D-I-TASSER results for P35544

Summary of the Protein

Uniprot ID: P35544


Protein Name: Ubiquitin-like protein FUBI


Gene Name: FAU

Input Sequence in FASTA format

>P35544 (74 residues)
MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVE
ALTTLEVAGRMLGG

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

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Sequence
1	P35544-D1	1-74	74	MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.8644


(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	5b83A	0.94	1.22	0.351	1.000
2	6px3C	0.93	1.00	0.351	1.000
3	2w9nA2	0.93	0.59	0.352	0.960
4	7bbdB	0.93	1.18	0.338	1.000
5	2fazA	0.91	0.83	0.236	0.973
6	2kanA	0.90	1.45	0.203	1.000
7	1wx8A	0.90	1.26	0.230	1.000
8	1v5oA	0.89	1.28	0.149	1.000
9	1wy8A	0.88	1.20	0.270	1.000
10	1wh3A	0.88	1.27	0.203	1.000



(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:0003735	0.68	structural constituent of ribosome
GO:1901363	0.50	heterocyclic compound binding
GO:0097159	0.50	organic cyclic compound 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:0009987	0.98	cellular process
GO:0008152	0.96	metabolic process
GO:0044238	0.95	primary metabolic process
GO:0044237	0.95	cellular metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0019538	0.92	protein metabolic process
GO:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0044267	0.87	cellular protein metabolic process
GO:0007165	0.85	signal transduction
GO:0006464	0.85	cellular protein modification process
GO:0044699	0.83	single-organism process
GO:0007219	0.83	Notch signaling pathway
GO:0034641	0.82	cellular nitrogen compound metabolic process
GO:0032446	0.82	protein modification by small protein conjugation
GO:0016567	0.80	protein ubiquitination
GO:0006508	0.80	proteolysis
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0044249	0.79	cellular biosynthetic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0019941	0.79	modification-dependent protein catabolic process
GO:0016043	0.79	cellular component organization
GO:0009059	0.79	macromolecule biosynthetic process
GO:0006139	0.79	nucleobase-containing compound metabolic process
GO:0090304	0.78	nucleic acid metabolic process
GO:0050896	0.78	response to stimulus
GO:0044763	0.78	single-organism cellular process
GO:0044271	0.78	cellular nitrogen compound biosynthetic process
GO:0034645	0.78	cellular macromolecule biosynthetic process
GO:0006511	0.78	ubiquitin-dependent protein catabolic process
GO:0051179	0.77	localization
GO:0051234	0.76	establishment of localization
GO:0010468	0.76	regulation of gene expression
GO:0051252	0.75	regulation of RNA metabolic process
GO:0048519	0.75	negative regulation of biological process
GO:0034654	0.75	nucleobase-containing compound biosynthetic process
GO:2000112	0.74	regulation of cellular macromolecule biosynthetic process
GO:0048523	0.74	negative regulation of cellular process
GO:0048522	0.74	positive regulation of cellular process
GO:0043933	0.74	macromolecular complex subunit organization
GO:0032268	0.74	regulation of cellular protein metabolic process
GO:0022607	0.74	cellular component assembly
GO:0006950	0.74	response to stress
GO:0006810	0.74	transport
GO:0065008	0.73	regulation of biological quality
GO:0048583	0.73	regulation of response to stimulus
GO:0044710	0.73	single-organism metabolic process
GO:0034622	0.73	cellular macromolecular complex assembly
GO:0033554	0.73	cellular response to stress
GO:0031324	0.73	negative regulation of cellular metabolic process
GO:0010605	0.73	negative regulation of macromolecule metabolic process
GO:0006996	0.73	organelle organization
GO:0006355	0.73	regulation of transcription, DNA-templated
GO:0006259	0.73	DNA metabolic process
GO:1903050	0.72	regulation of proteolysis involved in cellular protein catabolic process
GO:0080134	0.72	regulation of response to stress
GO:0046907	0.72	intracellular transport
GO:0042981	0.72	regulation of apoptotic process
GO:0032270	0.72	positive regulation of cellular protein metabolic process
GO:0032269	0.72	negative regulation of cellular protein metabolic process
GO:0031399	0.72	regulation of protein modification process
GO:0022402	0.72	cell cycle process
GO:0016032	0.72	viral process
GO:0009966	0.72	regulation of signal transduction
GO:1903052	0.71	positive regulation of proteolysis involved in cellular protein catabolic process
GO:1902533	0.71	positive regulation of intracellular signal transduction
GO:0050790	0.71	regulation of catalytic activity
GO:0044765	0.71	single-organism transport
GO:0043161	0.71	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0035556	0.71	intracellular signal transduction
GO:0031400	0.71	negative regulation of protein modification process
GO:0031396	0.71	regulation of protein ubiquitination
GO:0019985	0.71	translesion synthesis
GO:0010629	0.71	negative regulation of gene expression
GO:0006357	0.71	regulation of transcription from RNA polymerase II promoter
GO:0002376	0.71	immune system process
GO:0001932	0.71	regulation of protein phosphorylation
GO:0000209	0.71	protein polyubiquitination
GO:2000026	0.70	regulation of multicellular organismal development
GO:1903047	0.70	mitotic cell cycle process
GO:0090090	0.70	negative regulation of canonical Wnt signaling pathway
GO:0072331	0.70	signal transduction by p53 class mediator
GO:0071158	0.70	positive regulation of cell cycle arrest
GO:0065004	0.70	protein-DNA complex assembly
GO:0055114	0.70	oxidation-reduction process
GO:0055085	0.70	transmembrane transport
GO:0051438	0.70	regulation of ubiquitin-protein transferase activity
GO:0051348	0.70	negative regulation of transferase activity
GO:0051276	0.70	chromosome organization
GO:0045944	0.70	positive regulation of transcription from RNA polymerase II promoter
GO:0045930	0.70	negative regulation of mitotic cell cycle
GO:0045088	0.70	regulation of innate immune response
GO:0043549	0.70	regulation of kinase activity
GO:0043408	0.70	regulation of MAPK cascade
GO:0043123	0.70	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043085	0.70	positive regulation of catalytic activity
GO:0043066	0.70	negative regulation of apoptotic process
GO:0032480	0.70	negative regulation of type I interferon production
GO:0031398	0.70	positive regulation of protein ubiquitination
GO:0031397	0.70	negative regulation of protein ubiquitination
GO:0022603	0.70	regulation of anatomical structure morphogenesis
GO:0016051	0.70	carbohydrate biosynthetic process
GO:0010803	0.70	regulation of tumor necrosis factor-mediated signaling pathway
GO:0010608	0.70	posttranscriptional regulation of gene expression
GO:0006811	0.70	ion transport
GO:0006468	0.70	protein phosphorylation
GO:0006091	0.70	generation of precursor metabolites and energy
GO:0002757	0.70	immune response-activating signal transduction
GO:0001934	0.70	positive regulation of protein phosphorylation
GO:0000122	0.70	negative regulation of transcription from RNA polymerase II promoter
GO:0090263	0.69	positive regulation of canonical Wnt signaling pathway
GO:0075733	0.69	intracellular transport of virus
GO:0070987	0.69	error-free translesion synthesis
GO:0070911	0.69	global genome nucleotide-excision repair
GO:0070423	0.69	nucleotide-binding oligomerization domain containing signaling pathway
GO:0061418	0.69	regulation of transcription from RNA polymerase II promoter in response to hypoxia
GO:0060071	0.69	Wnt signaling pathway, planar cell polarity pathway
GO:0051437	0.69	positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
GO:0051436	0.69	negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
GO:0051092	0.69	positive regulation of NF-kappaB transcription factor activity
GO:0050852	0.69	T cell receptor signaling pathway
GO:0045742	0.69	positive regulation of epidermal growth factor receptor signaling pathway
GO:0043488	0.69	regulation of mRNA stability
GO:0042769	0.69	DNA damage response, detection of DNA damage
GO:0042276	0.69	error-prone translesion synthesis
GO:0042059	0.69	negative regulation of epidermal growth factor receptor signaling pathway
GO:0038128	0.69	ERBB2 signaling pathway
GO:0038095	0.69	Fc-epsilon receptor signaling pathway
GO:0038061	0.69	NIK/NF-kappaB signaling
GO:0036297	0.69	interstrand cross-link repair
GO:0035666	0.69	TRIF-dependent toll-like receptor signaling pathway
GO:0034220	0.69	ion transmembrane transport
GO:0031145	0.69	anaphase-promoting complex-dependent catabolic process
GO:0030512	0.69	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0019068	0.69	virion assembly
GO:0016197	0.69	endosomal transport
GO:0010939	0.69	regulation of necrotic cell death
GO:0008543	0.69	fibroblast growth factor receptor signaling pathway
GO:0007254	0.69	JNK cascade
GO:0006977	0.69	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0006297	0.69	nucleotide-excision repair, DNA gap filling
GO:0006296	0.69	nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006294	0.69	nucleotide-excision repair, preincision complex assembly
GO:0006283	0.69	transcription-coupled nucleotide-excision repair
GO:0005978	0.69	glycogen biosynthetic process
GO:0002755	0.69	MyD88-dependent toll-like receptor signaling pathway
GO:0002223	0.69	stimulatory C-type lectin receptor signaling pathway
GO:0000717	0.69	nucleotide-excision repair, DNA duplex unwinding
GO:0000715	0.69	nucleotide-excision repair, DNA damage recognition
GO:0000187	0.69	activation of MAPK activity
GO:0000086	0.69	G2/M transition of mitotic cell cycle
GO:0019725	0.59	cellular homeostasis
GO:0010992	0.58	ubiquitin homeostasis






(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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0044422	0.86	organelle part
GO:0044446	0.85	intracellular organelle part
GO:0032991	0.76	macromolecular complex
GO:0030529	0.63	intracellular ribonucleoprotein complex
GO:0044445	0.62	cytosolic part
GO:0044391	0.62	ribosomal subunit
GO:0022627	0.55	cytosolic small ribosomal subunit
GO:0043226	0.53	organelle
GO:0043229	0.51	intracellular organelle






(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	0.067	2jrhA	0.666	2.38	0.057	0.946	2.7.11.25	48,54
2	0.060	3c8yA	0.545	2.72	0.048	0.838	1.12.7.2	26
3	0.060	2j0lA	0.390	4.43	0.048	0.770	2.7.10.2	NA
4	0.060	1vz6A	0.553	3.17	0.041	0.919	2.3.1.35	NA
5	0.060	1mp8A	0.318	4.31	0.048	0.689	2.7.10.2 2.7.1.112	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	0.36	1nbf1	0.902	1.50	0.356	0.987	1.40	III	2,4,6,9,10,11,12,31,33,34,35,38,40,42,43,44,45,46,47,60,61,62,63,64,66,67,68,69,70
2	0.32	1aar0	0.936	1.16	0.365	1.000	1.41	III	42,45,46,47,66,68,69,70,73
3	0.21	1q0wB	0.890	1.22	0.351	1.000	1.41	III	40,42,43,44,45,47,60,66,67,68,69,70,71
4	0.10	2d3gB	0.895	0.77	0.357	0.946	1.00	III	42,45,46,47,66,68
5	0.08	2c7n1	0.915	0.70	0.352	0.960	1.44	III	6,7,40,42,43,44,45,47,61,62,64,66,68,69,70,71
6	0.06	2izv0	0.907	1.46	0.257	1.000	0.81	III	11,12,14,31



(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.