	POY	complex2.pdb.gz	42,46,49
3	0.01	1zedA	0.459	6.03	0.030	0.769	0.52	PNP	complex3.pdb.gz	112,113,116,117,120

	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.