I-TASSER results

I-TASSER results for job id Rv2597

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

Input Sequence in FASTA format

>protein (206 residues)
MGNLLVVIAVALFIAAIVVLVVAIRRPKTPATPGGRRDPLAFDAMPQFGPRQLGPGAIVS
HGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEDDGRLELAMWVKRTDLGLQPG
GQHVIDGVTFQETERGHAGYTTEGTTGLPAGGEMDYVDCASAGQGADESMLLSFERWAPD
MGWEIATGKSVLAGELTVYPAPPVSA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGNLLVVIAVALFIAAIVVLVVAIRRPKTPATPGGRRDPLAFDAMPQFGPRQLGPGAIVSHGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEDDGRLELAMWVKRTDLGLQPGGQHVIDGVTFQETERGHAGYTTEGTTGLPAGGEMDYVDCASAGQGADESMLLSFERWAPDMGWEIATGKSVLAGELTVYPAPPVSA
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCEEEEEEEEEEEEHCCCEEEEEEEHCCCCEEEEEEEHCCCCEEEEEEEHCCCCCCCCCCEEEHCCEEEEEEEEEEEEEEEEHCCCCCCCEEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCEEEEHCEEHCCEEEEEEHCCCCCC
Conf.Score	97466899999999999999998755555788888888888777778897556998899995789999999999878958999999769976999998569958999986656877899986999669999998787899999757888876899999857888888876899998589986899975685855799996899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGNLLVVIAVALFIAAIVVLVVAIRRPKTPATPGGRRDPLAFDAMPQFGPRQLGPGAIVSHGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEDDGRLELAMWVKRTDLGLQPGGQHVIDGVTFQETERGHAGYTTEGTTGLPAGGEMDYVDCASAGQGADESMLLSFERWAPDMGWEIATGKSVLAGELTVYPAPPVSA
Prediction	55211123133333222111021344555665555544315556664230540321110314443120213030444423011110435743300101454540200003515536362555131433413342524030314341534642302111032454554432100003127724100122340453303013255688
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCEEEEEEEEEEEEHCCCEEEEEEEHCCCCEEEEEEEHCCCCEEEEEEEHCCCCCCCCCCEEEHCCEEEEEEEEEEEEEEEEHCCCCCCCEEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCEEEEHCEEHCCEEEEEEHCCCCCC
MGNLLVVIAVALFIAAIVVLVVAIRRPKTPATPGGRRDPLAFDAMPQFGPRQLGPGAIVSHGGIDYVVRGSVTFREGPFVWWEHLLEGGDTPTWLSVQEDDGRLELAMWVKRTDLGLQPGGQHVIDGVTFQETERGHAGYTTEGTTGLPAGGEMDYVDCASAGQGADESMLLSFERWAPDMGWEIATGKSVLAGELTVYPAPPVSA

2mkvA

0.15

0.03

0.20

1.06

dPPAS2

VRNGGLIFAGLAFIVGLLILLSRRFRSGGNKKRRQINEDEP---------------------------------------------------------------------------------------------------------------------------------------------------------------------

4cp6A1

0.12

0.06

0.53

1.05

dPPAS2

----------------------------------------------------TKVGSIIQQNNIKYKVLTVEG--------NIGTVQVGNGVTPVEFEAGQDGKPFTI-----------PTKITVGDKVFTVTEVASQAFSYTGRIVYYPSSITIIKKIQKKGFHGSKAKTIIFDK-GSQL-------------------------

5ay6A2

0.11

0.10

0.85

0.76

MUSTER

-------------KTTRVGVNANLRSEQPYDPSTWSMSDYAKDNSKGVKPDEVQI-PLSDSKGGQRTVTLSMLKGPGPNQWYAELRAKPGDLA----NNGNGQISTGIIEFTTDGKLKNTGSLFGTTSPTAITIKSSGYIAPTVTPPAVQPPTPPTWA----DALGIDEQEVQIDLASAAGGLTQYN----SQSVVQSVNTN----

3x0uA2

0.12

0.10

0.83

dPPAS

-------HSNLISYSPAVGFPSGNFNYIATGTEDEIPQPLKPNMFGERRNRIVKIESWNSIEIHYYNRVGRLKLTYENGEVVELGKAHKYDEHYQSIELNGAYIKYVDVIANGPEAIDRIVFHFSDDRTFVVGENSGKPSVRLQL----EGHFICGMLADQEGSDKVAAFSVAYELFHPDGT------------------------

2coyA

0.19

0.10

0.52

0.88

wdPPAS

-------------------GSSGSSGMAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKG--HRGTVAYVGA----------LFATGKWVGVILDEAK----------------GKN-TVQGRKY----------------------------FTCDEGH----------------------GIFVRQSQIQVFEDSGPSS

5d74A

0.12

0.95

0.75

wMUSTER

NEALNNVRAQVGCYALASWYERMISPDATVVSGATGDTISAKNIGSSYNSGPFQAGQIVTLGANPYGHVVIVEAVDGD-RLTILEQNYGGKRYPTRNYYSAASYQVVHYITPPARTYRETGTMSVTVDAINIRRAPNTSGQIVAT--YKRGESFDYDTVII---DTNGYVWVSYIG-SSGIRNYVATGATKDGKRY----GDAWGT

2coyA

0.18

0.09

0.50

0.87

wPPAS

------------------------GSSGSSGMAQSKRTPSGSRMSAEASARPLRVGSRVEVIGKG--HRGTVAYVGA--------TLFATG-KWVGVILDEA----------------KGKN-TVQGRKY----------------------------FTCDEGH----------------------GIFVRQSQIQVFEDSGPSS

2m20A

0.18

0.04

0.24

0.96

dPPAS2

IATGLVGALLLLLVVALGIGLFIRRRHIVRKRTLRRVEPLTPSGEKLWS-------------------------------------------------------------------------------------------------------------------------------------------------------------

4mkmA1

0.13

0.08

0.64

0.81

PPAS

-------------------------EGTLKTTVAADGVNGSSEKEALVSFENSKDGDTIDYKNEKYNLTGKLHVKDDGS------LEEVATKTTEVTAVENGSGQWELDFGNQKLQ---------VGEKYVVFENAESVENLIDTDNNYELDTKQVVKHEDK---NDKAQTLIVE-------------------------------

2vv5A1

0.09

0.07

0.73

0.74

Env-PPAS

LSYAVNIVAALAIIIVGLIIARMISNAVNRLMISRKIDATVADF----------LSALVRY--GIIAFTLIAALGRVGVQTASVIAVLGAAGLVVGLALQGSNLAAGVLL-VMFRPFRAGEYVDLGGVAGTVLSVQSTTMRT------ADGKIIVIPN----------GKIIAIINFSRE--------------------------

(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=-4.17

Estimated TM-score = 0.27±0.08

Estimated RMSD = 15.6±3.3Å

Download Model 2

C-score=-4.52

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	3x0uA	0.783	1.99	0.117	0.850
2	3eb7A	0.632	3.18	0.042	0.791
3	1w99A	0.626	3.42	0.057	0.796
4	1dlcA	0.625	3.16	0.064	0.786
5	1ji6A	0.624	3.23	0.042	0.791
6	2c9kA	0.606	3.95	0.046	0.820
7	4w8jA	0.593	3.61	0.059	0.782
8	1ciyA2	0.590	3.63	0.075	0.772
9	1i5pA2	0.576	4.18	0.063	0.801
10	1zgsA1	0.574	2.68	0.042	0.684

(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	0.10	8	1jacA	AMG	Rep, Mult	114,116,164,165,166,168
2	0.08	6	3mitA	MAN	Rep, Mult	59,93,95,132,133,134
3	0.06	5	3lm1A	III	Rep, Mult	96,97,98,99,100,101,124
4	0.05	4	2gucA	MAN	Rep, Mult	68,113,114,116,118,136,137
5	0.04	3	1jotA	III	Rep, Mult	41,111,115,117,139,140,141,143,168,169,170,171,172,173,174
6	0.02	2	2bn0A	BGC	Rep, Mult	61,62,63,89,90,91,166
7	0.02	2	3ginA	CA	Rep, Mult	99,158,180,184
8	0.02	2	2bmzB	XLM	Rep, Mult	66,67,69,91,166
9	0.02	2	3t91A	MN	Rep, Mult	126,167
10	0.01	1	3mflB	DHY	Rep, Mult	50,66
11	0.01	1	2dsdB	AMP	Rep, Mult	183,184
12	0.01	1	2zyqB	TAR	Rep, Mult	55,56
13	0.01	1	3mxgD	XLS	Rep, Mult	167,177
14	0.01	1	1jacG	III	Rep, Mult	59,67,95,97,118,119,120,121,122,123,124
15	0.01	1	2wsc2	CLA	Rep, Mult	81,84,91
16	0.01	1	3e9tB	CA	Rep, Mult	99,158,184

	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	1kblA	0.390	5.38	0.041	0.665	2.7.9.1	NA
2	0.060	1eulA	0.278	5.90	0.016	0.495	3.6.3.8	NA
3	0.060	1k32A	0.374	5.90	0.087	0.680	3.4.21.-	NA
4	0.060	2w68C	0.294	5.72	0.038	0.505	3.2.1.18	105,126,180
5	0.060	2v5aB	0.373	5.29	0.063	0.612	6.3.4.14	54,122
6	0.060	2wybB	0.380	5.54	0.046	0.641	3.5.1.97	NA
7	0.060	1l9mB	0.382	5.93	0.076	0.684	2.3.2.13	NA
8	0.060	1y9mA	0.361	6.15	0.030	0.675	3.2.1.80	NA
9	0.060	1c9uB	0.365	6.00	0.016	0.680	1.1.5.2,1.1.99.17	NA
10	0.060	1a6qA	0.339	5.91	0.069	0.621	3.1.3.16	NA
11	0.060	1sllA	0.385	5.91	0.061	0.714	4.2.2.15	NA
12	0.060	1kc7A	0.392	5.44	0.042	0.670	2.7.9.1	NA
13	0.060	2vqdA	0.374	5.08	0.068	0.602	6.3.4.14,6.4.1.2	54
14	0.060	1sliA	0.382	5.98	0.061	0.714	4.2.2.15,3.2.1.18	NA
15	0.060	1f1sA	0.380	5.74	0.058	0.670	4.2.2.1	NA
16	0.060	1yniB	0.378	5.76	0.040	0.670	3.5.3.23	182
17	0.060	3dt7A	0.382	5.81	0.038	0.675	4.1.1.32	61
18	0.060	1cb8A	0.377	5.84	0.053	0.670	4.2.2.5	NA
19	0.060	1uwkA	0.391	5.73	0.033	0.684	4.2.1.49	96,121,171

(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	0.15	0.783	1.99	0.12	0.85	3x0uA	GO:0009405
1	0.08	0.548	2.62	0.09	0.65	3aqgB	GO:0001895 GO:0005576 GO:0005615 GO:0030246 GO:0070062
2	0.08	0.553	2.97	0.07	0.67	3apaA	GO:0005576 GO:0005578 GO:0005794 GO:0005796 GO:0006810 GO:0015031 GO:0030246 GO:0031012 GO:0031410 GO:0042589 GO:0060205
3	0.08	0.632	3.18	0.04	0.79	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
4	0.08	0.546	2.79	0.06	0.66	1xxqA	GO:0030246
5	0.07	0.511	2.73	0.04	0.61	1jotA	GO:0030246
6	0.07	0.625	3.37	0.06	0.80	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
7	0.07	0.624	3.23	0.04	0.79	1ji6A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
8	0.07	0.606	3.95	0.05	0.82	2c9kA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
9	0.07	0.593	3.61	0.06	0.78	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
10	0.07	0.576	4.18	0.06	0.80	1i5pA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
11	0.07	0.569	3.92	0.02	0.76	4d8mA	GO:0009405 GO:0030435
12	0.06	0.625	3.16	0.06	0.79	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
13	0.06	0.590	3.72	0.06	0.77	1ciyA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
14	0.06	0.332	6.09	0.05	0.63	4v6wAg	GO:0000398 GO:0005080 GO:0005737 GO:0005776 GO:0005829 GO:0005875 GO:0007626 GO:0009267 GO:0016243 GO:0018991 GO:0035220 GO:0042335 GO:0044829 GO:0045725 GO:0046716 GO:0048477 GO:0071011 GO:0071013 GO:0075522
15	0.06	0.298	6.24	0.02	0.56	4bvkB	GO:0016787
16	0.06	0.277	6.02	0.04	0.50	1xv2C	GO:0045151 GO:0047605
17	0.06	0.290	5.84	0.04	0.52	4k3vB	GO:0006810 GO:0007155 GO:0030001 GO:0046872
18	0.06	0.265	5.73	0.07	0.46	3o38A	GO:0004316 GO:0016491 GO:0055114 GO:0102132
19	0.06	0.256	5.61	0.04	0.44	2hhiA	GO:0005576 GO:0005618 GO:0009267
20	0.06	0.225	5.23	0.05	0.37	2rb4A	GO:0000166 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0006406 GO:0006417 GO:0006810 GO:0007275 GO:0007283 GO:0007286 GO:0010501 GO:0016787 GO:0030154 GO:0033391 GO:0051028
21	0.06	0.244	5.47	0.02	0.41	4pzkA	GO:0001510 GO:0003723 GO:0005737 GO:0006396 GO:0008033 GO:0008168 GO:0008173 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0032259
22	0.06	0.248	4.26	0.07	0.36	1yo7A	GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0005488
GO-Score	0.35
Biological Processes	GO:0051704
GO-Score	0.44
Cellular Component	GO:0070062	GO:0005615	GO:0005796	GO:0005578	GO:0060205	GO:0042589
GO-Score	0.08	0.08	0.08	0.08	0.08	0.08

(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.