D-I-TASSER Q9UBC1-D2

D-I-TASSER results for Q9UBC1-D2

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

Input Sequence in FASTA format

>Q9UBC1 (153 residues)
AEGSSQSWRQQEEEQRLFRERARAKEEELRESRARRAQEALGDREPKPTRAGPREEHPRG
AGRGSLWRFGDVPWPCPGGGDPEAMAAALVARGPPLEEQGALRRYLRVQQVRWHPDRFLQ
RFRSQIETWELGRVMGAVTALSQALNRHAEALK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AEGSSQSWRQQEEEQRLFRERARAKEEELRESRARRAQEALGDREPKPTRAGPREEHPRGAGRGSLWRFGDVPWPCPGGGDPEAMAAALVARGPPLEEQGALRRYLRVQQVRWHPDRFLQRFRSQIETWELGRVMGAVTALSQALNRHAEALK
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	716799999999999999999999999999999999999999999999987666543202577764202456899999997678889887537766665899999999986208178999998526856799999999999999999999719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AEGSSQSWRQQEEEQRLFRERARAKEEELRESRARRAQEALGDREPKPTRAGPREEHPRGAGRGSLWRFGDVPWPCPGGGDPEAMAAALVARGPPLEEQGALRRYLRVQQVRWHPDRFLQRFRSQIETWELGRVMGAVTALSQALNRHAEALK
Prediction	875546535545445443554455455534554444355426544542354445244554554533040540001145665464134213441424655642253036222401123025303640466236402620330041035117538
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCSCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC
AEGSSQSWRQQEEEQRLFRERARAKEEELRESRARRAQEALGDREPKPTRAGPREEHPRGAGRGSLWRFGDVPWPCPGGGDPEAMAAALVARGPPLEEQGALRRYLRVQQVRWHPDRFLQRFRSQIETWELGRVMGAVTALSQALNRHAEALK

3hr0A

0.07

2.93

0.61

CEthreader

LFSQGIGGEQAQAKFDSCLSDLAAVSNKFRDLLQEGLTELNSTAIKPQVQPW-INSFFSVSHNIEEEEFNDYEANDPWVQQFILNLEQQMAEFKASLSPVIYDSLTGLMTSLVAVELEKVVLKSTFNRLGGLQFDKELRSLIAYLTTVTTWTI

2fji11

0.07

2.76

0.83

EigenThreader

HMGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERLDGTKTCFQMFTQQVEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKVEYLIAVSNDQMAVAISSKYGKLVSKVYEKQITNHLEGFAEVAQCSSLGLI

6ybtu

0.10

0.07

2.69

0.68

FFAS-3D

-REKEELEQREAELQKVRKAEEERLRQEAKEREKERILQEHEQIKKKTVRERLEQIKKTELGAKAFKDIDI----------------------------EDLEELDPDFIMAKQVEQL---------EKEKKELQERLKNQEKKIDYFERAKR

5u30A4

0.09

0.08

3.02

0.79

SPARKS-K

--SWESWNQRVGQEYAKLVEQKNRFEQKNFVGQ-EHLVHLVNQLQQDKEASPGLES---KEQTAHYVTGRAL-------RGSDKVFEKWGK-LAPDAPFDLYDAEIKNVQRRN-TRRFHDLFAKLAEPEYQALWRSFLTRYAVYNSILRKLNH

5cwmA

0.18

0.13

4.25

0.46

CNFpred

---------DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALR----------------------------------TAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESSEEALERALRVAEEAARLAKRVLELAE

5hb4B

0.08

0.07

2.59

1.00

DEthreader

ATPEFLETVELEEKVLIEWLTVRNRANLLLTARLNLLQAWANLLLVMIESNDFKSPKMAF----L-LQ--LQAILPTL-EA--FSSL-KS-----------D--EAFELARVAKLLWKLDF--QFTVGNLIGDKLFQLFQLCLSAICSGTPEL

2fji1

0.08

3.07

0.87

MapAlign

-----MGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLEDGTKTCFQMFTQQVEVAAGTNQAL-VGVVERFSDLLTRQKNWISKISEPGGLVEYLIAVSNDQMKAADYA-V-AISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSS

2otoB

0.12

0.11

3.89

0.61

MUSTER

--AANNPAIQNIRLRHENKDLKARLENAEVAGRDFKRAEELEKAKQALEDQRKDLETKLKELQQDY---------------DLAKESTSWDRQRLEKELEEKKEALELAIDQASRDYHRATALEKELEEKKKALELAIDQASQDYNRANVLEK

6u3rA

0.18

0.07

2.35

1.06

HHsearch

-----------------------------------------------------------------------------GMVDY-----YEVLGVQRHASPEDIKKAYRKLALKWHPDKNP---------ENKEEAERKFKQVAEAYEVLSDAKK

5jggA

0.05

2.15

0.52

CEthreader

---------TLTSADKSHVKSIWSKASGKAEELGAEALGRMLEVFPNTKTYFSHYADLSVTSGQVHTHGKKILDAITTAVNHDITGVLTALSTLHAKTLRVDPANFKILSHTI-LVVLALYFPADFTPEVHLACDKFLASVSHTLATKYR---

(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	0.7257

(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	5hb4B	0.59	4.06	0.078	0.843	model1_5hb4B.pdb.gz
2	4ifqA	0.56	4.65	0.034	0.922	model1_4ifqA.pdb.gz
3	6xnsA	0.56	4.17	0.075	0.830	model1_6xnsA.pdb.gz
4	5yfpB	0.56	4.17	0.074	0.830	model1_5yfpB.pdb.gz
5	5j5kA	0.56	3.70	0.070	0.778	model1_5j5kA.pdb.gz
6	6tgbA	0.55	3.95	0.055	0.784	model1_6tgbA.pdb.gz
7	5ijnD	0.55	4.60	0.094	0.882	model1_5ijnD.pdb.gz
8	1y1uA	0.54	4.48	0.092	0.837	model1_1y1uA.pdb.gz
9	5e7xA	0.53	4.02	0.090	0.778	model1_5e7xA.pdb.gz
10	6m3pA	0.53	4.15	0.065	0.797	model1_6m3pA.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	0.23	heterocyclic compound binding
GO:0097159	0.23	organic cyclic compound binding
GO:0004872	0.13	receptor activity
GO:0005102	0.12	receptor binding
GO:0004871	0.12	signal transducer activity
GO:0003676	0.11	nucleic acid binding
GO:0000166	0.11	nucleotide 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:0034122	1.00	negative regulation of toll-like receptor signaling pathway
GO:0007249	1.00	I-kappaB kinase/NF-kappaB signaling
GO:0009987	0.67	cellular process
GO:0051239	0.57	regulation of multicellular organismal process
GO:0050896	0.56	response to stimulus
GO:0080090	0.55	regulation of primary metabolic process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0001817	0.55	regulation of cytokine production
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0051241	0.54	negative regulation of multicellular organismal process
GO:0010033	0.53	response to organic substance
GO:0043207	0.52	response to external biotic stimulus
GO:0010556	0.52	regulation of macromolecule biosynthetic process
GO:0001818	0.52	negative regulation of cytokine production
GO:0071222	0.51	cellular response to lipopolysaccharide
GO:0032720	0.51	negative regulation of tumor necrosis factor production
GO:0032088	0.51	negative regulation of NF-kappaB transcription factor activity
GO:0031665	0.51	negative regulation of lipopolysaccharide-mediated signaling pathway

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:0043229	1.00	intracellular organelle
GO:0043227	0.94	membrane-bounded organelle
GO:0005634	0.93	nucleus

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	3dysB	0.495	4.37	0.056	0.752	3.1.4.35	NA
2	0.060	2pfdB	0.513	4.29	0.079	0.784	2.1.2.5 4.3.1.4	NA
3	0.060	2r8qA	0.472	4.46	0.042	0.752	3.1.4.17	71
4	0.060	1z1lA	0.478	4.49	0.034	0.778	3.1.4.17	NA
5	0.060	2j2fA	0.460	4.62	0.075	0.758	1.14.19.2 1.14.99.6	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	3jsiA	0.493	4.38	0.063	0.752	0.29	WTC	complex1.pdb.gz	133,134,137
2	0.08	3sl5A	0.484	4.22	0.028	0.732	0.22	J25	complex2.pdb.gz	132,133,136,139
3	0.07	3i8vA	0.487	4.33	0.035	0.745	0.19	0MO	complex3.pdb.gz	79,131,134,135
4	0.03	1g9aA	0.461	5.17	0.041	0.758	0.11	BAB	complex4.pdb.gz	69,70,73,133,136
5	0.01	3g45B	0.490	4.29	0.028	0.745	0.18	988	complex5.pdb.gz	68,79,132
6	0.01	1mkdD	0.490	4.44	0.021	0.758	0.17	ZAR	complex6.pdb.gz	122,123,126
7	0.01	1xomB	0.483	4.34	0.021	0.745	0.16	CIO	complex7.pdb.gz	133,140,144
8	0.01	1oynC	0.490	4.22	0.014	0.739	0.17	ROL	complex8.pdb.gz	136,137,140
9	0.01	2fm0D	0.477	4.65	0.021	0.771	0.25	M98	complex9.pdb.gz	110,113,114,118,122,131,140
10	0.01	1xoqA	0.480	4.47	0.021	0.752	0.17	ROF	complex10.pdb.gz	78,114,115,121

	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.