D-I-TASSER results for P05556-D2

Input Sequence in FASTA format

>P05556 (158 residues)
RGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAESANS
SNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEV
QFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC

Predicted Secondary Structure

                  20                  40                  60                  80                 100                 120                 140
                   |                   |                   |                   |                   |                   |                   |
Sequence
RGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAESANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
Prediction
CCCSSSSCCCCCCCCCHHHHHHHHHHCCCSSSSSHHHHHHHHHHHHHCCCCSSSSCCCCCHHHHHHHHHHHHHHHSSSSSSCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCSCCCCSSSSSSSSSSSCCCCCCCSSSSSSSCCCCSSSSSSSSSCC
Confidence
98458851666778777899986450383566531456887542764587246770566336999999999986168999728999837999999859997444445761156138938999999999238899964999995246527999999559

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140
                   |                   |                   |                   |                   |                   |                   |
Sequence
RGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAESANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
Prediction
84444245357153433432541476523423246323502551363144332441374153014104610550364040425542740403130304645546446454056143564040403030451367454403020331434030404457

Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

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                    |                   |                   |                   |                   |                   |                   |
							SS	CCCSSSSCCCCCCCCCHHHHHHHHHHCCCSSSSSHHHHHHHHHHHHHCCCCSSSSCCCCCHHHHHHHHHHHHHHHSSSSSSCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCSCCCCSSSSSSSSSSSCCCCCCCSSSSSSSCCCCSSSSSSSSSCC
							Seq	RGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAESANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
1	3fcsB	0.23	0.18	5.75	1.00	DEthreader		-------LMDLM-DLWS-------------VFTTTIPSLGL---TEKLNLIFA-LSSN---LQ-LIVDAYGKIRSK-VELEVRDLPEELSLSFNATCLNNEVIP-GL-KSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDC
2	4g1eB1	0.31	0.28	8.62	2.59	SPARKS-K		VSEARVLEDRPLSDKGSG-----DSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDN----VLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPG--LKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDC
3	3vi3B	0.99	0.99	27.66	0.89	MapAlign		RGSKDIKKNKNVTNRSKGTAEKLKPEDIHQIQPQQLVLRLRSGEPQTFTLKFKRALSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
4	4g1eB1	0.31	0.28	8.62	1.02	CEthreader		VSEARVLEDRPLSD-----KGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVED----NVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPGL--KSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDC
5	3vi3B	0.69	0.68	19.27	1.78	MUSTER		NN--MYTMSHYYDYPSAHLVQKLSENNIQTIFVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
6	3k6sB	0.29	0.28	8.49	3.32	HHsearch		LYKRSNEFDYPS---VGQLAHKLAENNIQPIFATSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQ--EQSFVIRALGFTDIVTVQVLPQC
7	4g1eB1	0.30	0.28	8.44	1.96	FFAS-3D		-SEARVLEDRPLSDKGSG-----DSSQVTQVSPQRIALRLRPDDSKNFSIQVR----QVEDNVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEV--IPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDC
8	3v4pB1	0.38	0.35	10.50	0.95	EigenThreader		RGQQEVLQDQPLSQG-------ARGEGATQLAPQRVRVTLRPGEPQQLQVRFLRAEGYPV---VQLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEEGKAEDRGQCNHVRINQTVTFWVSLQATHCLPEP-HLLRLRALGFSEELIVELHTLC
9	4wjkB	0.75	0.67	19.01	2.71	CNFpred		-----------------HLVQKLSENNIQTIFAVTEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC
10	3vi3B	0.58	0.46	13.09	1.00	DEthreader		-------YLMD---MKDD--N-------L-LVFSFYPSIAH---VQSIQTIFA--------VIQLIIDAYNSLSSE-VILENGKLSEGVTISYKSYCKNGVNGT-GENGRKCSNISIDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYIC


(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

Rank^a	Estimated TM-score^b
1	0.747


(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.
1	3vi3B	0.85	2.48	0.865	0.975
2	4g1eB	0.85	2.47	0.272	0.956
3	4um8B	0.84	2.27	0.307	0.937
4	3v4pB	0.82	2.27	0.347	0.937
5	6bxbA	0.82	2.58	0.252	0.930
6	3k6sB	0.76	2.53	0.310	0.886
7	2jksA	0.46	3.91	0.102	0.658
8	1olzA	0.44	3.92	0.064	0.614
9	2ygqA	0.44	4.81	0.056	0.715
10	2e26A1	0.40	5.22	0.052	0.709



(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:0046983	0.60	protein dimerization activity
GO:0046982	0.54	protein heterodimerization activity
GO:0019960	0.52	C-X3-C chemokine binding






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0044699	0.97	single-organism process
GO:0044763	0.95	single-organism cellular process
GO:0065007	0.83	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.81	regulation of cellular process
GO:0050896	0.65	response to stimulus
GO:0032879	0.65	regulation of localization
GO:0016043	0.65	cellular component organization
GO:1902578	0.63	single-organism localization
GO:0048518	0.63	positive regulation of biological process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0071495	0.60	cellular response to endogenous stimulus
GO:0071310	0.60	cellular response to organic substance
GO:0071704	0.59	organic substance metabolic process
GO:0048522	0.59	positive regulation of cellular process
GO:0044765	0.59	single-organism transport
GO:0044710	0.59	single-organism metabolic process
GO:0016192	0.59	vesicle-mediated transport
GO:0071402	0.58	cellular response to lipoprotein particle stimulus
GO:0055098	0.58	response to low-density lipoprotein particle
GO:0043170	0.58	macromolecule metabolic process
GO:0006898	0.58	receptor-mediated endocytosis
GO:0051128	0.56	regulation of cellular component organization
GO:0051239	0.54	regulation of multicellular organismal process
GO:0007155	0.54	cell adhesion
GO:0051130	0.53	positive regulation of cellular component organization
GO:0044237	0.52	cellular metabolic process
GO:0007229	0.52	integrin-mediated signaling pathway
GO:0071404	0.51	cellular response to low-density lipoprotein particle stimulus
GO:0031623	0.51	receptor internalization






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044464	0.93	cell part
GO:0016020	0.88	membrane
GO:0044459	0.87	plasma membrane part
GO:0005886	0.63	plasma membrane
GO:0098590	0.56	plasma membrane region
GO:0044421	0.52	extracellular region part
GO:0043235	0.51	receptor complex
GO:0043226	0.51	organelle
GO:0031253	0.51	cell projection membrane
GO:0008305	0.50	integrin complex






(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:

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	0.066	2nqdA	0.472	3.02	0.125	0.595	3.4.22.15	81
2	0.060	2biiA	0.485	4.44	0.023	0.772	1.7.1.3	147
3	0.060	2dewX	0.540	3.78	0.052	0.778	3.5.3.15	NA
4	0.060	1f13A	0.484	3.72	0.066	0.677	2.3.2.13	NA
5	0.060	1kyaA	0.503	3.87	0.078	0.722	1.10.3.2	NA



(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	Predicted binding site residues
1	0.05	2vc2B	0.810	2.39	0.260	0.918	0.52	180	13,14,15,30,54,117,119



(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.

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.