D-I-TASSER Q0P5N6-D1

D-I-TASSER results for Q0P5N6-D1

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

Input Sequence in FASTA format

>Q0P5N6 (197 residues)
MRVAGGRALSRGAELRVPGGAKHGMCLLLGATGVGKTLLVKRLQEVSSRDGKGDLGEPPP
TRPTVGTNLTDIVAQRKITIRELGGCMGPIWSSYYGNCRSLLFVMDASDPTQLSASCVQL
LGLLSAEQLAEASVLILFNKIDLPCYMSTEEMKSLIRLPDIIACAKQNITTAEISAREGT
GLAGVLAWLQATHRAND

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MRVAGGRALSRGAELRVPGGAKHGMCLLLGATGVGKTLLVKRLQEVSSRDGKGDLGEPPPTRPTVGTNLTDIVAQRKITIRELGGCMGPIWSSYYGNCRSLLFVMDASDPTQLSASCVQLLGLLSAEQLAEASVLILFNKIDLPCYMSTEEMKSLIRLPDIIACAKQNITTAEISAREGTGLAGVLAWLQATHRAND
Prediction	CCCCHHHHHHHHHHHHCHCCCCSSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCSCCCCCSCSSSSSSSCCCSSSSSSCCCCSHHHHHHHHCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHCHHHCCCCSSSSSSCCCCCCCCCHHHHHHHHCCCCCCCCCCCCSSSSSSSCSCCCCHHHHHHHHHHHHHHCC
Confidence	98752589999999852046854899998779998689999997135666666788410124762247999835842999955896333799873266489998528836889999999999995020149948999855789899999999998398321335898459999875069599999999999998519
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MRVAGGRALSRGAELRVPGGAKHGMCLLLGATGVGKTLLVKRLQEVSSRDGKGDLGEPPPTRPTVGTNLTDIVAQRKITIRELGGCMGPIWSSYYGNCRSLLFVMDASDPTQLSASCVQLLGLLSAEQLAEASVLILFNKIDLPCYMSTEEMKSLIRLPDIIACAKQNITTAEISAREGTGLAGVLAWLQATHRAND
Prediction	63331131023334234324544010000003301010002203544355454444432423223302023134534020120442332003311440210000100234312420341033004324044001000002332641043642352040550463661402000000244541440053217404658
	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

CCCCHHHHHHHHHHHHCHCCCCSSSSSSSCCCCCCHHHHHHHHHCCCCCCCCCCCCCCSCCCCCSCSSSSSSSCCCSSSSSSCCCCSHHHHHHHHCCCCSSSSSSCCCCHHHHHHHHHHHHHHHHCHHHCCCCSSSSSSCCCCCCCCCHHHHHHHHCCCCCCCCCCCCSSSSSSSCSCCCCHHHHHHHHHHHHHHCC
MRVAGGRALSRGAELRVPGGAKHGMCLLLGATGVGKTLLVKRLQEVSSRDGKGDLGEPPPTRPTVGTNLTDIVAQRKITIRELGGCMGPIWSSYYGNCRSLLFVMDASDPTQLSASCVQLLGLLSAEQLAEASVLILFNKIDLPCYMSTEEMKSLIRLPDIIACAKQNITTAEISAREGTGLAGVLAWLQATHRAND

6bbpA

0.27

0.24

7.49

1.33

DEthreader

YFEKEPRGICVEGN-KSKIGNKEMRILMLGLDAAGKTTILYKLKL---------GQSV-TTIPTVGFNVETVTYNVKFNVWDVGGLIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLG---LTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY--N-

3dofA

0.24

0.22

6.79

1.55

SPARKS-K

--------GLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDT----------ISPTLGFNIKTLEHRGKLNIWDVGGQLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSSNAIREVLELDS---IRSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI

6bbpA2

0.29

0.24

7.42

0.45

MapAlign

--------------LSKIFGNKEMRILMLGLDAAGKTTILYKLKL----------GQSVTTIPTVGFNVETVTYKVKFNVWDVGGLIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKL---GLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY----

6bbpA2

0.28

0.25

7.77

0.39

CEthreader

ATRKRRIANKKGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKL----------GQSVTTIPTVGFNVETVTYNVKFNVWDVGGLIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLG---LTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYN---

3o47A

0.29

0.26

8.03

1.27

MUSTER

VALAEGREWSLES--WTPPQKKEMRILMVGLDAAGKTTILYKLKL----------GEIVTTIPTIGFNVETVEYKNSFTVWDVG---RPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL---RHRNWYIQATCATSGDGLYEGLDWLSNQLRN--

3dofA

0.26

0.23

7.06

0.82

HHsearch

----GLLTILKKM----KQKERELRLLMLGLDNAGKTTILKKFNGE----------DIDTISPTLGFNIKTLEHRGKLNIWDVGGQLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSSNAIREVLELDSI---RSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI

5di3A

0.25

0.20

6.30

2.41

FFAS-3D

----------------------EARILVLGLDNAGKTTILKALSEEDITTITPTQG----------FNIKSLSRDFNLKIWDGQKSIRPYWRNYFDQTDALIYVIDSADSKRLSESEFELTELLQEEKMTGVPLLVFANKQDLVGALAADEIASTLD---LTSIRDRPWQIQACSAKQGTGLKEGMEWMMKQVKLE-

3dofA

0.24

0.22

6.79

0.62

EigenThreader

----GLLTILKKMKQKE----RELRLLMLGLDNAGKTTILKKFNG----------EDIDTISPTLGFNIKTLEHRGFLNIWDVGGQLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSSNAIREVLELDS---IRSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI

6ii6C

0.28

0.23

6.98

1.56

CNFpred

---------------------KEMRILMVGLDAAGKTTILYKLKLGE----------IVTTIPTIGFNVETVEYKISFTVWDVGGLIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRH---RNWYIQATCATSGDGLYEGLDWLANQLE---

4zkdA

0.16

0.14

4.75

1.33

DEthreader

----------------IATHPLNLTCLFLGDTNAGKSTLLGHLLYDLNE--SMSSMSVILDEFSMFKKVIQVENLLTLTLIDTPGIFNKETLNSILDPEVYVLVIDCNSWEKSLNQIYEILKVISYLNKSKKHLIILLNKADLISDHRLEMIQSELNYVLKEQWTDAEFQFIPCSGLLGSNLNTFFSQLYLLVEHNN

(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	0.8564

(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	6bbpA	0.83	2.11	0.260	0.904	model1_6bbpA.pdb.gz
2	3dofA	0.80	1.73	0.239	0.848	model1_3dofA.pdb.gz
3	4m9qA	0.79	1.30	0.270	0.827	model1_4m9qA.pdb.gz
4	1r4aA	0.78	1.30	0.309	0.822	model1_1r4aA.pdb.gz
5	2h57B	0.78	1.28	0.235	0.822	model1_2h57B.pdb.gz
6	3lvqE2	0.78	1.38	0.280	0.817	model1_3lvqE2.pdb.gz
7	4basA	0.78	1.41	0.222	0.822	model1_4basA.pdb.gz
8	5di3A	0.78	1.34	0.273	0.817	model1_5di3A.pdb.gz
9	1tndA	0.77	2.16	0.175	0.868	model1_1tndA.pdb.gz
10	2rgnA	0.77	2.36	0.174	0.873	model1_2rgnA.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:1901363	0.99	heterocyclic compound binding
GO:0097159	0.99	organic cyclic compound binding
GO:0005525	0.98	GTP binding
GO:0003924	0.97	GTPase activity
GO:0019003	0.65	GDP binding
GO:0098772	0.60	molecular function regulator
GO:0030234	0.58	enzyme regulator activity
GO:0008047	0.57	enzyme activator activity
GO:0043169	0.51	cation binding
GO:0046872	0.50	metal ion 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:0065007	0.95	biological regulation
GO:0050794	0.94	regulation of cellular process
GO:0007165	0.90	signal transduction
GO:0035556	0.89	intracellular signal transduction
GO:0007264	0.88	small GTPase mediated signal transduction
GO:0009987	0.86	cellular process
GO:0044699	0.83	single-organism process
GO:0051179	0.81	localization
GO:0006810	0.79	transport
GO:0044763	0.77	single-organism cellular process
GO:0051641	0.70	cellular localization
GO:0051649	0.67	establishment of localization in cell
GO:0016192	0.67	vesicle-mediated transport
GO:0016043	0.67	cellular component organization
GO:0046907	0.64	intracellular transport
GO:0008104	0.61	protein localization
GO:0006996	0.60	organelle organization
GO:0008152	0.59	metabolic process
GO:0044237	0.56	cellular metabolic process
GO:0071702	0.55	organic substance transport
GO:0007034	0.55	vacuolar transport
GO:1902578	0.54	single-organism localization
GO:0034613	0.54	cellular protein localization
GO:0016197	0.54	endosomal transport
GO:0015031	0.54	protein transport
GO:0048193	0.53	Golgi vesicle transport
GO:0071704	0.52	organic substance metabolic process
GO:0051128	0.52	regulation of cellular component organization
GO:0044765	0.52	single-organism transport
GO:0044710	0.52	single-organism metabolic process
GO:0044238	0.51	primary metabolic process
GO:0016482	0.51	cytosolic transport
GO:0033365	0.50	protein localization to organelle
GO:0032879	0.50	regulation of localization

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.97	cytoplasmic part
GO:0043226	0.95	organelle
GO:0043227	0.94	membrane-bounded organelle
GO:0043229	0.92	intracellular organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0016020	0.85	membrane
GO:0044422	0.81	organelle part
GO:0044446	0.80	intracellular organelle part
GO:0031982	0.71	vesicle
GO:0031988	0.68	membrane-bounded vesicle
GO:0098588	0.58	bounding membrane of organelle
GO:0005886	0.57	plasma membrane
GO:0031410	0.55	cytoplasmic vesicle
GO:0005773	0.54	vacuole
GO:0016023	0.53	cytoplasmic, membrane-bounded vesicle
GO:0005794	0.50	Golgi apparatus
GO:0005768	0.50	endosome

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	0.349	3bfkB	0.723	2.08	0.213	0.812	3.6.5.2	33
2	0.325	2yxbA	0.502	3.32	0.070	0.655	5.4.99.2	43
3	0.165	1m2oB	0.747	1.91	0.266	0.802	3.6.5.-	NA
4	0.128	1e0sA	0.708	2.02	0.222	0.777	3.6.1.47	NA
5	0.121	2atxA	0.711	2.46	0.170	0.822	3.6.5.2	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.69	1r4aA	0.785	1.30	0.309	0.822	1.42	GNP	complex1.pdb.gz	33,34,35,36,37,38,61,64,84,85,139,140,142,143,175,176,177
2	0.20	2zjyA	0.767	2.21	0.175	0.868	0.99	ALF	complex2.pdb.gz	31,32,33,36,64,83,84,85,86
3	0.06	1ksh0	0.781	1.27	0.261	0.817	1.21	III	complex3.pdb.gz	65,66,67,68,69,70,71,79,81,90,93,94
4	0.04	1y3aB	0.723	2.58	0.170	0.838	1.12	III	complex4.pdb.gz	83,84,95,118,119,122,123,126
5	0.04	2ik80	0.764	2.30	0.175	0.868	0.86	III	complex5.pdb.gz	63,64,65,66,67,68,86,87,89,90,93
6	0.04	1gitA	0.756	2.33	0.165	0.863	0.84	PO4	complex6.pdb.gz	32,36,63,64,86
7	0.04	1gg22	0.760	2.99	0.152	0.904	0.80	III	complex7.pdb.gz	65,66,67,69,81,89,94,95,96,128

	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.