D-I-TASSER O43684-D1

D-I-TASSER results for O43684-D1

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

Input Sequence in FASTA format

>O43684 (166 residues)
MTGSNEFKLNQPPEDGKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFK
CHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASL
AFSNDGTTLAIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKSPCT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTGSNEFKLNQPPEDGKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKSPCT
Prediction	CCCCCCSSSCCCCCCCCCCSSSSSSSCCCCSSSSSSCCCCSSSSSCCCCCCCCSSSSSCCCCCSSCCCCCCSSSSSSSSSCCCCCSSSSSCCCCSSSSSSCCCCCSSSSCCCCCCCSSSSSSCCCCCSSSSSSCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCC
Confidence	9887631202377788643589999159997999975993899983688886267223335813115875101068999869999799981899599986899928986179999788999989999999996764135765578980899976864457899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTGSNEFKLNQPPEDGKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKSPCT
Prediction	8564552443444563421020000024330000002213000210243644333213361342345444332002002013633200001323201001274453234066174312000104514200000011123244734642010130557514546678
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSSCCCCCCCCCCSSSSSSSCCCCSSSSSSCCCCSSSSSCCCCCCCCSSSSSCCCCCSSCCCCCCSSSSSSSSSCCCCCSSSSSCCCCSSSSSSCCCCCSSSSCCCCCCCSSSSSSCCCCCSSSSSSCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCC
MTGSNEFKLNQPPEDGKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKSPCT

5wlcLN

0.14

0.12

4.12

1.33

DEthreader

RNYVLEHDTILMR--QEARVLTLAWK-KDDFVIGGCSDGRIRIWSAQKNDEMGRLLHTMKVDKAKK----ESTLVWSVIYLPRTDQIASGDSTGSIKFWDFQFATLNQSFKAHDADVLCLTTDTDNNYVFSAGVD-----------RKIFQFSQNTKSQKNN----

5mzhA2

0.15

0.13

4.43

1.55

SPARKS-K

------FTLFKVLRAHILPLTNCAFNKSGDRFITGSYDRTCKVWNT----FTGEEVFTLEGHKN---------VVYAIAFNPYGDKIVTGSFDKTCKLWDAYTGQLYYTLKGHQTEIVCLSFNPQSTIIATGSMDLWDVETGQEHTD-----EIFSCAFNYEGDFI

1fwxA1

0.12

0.10

3.37

0.42

MapAlign

----------------NGDLHHVHMSFTGRFLFMNDKATRVARVRC----DVMKCDAILEIA----------KGIHGLRPQKWSNYVFCNGEVNVFTAVDADKWEVAWQVL-VSGNLDNCDADYEGKWAFSTSNSEKGMTLPEMAMDHIVVFNIAEIEK-------

5nnzB

0.12

0.10

3.62

0.28

CEthreader

VWDADTGRKVNILIGHCAEISSASFNWDCSLILTGSMDKTCKLWDATN----GKCVATLTGHD---------DEILDSCFDYTGKLIATASADGTARIFSAATRKCIAKLEGHEGEISKISFNPQGNHLLTGSSD-----------KTARIWDAQTGQCLQVLEGH

5xyig1

0.13

0.11

3.77

1.39

MUSTER

----AHFAPRATFVGHNAAIESIEIDNEHNYLVSASRDKSALVWKLNRTQEQW--------ATPFTRLIGHNHFVSDVSLSRDASHLLTSSWDSTLRLWDLSTRTTKKLFLGHKKDVLGVTFSPCNRRIISVGRDQVKIWNI-LGENKAELQ--------------

3dm0A

0.12

4.23

0.64

HHsearch

TKDDAYGVAQRRLTGHSHFVEDVVLSSDGQFALSGSWDGELRLWDLAA----GVSTRRFVGHTKDVTIEGHRDWVSCVRFSPNTLTIVSASWDKTVKVWNLSNCKLRSTLAGHTGYVSTVAVSPDGSLCASGGKDLWDLAEGKKLYSLEANSVIHALCFSPNRYWL

4lg8A2

0.18

0.14

4.51

1.47

FFAS-3D

--------------AHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGR----VLTKVTDE-------TSGCSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSVKLWDLRKLKNFKTLQ--------------

3mmyA

0.31

0.30

8.92

0.48

EigenThreader

SSNPMERGENQPESPLKHQHRCVAIFKKQNKFALGSIEGRVAIHYINPPNPAKDN-FTFKCHSNSAPQ--DIYAVNGIAFHPVHGTLATVGSDGRFSFWDKDAR-TKLKTSQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNKKNYIFLRNAA---EELKPR-

4nsxA

0.18

0.15

4.91

1.97

CNFpred

--------LRKKYKLHKRAVTGISLDGMNRKMVSCGLDGIVGFYDFNK----STLLGKLKL----------DAPITAMVYHRSSDLFALALDDLSIVVIDAVTQRVVRQLWGHSNRITAFDFSPEGRWIVSASIRTWDLPT----GGCIDGIIVTNVKFSPNGDLL

3mmyA

0.37

0.33

9.84

1.17

DEthreader

TVLQPSEFRRIESP-LKHQHRCVAIFKNPTGFALGSIEGRVAIHYINPP--PAKDNFTFKCHRS-NSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSY---------KKNYIFLRNAA-EELKPR----

(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	0.7924

(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 AttentionPotential, 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	3mmyA	0.75	2.88	0.335	0.879	model1_3mmyA.pdb.gz
2	6f3tA	0.74	2.05	0.197	0.825	model1_6f3tA.pdb.gz
3	4ozuA	0.74	3.40	0.123	0.898	model1_4ozuA.pdb.gz
4	2eceA	0.74	2.55	0.085	0.874	model1_2eceA.pdb.gz
5	1vyhT	0.72	2.03	0.099	0.789	model1_1vyhT.pdb.gz
6	2h9lA	0.72	2.23	0.162	0.789	model1_2h9lA.pdb.gz
7	1u2vC	0.71	2.65	0.118	0.831	model1_1u2vC.pdb.gz
8	2ymuA1	0.70	2.09	0.186	0.771	model1_2ymuA1.pdb.gz
9	1erjC	0.69	1.91	0.142	0.753	model1_1erjC.pdb.gz
10	1pevA	0.68	3.08	0.111	0.831	model1_1pevA.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:0043130	0.87	ubiquitin binding
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound 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	0.99	cellular process
GO:0065007	0.73	biological regulation
GO:0050794	0.71	regulation of cellular process
GO:0022402	0.66	cell cycle process
GO:1903047	0.63	mitotic cell cycle process
GO:0048519	0.62	negative regulation of biological process
GO:0048523	0.61	negative regulation of cellular process
GO:0010564	0.61	regulation of cell cycle process
GO:0000075	0.60	cell cycle checkpoint
GO:1901987	0.59	regulation of cell cycle phase transition
GO:0045786	0.59	negative regulation of cell cycle
GO:1901988	0.58	negative regulation of cell cycle phase transition
GO:0071173	0.58	spindle assembly checkpoint
GO:0051983	0.58	regulation of chromosome segregation
GO:0051128	0.58	regulation of cellular component organization
GO:0007346	0.58	regulation of mitotic cell cycle
GO:1901990	0.57	regulation of mitotic cell cycle phase transition
GO:0051129	0.57	negative regulation of cellular component organization
GO:0010965	0.57	regulation of mitotic sister chromatid separation
GO:0007093	0.57	mitotic cell cycle checkpoint
GO:0007094	0.56	mitotic spindle assembly checkpoint
GO:0016043	0.51	cellular component organization
GO:0044699	0.50	single-organism process

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:0044446	0.98	intracellular organelle part
GO:0044428	0.95	nuclear part
GO:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0032991	0.79	macromolecular complex
GO:0043234	0.76	protein complex
GO:0043232	0.66	intracellular non-membrane-bounded organelle
GO:0044427	0.62	chromosomal part
GO:0000776	0.60	kinetochore
GO:1990298	0.54	bub1-bub3 complex
GO:0033597	0.54	mitotic checkpoint complex

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	1s0kA	0.648	3.58	0.078	0.885	3.2.1.18	NA
2	0.060	2gbcA	0.620	3.60	0.098	0.861	3.4.14.5 3.4.15.5	NA
3	0.060	1kv9A	0.637	3.33	0.109	0.813	1.1.99.-	NA
4	0.060	1yiqA	0.667	3.37	0.075	0.855	1.1.99.-	NA
5	0.060	1orvA	0.625	3.52	0.085	0.861	3.4.14.5	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	0.08	2xl3B	0.716	2.24	0.162	0.789	0.60	III	complex1.pdb.gz	74,92,118,134
2	0.07	3smrA	0.718	2.36	0.162	0.795	0.46	NP7	complex2.pdb.gz	76,77,92,117,118,119
3	0.05	2i3s0	0.710	2.82	0.318	0.837	0.47	III	complex3.pdb.gz	18,19,21,37,38,40,63,69,70,71,72,73,74
4	0.03	1qniA	0.719	2.68	0.095	0.843	0.63	CUA	complex4.pdb.gz	90,96,111,114
5	0.02	3sbpB	0.715	2.70	0.081	0.843	0.65	CUA	complex5.pdb.gz	78,87,90,97

	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.