D-I-TASSER Q4G0X4-D1

D-I-TASSER results for Q4G0X4-D1

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

Input Sequence in FASTA format

>Q4G0X4 (260 residues)
MSDPITLNVGGKLYTTSLATLTSFPDSMLGAMFSGKMPTKRDSQGNCFIDRDGKVFRYIL
NFLRTSHLDLPEDFQEMGLLRREADFYQVQPLIEALQEKEVELSKAEKNAMLNITLNQRV
QTVHFTVREAPQIYSLSSSSMEVFNANIFSTSCLFLKLLGSKLFYCSNGNLSSITSHLQD
PNHLTLDWVANVEGLPEEEYTKQNLKRLWVVPANKQINSFQVFVEEVLKIALSDGFCIDS
SHPHALDFMNNKIIRLIRYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSDPITLNVGGKLYTTSLATLTSFPDSMLGAMFSGKMPTKRDSQGNCFIDRDGKVFRYILNFLRTSHLDLPEDFQEMGLLRREADFYQVQPLIEALQEKEVELSKAEKNAMLNITLNQRVQTVHFTVREAPQIYSLSSSSMEVFNANIFSTSCLFLKLLGSKLFYCSNGNLSSITSHLQDPNHLTLDWVANVEGLPEEEYTKQNLKRLWVVPANKQINSFQVFVEEVLKIALSDGFCIDSSHPHALDFMNNKIIRLIRYR
Prediction	CCCSSSSSSCCSSSSSSHHHHHHCCCCHHHHHHCCCCCCCCCCCCCSSSCCCHHHHHHHHHHHHCCCSCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSSSSSSSSSSSSSSCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCSSSSSCCCCHHHCCCCHHHHHHHHHHHHHCCCSSSSCCCCSSSSCCSSSSSSSCC
Confidence	99569998499899986889965998502122136565667777418972992499999999806963379986159999999998099689999998766553433445421321222431002434465699986787110024457888888996202788627998566765557875344543233443430366331123578727741213651349999998786467356532783468711799998529
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSDPITLNVGGKLYTTSLATLTSFPDSMLGAMFSGKMPTKRDSQGNCFIDRDGKVFRYILNFLRTSHLDLPEDFQEMGLLRREADFYQVQPLIEALQEKEVELSKAEKNAMLNITLNQRVQTVHFTVREAPQIYSLSSSSMEVFNANIFSTSCLFLKLLGSKLFYCSNGNLSSITSHLQDPNHLTLDWVANVEGLPEEEYTKQNLKRLWVVPANKQINSFQVFVEEVLKIALSDGFCIDSSHPHALDFMNNKIIRLIRYR
Prediction	86440301012331302230044234120032244314124234120001121600200020013240211762541630250052160650153046244634655454236244534242041236332301102233333110301010001010322201203343154144415514233031214245144240334102200222453402513312120030015303302232443320311211312438
	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

CCCSSSSSSCCSSSSSSHHHHHHCCCCHHHHHHCCCCCCCCCCCCCSSSCCCHHHHHHHHHHHHCCCSCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSSSSSSSSSSSSSSCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCSSSSSCCCCHHHCCCCHHHHHHHHHHHHHCCCSSSSCCCCSSSSCCSSSSSSSCC
MSDPITLNVGGKLYTTSLATLTSFPDSMLGAMFSGKMPTKRDSQGNCFIDRDGKVFRYILNFLRTSHLDLPEDFQEMGLLRREADFYQVQPLIEALQEKEVELSKAEKNAMLNITLNQRVQTVHFTVREAPQIYSLSSSSMEVFNANIFSTSCLFLKLLGSKLFYCSNGNLSSITSHLQDPNHLTLDWVANVEGLPEEEYTKQNLKRLWVVPANKQINSFQVFVEEVLKIALSDGFCIDSSHPHALDFMNNKIIRLIRYR

3p8cB

0.05

0.04

1.84

0.83

DEthreader

FFTYLIITTILLP-LSALSLQMVYPNLDMEKWIIF--FILCHGIL-WLCLSLFRDEV----FM-LSFARD---IIWLLRHADN-MP------FI-DKHIAELFQQCLESMKQARNTHIRFTKSIVGTQTITSLYTNLLESLMWHISSQVAELKKLVVNVLTQMRTSF-DKPQMAALFK-RLSSVDLFVALAINQA--SIEDRLKEFALASSLLKIGTRESVYLLL--------------M--VQESPFL-----------

6s4lA

0.31

0.23

7.10

2.00

SPARKS-K

SNAPVHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPIVLDSKQHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERWKQDRETG-------RFSRPCECLVVRVAPDL--------GERITLSGDK-----SLIEEVFPEIG---DVMSTHVRFPLNGYCHLN--------------------------------------SVQVLERLQQRGFEIVGSCGGGVDSSQFSEYVLRREL

6s4lA

0.31

0.24

7.21

1.34

MapAlign

SNAPVHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPIVLDSLKHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERWKQDRET-------------------------------GRFSRPCECLVVRVA-------PDLGERITLSGDKSLIEEVFPEIGDVMSTHVIRFP----------------------LNGYCHLNSVQVLERLQQRGFEIVGSCGGGVDSSQFSEYVLRREL

6s4lA

0.31

0.24

7.21

1.16

CEthreader

SNAPVHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPIVLDSKQHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERWKQDRETGRFS-------------------------------RPCECLVVR-----VAPDLGERITLSGDKSLIEEVFPEIGDVMST-------------------HVIRFPLNGYCHLN-----SVQVLERLQQRGFEIVGSCGGGVDSSQFSEYVLRREL

2r9rB

0.20

6.27

1.27

MUSTER

-SERVVINISGLRFETQLKTLAQFPETLLGDPKK-RMRYFDPLRNEYFFDRNRPSFDAILYYYQSGRLRRPVNVP-LDIFSEEIRFYELGEAMEMFREDEGYIKEEERP---LPENEFQRQV--WLLFEYPRIIAIVSVMVILISIVSFCLEPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPFFIVETLCIIWFSFEFLVRFFACPSKAGFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQNVRIFKLSRHS

6s4lA

0.30

0.25

7.46

3.86

HHsearch

SNAPVHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPIVLDSKQHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERWKQDRET--G-R---FSRPCECLV--VR--VAPDL----------GERITLSGDKSLIEEFPEIGD----VMSHVIRFPLNGYCHLN-----SVQVL-----ERLQQRGFEIVGSCGGGVDSSQFSEYVLRRELRRTPRVPSVIRIKQ--------------

6s4lA

0.31

0.23

7.09

1.78

FFAS-3D

-NAPVHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPILDSLKQHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERW------KQDRETGRFSRPCECLVVRVAPDLGERITLSGD----------KSLIEEVF-----------------------------------------PEIGDVMSTHVIRFPLNGYCHL---NSVQVLERLQQRGFEIVGSCGGGVDSSQFSEYVLRR--

6s4lA

0.24

0.18

5.63

0.82

EigenThreader

SMSNAHIDVGGHMYTSSLATLTKYPESRIGRLFDGTDPIVLDSLKQHYFIDRDGQFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPMLLEMERWKQDRETG------RFSRPCECLVVRVAPDLG--ERITLSGD---KSLIEEVF-----------------------------------------PEIGD------VMSTIRFPLNGYCHLN---SVQVLERLQQRGFEIVGSCGDSS----QFSEYVLRREL

5wieB

0.22

0.13

4.01

1.51

CNFpred

SSERVVINISGLRFETQLKTLAQFPETLLGDPKKRMRYFDPL-RNEYFFDRNRPSFDAILYYYQSGRLRRPVNV-PLDIFSEEIRFYELGEAMEMFREDEGYIKEEERPLPEN-----EFQRQVWLLFEYARIIAIVSVMVILISIVSFCLLPIFRDEN-----------------------------------------------------------------------------------------------------

5yfpC

0.07

0.06

2.36

0.83

DEthreader

VAERVAELAEDAETPLEIHFLLSA---------------------DGYDIVEMARQIFKDGYKHFLINGNSEGIFLIIVKEHIANC--CPPHW-NIFEVYFDYQDKSVIGD-KEVAGTNQILVGVVERFSDLATDGFAEVAQCSSLGLITLMFDDLRKPYQ-E-IFS-KTWYMGSQAQ--QIADTLETIIKFL-TAL--SF--EHSF-FLEAMKRDFE---IF-YQLFVKVLDGNSKL-Q--DREPTLMRRF--------

(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	0.5411

(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	6s4lA	0.64	3.20	0.295	0.746	model1_6s4lA.pdb.gz
2	3dryC	0.49	3.06	0.206	0.577	model1_3dryC.pdb.gz
3	2r9rB	0.47	4.04	0.191	0.592	model1_2r9rB.pdb.gz
4	3sqiA	0.42	5.86	0.066	0.704	model1_3sqiA.pdb.gz
5	5oy5A	0.42	5.98	0.058	0.704	model1_5oy5A.pdb.gz
6	6u5vB	0.42	6.12	0.043	0.742	model1_6u5vB.pdb.gz
7	6fec2	0.42	5.70	0.042	0.669	model1_6fec2.pdb.gz
8	3la4A	0.42	6.75	0.042	0.792	model1_3la4A.pdb.gz
9	6hqvA	0.42	6.23	0.058	0.742	model1_6hqvA.pdb.gz
10	5mu5A	0.42	5.82	0.056	0.673	model1_5mu5A.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:0005267	0.84	potassium channel activity
GO:0005244	0.84	voltage-gated ion channel activity
GO:0005249	0.83	voltage-gated potassium channel activity
GO:0005251	0.81	delayed rectifier potassium channel activity
GO:0003824	0.57	catalytic activity
GO:0016740	0.52	transferase activity
GO:0019899	0.50	enzyme 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	0.95	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0044699	0.85	single-organism process
GO:0050794	0.84	regulation of cellular process
GO:0016043	0.80	cellular component organization
GO:0044763	0.79	single-organism cellular process
GO:0022607	0.79	cellular component assembly
GO:0051259	0.76	protein oligomerization
GO:0051260	0.75	protein homooligomerization
GO:0008152	0.67	metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0044238	0.64	primary metabolic process
GO:0043170	0.64	macromolecule metabolic process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:0023051	0.63	regulation of signaling
GO:0010646	0.63	regulation of cell communication
GO:0048518	0.62	positive regulation of biological process
GO:0048583	0.61	regulation of response to stimulus
GO:0048522	0.61	positive regulation of cellular process
GO:0048519	0.60	negative regulation of biological process
GO:0009966	0.60	regulation of signal transduction
GO:0048523	0.59	negative regulation of cellular process
GO:0019538	0.58	protein metabolic process
GO:0044267	0.55	cellular protein metabolic process
GO:0006464	0.54	cellular protein modification process
GO:0023057	0.53	negative regulation of signaling
GO:0019222	0.53	regulation of metabolic process
GO:0010648	0.53	negative regulation of cell communication
GO:0031323	0.52	regulation of cellular metabolic process
GO:0080090	0.51	regulation of primary metabolic process
GO:0070647	0.51	protein modification by small protein conjugation or removal
GO:0060255	0.51	regulation of macromolecule metabolic process
GO:0030036	0.51	actin cytoskeleton organization
GO:0009968	0.51	negative regulation of signal transduction
GO:0006928	0.51	movement of cell or subcellular component
GO:0006508	0.51	proteolysis
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0048870	0.50	cell motility
GO:0046580	0.50	negative regulation of Ras protein signal transduction
GO:0035023	0.50	regulation of Rho protein signal transduction
GO:0031032	0.50	actomyosin structure organization
GO:0030038	0.50	contractile actin filament bundle assembly
GO:0019219	0.50	regulation of nucleobase-containing compound metabolic process
GO:0016567	0.50	protein ubiquitination

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	0.96	cell part
GO:0044425	0.93	membrane part
GO:0044424	0.88	intracellular part
GO:0016021	0.88	integral component of membrane
GO:0043234	0.71	protein complex
GO:0016020	0.68	membrane
GO:0043226	0.64	organelle
GO:0043229	0.63	intracellular organelle
GO:0044444	0.62	cytoplasmic part
GO:0044422	0.58	organelle part
GO:0043227	0.57	membrane-bounded organelle
GO:0043231	0.56	intracellular membrane-bounded organelle
GO:0044446	0.55	intracellular 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	3la4A	0.417	6.75	0.042	0.792	3.5.1.5	82
2	0.060	2hpiA	0.361	6.38	0.072	0.646	2.7.7.7	NA
3	0.060	3h8eA	0.396	6.57	0.050	0.715	3.4.11.1	53
4	0.060	3ecqB	0.375	6.17	0.037	0.654	3.2.1.97	NA
5	0.060	1ea0A	0.401	6.31	0.041	0.700	1.4.1.13	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	1hkbA	0.397	6.18	0.044	0.681	0.49	CA	complex1.pdb.gz	9,51,53
	2	0.01	2vdcA	0.401	6.31	0.041	0.700	0.52	F3S	complex2.pdb.gz	10,11,12,13,55,56

	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.