I-TASSER results

I-TASSER results for job id Rv1507A

[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)
MQSGQNILAKVCNLIEQSRLSSTRCLQFRITNTSRPRQLRWSEFKRFCDIFNMVLGKARM
GRDPGRPVRDERRIVSCEIIASDHIGLAAARLLAKRYRGRSVSGFVLMIKSASVHEIDSW
SSPSVAMSIGVALCSYPHYAAARTSPPNRDWGEDTTRSRPVTGLLAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQSGQNILAKVCNLIEQSRLSSTRCLQFRITNTSRPRQLRWSEFKRFCDIFNMVLGKARMGRDPGRPVRDERRIVSCEIIASDHIGLAAARLLAKRYRGRSVSGFVLMIKSASVHEIDSWSSPSVAMSIGVALCSYPHYAAARTSPPNRDWGEDTTRSRPVTGLLAG
Prediction	CCCHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEHCCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCEEEHCCCCCCCEEEEEEEEEHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98667899999999988655655467888757898644458899999999999875554578899888654457888887556547899999999986976546899987464565456788754555554544576544445789887666666667765444589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQSGQNILAKVCNLIEQSRLSSTRCLQFRITNTSRPRQLRWSEFKRFCDIFNMVLGKARMGRDPGRPVRDERRIVSCEIIASDHIGLAAARLLAKRYRGRSVSGFVLMIKSASVHEIDSWSSPSVAMSIGVALCSYPHYAAARTSPPNRDWGEDTTRSRPVTGLLAG
Prediction	76534410230041045541443311413035374445142540440041033013304345544442456432130412144311110031015415444031000103324244145154340022001100323322334453464523663345431322258
	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

CCCHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEHCCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCEEEHCCCCCCCEEEEEEEEEHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
MQSGQNILAKVCNLIEQSRLSSTRCLQFRITNTSRPRQLRWSEFKRFCDIFNMVLGKARMGRDPGRPVRDERRIVSCEIIASDHIGLAAARLLAKRYRGRSVSGFVLMIKSASVHEIDSWSSPSVAMSIGVALCSYPHYAAARTSPPNRDWGEDTTRSRPVTGLLAG

4qanA2

0.15

0.14

0.91

0.60

MUSTER

EKTPQRAVEQFIYAIEKGDL--TRALAF--ATTESSQDTSPELLKKQGEYAKELKTLYGLGTEDARLYGK-----------SEEQLNKLRGKLNPEYVYLDLIKVIPIENTETVKQYAGYSYNGKNYLTGYTLCRQLSAPALSLESGEVRLSKEESRKTSEQSVLKA

3hcyA

0.08

0.07

0.78

0.55

dPPAS

SNAIEEVYEATLDAIQGAL-NCDRASILLFDEAGTMRFVAARGLEHYQRAVDGH----------SPWINEPEPIFVENVDDAEF--SRELKESIVGEGIAALGFFPLVTEGKFMTYYDRPHRFAIARQLGFSIQRMRAEYARRQ-----------------------

4r1dB2

0.17

0.12

0.72

0.56

wdPPAS

--------------V---TFPEHPGARFEFRSSTGAEL---SLLERVDGFVQNMLSTF-----AGETLRKGKHPVG---------SLPGEEYLVAG-KGQRGYTFMWEVQGKE----ESLTEPNLTAGLAVLERSNENGKPPPPAFKSDKW--DSIRVRPTS-----

1t1eA2

0.16

0.14

0.88

0.57

wMUSTER

PNTDAGFLNAITTAVHDPTHKPS------IVSISPEDSWAPASIAAMNRAFLDAAALAAAG-DSGSTDGEQDGLYHVDFPAASPYVLA-------------CGGTRLVASAGRIERETVWNDGPDGGSTGGGVSRIPSWQERANVPPSANPGAGSGRGVPVAGNADP

4r1dB2

0.18

0.13

0.71

0.47

wPPAS

--------------V---TFPEH--ARFEFRSSTGAEL---SLLERVDGFVQNMLSTF-----AGETLRKGKHPVG---------SLPGEEYLVAGSKGQRGYTFMWEVQGKE----ESLTEPNLTAGLAVLERSNENGKPPPPAFKS-DW--DSIRVRP--T--S-

1wh4A

0.21

0.16

0.74

0.60

dPPAS2

-------------------GSSGSSMNKPLTPSTYIRNLNVGILRKLSDFIDPEGWKKLAVAIK-KPSGDDR-----------YNQFHIRRFEALLQTGKS--------PTCEL--LFDWTNCTVG-DLVDLLVQIELFAPATLLLP--DAVPQTVKSLPPSGPSSG

1wh4A

0.21

0.16

0.73

0.67

PPAS

-------------------GSSGSSMNKPLTPSTYIRNLNVGILRKLSDFID-EGWKKLAVAIK-KPSGDDR-----------YNQFHIRRFEALLQTGKS--------PTCEL--LFDWTNCTVGDLVDL-LVQIELFAPATLLLP--DAVPQTVKSLPPSGPSSG

1wh4A

0.22

0.16

0.74

0.65

Env-PPAS

-------------------GSSGSSMNKPLTPSTYIRNLNVGILRKLSDFIDPEGWKKLAVAIK-KPSGDDR-----------YNQFHIRRFEALLQTGKSPTCELL----------FDWTNCTVGDLVDL-LVQIELFAPATLLLP--DAVPQTVKSLPPSGPSSG

1u8sB

0.14

0.12

0.84

0.60

MUSTER

LTQGTGICNEVVRLVTQAGC---NIIDSRIAMFGK--SGSPSNITRVETTLPLLGQQTMMKRTSPHDHQTHAYTVEVYVESDDGLTEKFTQFFAQR----------IGMASLSAQTIS---KNQFHIAISARVDSGCNLMQLQEE---DALCTALD--NFIKN----

1i6wB

0.12

0.10

0.86

0.55

dPPAS

IGGASFNFAGIKSYLVSQGWSRDKLYAV---DFWDKTGTNYNNGPVLSRFVQKVLDETGAKK--------------VDIVAHS-MGGANTLYYIKNLDGGNKVANVVTLGGATTGKALPGTDPNQKILYTSIYSSADM-----IVMNYLSR-LDGARNVQIHGVGHI

(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=-4.06

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.7±3.6Å

Download Model 2

C-score=-4.88

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	3eblA	0.600	3.98	0.101	0.886
2	2o7vA	0.596	4.13	0.074	0.892
3	5jd4A	0.595	3.79	0.092	0.850
4	3mbfA	0.594	4.09	0.079	0.868
5	2zsiA	0.593	3.96	0.088	0.886
6	1evqA	0.591	3.91	0.097	0.868
7	4ypvA	0.589	3.97	0.083	0.868
8	3qh4A	0.588	3.90	0.104	0.856
9	4ob6A	0.588	3.92	0.056	0.856
10	4v2iA	0.588	4.02	0.083	0.868

(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	0.06	3	4ub8d	CLA	Rep, Mult	47,50,53,54
2	0.06	3	3wmmE	CRT	Rep, Mult	46,47,50,51
3	0.04	2	1vltA	ASP	Rep, Mult	62,69
4	0.04	2	5curA	BM0	Rep, Mult	9,10,167
5	0.04	2	3cejB	AVF	Rep, Mult	8,9,28
6	0.04	2	3cuxA	MG	Rep, Mult	27,110,134
7	0.04	2	3iabA	NUC	Rep, Mult	5,32,43,44,45,48,49,50,84,85,88,91,92,95,137,138
8	0.04	2	1c8lA	CFF	Rep, Mult	23,63,65
9	0.02	1	3sfwA	ZN	Rep, Mult	57,84,115
10	0.02	1	4e5tA	MG	Rep, Mult	26,130,166
11	0.02	1	1ldbA	SO4	Rep, Mult	96,115,141,144
12	0.02	1	4tnhH	CLA	Rep, Mult	51,55
13	0.02	1	3nl3A	MG	Rep, Mult	63,64,78
14	0.02	1	1eccA	MN	Rep, Mult	123,153,154
15	0.02	1	3nl5A	TZE	Rep, Mult	32,69
16	0.02	1	2gm9A	3TH	Rep, Mult	7,11,14,109,165

	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	1aldA	0.580	4.25	0.026	0.862	4.1.2.13	NA
2	0.060	3gpbA	0.572	4.07	0.041	0.856	2.4.1.1	19
3	0.060	2o7vA	0.596	4.13	0.074	0.892	3.4.23.16	4,39,82
4	0.060	1jjiA	0.587	3.93	0.103	0.868	3.1.1.1	NA
5	0.060	1b41A	0.567	4.83	0.075	0.946	3.1.1.7	NA
6	0.060	1fbaC	0.581	4.29	0.039	0.868	4.1.2.13	107,130
7	0.060	1j33A	0.573	3.91	0.056	0.844	2.4.2.21	71
8	0.060	3mmtA	0.587	4.16	0.033	0.862	4.1.2.13	43
9	0.060	1maaD	0.569	4.89	0.082	0.946	3.1.1.7	NA
10	0.060	1f6wA	0.579	4.78	0.038	0.940	3.1.1.13,3.1.1.3	NA
11	0.060	1cleA	0.568	4.80	0.063	0.946	3.1.1.3	NA
12	0.060	1fdjA	0.582	4.29	0.026	0.868	4.1.2.13	NA
13	0.060	1lpsA	0.567	4.82	0.057	0.946	3.1.1.3	129,165
14	0.060	1adoA	0.579	4.27	0.026	0.868	4.1.2.13	NA
15	0.060	1vbgA	0.572	4.44	0.059	0.874	2.7.9.1	NA
16	0.060	1aknA	0.578	4.78	0.032	0.946	3.1.1.13,3.1.1.3	NA
17	0.060	2pc4C	0.576	4.32	0.033	0.868	4.1.2.13	NA
18	0.060	2qdgA	0.581	4.23	0.053	0.868	4.1.2.13	NA
19	0.060	3kx6A	0.582	4.24	0.033	0.868	4.1.2.13	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	0.07	0.575	4.34	0.07	0.88	4kryE	GO:0005737 GO:0008126 GO:0008152 GO:0009056 GO:0016787 GO:0034338 GO:0043433 GO:0051346 GO:0052689
1	0.07	0.600	3.98	0.10	0.89	3eblA	GO:0005634 GO:0005737 GO:0008152 GO:0009056 GO:0009739 GO:0009740 GO:0009939 GO:0010325 GO:0010331 GO:0016787 GO:0048444
2	0.07	0.599	4.09	0.07	0.89	2o7rA	GO:0008152 GO:0016787 GO:0052689
3	0.07	0.593	3.96	0.09	0.89	2zsiA	GO:0005634 GO:0005737 GO:0008152 GO:0009739 GO:0009740 GO:0009939 GO:0010331 GO:0010476 GO:0016787 GO:0048444
4	0.07	0.588	4.02	0.08	0.87	4v2iA	GO:0008152 GO:0016787 GO:0052689
5	0.07	0.565	4.39	0.05	0.88	4n5hX	GO:0008152 GO:0016787
6	0.07	0.584	3.94	0.11	0.87	3zwqA	GO:0008152 GO:0016787
7	0.07	0.585	4.16	0.07	0.88	1lzkA	GO:0008152 GO:0016787
8	0.07	0.579	4.78	0.04	0.94	1f6wA	GO:0003824 GO:0004771 GO:0004806 GO:0004872 GO:0005576 GO:0005615 GO:0005737 GO:0005887 GO:0006629 GO:0006641 GO:0006707 GO:0007158 GO:0007416 GO:0008201 GO:0009062 GO:0009986 GO:0016042 GO:0016787 GO:0018350 GO:0030157 GO:0030299 GO:0042043 GO:0044241 GO:0044258 GO:0045202 GO:0047372 GO:0050804 GO:0052689 GO:0070062
9	0.07	0.588	3.90	0.10	0.86	3qh4A	GO:0008152 GO:0016787
10	0.07	0.572	4.23	0.12	0.88	4j7aA	GO:0008152 GO:0016787
11	0.07	0.556	4.04	0.07	0.83	3h04A	GO:0008152 GO:0016787
12	0.07	0.587	3.91	0.05	0.86	4ou5A	GO:0008152 GO:0016787
13	0.07	0.594	4.04	0.10	0.88	1qz3A	GO:0008152 GO:0016787
14	0.07	0.568	4.12	0.16	0.86	4c87A	GO:0008152 GO:0016787
15	0.07	0.587	3.93	0.10	0.87	1jjiA	GO:0008152 GO:0016787
16	0.07	0.585	3.84	0.13	0.86	4p9nA	GO:0008152 GO:0016787
17	0.07	0.549	4.88	0.04	0.93	1thgA	GO:0004806 GO:0005576 GO:0006629 GO:0016042 GO:0016787
18	0.07	0.587	3.86	0.11	0.87	3aikA	GO:0008152 GO:0016787 GO:0042802 GO:0052689

Consensus prediction of GO terms

Molecular Function	GO:0016788
GO-Score	0.37
Biological Processes	GO:0009939	GO:0009056	GO:0048444	GO:0043433	GO:0010325	GO:0051346
GO-Score	0.13	0.13	0.13	0.07	0.07	0.07
Cellular Component	GO:0044424
GO-Score	0.38

(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.