D-I-TASSER P36888-D2

D-I-TASSER results for P36888-D2

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

Input Sequence in FASTA format

>P36888 (162 residues)
VDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMTETQAGEYL
LFIQSEATNYTILFTVSIRNTLLYTLRRPYFRKMENQDALVCISESVPEPIVEWVLCDSQ
GESCKEESPAVVKKEEKVLHELFGTDIRCCARNELGRECTRL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMTETQAGEYLLFIQSEATNYTILFTVSIRNTLLYTLRRPYFRKMENQDALVCISESVPEPIVEWVLCDSQGESCKEESPAVVKKEEKVLHELFGTDIRCCARNELGRECTRL
Prediction	CCCCCCSSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSCCCSSSSSSSCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSCCCSSSSCCCSSSSCCCCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCC
Confidence	987752899999967999759999899524776531352265799999137855575899999938984899999999369779842541776178429999998516987999978996655566676531214899851169825999892224232359
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMTETQAGEYLLFIQSEATNYTILFTVSIRNTLLYTLRRPYFRKMENQDALVCISESVPEPIVEWVLCDSQGESCKEESPAVVKKEEKVLHELFGTDIRCCARNELGRECTRL
Prediction	673445140303042344021202246551545442535442303030450456331401020306444331303030443132224453244466532030304432414030131753463156644444554433344435330302031632451477
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSCCCSSSSSSSCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSCCCSSSSCCCSSSSCCCCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCC
VDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMTETQAGEYLLFIQSEATNYTILFTVSIRNTLLYTLRRPYFRKMENQDALVCISESVPEPIVEWVLCDSQGESCKEESPAVVKKEEKVLHELFGTDIRCCARNELGRECTRL

5o5gA

0.13

0.12

4.28

1.33

DEthreader

VTVDDSAEFKCEARGDPVPTVRWRKDDGELPKSRYEIRDD---HTLKIRKVTAGDMGSYTCVAENMVGKAEASATLTVQEPP-H-FVVKPRDQVVRTVTFQCEATGNPQPAIFWRREGS--QNLLSSFSVSQT--GDLTITVDVGYYICQTLNVAGSIITKA

6fwxB

0.12

4.17

1.36

SPARKS-K

VRQGSQVRLQVRVTGIPTPVVKFYRDGAEIQSSLDFQISQGDLYSLLIAEAYPEDSGTYSVNATNSVGRATSTAELLVQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVIGDSSPGVQISFSDGRAKLTIANSGRYSLKATNGSGQATSTA

4liqE

0.16

0.15

5.12

0.39

MapAlign

VTVGEGLNLKVMVEAYPGLGFNWTYLGHQP---EKLANAYRHTFTLSLPRLKPSEAGRYSFLARNPGGWRALTFELTLRYPPEVSV---IWTFINGSGTLLCAASGYPQPNVTWLQCCDEAQVLQ--VWDDPVTVQSLLTVEHNQTYECRAHNSVGSGSWAF

4liqE

0.17

5.48

0.39

CEthreader

VTVGEGLNLKVMVEAYPGLGFNWTYLGPFSDHQPEKLANATHTFTLSLPRLKPSEAGRYSFLARNPGGWRALTFELTLRYPPEVSVIW---TFINGSGTLLCAASGYPQPNVTWLQCSGHTDRCVLQVWDDPYKVTVQSLLTHNQTYECRAHNSVGSGSWAF

3b43A

0.16

5.33

1.16

MUSTER

LALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLENTATLTVLKVTKGDAGQYTCYASNVAGKDSCSAQLGVQEPFIKKLEPSRIVKQDEHTRYECKIGGSPEIKVLWYKDETEIQESSKFRMSFVESVMYNLSVEDSGDYTCEAHNAAGSASSST

3p3yA

0.15

4.99

0.53

HHsearch

VLRGMDLLLECIASGVPTPDIAWYKKGGDLPSDKAKF--ENFNKALRITNVSEEDSGEYFCLASNKMGSIRHTISVRVAAPYWLDEPKNLILAPGEDGRLVCRANGNPKPTVQWMVNGEPLQSAPPNPNREVAGDTIIFQISSRAVYQCNTSNEHGYLLANA

2va4A

0.11

3.99

1.98

FFAS-3D

AERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSN-TELTVRNIINSDGGPYVCRATNKAGEDEKQAFLQVFVQPHIIQLKNETTYENGQVTLVCDAEGEPIPEITWKRAVDGFTFTEGDKSGSSSLHIKDVKLSDSGRYDCEAASRIGGHQKSM

3lcyA

0.09

3.48

0.60

EigenThreader

TKLGEAAQLSCQIVGRPLPDIKWYRFGELIQSRKYKMSSDGRTHTLTVMTEEQEDEGVYTCIATNEVGEVETSSKLLLQATPQHPGYPLKYGAVGSTLRLHVMYIGRPVPAMTWFHGQ---KLQNSENIIENTEHYTHLVMKHAGKYKVQLSNVFGTVDAIL

2rikA

0.14

4.66

2.35

CNFpred

VKQDEHTRYECKIGGSPEIKVLWYKDETEIQESSKFRMSFESVAVLEMYNLSVEDSGDYTCEAHNAAGSASSSTSLKVKEPVFRKKPHPVETLKGADVHLECELQGTPPFQVSWHKDKRELRS-GKKYKIMSENFLTSIHILDIGEYQCKASNDVGSYTCVG

3jz7A

0.13

0.12

4.30

1.17

DEthreader

KAKGETAYLPCKFTLSPDLDIEWLISVQVIILDVHFTSDVSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKFLLTVLVKPSG-T-RCFVDSEENDFKLKCEPKEGSLPLQFEWQKLSDSQTMPTLAEMTS---PVISVAEYSGTYSCTVQNRVGSDQCML

(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	0.8486

(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	3b43A	0.85	2.20	0.176	0.982	model1_3b43A.pdb.gz
2	2jllA	0.84	2.13	0.139	0.975	model1_2jllA.pdb.gz
3	2va4A	0.83	2.29	0.121	0.969	model1_2va4A.pdb.gz
4	6nrrB	0.82	2.22	0.149	0.951	model1_6nrrB.pdb.gz
5	6eg0B	0.81	2.34	0.162	0.951	model1_6eg0B.pdb.gz
6	2e9wB	0.80	2.25	0.164	0.938	model1_2e9wB.pdb.gz
7	5t89X	0.80	2.71	0.153	0.969	model1_5t89X.pdb.gz
8	2wngA	0.80	2.67	0.122	0.963	model1_2wngA.pdb.gz
9	4liqE	0.79	2.78	0.159	0.944	model1_4liqE.pdb.gz
10	4bsjA	0.79	2.64	0.162	0.951	model1_4bsjA.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:0003824	0.79	catalytic activity
GO:0016740	0.76	transferase activity
GO:0004888	0.75	transmembrane signaling receptor activity
GO:0004672	0.75	protein kinase activity
GO:0004713	0.74	protein tyrosine kinase activity
GO:0004896	0.61	cytokine receptor 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	1.00	single-organism process
GO:0009987	1.00	cellular process
GO:0048856	0.94	anatomical structure development
GO:0044767	0.94	single-organism developmental process
GO:0050896	0.93	response to stimulus
GO:0071310	0.92	cellular response to organic substance
GO:0048513	0.86	animal organ development
GO:0065007	0.80	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0044763	0.79	single-organism cellular process
GO:0008152	0.79	metabolic process
GO:0071704	0.78	organic substance metabolic process
GO:0050794	0.78	regulation of cellular process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0043170	0.77	macromolecule metabolic process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0080090	0.72	regulation of primary metabolic process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0048518	0.72	positive regulation of biological process
GO:0031323	0.72	regulation of cellular metabolic process
GO:0007165	0.72	signal transduction
GO:0048522	0.71	positive regulation of cellular process
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0006464	0.70	cellular protein modification process
GO:0001932	0.70	regulation of protein phosphorylation
GO:0065008	0.69	regulation of biological quality
GO:0042127	0.69	regulation of cell proliferation
GO:0034097	0.69	response to cytokine
GO:0007166	0.69	cell surface receptor signaling pathway
GO:0006468	0.69	protein phosphorylation
GO:0002521	0.69	leukocyte differentiation
GO:0001934	0.69	positive regulation of protein phosphorylation
GO:0071345	0.68	cellular response to cytokine stimulus
GO:0046777	0.68	protein autophosphorylation
GO:0030097	0.62	hemopoiesis
GO:0019221	0.62	cytokine-mediated signaling pathway
GO:0008283	0.62	cell proliferation
GO:0002376	0.58	immune system process
GO:0045321	0.57	leukocyte activation
GO:0042592	0.57	homeostatic process
GO:0097028	0.56	dendritic cell differentiation
GO:0046651	0.56	lymphocyte proliferation
GO:0035726	0.56	common myeloid progenitor cell proliferation
GO:0030183	0.56	B cell differentiation
GO:0002328	0.56	pro-B cell differentiation
GO:0002318	0.56	myeloid progenitor cell differentiation
GO:0001776	0.56	leukocyte homeostasis

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	0.76	intracellular part
GO:0016020	0.71	membrane
GO:0044425	0.69	membrane part
GO:0005886	0.69	plasma membrane
GO:0044459	0.68	plasma membrane part
GO:0043226	0.54	organelle
GO:0043229	0.52	intracellular organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.50	intracellular membrane-bounded 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	0.068	1u2hA	0.470	1.18	0.138	0.494	2.7.11.1	NA
2	0.067	1cvsC	0.678	3.30	0.081	0.883	2.7.10.1	23
3	0.067	1ry7B	0.694	3.34	0.093	0.889	2.7.10.1	1,26,47,75
4	0.066	2wwmD	0.474	1.00	0.150	0.494	2.7.11.1	NA
5	0.060	1wd8A	0.452	5.73	0.063	0.864	3.5.3.15	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	0.03	2vraA	0.747	2.86	0.151	0.938	0.30	UUU	complex1.pdb.gz	17,19,20,21
2	0.03	1ry71	0.694	3.34	0.093	0.889	0.36	III	complex2.pdb.gz	103,104,105,106,109,110,111,136,137,153,157
3	0.03	2iep0	0.733	3.02	0.137	0.944	0.26	III	complex3.pdb.gz	9,11,13,15,42
4	0.03	2j8o0	0.695	3.38	0.132	0.926	0.30	III	complex4.pdb.gz	1,2,10,40,43,45,152,154,155,156
5	0.02	2ch80	0.624	3.95	0.135	0.883	0.24	III	complex5.pdb.gz	76,78,79,83,84,85,86,155,156,157,158,159,160
6	0.02	2o264	0.654	3.62	0.078	0.944	0.12	III	complex6.pdb.gz	56,57,75,77,79
7	0.02	1n26A	0.551	4.26	0.137	0.852	0.11	UUU	complex7.pdb.gz	17,20,39
8	0.01	1ncg0	0.362	3.23	0.013	0.469	0.29	III	complex8.pdb.gz	11,12,16,63,64,66,69
9	0.01	1bqu0	0.472	4.26	0.035	0.728	0.21	III	complex9.pdb.gz	58,76,109
10	0.01	1pvh0	0.478	4.29	0.043	0.735	0.32	III	complex10.pdb.gz	61,62,64,69

	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.