D-I-TASSER Q6NUM6-D1

D-I-TASSER results for Q6NUM6-D1

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

Input Sequence in FASTA format

>Q6NUM6 (307 residues)
MDPSADTWDLSSPLISLWINRFYIYLGFAVSISLWICVQIVIEMQGFATVLAEAVTSLDL
PVAIINLKEYDPDDHLIEEVTSKNVCVFLVATYTDGLPTESAEWFCKWLEEASIDFRFGK
TYLKGMRDAVFGLGNSAYASHFNKVGKNVDKWLWMLGVHRVMSRGEGDCDVVKSKHGSIE
ANFRAWKTKFISQLQALQKGERKKSCGGHCKKGKCESHQHGSEEREEGSQEQDELHHRDT
KEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGR
NEDGERR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MDPSADTWDLSSPLISLWINRFYIYLGFAVSISLWICVQIVIEMQGFATVLAEAVTSLDLPVAIINLKEYDPDDHLIEEVTSKNVCVFLVATYTDGLPTESAEWFCKWLEEASIDFRFGKTYLKGMRDAVFGLGNSAYASHFNKVGKNVDKWLWMLGVHRVMSRGEGDCDVVKSKHGSIEANFRAWKTKFISQLQALQKGERKKSCGGHCKKGKCESHQHGSEEREEGSQEQDELHHRDTKEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGRNEDGERR
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCSSSSSSSSSSCCHHHHHHHHHHHHHHCCCCSSSSCHHHCCCCHHHHHHCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHHHHCCSSSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence	9998888777652455666545553056752699999985113899999999999980998089567887941001441477877999984899999866899999999841511246765457975999935699647888798999999999809938650254047765545577789999999999999997424444556666555566432354432234564323454456654456655654211577776676630447788899875201245577764321454311124578899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MDPSADTWDLSSPLISLWINRFYIYLGFAVSISLWICVQIVIEMQGFATVLAEAVTSLDLPVAIINLKEYDPDDHLIEEVTSKNVCVFLVATYTDGLPTESAEWFCKWLEEASIDFRFGKTYLKGMRDAVFGLGNSAYASHFNKVGKNVDKWLWMLGVHRVMSRGEGDCDVVKSKHGSIEANFRAWKTKFISQLQALQKGERKKSCGGHCKKGKCESHQHGSEEREEGSQEQDELHHRDTKEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGRNEDGERR
Prediction	8636265341233203212541232233324010100000002032005300530573605030220530326433255046420000000012414104003400410363344354545304302000000214413620130043015104624042003003002424443442035304531550052047245465554445545545354454455554555555553454525575414364655364654423200010131141055355455445445664542453465575668
	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                 280                 300

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

SS
Seq

CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCSSSSSSSSSSCCHHHHHHHHHHHHHHCCCCSSSSCHHHCCCCHHHHHHCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSSCCCCCHHHHHHHHHHHHHHHHHHHCCSSSSSSSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
MDPSADTWDLSSPLISLWINRFYIYLGFAVSISLWICVQIVIEMQGFATVLAEAVTSLDLPVAIINLKEYDPDDHLIEEVTSKNVCVFLVATYTDGLPTESAEWFCKWLEEASIDFRFGKTYLKGMRDAVFGLGNSAYASHFNKVGKNVDKWLWMLGVHRVMSRGEGDCDVVKSKHGSIEANFRAWKTKFISQLQALQKGERKKSCGGHCKKGKCESHQHGSEEREEGSQEQDELHHRDTKEEEPFESSSEEEFGGEDHQSLNSIVDVEDLGKIMDHVKKEKREKEQQEEKSGLFRNMGRNEDGERR

1tllA1

0.25

0.14

4.34

1.03

SPARKS-K

---------------------------AKRVKATILYATETGKSQAYAKTLCEIFK-HAFDAKAMSMEEYDIVHL-----EHEALVLVVTSTFGNGDPPENGEKFGCALMEMKVRFNSVSGPLANVRFSVFGLGSRAY-PHFCAFGHAVDTLLEELGGERILKMREGDEL------CGQEEAFRTWAKKVFKAACDVFC------VGDDVNIESNDRS-----------------------------------------------------------------------------------------

1tllA

0.22

0.19

5.87

2.72

HHsearch

----------------------------AKRVKATILYAT-ETSQAYAKTLCEIFK-HAFDAKAMSMEEYDIVHLEH-----EALVLVVTSTFGNGDPPENGEKFGCALMEMRHEFNSVSGPLANVRFSVFGLGSRAYP-HFCAFGHAVDTLLEELGGERILKMREGDEL------CGQEEAFRTWAKKVFKAACDVFCVGDDVNINKRLTVAEAPDLHKKRVSALSRQNLRSFVRLHTNGQELQYQPGDHLGPGNEDAPPANHVVKVEMLEERNPTPLQLQQFASLEKEKQRLLVLS--KGLQQPR

5b3kA

0.17

0.08

2.67

1.37

FFAS-3D

----------------------------------ILSGSVYGTAEEVARHAQKLLSAAGLEASHLPRASLDELKAF-----APEAFLVVTSTTGMGELPDNLQPLYYAIRDQLPA-------WHGLPGGVIGLGDSSYGDTFAGGGEQVRELFGELGVREVLPMLRLDA----SETVTPETDAEPWLAEFAAALK----------------------------------------------------------------------------------------------------------------

2bf4A

0.16

0.14

4.57

1.01

SPARKS-K

------------------NRDIAQVVTENNKNYLVLYASQTGTAEDYAKKFSKELVAKFLNVMCADVENYDFESLNDV----PVIVSIFISTYGEGDFPDGAVNFEDFICNA------EAGALSNLRYNMFGLGNSTY-EFFNGAAKKAEKHLSAAGAIRLGKLGEADD-----GAGTTDEDYMAWKDSILEVLKDELH-LDEQEAKFTS----QFQYTVLNEITDSMSLGEPSAHYLPSHQLNRNADGIQLGPFDLSSSNDRNCIHSEDLSGSNIKYSTGDHLAVWPSNPLEKVEQFLSIFNLDPE

1j9zA

0.31

0.16

4.93

1.26

CNFpred

----------------------FVEKMKKTGRNIIVFYGSTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDKSLVVFCMATYGEGDPTDNAQDFYDWLQETD-------VDLTGVKFAVFGLGNKTY-EHFNAMGKYVDQRLEQLGAQRIFELGLGDD------DGNLEEDFITWREQFWPAVCEFFG------------------------------------------------------------------------------------------------------------

2bf4A

0.16

0.14

4.65

2.72

HHsearch

------NRDI--------AQ-----VVTENNKNYLVLYAS-QTAEDYAKKFSKELVAKNLNVMCADVENYDFESLND-----VVIVSIFISTYGEGDFPDGAVNFEDFICNAE------AGALSNLRYNMFGLGNSTYE-FFNGAAKKAEKHLSAAGAIRLGKLGEADDG-----AGTTDEDYMAWKDSILEVLKDELHLDEQEKTSQQYTNEITDSMSLGEPQLGPFSQKSRFSSNDRNCINIKYSTGDHLAPSNPLNLDPETIFDLKPLDPPVSRQPNADVKEKLTLLSKDKQFAVEIT--SKYF

1ykgA

0.24

0.11

3.54

1.35

FFAS-3D

---------------------------------TIISASQTGNARRVAEALRDDLLAAKLNVKLVNAGDYKFKQIA-----SEKLLIVVTSTQGEGEPPEEAVALHKFLFSKKAP------KLENTAFAVFSLGDTSY-EFFCQSGKDFDSKLAELGGERLLDRVDADVEY--------QAAASEWRARVVDALKS---------------------------------------------------------------------------------------------------------------

6t1tA

0.21

0.19

5.89

2.72

HHsearch

---SRDVL-----------S-----TLKKNNKNTLLLFGS-QTAEDYANKLSRELHSFGLKTMVADFADYDWDNFGD--ITEDILVFFIVATYGEGEPTDNADEFHTWLTEEA-------DTLSTLRYTVFGLGNSTYE-FFNAIGRKFDRLLSEKGGDRFAEYAEGDDG-----TGTLDEDFMAWKDNVFDALKNDLNFEEKELKPNKLTERDDLASSLGEPTKFDHTHETRFSSKERHCINLKYTTGDHLAPSNGLEDKLDTVIELKALDSTVSRQPDEETKKTFTRLGGDKEFATKVT--RRKF

3ojwA

0.31

0.16

4.93

1.24

CNFpred

----------------------FVEKMKKTGRNIIVFYGSQGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDKSLVVFAMATYGEGDPTCNAQDFYDWLQETD-------VDLTGVKFAVFGLGNKTY-EHFNAMGKYVDQRLEQLGAQRIFELGLGDDDG------NLEEDFITWREQFWPAVAEFFG------------------------------------------------------------------------------------------------------------

1ja0A

0.22

0.20

6.26

2.66

HHsearch

PVKESSFV-----------E-----KMKKTGRNIIVFYGS-QTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDKSLVVFCMATYGEGDPTDNAQDFYDWLQETD-------VDLTGVKFAVFGLGNKTYE-HFNAMGKYVDQRLEQLGAQRIFELGLGDDD------GNLEEDFITWREQFWPAVCEFFGVEATGEIRQELVEDDVATGKSNQKPPFDAKNANRNQGTERHLMKIRYESGDHVAPANDLGADLDVIMSLNNLDEPPRTN-VLYELAQYPSEQEHLHKMASGEGKEARR

(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	0.6138

(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	1ja0A	0.62	3.97	0.233	0.746	model1_1ja0A.pdb.gz
2	6t1tA	0.61	3.81	0.207	0.723	model1_6t1tA.pdb.gz
3	2bf4A	0.60	3.74	0.154	0.713	model1_2bf4A.pdb.gz
4	1tllA	0.58	4.28	0.186	0.710	model1_1tllA.pdb.gz
5	5gxuA	0.52	3.06	0.204	0.593	model1_5gxuA.pdb.gz
6	4bb9A	0.52	5.28	0.042	0.752	model1_4bb9A.pdb.gz
7	3hr4A	0.48	2.39	0.180	0.518	model1_3hr4A.pdb.gz
8	1ykgA	0.46	1.28	0.247	0.476	model1_1ykgA.pdb.gz
9	1ofvA	0.44	2.13	0.155	0.482	model1_1ofvA.pdb.gz
10	2wc1A	0.44	2.65	0.144	0.492	model1_2wc1A.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:0016491	0.99	oxidoreductase activity
GO:1901363	0.79	heterocyclic compound binding
GO:0097159	0.79	organic cyclic compound binding
GO:0030586	0.78	[methionine synthase] reductase activity
GO:0016651	0.74	oxidoreductase activity, acting on NAD(P)H
GO:0003958	0.73	NADPH-hemoprotein reductase activity
GO:0032553	0.72	ribonucleotide binding
GO:0048037	0.67	cofactor binding
GO:0050660	0.66	flavin adenine dinucleotide binding
GO:0010181	0.66	FMN binding
GO:0050661	0.65	NADP binding
GO:0009055	0.57	electron carrier activity
GO:0016705	0.54	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

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	0.90	cellular process
GO:0008152	0.87	metabolic process
GO:0044699	0.81	single-organism process
GO:0044237	0.81	cellular metabolic process
GO:0065007	0.76	biological regulation
GO:0071704	0.75	organic substance metabolic process
GO:0050789	0.75	regulation of biological process
GO:0044763	0.73	single-organism cellular process
GO:0044710	0.73	single-organism metabolic process
GO:0050794	0.72	regulation of cellular process
GO:0044238	0.70	primary metabolic process
GO:0050790	0.67	regulation of catalytic activity
GO:0048518	0.67	positive regulation of biological process
GO:0019222	0.67	regulation of metabolic process
GO:0050896	0.66	response to stimulus
GO:0009893	0.66	positive regulation of metabolic process
GO:0065008	0.65	regulation of biological quality
GO:0080090	0.64	regulation of primary metabolic process
GO:0048522	0.64	positive regulation of cellular process
GO:0043085	0.64	positive regulation of catalytic activity
GO:0031326	0.64	regulation of cellular biosynthetic process
GO:0043170	0.63	macromolecule metabolic process
GO:0031328	0.63	positive regulation of cellular biosynthetic process
GO:0055114	0.62	oxidation-reduction process
GO:0051239	0.62	regulation of multicellular organismal process
GO:0034641	0.62	cellular nitrogen compound metabolic process
GO:0051240	0.61	positive regulation of multicellular organismal process
GO:0044260	0.61	cellular macromolecule metabolic process
GO:0019932	0.56	second-messenger-mediated signaling
GO:1901360	0.55	organic cyclic compound metabolic process
GO:0019219	0.55	regulation of nucleobase-containing compound metabolic process
GO:0051339	0.54	regulation of lyase activity
GO:0048519	0.54	negative regulation of biological process
GO:0044281	0.54	small molecule metabolic process
GO:0051349	0.53	positive regulation of lyase activity
GO:0048523	0.53	negative regulation of cellular process
GO:0031282	0.53	regulation of guanylate cyclase activity
GO:0031281	0.53	positive regulation of cyclase activity
GO:0030828	0.53	positive regulation of cGMP biosynthetic process
GO:0006950	0.53	response to stress
GO:1903522	0.52	regulation of blood circulation
GO:0032501	0.52	multicellular organismal process
GO:0009058	0.52	biosynthetic process
GO:0008217	0.52	regulation of blood pressure
GO:0006629	0.52	lipid metabolic process
GO:0006082	0.52	organic acid metabolic process
GO:1903524	0.51	positive regulation of blood circulation
GO:0051716	0.51	cellular response to stimulus
GO:0044249	0.51	cellular biosynthetic process
GO:0042312	0.51	regulation of vasodilation
GO:0042221	0.51	response to chemical
GO:0042127	0.51	regulation of cell proliferation
GO:0019752	0.51	carboxylic acid metabolic process
GO:0044712	0.50	single-organism catabolic process
GO:0010033	0.50	response to organic substance

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:0044444	0.93	cytoplasmic part
GO:0043229	0.89	intracellular organelle
GO:0043231	0.85	intracellular membrane-bounded organelle
GO:0005737	0.79	cytoplasm
GO:0044422	0.65	organelle part
GO:0016020	0.65	membrane
GO:0044446	0.64	intracellular organelle part
GO:0005829	0.59	cytosol
GO:0044425	0.54	membrane 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	0.252	1b1cA	0.514	1.43	0.303	0.537	1.6.2.4	91,133,150
2	0.060	3hr4A	0.481	2.39	0.180	0.518	1.14.13.39	92,134,165,180
3	0.060	1f20A	0.313	6.25	0.050	0.508	1.14.13.39	NA
4	0.060	1i3kA	0.477	4.91	0.069	0.677	5.1.3.2	NA
5	0.060	3enkA	0.479	5.00	0.104	0.687	5.1.3.2	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	0.33	1j9zA	0.625	4.05	0.229	0.749	1.42	FMN	complex1.pdb.gz	39,40,41,43,44,91,92,93,94,133,134,135,138,141,142,143,179

	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.