D-I-TASSER Q9HC07-D1

D-I-TASSER results for Q9HC07-D1

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

Input Sequence in FASTA format

>Q9HC07 (324 residues)
MAAAAPGNGRASAPRLLLLFLVPLLWAPAAVRAGPDEDLSHRNKEPPAPAQQLQPQPVAV
QGPEPARVEKIFTPAAPVHTNKEDPATQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIM
AMRYNRLTVLAGAMLALGLMTCLSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLK
MSPDEGQEELEEVQAELKKKDEEFQRTKLLNGPGDVETGTSITVPQKKWLHFISPIFVQA
LTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGGTVGHCLCTGLAVIGGRMIAQKISVRTV
TIIGGIVFLAFAFSALFISPDSGF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAAAPGNGRASAPRLLLLFLVPLLWAPAAVRAGPDEDLSHRNKEPPAPAQQLQPQPVAVQGPEPARVEKIFTPAAPVHTNKEDPATQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIMAMRYNRLTVLAGAMLALGLMTCLSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLKMSPDEGQEELEEVQAELKKKDEEFQRTKLLNGPGDVETGTSITVPQKKWLHFISPIFVQALTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGGTVGHCLCTGLAVIGGRMIAQKISVRTVTIIGGIVFLAFAFSALFISPDSGF
Prediction	CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence	986467876323278999999999999764213675431112345655432234443111356776544466666655666555434444218999999999999996263899999999942884689999999999999999999999996689999999999999999999999874687544157776676665545554311023577653235565554443222222199999999999985208899999998348832569999999999999999999999953899999999999999999999961766799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAAAAPGNGRASAPRLLLLFLVPLLWAPAAVRAGPDEDLSHRNKEPPAPAQQLQPQPVAVQGPEPARVEKIFTPAAPVHTNKEDPATQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIMAMRYNRLTVLAGAMLALGLMTCLSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLKMSPDEGQEELEEVQAELKKKDEEFQRTKLLNGPGDVETGTSITVPQKKWLHFISPIFVQALTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGGTVGHCLCTGLAVIGGRMIAQKISVRTVTIIGGIVFLAFAFSALFISPDSGF
Prediction	734236332211202200000010000000043355743554555456546535645453546444546644464553545655456644321010033022101100331210000000003343210000012013210110021120011024300200001102210010012125256553464355355515545553544345645444554454544444344222100100020101013322100000000043311000200120000000000000220063023400320001001210210002237733
	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                 320

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

SS
Seq

CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MAAAAPGNGRASAPRLLLLFLVPLLWAPAAVRAGPDEDLSHRNKEPPAPAQQLQPQPVAVQGPEPARVEKIFTPAAPVHTNKEDPATQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIMAMRYNRLTVLAGAMLALGLMTCLSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLKMSPDEGQEELEEVQAELKKKDEEFQRTKLLNGPGDVETGTSITVPQKKWLHFISPIFVQALTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGGTVGHCLCTGLAVIGGRMIAQKISVRTVTIIGGIVFLAFAFSALFISPDSGF

5m87A

0.06

0.05

1.99

1.12

EigenThreader

-----------------------------------------------------------------------DLSLSDINSTVEVPEG--HSFWKTLLAYPGALVAVGYMDPGNWSTSITGGQNFLLLSIIVISSLLAMLLQNMAAKLGIVCQLDIFWILTELAIMATDIAEVIGAAIALYLLFKIPIFLAVVITV----LDVFLLLLLNRIGIPSWASVQTSPKIGGQT---PLSASLGIIGATI----MPHNLFLHSAISQSRKIDFSNWDSNIQLSLAMVVNALLLIMGVASTLFAVALLASGQTGTITGQVIMEGFIHLRL

3rkoC

0.12

0.09

3.08

1.09

CNFpred

-----------FFHLNLMWILGGVIGVFLAIDMFLFFFFWEMM-------VPMYFLIALWGHKASDGKTRITAATKF----------IYTQASGLVMLIAILALVFVHYGVWTFNYEELLNTPMVEYLLMLGFFIAFAVKMPVHGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLR----------------------------------------------------FSLPLFPNASAEFAPIAM-WLGVIGIFYGAWMAFAQDIKRLIAYTSVSHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTR

7crzA

0.12

0.10

3.52

0.43

CEthreader

LEFILGSEELWPLLLGFTILPAILQSAALPFCPESPRFLLINRKEEENAKQILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQLSGAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKDNYNG----------------------------------------------MSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAALGAYVFIIFTGFLITFLAFTFFKVPETRG

5oqtA

0.09

0.07

2.69

1.07

EigenThreader

-----------------------------------------------------------LFRKKPIQLLMKESGAKGASLRK-------ELGAFDLTMLGIGAII----GTGIFVLTGVAAAEHAGPALVLSFILSGLACAEFASTVIAWILGWDLILEYGVASSAVAVGWSGYFQGLLSGELPKALIVLFITFLLNLGAKVAIKVAVVLLFLAVGVWYVKPENWTPFM--PYGFSGVATGAATVFFAYIG--FDAVSTAAEEVRNPIGIIVSLLVCTLLYIAVSLVLTGIVPYEQLNFISLGAIAGITTVLLVMMYGQTRLFY

4k1cA

0.17

0.13

4.37

0.88

FFAS-3D

-------HFQLSHTLTFLFNFLAIIPLAAILANATEELADKAG-------------------------------------------------------NTIGGLLNATFGNAVELIVSIIALKKGQVRIVQASMLGSLLSNLLLVLGLCFIFTFNQTAAQTMSSLLAIACASLLIPAAFRATLPFIDGKILELSHALFEQQEEETDEVMSTISRNPHHSLSVKSSLVILLGTTVIISFCAIGLIVIPIVGNAAEHVTSVLVAMKDKMDLALGVAIGSSLQVAFMVLVGWMIDVPMTFETATLFIAVFLSNYGVMSLA-------

7duwA1

0.11

0.09

3.23

0.95

SPARKS-K

------LNRYRALIVAVLTVAVFCIAAYAIYDLT-------------------------TEVRYDDVVHALTTTK------------------ISSVLLALLFTGLSFASLIFYDQNALEYIRLPFPHVALTSFSAYAVGNAGAIRYRAYTRLFVTLAFGLGLASVGAMALLVIADEIGPLISVDGLWLRLIAIAILAALAFVVYAG--RNGREVRIGPVAVRLPDS-------RTWSRQFLVTAFDIAASASVLYVLLPETSIGWPGFFAIYAIAVGLGVLSETIIIAWLGSSVNE-DAVLSSLVLYRVIYNVIPLVIAIAAI

5gpjA

0.10

0.06

2.27

1.08

CNFpred

---------------LATAIFSTVSFLLGGVTSLV-------------------------------------------------------SGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLAANGLLVLYIAINLFKIYYGDDWGGLFEAITGYGLGGSSMALFG------------------------------------------------------RVGGGIYTKAADVGA---PRNPAVIADNVGDNVGDIAGMGSDLFGSYAESSCAALVVASISSFGLNHELTAMLYPLIVSSVGILVCLLTTLFAT

6l85A

0.08

0.06

2.15

0.67

DEthreader

-------------------------------------------------------------------------------------------M-TILIIAGILGFIMAFS-I-GANDVANSMATAVAAIAMFLEFLGAVMFGSHVSQTIVKV-VEKVQPLGAVMMVNWTFL-IVL-WV---P---V--GLISFVMFKLISLSVSSTVAIPFLFFV-----FAVRKLIVVFRAQILTSCYVSFSHGANDVA-NAAGPVAAVMIVASTPFLALLLGGIGISLGVFFLGQKVMETVGEKVNIISWLLIVPTVAATSAAVYWVL-KLIL

5m87A

0.09

0.07

2.58

0.76

MapAlign

-----------------------------------------------------------------------LSLSDINSTVEVPEGHSFWKTLLAYS-GPGALVAVGYMDPGNWSTSITGGQNFQY-LLLSIIVISSMLLQNMAAKLGIVDLGFIFWILTELAIMATDIAEVIGAAIALYLLRIGFRKIEALVVCLIFVILFVFLYQIILSQPA--------WHQVAKGLIPSWASPLSASLGIIGATIMPHNLFLHSAISQSRKVRFSNWDSNIQLSLANALLLIMGVVFVQDPSFAVALLASGQNSTITGTITGQVIMEGFI

4gbyA

0.14

0.13

4.29

0.62

MUSTER

AANSLLGFCVASALRRDSLKIAAVLFFISGVGSAW-------------------PELGFTSINPDNTVPVYLAGYVPE------------GGIGVGLASMLSPMYIAELPAHIRGKLVSFNQ----FAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYPRWLMSRGK-QEQAEGILRKIMGNTLATQAVQEIKHSLDHG----RKTGGRLLMFGVGVIVIGVMLSIFQQFVG-VLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAP

(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	0.5143

(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	5nv9A	0.42	6.09	0.084	0.657	model1_5nv9A.pdb.gz
2	6rutB	0.42	6.34	0.049	0.688	model1_6rutB.pdb.gz
3	6l85A	0.41	5.81	0.085	0.636	model1_6l85A.pdb.gz
4	6rkoA	0.41	6.22	0.044	0.685	model1_6rkoA.pdb.gz
5	7d8zB1	0.41	5.87	0.055	0.624	model1_7d8zB1.pdb.gz
6	4a01A	0.40	6.31	0.097	0.654	model1_4a01A.pdb.gz
7	5w1hA	0.40	6.26	0.028	0.654	model1_5w1hA.pdb.gz
8	2witA	0.40	5.47	0.088	0.580	model1_2witA.pdb.gz
9	6s8bK1	0.40	6.43	0.052	0.657	model1_6s8bK1.pdb.gz
10	6me2A	0.39	5.84	0.050	0.608	model1_6me2A.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:0072509	1.00	divalent inorganic cation transmembrane transporter activity
GO:0046873	1.00	metal ion transmembrane transporter activity
GO:0046915	0.51	transition metal ion transmembrane transporter activity
GO:0015095	0.50	magnesium ion transmembrane transporter activity
GO:0015085	0.50	calcium ion transmembrane transporter activity
GO:0005384	0.50	manganese ion transmembrane transporter activity

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	0.97	cellular process
GO:0044699	0.93	single-organism process
GO:0044763	0.90	single-organism cellular process
GO:0008152	0.85	metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0044238	0.83	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0065007	0.80	biological regulation
GO:0044710	0.80	single-organism metabolic process
GO:0044267	0.79	cellular protein metabolic process
GO:0044723	0.77	single-organism carbohydrate metabolic process
GO:0006464	0.77	cellular protein modification process
GO:0006810	0.76	transport
GO:0006487	0.76	protein N-linked glycosylation
GO:0030001	0.73	metal ion transport
GO:0006874	0.73	cellular calcium ion homeostasis
GO:0006816	0.66	calcium ion transport
GO:0035751	0.61	regulation of lysosomal lumen pH
GO:0032472	0.61	Golgi calcium ion transport

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:0044444	1.00	cytoplasmic part
GO:0043226	0.96	organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0044446	0.86	intracellular organelle part
GO:0016020	0.82	membrane
GO:0005794	0.82	Golgi apparatus
GO:0031090	0.71	organelle membrane
GO:0044431	0.69	Golgi apparatus part
GO:0098588	0.65	bounding membrane of organelle
GO:0010008	0.63	endosome membrane
GO:0000139	0.63	Golgi membrane
GO:0032588	0.62	trans-Golgi network membrane
GO:0005765	0.62	lysosomal membrane

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	1kqfA	0.355	6.79	0.066	0.617	1.2.1.2	NA
2	0.060	3hmjA	0.359	6.38	0.032	0.596	2.3.1.86	NA
3	0.060	3hf2A	0.279	6.75	0.046	0.491	1.14.14.1 1.6.2.4	113,278
4	0.060	3a4gA	0.362	5.99	0.073	0.562	1.14.13.15	166
5	0.060	1po5A	0.358	6.67	0.027	0.608	1.14.14.1	113,278

	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	0.01	2qeiA	0.393	6.26	0.051	0.617	0.56	CXX	complex1.pdb.gz	107,111,113,273
2	0.01	2p85C	0.386	6.35	0.047	0.626	0.58	IND	complex2.pdb.gz	277,280,281
3	0.01	3f3aA	0.396	6.10	0.060	0.611	0.45	TRP	complex3.pdb.gz	111,115,116,132

	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.