D-I-TASSER Q08AF3-D4

D-I-TASSER results for Q08AF3-D4

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

Input Sequence in FASTA format

>Q08AF3 (189 residues)
YPREEINRVVRNAGPIANYLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIE
DLNLEEILIYVANKCRFLLRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEE
SDLLLQIGDASDVLTDHIVLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKR
HLYILKASV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| YPREEINRVVRNAGPIANYLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIEDLNLEEILIYVANKCRFLLRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEESDLLLQIGDASDVLTDHIVLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKRHLYILKASV
Prediction	CCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSCCHHHCCCCCCSSSSSSHHHCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHSSSSSSSC
Confidence	956777778753178999999999999848999999788898741455678873589854788999999999999999981999220799980568899999999999997444321353110020230104558816874213415875216998577766614678899999999865156888629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| YPREEINRVVRNAGPIANYLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIEDLNLEEILIYVANKCRFLLRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEESDLLLQIGDASDVLTDHIVLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKRHLYILKASV
Prediction	744541241042034005203620550473434513461032034272264130313146414263004200630431064113351000002356215403530152035443453453443224045335333310001003313514220000001433447213200000013034201003256
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCSSSSSCCCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSCCHHHCCCCCCSSSSSSHHHCCCCCSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHSSSSSSSC
YPREEINRVVRNAGPIANYLQQVMQEARQNPPPNLPPGSLVMLYEPKWAQGVPGNLEIIEDLNLEEILIYVANKCRFLLRNGYSPKDIAVLFTKASEVEKYKDRLLTAMRKRKLSQLHEESDLLLQIGDASDVLTDHIVLDSVCRFSGLERNIVFGINPGVAPPAGAYNLLLCLASRAKRHLYILKASV

1w36E

0.14

0.13

4.34

1.33

DEthreader

KRSHYTLDNWRSAPGMVNSVNKLFSQTDDAFMF-RE-IPFIPVKSAGNQALRFPAMKMWLMCYQSTMAQVCAAQIRDWLQAGVRASDISVLVRSRQEAAQVRDALTLLE---------------IPSVYLNRLSDKLVQIVTIHKSKGLEYPLVWLPFITNFRLAEDLRLLYVALTRSVWHCSLGVAPL

1uaaA3

0.15

0.12

4.12

1.67

SPARKS-K

------EQNYRSSGRILKAANILIANNPHVFEKRLF-----------SELGYGAELKVLSANNEEHEAERVTGELIAHHFVNTQYKDYAILYRGNHQSR----VFEKFLMQN-----------RIPYKISGEEELDQVQLMTLHASKGLEFPYVYMVGMEEGNIDEERRLAYVGITRAQKELTFTLCKE

4c2tA

0.13

0.12

4.21

0.74

MapAlign

----MLEHNYRSSARVLEAANKLIENN-----------TERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVIAMSEAADYEPAAFLRFVMETSGYLAEDAVTLMTLHNAKGLEFPVVFIVGVEPSGIEEERRLFYVGITRAMERLLMTAAQN

2is6A3

0.17

0.14

4.54

0.70

CEthreader

------EQNYRSTSNILSAANALIENNNG-----RLGKKLWT------DGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQSRVLEEALLQA---------------SMPYRIYADTWQDAVQLMTLHSAKGLEFPQVFIVGMEGGRLEEERRLAYVGVTRAMQKLTLTYAET

4b3fX

0.16

0.14

4.58

0.98

MUSTER

RVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDTAGCPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRH--------------------------PELEIKSVDGFQGREKEAVILSFVRSNRFLAEDRRINVAVTRARRHVAVICDSR

3u44A5

0.15

0.13

4.30

1.98

HHsearch

------NKNFRSRADILDSTNFLFKQLMGGKIGEVYDEQAELKLGAAYPDETE--TELLLIETVQFEAKAIAKEIRKLISSNIQYRDIVILLRS-MPAPQIMEELRAQ---------------GIPVYANL-TQEDVVRLMTIHSSKGLEFPVVFVAGLGRNFLSEELRVLYVALTRAKEKLFLIGSCK

6vsxA

0.16

0.12

3.88

1.51

FFAS-3D

----------RSTRQIVEFTKAMLQD---------------------NRSGEMP--LVVKTEGHESLCQKLAQEIGRLKKKGHE--TIAVICKTAHQCIQAHAHMSE-------------YTDVRLIHKENQPFQKGVCVIPVYLAKGIEFDAVLVYDASEEHTEHDRRLLYTACTRAMHMLAVFYTG-

1w36E4

0.15

0.14

4.62

0.83

EigenThreader

------DTNWRSAPGMVNSVNKLFSDAFMFREIPFIPVKSAGKNQALRFGETQPAMKMWLMCGVGDYQSTMAQVCAAQIRRGERASDISVLVRSRQEAAQVRDA---------LTLLEI---PSVYLSNRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEDLRLLYVALTRSVWHCSLGVAPL

4b3fX

0.16

0.14

4.56

1.27

CNFpred

--VRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDTA-NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRH--------------------------PELEIKSVDGFQGREKEAVILSFVREVGFLAEDRRINVAVTRARRHVAVICDSR

3u44A

0.15

0.13

4.48

1.33

DEthreader

LSKYIDLNNFRSRADILDSTNFLFKQLMGGKIG-EVDYDQAELKLGAAYPDNDTETELLLIDTVQFEAKAIAKEIRKLISSNIQYRDIVILLRSMPWAPQIMEELRAQG---------------I-PVYANK-QEDVVRLMTIHSSKGLEFPVVFVAGLGRNFLSEELRVLYVALTRAKEKLFLIGSCK

(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	0.8702

(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	3u44A	0.79	2.78	0.145	0.915	model1_3u44A.pdb.gz
2	1w36E	0.79	2.38	0.145	0.910	model1_1w36E.pdb.gz
3	4c2tA	0.77	2.04	0.135	0.841	model1_4c2tA.pdb.gz
4	3pjrA	0.76	2.24	0.184	0.847	model1_3pjrA.pdb.gz
5	2is6A3	0.75	1.92	0.159	0.831	model1_2is6A3.pdb.gz
6	1uaaA3	0.75	1.89	0.159	0.820	model1_1uaaA3.pdb.gz
7	2db3A	0.56	3.70	0.060	0.735	model1_2db3A.pdb.gz
8	1s2mA	0.53	3.18	0.062	0.661	model1_1s2mA.pdb.gz
9	2gszA	0.39	4.04	0.056	0.545	model1_2gszA.pdb.gz
10	1ni3A	0.37	4.26	0.045	0.534	model1_1ni3A.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:0003824	0.83	catalytic activity
GO:0016787	0.79	hydrolase activity
GO:0004518	0.71	nuclease activity
GO:0044877	0.66	macromolecular complex binding
GO:0043022	0.65	ribosome binding
GO:0004521	0.65	endoribonuclease activity
GO:1901363	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0003676	0.58	nucleic acid 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:0050896	1.00	response to stimulus
GO:0009987	1.00	cellular process
GO:0008152	0.81	metabolic process
GO:0071704	0.80	organic substance metabolic process
GO:0044238	0.79	primary metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0043170	0.78	macromolecule metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0006139	0.76	nucleobase-containing compound metabolic process
GO:0090304	0.75	nucleic acid metabolic process
GO:0090305	0.74	nucleic acid phosphodiester bond hydrolysis
GO:0051716	0.74	cellular response to stimulus
GO:0044699	0.74	single-organism process
GO:0044763	0.73	single-organism cellular process
GO:0042221	0.69	response to chemical
GO:0044767	0.68	single-organism developmental process
GO:0016070	0.68	RNA metabolic process
GO:0090502	0.67	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0071287	0.67	cellular response to manganese ion
GO:0071286	0.67	cellular response to magnesium ion
GO:0036345	0.67	platelet maturation
GO:0016075	0.67	rRNA catabolic process
GO:0006402	0.67	mRNA catabolic process
GO:0065007	0.64	biological regulation
GO:0050789	0.64	regulation of biological process
GO:0050794	0.62	regulation of cellular process
GO:0006950	0.50	response to stress

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:0044424	1.00	intracellular part
GO:0043226	0.76	organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0005622	0.73	intracellular
GO:0043229	0.72	intracellular organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0005634	0.67	nucleus
GO:0005737	0.56	cytoplasm

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	1rgqB	0.251	6.69	0.071	0.518	3.4.21.98	NA
2	0.060	2i4iA	0.540	3.26	0.037	0.667	3.6.4.13	84
3	0.060	2hyiI	0.575	3.44	0.069	0.741	3.6.4.13	148
4	0.060	3crvA	0.583	3.63	0.100	0.778	3.6.4.12	NA
5	0.060	3l9oA	0.559	3.84	0.069	0.751	3.6.4.13	146

	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	0.03	2pjrG	0.278	1.16	0.236	0.291	0.23	QNA	complex1.pdb.gz	54,78,80
2	0.03	2y3tA	0.614	4.05	0.096	0.862	0.12	ATP	complex2.pdb.gz	54,55,81,82,83,84
3	0.03	3gplA	0.620	3.31	0.172	0.757	0.18	QNA	complex3.pdb.gz	142,144,145
4	0.02	2gk6A	0.693	2.84	0.129	0.820	0.14	UUU	complex4.pdb.gz	58,92,93
5	0.01	1tf2A	0.599	3.68	0.087	0.799	0.21	ADP	complex5.pdb.gz	51,52,54

	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.