I-TASSER results

I-TASSER results for job id Rv3555c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (289 residues)
MDELPWPVLGSEVLAAKAIPERAMRQLYEPVYPGVYAPAGVELTARQRAHAAWLWSRRRA
VVAGNSAAALLGAKWVNPALDAELVHANRKPPPRIVVHTDRLAPHETVAVDGVAVTTPAR
TAFDIGRRTPSRLQAVQRLDALANSTDVKVADVQAVIAEHTGARGLVRLRAVLPLIDGGA
ESPQETWTRLVLIDAGLPKPQTQIRVFDDYGDFVARIDLGYEQLRVGVEYDGPQHWTDPA
QRARDIERSTALLDLGWTIIRVTSELLWYRRGTFVGRVDAAMRAAGWRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MDELPWPVLGSEVLAAKAIPERAMRQLYEPVYPGVYAPAGVELTARQRAHAAWLWSRRRAVVAGNSAAALLGAKWVNPALDAELVHANRKPPPRIVVHTDRLAPHETVAVDGVAVTTPARTAFDIGRRTPSRLQAVQRLDALANSTDVKVADVQAVIAEHTGARGLVRLRAVLPLIDGGAESPQETWTRLVLIDAGLPKPQTQIRVFDDYGDFVARIDLGYEQLRVGVEYDGPQHWTDPAQRARDIERSTALLDLGWTIIRVTSELLWYRRGTFVGRVDAAMRAAGWRP
Prediction	CCCCCCCCEHHHHHHHHHHHHHHHHCCEEEHCCCEEHCCCCCCCHHHHHHHHHHHHCCCEEEHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCEEEEHCCCCCCEEEEHCCEEHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEHCCCCCEEEEEEEEHCCCEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHHHHHHCHHHHHHHHHHHHHHHCCCC
Conf.Score	9988876444666666567899988986885698887799999999999999998689847744899999899888899868996799999997899866888875899888886689999999998578788999999999985698999999999976888768999999986556778979999999999999998767589986898767888667567569999879876789899999999999999989989998778878689999999999999988999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MDELPWPVLGSEVLAAKAIPERAMRQLYEPVYPGVYAPAGVELTARQRAHAAWLWSRRRAVVAGNSAAALLGAKWVNPALDAELVHANRKPPPRIVVHTDRLAPHETVAVDGVAVTTPARTAFDIGRRTPSRLQAVQRLDALANSTDVKVADVQAVIAEHTGARGLVRLRAVLPLIDGGAESPQETWTRLVLIDAGLPKPQTQIRVFDDYGDFVARIDLGYEQLRVGVEYDGPQHWTDPAQRARDIERSTALLDLGWTIIRVTSELLWYRRGTFVGRVDAAMRAAGWRP
Prediction	7642432021110122330322124442220132120246242322000100010032300001100000120311445330111223333221000011313333113234120030020000011203332201000010112341224102202342332220320221022233324322002000001213113222001021443322010000044210000001333245452243034024203714010000114101521430042014004415548
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280

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

Sec.Str
Seq

CCCCCCCCEHHHHHHHHHHHHHHHHCCEEEHCCCEEHCCCCCCCHHHHHHHHHHHHCCCEEEHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCEEEEHCCCCCCEEEEHCCEEHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEHCCCCCEEEEEEEEHCCCEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHHHHHHCHHHHHHHHHHHHHHHCCCC
MDELPWPVLGSEVLAAKAIPERAMRQLYEPVYPGVYAPAGVELTARQRAHAAWLWSRRRAVVAGNSAAALLGAKWVNPALDAELVHANRKPPPRIVVHTDRLAPHETVAVDGVAVTTPARTAFDIGRRTPSRLQAVQRLDALANSTDVKVADVQAVIAEHTGARGLVRLRAVLPLIDGGAESPQETWTRLVLIDAGLPKPQTQIRVFDDYGDFVARIDLGYEQLRVGVEYDGPQHWTDPAQRARDIERSTALLDLGWTIIRVTSELLWYRRGTFVGRVDAAMRAAGWRP

4oq2A1

0.17

0.08

0.46

1.46

wdPPAS

-----------------------------------------------------------------------------------------------------------------------------------------------------------HHHHHEFSKTDYILRALSKISHKRWEHYIINRVVHTLDDPDIEFVCQQCIRKEGHLGKIYLADLLFPQLNLYLEIDE-AHHDSNDARKADAVRRLDVEATGFQEERIPLSEVNKLVDEFVRLVKDKKEEL-FFR

4oq2A1

0.17

0.08

0.46

1.52

wPPAS

-----------------------------------------------------------------------------------------------------------------------------------------------------------HHHHHEFSKTDYILRALSKISHKRWEHYIINRVVHTLDDPDIEFVCQQCIRKEGHLGKIYLADLLFPQLNLYLEIDE-AHHDSNDARKADAVRRLDVEATGFQEERIPLSEVNKLVDEFVRLVKDKKEEL-FFR

3hrlA

0.18

0.06

0.31

1.49

Env-PPAS

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASEAEAKLWQHLRAGRLNGYKFRRQQPGN-----YIVDFCVT-PKLIVEADGVY----------DHARTVYLNSLGFTVLRFWNHEILQQTNDVLAEILRVLQELEK--

4parB1

0.18

0.08

0.43

1.06

wdPPAS

-------------------------------------------------------------------------------------------------------------------------------------------------------------------ASSDLTDYVIRQLNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKK--IALTDLYFPQLGIHIEVDEGHHFLRISQTESDAMREEDISITGHKIFRVNVFKNLENIHQQIDKIIEEIKTA-FKE

4parB1

0.18

0.08

0.43

1.15

wPPAS

-------------------------------------------------------------------------------------------------------------------------------------------------------------------ASSDLTDYVIRQLNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKK--IALTDLYFPQLGIHIEVDEGHHFLRISQTESDAMREEDISITGHKIFRVNVFKNLENIHQQIDKIIEEIKTA-FKE

4oq2A1

0.16

0.07

0.44

1.10

Env-PPAS

---------------------------------------------------------------------------------------------------------------------------------------------------------------HHHHHEFSKTDYILRALSKISHKRWEHYIINRVVHT-LDDPDIQCIRKEGHLGKIYLADLLFPQLNLYLEIDEA-HHDSNDARKADAVRRLDIVEAGFQEERIPLSEVNKLVDEFVRLVKDKKEELEFFR

3hrlA

0.22

0.07

0.30

1.12

wPPAS

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASEAEAKLWQHLRAGRLNKFRRQQP-----GN--YIVDF--VTPKLIVEADGV----------YDHARTVYLNSLGFTVLRFWNHEILQQTNDVLAEILRVLQEL--K-

1cw0A

0.18

0.08

0.42

1.01

Env-PPAS

-----------------------------------------------------------------------------------------------------------------------------------------------------------------ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGL-----AFRVQDAS--LPGRPDFVVDEYRCVIFTHGYLFKVPGKNVERDRRDISRLQELGWRVLIVWECALKLTDEALTERLEEWICGEGASA

3r3pA

0.12

0.04

0.33

0.96

wPPAS

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTPERRVKEILDEMDIV--FTHHVV--------GWNVAFYLGKKLAIEVNGVYWASKQKNVNKDKRKLSELHSKGYRVLTIEDDELND-IDKVKQQIQKFWVTH--S-

1cw0A

0.18

0.07

0.41

0.95

wPPAS

----------------------------------------------------------------------------------------------------------------------------------------------------------------ADVHDKATRSKNMRAIA-TRDTAIEKRLASLLTGQGL-----AFRVQDASLP--GRPDFVVDEYRCVIFTHGCFWHH-GKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEW--GA

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-4.54

Estimated TM-score = 0.24±0.07

Estimated RMSD = 17.6±2.6Å

Download Model 2

C-score=-4.81

Download Model 3

C-score=-4.89

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.95

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	4oq2A	0.414	2.52	0.158	0.460
2	2f3oA	0.413	6.44	0.060	0.716
3	3efoB	0.411	5.87	0.054	0.668
4	3eh1A	0.406	5.85	0.071	0.654
5	3k30A	0.406	6.42	0.038	0.699
6	3o3mA	0.404	5.93	0.050	0.637
7	3eh2A	0.403	5.81	0.063	0.654
8	3f93C	0.401	6.04	0.066	0.661
9	3to3A	0.401	5.99	0.062	0.657
10	1pcxA	0.399	5.93	0.039	0.650

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.17	8	1stxA	MN	Rep, Mult	181,218,229,230
2	0.11	5	2jfrA	MG	Rep, Mult	231,232
3	0.07	3	3k30A	SF4	Rep, Mult	184,187,188,228,229,230,231,271,272
4	0.04	2	1a9xA	MN	Rep, Mult	203,218
5	0.02	1	4v1fA	BQ1	Rep, Mult	15,16,19
6	0.02	1	2fkwD	BCL	Rep, Mult	10,13
7	0.02	1	3attA	MG	Rep, Mult	218,222
8	0.02	1	5ezmA	MPG	Rep, Mult	9,73
9	0.02	1	3kziT	CLA	Rep, Mult	274,278

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1q0lA	0.359	5.95	0.040	0.585	1.1.1.267	55,172,181
2	0.060	3fsnB	0.385	6.39	0.050	0.657	5.2.1.7	255
3	0.060	2a8iA	0.384	5.94	0.046	0.623	3.4.25.-	NA
4	0.060	1j6uA	0.374	6.41	0.060	0.654	6.3.2.8	188
5	0.060	1n1hA	0.368	6.45	0.069	0.640	2.7.7.48	NA
6	0.060	3bfjT	0.378	5.89	0.049	0.609	1.1.1.202	NA
7	0.060	1aroP	0.391	5.70	0.063	0.599	2.7.7.6	NA
8	0.060	1p4kA	0.373	6.15	0.042	0.613	3.5.1.26	NA
9	0.060	1myrA	0.384	6.54	0.034	0.664	3.2.1.147	NA
10	0.060	1l7qA	0.374	6.57	0.056	0.668	3.1.1.1	NA
11	0.060	2gl9D	0.223	5.11	0.093	0.332	3.5.1.26	173
12	0.060	2tmdA	0.398	6.34	0.049	0.682	1.5.8.2	180
13	0.060	2a8jB	0.351	5.93	0.062	0.564	3.4.25.-	NA
14	0.060	3a06A	0.378	5.17	0.041	0.554	1.1.1.267	NA
15	0.060	1w4xA	0.387	6.15	0.053	0.654	1.14.13.92	NA
16	0.060	1gqqA	0.321	6.31	0.061	0.533	6.3.2.8	NA
17	0.060	2nsmA	0.379	6.48	0.065	0.661	3.4.17.3	NA
18	0.060	1ayyD	0.221	5.18	0.101	0.332	3.5.1.26	NA
19	0.060	1br2A	0.305	6.97	0.076	0.564	3.6.1.32	NA

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.06	0.446	6.17	0.04	0.74	2yajC	GO:0003824 GO:0008152 GO:0016829 GO:0043722
1	0.06	0.413	6.44	0.06	0.72	2f3oA	GO:0003824 GO:0008152 GO:0016829
2	0.06	0.419	5.87	0.06	0.69	5i2gA	GO:0003824 GO:0008152
3	0.06	0.415	2.57	0.16	0.46	4oq2A	GO:0004519 GO:0090305
4	0.06	0.335	6.29	0.01	0.56	4mtjA	GO:0003824 GO:0008152
5	0.06	0.382	5.56	0.04	0.60	5i2aB	GO:0003824 GO:0008152
6	0.06	0.328	6.22	0.03	0.55	5bweA	GO:0003824 GO:0008152
7	0.06	0.313	6.21	0.05	0.52	3t1iD	GO:0000014 GO:0000019 GO:0000724 GO:0000729 GO:0000731 GO:0000732 GO:0000781 GO:0000784 GO:0000790 GO:0000794 GO:0003677 GO:0003690 GO:0004003 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005829 GO:0005913 GO:0006260 GO:0006281 GO:0006302 GO:0006303 GO:0006310 GO:0006974 GO:0007004 GO:0007062 GO:0007095 GO:0007129 GO:0007131 GO:0007507 GO:0008022 GO:0008283 GO:0008408 GO:0016032 GO:0016605 GO:0016787 GO:0030145 GO:0030870 GO:0031573 GO:0031860 GO:0031954 GO:0032206 GO:0032481 GO:0032508 GO:0032876 GO:0033674 GO:0035861 GO:0043066 GO:0046597 GO:0048471 GO:0051276 GO:0051321 GO:0090305 GO:0098609 GO:0098641 GO:1901796
8	0.06	0.339	6.53	0.04	0.61	3owaC	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
9	0.06	0.309	6.26	0.06	0.52	1cm5A	GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
10	0.06	0.280	6.19	0.05	0.47	3zx8C	GO:0003723 GO:0005198 GO:0016032 GO:0019012 GO:0019028 GO:0039617
11	0.06	0.294	6.22	0.04	0.50	3zq5A	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009585 GO:0009639 GO:0009881 GO:0009883 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0018298 GO:0023014 GO:0042802 GO:0046777 GO:0050896
12	0.06	0.254	6.03	0.06	0.42	3cx3A	GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0030001 GO:0046872
13	0.06	0.240	5.60	0.05	0.37	1v75A	GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
14	0.06	0.239	5.59	0.04	0.38	4dzrA	GO:0003676 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0018364 GO:0032259 GO:0036009 GO:0046872
15	0.06	0.241	6.05	0.05	0.40	2gauA	GO:0003677 GO:0006351 GO:0006355
16	0.06	0.219	4.74	0.04	0.31	2go51	GO:0000166 GO:0003924 GO:0005047 GO:0005525 GO:0005783 GO:0005785 GO:0005789 GO:0006613 GO:0006614 GO:0006810 GO:0006886 GO:0016020 GO:0016021 GO:0036498 GO:0044822 GO:0070062
17	0.06	0.224	5.64	0.03	0.35	2i88A	GO:0005886 GO:0016020 GO:0016021 GO:0019835 GO:0042742 GO:0050829
18	0.06	0.240	5.92	0.02	0.39	1d5cA	GO:0005525 GO:0005622 GO:0007264

Consensus prediction of GO terms

Molecular Function	GO:0043722	GO:0004519
GO-Score	0.07	0.06
Biological Processes	GO:0090305
GO-Score	0.06
Cellular Component
GO-Score

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.