I-TASSER results

I-TASSER results for job id Rv2253

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

Input Sequence in FASTA format

>protein (167 residues)
MSGHRKKAMLALAAASLAATLAPNAVAAAEPSWNGQYLVTLSANAKTGTSMAANRPEYPH
KANYTFSSRCASDVCIATVVDAPPPKNEFIPRPIEYTWNGTQWVREISWQWDCLLPDGTI
EYAPAKSITAYTPGQYGILTGVFHTDIASGTCKGNVDMPVSAKPIVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSGHRKKAMLALAAASLAATLAPNAVAAAEPSWNGQYLVTLSANAKTGTSMAANRPEYPHKANYTFSSRCASDVCIATVVDAPPPKNEFIPRPIEYTWNGTQWVREISWQWDCLLPDGTIEYAPAKSITAYTPGQYGILTGVFHTDIASGTCKGNVDMPVSAKPIVG
Prediction	CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCEEEEEHCCCCCCCCCCCCCCEEEEEHCCEEEEEEEHCCEEHCCCCCCCCCCCEEEEEEHCCCCCEEEEEEEEEEHCCCCCCEEEEEEEEEHCCC
Conf.Score	99756788999999998755678888888988767999999856676777777888887655799999975997899965799988999998858999597589998554455479987666764688998568996689999999747887766898666665689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSGHRKKAMLALAAASLAATLAPNAVAAAEPSWNGQYLVTLSANAKTGTSMAANRPEYPHKANYTFSSRCASDVCIATVVDAPPPKNEFIPRPIEYTWNGTQWVREISWQWDCLLPDGTIEYAPAKSITAYTPGQYGILTGVFHTDIASGTCKGNVDMPVSAKPIVG
Prediction	85544331000011121121322344346524041312032223543344333544535244513031314443010103434556355344334130444513562514120225644452420433232314441304130313146340413131313333348
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCEEEEEHCCCCCCCCCCCCCCEEEEEHCCEEEEEEEHCCEEHCCCCCCCCCCCEEEEEEHCCCCCEEEEEEEEEEHCCCCCCEEEEEEEEEHCCC
MSGHRKKAMLALAAASLAATLAPNAVAAAEPSWNGQYLVTLSANAKTGTSMAANRPEYPHKANYTFSSRCASDVCIATVVDAPPPKNEFIPRPIEYTWNGTQWVREISWQWDCLLPDGTIEYAPAKSITAYTPGQYGILTGVFHTDIASGTCKGNVDMPVSAKPIVG

4z28A

0.12

0.09

0.76

0.71

MUSTER

MSP-DMKLLAGASNWVNQSGSVAQFVFTPSPTQPQTYEVSGNYINNAQGTGCKG-------TPYPLSGAYYSGNQIISFS-------------VVWSNASANCQSATGWTGYFDFSGSQ-----------------AVLKTDWNLAFYSGSTPAIQQGQDDFMQS--

2ztnA2

0.11

0.10

0.89

0.76

dPPAS

------------------TPSPAPSRPFSVLRANDVLWLSLTAAEYDQTTYGSSTNPMYVSDTVTFVNVATGAQAVARSLDWSKVTLDGRPLTTIQQYSKTFYVLPLRGK-LSFWEASTTKYNTTASDQILIENAAGHRVAISTYTTSLGAGPTSISAVGVLAPHSA

1g8kB

0.13

0.09

0.71

0.76

wdPPAS

---RTTLAYPATAVSVAKNLAANEPVSFTYPD-TSSPCVAVKLGAPVPGGVGPDD------DIVAYSVLCTHMGCPTSYDSSSK-------------------------TFSCPCHFT-----------EFDAEKAGMICGRVLLRYDAA---SDALTAVGVDGLIY

3wajA

0.11

0.10

0.90

0.77

wMUSTER

QVNLNNESQVLQTALYEAVMRARYGVSPTMGTQEVLYKYAYTQLYEKKMGIPVKIAPSG----YVKIFERVKG---AVVTGKVSANVTEVSVNATIKTNQN---RTFEYWQTVEVKNGT-----YTVVLPYSHNSDYPVKPITPYHIKAGN--VVKEITIYESQVQG

3pg0A

0.18

0.11

0.64

0.73

wPPAS

---------------------------------DGYYKLVARHSGKTSDG-GDNQQVDLGDGYYKLVAR-HSGKALDVENASTSDGAN----VIQYSYSGGQWRLVDL-------GDGYYKLVARHSGKALD-TSDG-------ANVIQYSYSGG----WRLVDL--

2pq4B

0.33

0.07

0.20

0.90

dPPAS2

LSRRSFMKANAVAAAAAAAGLSVPGVARAVVGQ--------------------------------------------------------------------------------------------------------------------------------------

4qzvB

0.15

0.14

0.95

0.80

PPAS

YNFKRLTKLLSLFAVDEFSCNGISPDSIARGCYSTLTVDYFAYPLSMKSYIRPGSAGNIPLYNYKQSF--ANPTCRVMAS---VLANVTITKPHAYGYI-SKCSRLTGADVETPLYINPGEYSICRD---FSPGGFSEDGQVFKRTLTQFEGGGLLIGVGTRVPMTD

3li8A1

0.13

0.10

0.72

0.76

Env-PPAS

------EANQAIARTLACTAEYGSQDREEAPQLIGVYLGYFDGRDKNYINAPGHDSTGRFV-PYCNK---INGPVIIEPLVHYDSSD----------Y----YQLPKTTGKDTLTE---PYFYEGIFVSYDSPFKNGEFAGIAGVDVP-------------------

4lzkA

0.09

0.08

0.88

0.69

MUSTER

KAAQSIQILAVITNYIKRSHPNPSLNAQNPTSIPALFLNGHAPGVSSSEGNGNLGLKLNVGDKVSLGTSLADNS-AALIYHVQQYSGAQVFAPFTAVTIEQQ----VFQAFESVAKSAGSEYLATSFALYTRSQNRKSLFGYFFWVWQAAAA---------------

4qzvB

0.15

0.14

0.95

0.75

dPPAS

NCNYNLTKLLSLFAVDEFSCNGISPDSIARGCYSTLTVDYFAYPLSMKSYIRPGSAGNIPLYNYKQSF--ANPTCRVMAS---VLANVTITKPHAYGYI-SKCSRLTGADVETPLYINPGEYSICRD---FSPGGFSEDGQVFKRTLTQFEGGGLLIGVGTRVPMTD

(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=-4.04

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.6±3.7Å

Download Model 2

C-score=-4.07

Download Model 3

C-score=-4.53

Download Model 4

C-score=-4.91

Download Model 5

C-score=-5.00

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	5cwiA	0.445	4.75	0.055	0.713
2	3w6qA	0.440	5.31	0.036	0.766
3	4kqzA	0.432	5.52	0.108	0.814
4	4ouaB	0.430	5.23	0.075	0.754
5	1tubA	0.430	4.83	0.035	0.707
6	3h0lA	0.428	5.17	0.043	0.749
7	5cwoA	0.427	4.80	0.038	0.689
8	2wdaA	0.425	4.26	0.042	0.653
9	4yusA2	0.425	4.71	0.057	0.695
10	3zbpA	0.423	4.89	0.071	0.683

(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	0.07	4	4n6hA	OLA	Rep, Mult	8,11,12,15
2	0.07	4	1wc0B	APC	Rep, Mult	146,147,148,149,150,151,154
3	0.05	3	1wc1A	TAT	Rep, Mult	36,37,39,40,72,73
4	0.05	3	2kdxA	ZN	Rep, Mult	70,75,113,152
5	0.03	2	3cf4A	SF4	Rep, Mult	31,32,33,34,35,36,37,70,72,76
6	0.03	2	1izlM	CLA	Rep, Mult	12,19
7	0.02	1	3du7A	MG	Rep, Mult	68,69,71,118,119
8	0.02	1	1ud9A	ZN	Rep, Mult	46,164
9	0.02	1	3a0bH	CLA	Rep, Mult	9,17
10	0.02	1	1wc1C	TAT	Rep, Mult	137,138,140,163
11	0.02	1	4cv7A	CO	Rep, Mult	144,157
12	0.02	1	2pe7A	PDC	Rep, Mult	92,93
13	0.02	1	1rneA	NGA	Rep, Mult	99,101
14	0.02	1	2ei3A	MG	Rep, Mult	95,117
15	0.02	1	3cf4A	SF4	Rep, Mult	122,123,125,127,145,146,147,156
16	0.02	1	3m9iA	3PE	Rep, Mult	19,50
17	0.02	1	2bw7B	APC	Rep, Mult	131,132,133,134,135,140
18	0.02	1	1l6mB	DBH	Rep, Mult	42,67,158

	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	2ivfA	0.404	4.91	0.051	0.683	1.17.99.2	NA
2	0.060	1yx2B	0.404	4.80	0.075	0.665	2.1.2.10	NA
3	0.060	3dt7A	0.403	5.34	0.036	0.713	4.1.1.32	NA
4	0.060	1pj6A	0.401	5.41	0.063	0.713	1.5.3.10	NA
5	0.060	1occA	0.371	5.26	0.050	0.635	1.9.3.1	NA
6	0.060	3hsiB	0.397	4.83	0.050	0.677	2.7.8.8	NA
7	0.060	1s9iA	0.375	6.20	0.068	0.778	2.7.12.2,2.7.1.37	NA
8	0.060	1ua2A	0.411	5.37	0.040	0.754	2.7.11.22,2.7.11.23	NA
9	0.060	1bi7A	0.304	6.06	0.033	0.611	2.7.11.22,2.7.1.-	NA
10	0.060	2qx1A	0.394	5.18	0.089	0.701	2.3.1.180	NA
11	0.060	1t3qB	0.394	5.60	0.042	0.731	1.3.99.17	NA
12	0.060	2w01A	0.408	4.93	0.076	0.689	4.6.1.2	5
13	0.060	1rw9A	0.419	4.66	0.090	0.677	4.2.2.5	NA
14	0.060	2wz1A	0.402	5.27	0.023	0.707	4.6.1.2	5
15	0.060	3eqdA	0.397	5.97	0.067	0.784	2.7.12.2	81,87
16	0.060	2w96B	0.342	5.42	0.045	0.593	2.7.11.22	86,88
17	0.060	1ybtB	0.410	4.71	0.067	0.665	4.6.1.1	NA
18	0.060	3cf4A	0.422	5.53	0.079	0.766	1.2.99.2	76
19	0.060	3girA	0.405	5.12	0.077	0.695	2.1.2.10	132

(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	0.07	0.426	5.63	0.10	0.81	4xakA	GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
1	0.06	0.422	5.56	0.06	0.80	4qzvB	GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
2	0.06	0.440	5.31	0.04	0.77	3w6qA	GO:0004503 GO:0005634 GO:0008152 GO:0016491 GO:0046872 GO:0055114
3	0.06	0.354	5.38	0.04	0.65	1js8A	GO:0005344 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
4	0.06	0.343	5.61	0.02	0.65	2dd8S	GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0044173 GO:0046718 GO:0046789 GO:0046813 GO:0055036 GO:0061025
5	0.06	0.327	5.64	0.07	0.61	1gu6A	GO:0005506 GO:0005509 GO:0006807 GO:0016491 GO:0016966 GO:0019645 GO:0020037 GO:0030288 GO:0042128 GO:0042279 GO:0042597 GO:0046872 GO:0055114
6	0.06	0.342	5.46	0.07	0.62	3qjoA	GO:0008152 GO:0016491 GO:0046872 GO:0055114
7	0.06	0.283	5.40	0.07	0.51	4j3rA	GO:0004097 GO:0008152 GO:0016491 GO:0046872 GO:0055114
8	0.06	0.354	5.27	0.06	0.62	5a97C	GO:0003723 GO:0019012 GO:0019013 GO:0019028 GO:0019029
9	0.06	0.317	6.08	0.06	0.65	5i08A	GO:0005198 GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044173 GO:0046718 GO:0046813 GO:0055036 GO:0061025
10	0.06	0.280	5.56	0.01	0.50	5ce9A	GO:0004097 GO:0004503 GO:0008152 GO:0016491 GO:0036263 GO:0046148 GO:0046872 GO:0055114
11	0.06	0.413	5.57	0.04	0.78	4z11A	GO:0004097 GO:0008152 GO:0016491 GO:0046148 GO:0046872 GO:0055114
12	0.06	0.253	5.84	0.01	0.47	3awtA	GO:0008152 GO:0016491 GO:0046872 GO:0055114
13	0.06	0.406	5.80	0.08	0.80	3jclA	GO:0009405 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0033644 GO:0039663 GO:0044165 GO:0044173 GO:0044177 GO:0046718 GO:0046813 GO:0055036 GO:0061025
14	0.06	0.430	5.23	0.07	0.75	4ouaB	GO:0004503 GO:0008152 GO:0016491 GO:0046872 GO:0055114
15	0.06	0.337	5.02	0.04	0.58	1lnlA	GO:0005344 GO:0005576 GO:0005615 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.294	5.35	0.04	0.53	4hd4A	GO:0008152 GO:0016491 GO:0046872 GO:0055114
17	0.06	0.432	5.31	0.06	0.77	3w6wA	GO:0004503 GO:0005634 GO:0008152 GO:0016491 GO:0046872 GO:0055114
18	0.06	0.305	5.54	0.04	0.56	2p3xA	GO:0004097 GO:0008152 GO:0009507 GO:0009536 GO:0009543 GO:0009579 GO:0016491 GO:0046148 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0004503	GO:0046789	GO:0005344
GO-Score	0.12	0.07	0.06	0.06
Biological Processes	GO:0044800	GO:0019062	GO:0046718
GO-Score	0.36	0.36	0.36
Cellular Component	GO:0036338	GO:0033644	GO:0044172
GO-Score	0.36	0.36	0.36

(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.