D-I-TASSER Q2I0M4-D1

D-I-TASSER results for Q2I0M4-D1

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

Input Sequence in FASTA format

>Q2I0M4 (334 residues)
MRGPSWSRPRPLLLLLLLLSPWPVWAQVSATASPSGSLGAPDCPEVCTCVPGGLASCSAL
SLPAVPPGLSLRLRALLLDHNRVRALPPGAFAGAGALQRLDLRENGLHSVHVRAFWGLGA
LQLLDLSANQLEALAPGTFAPLRALRNLSLAGNRLARLEPAALGALPLLRSLSLQDNELA
ALAPGLLGRLPALDALHLRGNPWGCGCALRPLCAWLRRHPLPASEAETVLCVWPGRLTLS
PLTAFSDAAFSHCAQPLALRDLAVVYTLGPASFLVSLASCLALGSGLTACRARRRRLRTA
ALRPPRPPDPNPDPDPHGCASPADPGSPAAAAQA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MRGPSWSRPRPLLLLLLLLSPWPVWAQVSATASPSGSLGAPDCPEVCTCVPGGLASCSALSLPAVPPGLSLRLRALLLDHNRVRALPPGAFAGAGALQRLDLRENGLHSVHVRAFWGLGALQLLDLSANQLEALAPGTFAPLRALRNLSLAGNRLARLEPAALGALPLLRSLSLQDNELAALAPGLLGRLPALDALHLRGNPWGCGCALRPLCAWLRRHPLPASEAETVLCVWPGRLTLSPLTAFSDAAFSHCAQPLALRDLAVVYTLGPASFLVSLASCLALGSGLTACRARRRRLRTAALRPPRPPDPNPDPDPHGCASPADPGSPAAAAQA
Prediction	CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSCCCCCSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCSCCCCCCCCCCCCCSSSCCCCCCCSCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCSSCCHHHCCCCCCCSSSCCCCCCCCCCHHHHCCCCCCCSSSCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCSSCCCHHHCCCSSSSCCHHHHCCCCCCCCCCCCCCCCCCCCCCSSSCCHHHCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9988766530578888998888998878875177666566789997565897989847999986899999987699879996873382325688889899898997974381232086469887899993873492203898668876677998964470131788789887778999872583563578889899837998678666189999999837777887552747972326965115598885269997623455531235663055424011024665324541247523566666777888886567666687779997663679
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MRGPSWSRPRPLLLLLLLLSPWPVWAQVSATASPSGSLGAPDCPEVCTCVPGGLASCSALSLPAVPPGLSLRLRALLLDHNRVRALPPGAFAGAGALQRLDLRENGLHSVHVRAFWGLGALQLLDLSANQLEALAPGTFAPLRALRNLSLAGNRLARLEPAALGALPLLRSLSLQDNELAALAPGLLGRLPALDALHLRGNPWGCGCALRPLCAWLRRHPLPASEAETVLCVWPGRLTLSPLTAFSDAAFSHCAQPLALRDLAVVYTLGPASFLVSLASCLALGSGLTACRARRRRLRTAALRPPRPPDPNPDPDPHGCASPADPGSPAAAAQA
Prediction	7544525301000000001201000021010133333443440044130576330212444033106603540340205503034035510550440320105503034036402530440344247403043035410550430340205603043036500560540330304402034025300550430320304601030202022014004525252452630303315504734045035720540453341442432332221211122021212222012022444504323342343347645343423344444533523468
	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                 180                 200                 220                 240                 260                 280                 300                 320

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

SS
Seq

CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSCCCCCSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCCSCCCCCCCCCCCCCSSSCCCCCCCSCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCSSCCHHHCCCCCCCSSSCCCCCCCCCCHHHHCCCCCCCSSSCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCSSCCCHHHCCCSSSSCCHHHHCCCCCCCCCCCCCCCCCCCCCCSSSCCHHHCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MRGPSWSRPRPLLLLLLLLSPWPVWAQVSATASPSGSLGAPDCPEVCTCVPGGLASCSALSLPAVPPGLSLRLRALLLDHNRVRALPPGAFAGAGALQRLDLRENGLHSVHVRAFWGLGALQLLDLSANQLEALAPGTFAPLRALRNLSLAGNRLARLEPAALGALPLLRSLSLQDNELAALAPGLLGRLPALDALHLRGNPWGCGCALRPLCAWLRRHPLPASEAETVLCVWPGRLTLSPLTAFSDAAFSHCAQPLALRDLAVVYTLGPASFLVSLASCLALGSGLTACRARRRRLRTAALRPPRPPDPNPDPDPHGCASPADPGSPAAAAQA

4u7lA

0.22

0.16

5.12

1.00

DEthreader

-PSRCCGGLNSVYLNSLFVLDKELLTLTQLSLEV-GLSKMHLHLLEVSLLALHQLHLSNNSIARIHRGWCQKLHELVLSFNNLTRLDEESLAELSSLSVLRLSHNSISHIAEGAFKGLRSLRVLDLDHNEISGTTSGAFSGLDSLSKLTLFGNKIKSVAKRAFSGLEGLEHLNLGGNAIRSVQFDAFVKMKNLKELHISSDSFLCDCQLKWLPPWLIGRML-QAFV-TATCAHPESLKGQSIFSVPPESFV--CDD-F----------------------------------------------------------------------------

4r5dA

0.22

0.19

6.05

0.53

MapAlign

STPIKQIFPDDAFAETIKANLKKAVTQNELNSIDQIIANNSDIKALGGNTNLGWLNLSNNQLETLQGVFLTNLTTLNLSNNQLTSLPQGVFERLASLTTLNLSNNQLTSLPQGVFERLTNLTTLNLSNNQLTSLPQGVFERLTNLTTLNLSNNQLTSLPQGVFERLTSLTTLNLSNNQLTSLPDGVFERLTNLKTLNLSNNQLTKE-ACRAVANALKQASLHELHLSNNNIGEGAAELLSNCNLLHELHLSNNNIGEEGAAELVEALACREIARALAAELVEALKEACREIARAL---------------------------------------

3wo9A

0.30

0.20

5.99

2.50

SPARKS-K

----------------------------------HMACLAVGKDDICTCSNKETVDCSSKKLTAVPTGIPANTEKLQLDFNQLANIPAEAFHGLTRLTYLALDYNQLQSLPVGVFDQLNNLNELRLQDNQLTSLPPGVFDSLTKLTYLTLSQNQLQSIPAGVFDKLTNLNRLELSTNQLQSVPHGAFDSLVNLETLHLELNPWDCACSIIYLRTFIAKNTDKISGMESAQCN----GTSTAVKDVNTEKIKNVTC-------------------------------------------------------------------------------

5xnpA

0.24

0.20

6.35

0.96

HHsearch

------------------------------------PGDPQICPKRCVCQILLATLCAKKGLLFVPPNIDRRTVELRLADNFVTNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFSGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSMTRLSFGGNPLHCNCELLWLRRLSRE-------DDLETCASPPLLTGRYFWSIPEEEFL-CEPPLITRHHEMRVLEGQR----ATLRCKARGDP-EPAI-HWISPEGKATRSLYDNTTVKDTGAFTCIASNPAGEATQIVDL

2v9tB

0.32

0.20

6.04

0.34

CEthreader

--------------------------------------GSLHCPAACTCSN-NIVDCRGKGLTEIPTNLPETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHLAQNPFICDCHLKWLADYLHTNPI---ETSGARCTSPRRLANKRIGQIKSKKFRC----------------------------------------------------------------------------------

4r5dA

0.21

0.19

6.20

0.88

EigenThreader

-ATITVSTPIKQIFAFAETIKANLKNELNSIKSVQGIQYLPNVRALKELTNLGWLNLSNNQLETLVFEKLTNLTTLNLSNNQLTSLPQGVFERLASLTTLNLSNNQLTSLPQGVFERLTNLTTLNLSNNQLTSLPQGVFERLTNLTTLNLSNNQLTSLPQGVFERLTSLTTLNLSNNQLTSLPDGVFERLTNLKTLNLSNNQLTKEA-CRAVANALKQAA--SLHLSNNN--------IGEEGAAELVEALLSNCNLTKEACREIARALKQAEEGAAELVEALLEACREIARALK------QATTLHSNNNIGHPGSTLESNCNLTKEACREIA

2v9tB

0.32

0.20

6.13

1.64

MUSTER

--------------------------------------GSLHCPAACTCSN-NIVDCRGKGLTEIPTNLPETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHLAQNPFICDCHLKWLADYLHTNPI---ETSGARCTSPRRLANKRIGQIKSKKFR-C---------------------------------------------------------------------------------

2v9tB

0.32

0.20

6.04

1.98

FFAS-3D

--------------------------------------GSLHCPAACTCSN-NIVDCRGKGLTEIPTNLPETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHLAQNPFICDCHLKWLADYLHTNPIET---SGARCTSPRRLANKRIGQIKSKKF-RC---------------------------------------------------------------------------------

2v9sA

0.32

0.19

5.87

2.99

CNFpred

------------------------------------------CPAACTCSN-NIVDCRGKGLTEIPTNLPETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINMLRVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHLAQNPFICDCHLKWLADYLHTNPIE---TSGARCTSPRRLANKRIGQIKSKKFR-----------------------------------------------------------------------------------

2a0zA

0.21

0.16

5.03

1.00

DEthreader

-LGPQLSTLNNLLENLNLKLNMLYLSHILLEVLGLENIFEI-LYLQLSFVSLQRLMLRVALKNVDSSPFLRNLTILDLSNNNIANINDDMLEGLEKLEILDLQHNNLALWPIYFLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQKNLITSVEKKVFGPARNLTELDMRFNPFDCTCESAWFVNWINETHTNIPELSHYLCNTPPHYHGFPVRLFDTS-SC-----------------------------------------------------------------------------------

(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	0.7077

(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	1p8tA	0.65	3.04	0.296	0.719	model1_1p8tA.pdb.gz
2	3rfjA	0.64	3.10	0.251	0.728	model1_3rfjA.pdb.gz
3	4p8sA	0.64	3.12	0.287	0.716	model1_4p8sA.pdb.gz
4	4r5dA	0.64	4.26	0.178	0.790	model1_4r5dA.pdb.gz
5	2o6qA	0.63	3.31	0.236	0.719	model1_2o6qA.pdb.gz
6	5a5cA	0.63	3.36	0.232	0.722	model1_5a5cA.pdb.gz
7	5z8xA	0.63	3.74	0.215	0.734	model1_5z8xA.pdb.gz
8	4u7lA	0.63	4.48	0.187	0.787	model1_4u7lA.pdb.gz
9	4v2cA	0.63	3.59	0.231	0.722	model1_4v2cA.pdb.gz
10	6lbxA	0.63	3.32	0.232	0.713	model1_6lbxA.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	0.47	heterocyclic compound binding
GO:0097367	0.47	carbohydrate derivative binding
GO:0097159	0.47	organic cyclic compound binding
GO:0098772	0.45	molecular function regulator
GO:0030234	0.42	enzyme regulator activity
GO:0019887	0.41	protein kinase regulator activity
GO:0004857	0.41	enzyme inhibitor activity
GO:0004860	0.40	protein kinase inhibitor activity
GO:0000166	0.34	nucleotide binding
GO:0032555	0.33	purine ribonucleotide binding
GO:0032550	0.33	purine ribonucleoside binding
GO:0035639	0.31	purine ribonucleoside triphosphate 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	0.91	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0009987	0.84	cellular process
GO:0007165	0.83	signal transduction
GO:0044699	0.81	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0048583	0.72	regulation of response to stimulus
GO:0007166	0.71	cell surface receptor signaling pathway
GO:0048523	0.69	negative regulation of cellular process
GO:0031323	0.69	regulation of cellular metabolic process
GO:0080090	0.68	regulation of primary metabolic process
GO:0060255	0.68	regulation of macromolecule metabolic process
GO:0009966	0.68	regulation of signal transduction
GO:0065009	0.67	regulation of molecular function
GO:0051246	0.67	regulation of protein metabolic process
GO:1902531	0.66	regulation of intracellular signal transduction
GO:0050790	0.66	regulation of catalytic activity
GO:0031399	0.66	regulation of protein modification process
GO:0019220	0.66	regulation of phosphate metabolic process
GO:0009968	0.66	negative regulation of signal transduction
GO:0009892	0.66	negative regulation of metabolic process
GO:1902532	0.65	negative regulation of intracellular signal transduction
GO:0045936	0.65	negative regulation of phosphate metabolic process
GO:0045859	0.65	regulation of protein kinase activity
GO:0043086	0.65	negative regulation of catalytic activity
GO:0032269	0.65	negative regulation of cellular protein metabolic process
GO:0046426	0.64	negative regulation of JAK-STAT cascade
GO:0019221	0.64	cytokine-mediated signaling pathway
GO:0006469	0.64	negative regulation of protein kinase activity
GO:0008152	0.57	metabolic process
GO:0071704	0.55	organic substance metabolic process
GO:0051239	0.55	regulation of multicellular organismal process
GO:0050896	0.55	response to stimulus
GO:0051128	0.54	regulation of cellular component organization
GO:0044238	0.54	primary metabolic process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0045595	0.53	regulation of cell differentiation
GO:0051960	0.52	regulation of nervous system development
GO:0043170	0.52	macromolecule metabolic process
GO:0032502	0.52	developmental process
GO:0044767	0.51	single-organism developmental process
GO:0010975	0.51	regulation of neuron projection development
GO:0010769	0.51	regulation of cell morphogenesis involved in differentiation
GO:0080134	0.50	regulation of response to stress
GO:0050770	0.50	regulation of axonogenesis

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	0.97	cell part
GO:0044424	0.80	intracellular part
GO:0005737	0.42	cytoplasm
GO:0016020	0.41	membrane
GO:0044444	0.39	cytoplasmic part
GO:0044421	0.32	extracellular region part
GO:0043226	0.31	organelle

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	1dboA	0.466	5.46	0.039	0.689	4.2.2.19	NA
2	0.060	1jtaA	0.429	5.35	0.037	0.611	4.2.2.2	154
3	0.060	2ntqB	0.407	4.99	0.040	0.572	3.1.1.11	NA
4	0.060	1airA	0.429	5.52	0.053	0.629	4.2.2.2	NA
5	0.060	1pclA	0.438	5.07	0.041	0.617	4.2.2.2	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	0.10	2z7xB	0.582	3.53	0.181	0.683	0.87	UUU	complex1.pdb.gz	58,79,80,101,103,125,127
2	0.03	3a79B	0.594	3.61	0.183	0.695	0.88	UUU	complex2.pdb.gz	63,81,83,105,107
3	0.03	2z62A	0.536	4.20	0.176	0.668	0.85	UUU	complex3.pdb.gz	95,96,117,120

	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.