D-I-TASSER Q06055-D1

D-I-TASSER results for Q06055-D1

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

Input Sequence in FASTA format

>Q06055 (141 residues)
MFACSKFVSTPSLVKSTSQLLSRPLSAVVLKRPEILTDESLSSLAVSCPLTSLVSSRSFQ
TSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGF
ALSEAMGLFCLMVAFLILFAM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFACSKFVSTPSLVKSTSQLLSRPLSAVVLKRPEILTDESLSSLAVSCPLTSLVSSRSFQTSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
Prediction	CCCHHHHHHCHHHHHCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	963146552156553244254005777774387302103421113466521234333467889999999999986577776533022134899999999999819668999999999999999999999999999999829
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MFACSKFVSTPSLVKSTSQLLSRPLSAVVLKRPEILTDESLSSLAVSCPLTSLVSSRSFQTSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
Prediction	742313221332323432430323221223444543454444444444434434454422333335404401432212120112133331203012310211043362464033201111031213333233323333336
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHCHHHHHCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MFACSKFVSTPSLVKSTSQLLSRPLSAVVLKRPEILTDESLSSLAVSCPLTSLVSSRSFQTSAISRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM

6l7eA

0.07

0.06

2.68

1.17

DEthreader

---HQASLGFLKAT-IRKLNTI-WLLMTQLMVYHSTGITAD-NGEQNAAELILTNLSIQDKTIEELDAEKTVLEKSKAGAQSRFDSYGKLYDENINGENQAMTLRATDKISQSETYRRRRQEWEIQRNNAEAELKQIDAQL

4bemJ

0.18

0.15

4.85

1.51

SPARKS-K

KSNDIVMIMLLGAAVAETSGIFSLVIALILLFANPFISSTAS------------------------VWILSASAMASGIAMIAGIGPGTGQGYAAGKGAEAVGIRPEMKSAILRVMLLGQAVAQTTGIYALIVALILMYAN

3jacA

0.14

0.08

2.65

1.05

MapAlign

-----------------------------------------------------------------GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

4bemJ

0.16

5.21

0.43

CEthreader

GVGPGIGQGFAAGKGAEAVGKNPTKSNDIVMIMLLGAAVAETSGIFSLVIALILLFANPFISSTASVWILSASAMASGIAMIAGIGPGTGQGYAAGKGAEAVGIRPEMKSAILRVMLLGQAVAQTTGIYALIVALILMYAN

1ycev

0.30

0.18

5.37

1.26

MUSTER

-----------------------------------------------------------MDMLFAKTVVLAASAVGAGTAMIAGIGPGVGQGYAAGKAVESVARQPEAKGDIISTMVLGQAVAESTGIYSLVIALILLYAN

6ynwP

0.28

0.15

4.55

2.35

HHsearch

-----------------------------------------------------------------MLLVKAVKVLVMGGCMLPIAFGALGTGVLFAGFNVALSRNPEETESLFNNTLMGFALIETFIFMSIGLGFFVLFA-

5dn6J

0.39

0.21

6.08

1.42

FFAS-3D

------------------------------------------------------------------NLGQLGQYLGAGLACVGMAGAAMGVGNVAGNYLAGALRNPSAAASQTATLFIGMAFAEALGIFSFLVALLLLFA-

6m32A

0.06

2.53

0.62

EigenThreader

MGIYYISGIGARLLGWAAFHFLVGSVLIFGGWRHWTHNCGNFRDFSAKSYKEALGPHAVYMSLLFLGWGIVMWAILAAFSVHLTAIGYINIALGCIAFVAFQQPSFAPYYKTNLIVFNHIICGVLYVFAGVYHGGQYLLKI

4bemJ

0.24

0.13

3.97

0.79

CNFpred

-------------------------------------------------------------------WILSASAMASGIAMIAGIGPGTGQGYAAGKGAEAVGIRPEMKSAILRVMLLGQAVAQTTGIYALIVALILMYAN

6rw8A

0.06

2.50

1.17

DEthreader

IVLGKLFYVYYTQISFLFQCTQWLQWVDVMLIVRNIG--A--RGTSELLQSIKMQDKVMA-EIDADKLALQESRHGAQSRFDSFNTLYDEDVNGEKQAMDLYLSSSAIAADKISQSEIYRRRRQEWEIQRNNAEAEIKQIQ

(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	0.5743

(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	7jh5A	0.58	4.27	0.075	0.837	model1_7jh5A.pdb.gz
2	4akkA	0.58	3.84	0.098	0.837	model1_4akkA.pdb.gz
3	3o0rB3	0.57	3.64	0.035	0.794	model1_3o0rB3.pdb.gz
4	4f4cA	0.57	3.84	0.140	0.780	model1_4f4cA.pdb.gz
5	6vq6g	0.56	3.28	0.221	0.731	model1_6vq6g.pdb.gz
6	4xzyA1	0.56	3.78	0.037	0.808	model1_4xzyA1.pdb.gz
7	3mk7A	0.56	4.26	0.044	0.872	model1_3mk7A.pdb.gz
8	4xydA	0.54	4.50	0.073	0.865	model1_4xydA.pdb.gz
9	3ayfA2	0.52	4.68	0.051	0.858	model1_3ayfA2.pdb.gz
10	2yevA1	0.51	3.97	0.046	0.731	model1_2yevA1.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:0005215	0.94	transporter activity
GO:0003824	0.63	catalytic activity
GO:0022857	0.60	transmembrane transporter activity
GO:0022891	0.58	substrate-specific transmembrane transporter activity
GO:0022890	0.57	inorganic cation transmembrane transporter activity
GO:0015078	0.56	hydrogen ion transmembrane transporter activity
GO:0016787	0.53	hydrolase activity
GO:0022804	0.51	active transmembrane transporter activity
GO:0016817	0.51	hydrolase activity, acting on acid anhydrides
GO:0019829	0.50	cation-transporting ATPase 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:0044699	0.91	single-organism process
GO:0008152	0.89	metabolic process
GO:0009987	0.88	cellular process
GO:0044237	0.83	cellular metabolic process
GO:0044710	0.81	single-organism metabolic process
GO:0071704	0.79	organic substance metabolic process
GO:0044281	0.79	small molecule metabolic process
GO:0044763	0.78	single-organism cellular process
GO:0044238	0.78	primary metabolic process
GO:0034641	0.77	cellular nitrogen compound metabolic process
GO:1901564	0.76	organonitrogen compound metabolic process
GO:0006139	0.74	nucleobase-containing compound metabolic process
GO:1901135	0.73	carbohydrate derivative metabolic process
GO:0055086	0.73	nucleobase-containing small molecule metabolic process
GO:0019637	0.73	organophosphate metabolic process
GO:0006796	0.73	phosphate-containing compound metabolic process
GO:0046034	0.72	ATP metabolic process
GO:0006810	0.69	transport
GO:1901576	0.68	organic substance biosynthetic process
GO:0044249	0.68	cellular biosynthetic process
GO:1901566	0.67	organonitrogen compound biosynthetic process
GO:0044271	0.67	cellular nitrogen compound biosynthetic process
GO:1902578	0.65	single-organism localization
GO:0044765	0.64	single-organism transport
GO:0044711	0.64	single-organism biosynthetic process
GO:0034654	0.64	nucleobase-containing compound biosynthetic process
GO:0055085	0.63	transmembrane transport
GO:0006812	0.63	cation transport
GO:0006754	0.63	ATP biosynthetic process
GO:0015986	0.62	ATP synthesis coupled proton 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:0044446	0.82	intracellular organelle part
GO:0044429	0.76	mitochondrial part
GO:0043226	0.70	organelle
GO:0043229	0.68	intracellular organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0032991	0.68	macromolecular complex
GO:0044425	0.67	membrane part
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0043234	0.66	protein complex
GO:0098796	0.64	membrane protein complex
GO:0044455	0.64	mitochondrial membrane part
GO:0098800	0.63	inner mitochondrial membrane protein complex
GO:0005739	0.56	mitochondrion
GO:0005753	0.53	mitochondrial proton-transporting ATP synthase complex
GO:0016020	0.50	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	3gpbA	0.498	4.66	0.086	0.844	2.4.1.1	NA
2	0.060	2occN	0.511	4.28	0.068	0.780	1.9.3.1	95,98,127
3	0.060	2ohyB	0.526	3.91	0.053	0.773	5.4.3.6	NA
4	0.060	2f8zF	0.523	3.77	0.017	0.759	2.5.1.10 2.5.1.1	86
5	0.060	1ahpA	0.499	4.61	0.068	0.837	2.4.1.1	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	0.04	3mk7D	0.567	3.50	0.103	0.794	0.61	CA	complex1.pdb.gz	80,82,131
2	0.01	2i19B	0.537	3.97	0.074	0.780	0.41	1BY	complex2.pdb.gz	84,88,127
3	0.01	1i490	0.546	3.04	0.068	0.716	0.49	III	complex3.pdb.gz	54,55,78,91,112,116,120,121,123,124,127,131,132,134,135
4	0.01	2hydA	0.526	3.88	0.031	0.766	0.44	ADP	complex4.pdb.gz	99,100,102,108
5	0.01	2hydA	0.526	3.88	0.031	0.766	0.42	ADP	complex5.pdb.gz	90,118,119,123,124,125,126
6	0.01	2onjB	0.525	3.70	0.031	0.759	0.51	ANP	complex6.pdb.gz	103,106,107

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.