I-TASSER results

I-TASSER results for job id Rv1401

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

Input Sequence in FASTA format

>Rv1401 (200 residues)
MLQPAFKASMAVLLAAAAVAHPIGRERRWLVPALLLSATGDWLLAIPWWTWAFVFGLGAF
LLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNLTIPVTVYIV
ALSAMVCTALLARLPTIWTAVGAVCFAASDSMIGIGRFILGNEALAVPIWWSYAAAEILI
TAGFFFGREVPDNAAAPTDS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLQPAFKASMAVLLAAAAVAHPIGRERRWLVPALLLSATGDWLLAIPWWTWAFVFGLGAFLLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNLTIPVTVYIVALSAMVCTALLARLPTIWTAVGAVCFAASDSMIGIGRFILGNEALAVPIWWSYAAAEILITAGFFFGREVPDNAAAPTDS
Prediction	CCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	98778799999999999998898755689999999999977997589986643458999999999999999765567777656899999999999999999986579988634888999999999999999869888999999999998788776556667775557999999999999999855477778777888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLQPAFKASMAVLLAAAAVAHPIGRERRWLVPALLLSATGDWLLAIPWWTWAFVFGLGAFLLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNLTIPVTVYIVALSAMVCTALLARLPTIWTAVGAVCFAASDSMIGIGRFILGNEALAVPIWWSYAAAEILITAGFFFGREVPDNAAAPTDS
Prediction	72321020200220021013144442210000002102200200023235320020010000001000100132143333332221102111122222221013323354020000000000000000001133422000200110030023003311131043131100201331032002011333544654555488
	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

CCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
MLQPAFKASMAVLLAAAAVAHPIGRERRWLVPALLLSATGDWLLAIPWWTWAFVFGLGAFLLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNLTIPVTVYIVALSAMVCTALLARLPTIWTAVGAVCFAASDSMIGIGRFILGNEALAVPIWWSYAAAEILITAGFFFGREVPDNAAAPTDS

5jkiA

0.18

0.17

0.93

0.91

MUSTER

MYKPVSLFLFFLILAAAIHTNAVQSADEAISKAAVLIRQ-PWLNEV--MTGITHLGASSFLLPLIVIIGAGMFFYRKTWDGLLMLLVFGTDRLLNKVLKEWIFAPLVHESSF-GHSMNAACVYPVIAYFLVKHLPFLHKKMVYIIAGVIAVLVGISRVYLG--VTDVLGGFSLGLLLFFLVKGFDEKIKRFR--------

4ke2A

0.15

0.97

1.08

dPPAS

NIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATA----ATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-

2mgyA

0.10

0.08

0.82

1.11

wdPPAS

----MPESWVPAVGLTLVPS-----LGGFMGAYFVRGEGLRWYAGLPSWH-RWTLAPIWGTLYSAMGYGSYIVWKELGGFTEDAMVPLGLYTGQLALNWAWPPIFFGARQMGWALADLLLVSGVATATTLAWHRVSPPAARLLY----------------------YLAWLAFATVLNYYVWRDNSGRRGGSRLAE----

3wajA

0.17

0.16

0.95

1.07

wMUSTER

AFIPAIGGVLAILPVYLLTRE-VFDKRAAVIAAFLIAIVGQFLQRILGFNDHHIWEAFWQVSALGTFLLAYN-RWKGHDLTARQ-MAYPVIAGITIGLYVLSWGAG----FIIAPIILAFMFFAFVLAGFVNADRKNLSLVAVVTFAVSALIYLP--FAFNYPGFSTPFQLLVLLGSAVIAAAFYQIEKWNDVGRVGLGR

4zowA2

0.17

0.14

0.83

1.05

wPPAS

LLKELGRDYKLVL-------------GRFVAGALALGFVSLPLLA-P----LQVPIFGALIAGNLLLARLT----RRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRLTLDTVSAAMGMLQMLIFTVGIEISKHAWLNGGNGLFNLFNLVNGILWLSLMVIFLK------------

5i20A

0.14

0.94

1.91

dPPAS2

A--GLVAYLWPLLIVLFSAFLPGERLRPAHVAGALMGLAGTVVLLGARAGGFYVPGYLAAAACAVIWSVYSVASRRFARVPTEVVAGFCLATAALSALCHILFEPSVWPVGSLAVVALGIGIAFYTWDIGMKRGDVRLLGVLSYAAPVLSTLLLV---VAGFAAPS----GALAIACALIVGGAAVATLLARRLES----

4zowA2

0.16

0.14

0.82

0.99

PPAS

SLKELGRDYKLVL-------------GRFVAGALALGFVSLPLLA-P----LQVPIFGALIAGNLLLARLT----RRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRL-KGTVSAAMGMLQMLIFTVGIEISKHAWLNGGNGLFNLFNLVNGILWLSLMVIFLK------------

3h2zA1

0.17

0.16

0.94

0.70

Env-PPAS

ALHNIGRGFIGKLLADAGIQLTFADVNQVVLDALNARHSYQVHVVGETEQVDTVSGVNAVSSIGDDVVDLIAQ-VDLVTTAVGPVVLERIAPAIAKGLVKRKEQGNE-SPLNI-IACENVRGTTQLKGHVNALPEDAKAWVEEHVFV--DSAV--DRIVPPNDPLEVTV-ETFS--EWIVDKTQFKGA-LPNIPGELTDN

4m58A

0.14

0.98

0.91

MUSTER

YLSPQTCAVMGAAMVPVLTVA-AKKVNKSFKDVPAMAIGSAFAFTIPIPGGTTAATLLATTLPWAASISLTLALFIQAGGILALGANSFNMAFIAPFVGYGIYRLMLSLKLNKVLSSAIGGYVGINAAALAT---AIELGLQPLLFHTANGTPLYFPYGLAIPAMMFAHLTVAGIVEAVITGLVVYQKVDEEKFSYRLRG

4pgrA

0.09

0.90

1.02

dPPAS

---------------HESKQSIMQRILTVFVFTLLIATVGLFIGQFVPVALM-----LPLSILEVAMIILAFWMRRRKAVGYAFVYTFAFVSGITLFPIVSHYASIAGAY-VVLEAFGSTFVIFAVLGTIGAKMKKDLSFLWSFLLVAVLALAVVGIFNIFSPLNSAAMMAYSVIGTIVFSLYILYDLNQIKHRHITEDL

(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=-2.74

Estimated TM-score = 0.40±0.13

Estimated RMSD = 11.7±4.5Å

Download Model 2

C-score=-3.14

Download Model 3

C-score=-2.93

Download Model 4

C-score=-4.17

Download Model 5

C-score=-3.99

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	5i20A	0.655	4.23	0.134	0.930
2	5doqB	0.574	5.09	0.056	0.930
3	2innA	0.564	4.78	0.068	0.870
4	1mhzD	0.555	5.07	0.067	0.885
5	3vvnA	0.552	4.29	0.071	0.795
6	5doqA	0.550	5.39	0.088	0.930
7	3mktA	0.546	4.61	0.080	0.835
8	2j8sA	0.546	4.68	0.058	0.840
9	3jd8A3	0.539	5.15	0.073	0.890
10	4mt1A2	0.532	4.89	0.078	0.845

(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	1xvgB	BRJ	Rep, Mult	10,11,15,64,72
2	0.07	4	3sidA	FE	Rep, Mult	5,8,38,180
3	0.07	4	3wu2D	CLA	Rep, Mult	146,149,152,153,177
4	0.04	2	1smyF	MG	Rep, Mult	114,115,118
5	0.04	2	2dyrD	PGV	Rep, Mult	139,143,146
6	0.02	1	2q69A	CA	Rep, Mult	136,153,154
7	0.02	1	1xvgC	BRJ	Rep, Mult	53,56,60
8	0.02	1	4o6mB	MPG	Rep, Mult	121,122
9	0.02	1	1xveA	3BB	Rep, Mult	42,45,46,53,54
10	0.02	1	4kvrA	6NA	Rep, Mult	7,8,11,37,140,143,144,146,147,180
11	0.02	1	3pf7B	FE	Rep, Mult	5,41,44,176
12	0.02	1	2np5C	NDS	Rep, Mult	78,79,81,85
13	0.02	1	2qx6A	ML1	Rep, Mult	138,183
14	0.02	1	1xvfA	3CL	Rep, Mult	30,34,180,182,183
15	0.02	1	3e6sA	FE	Rep, Mult	12,34,38,144,183
16	0.02	1	2o012	CLA	Rep, Mult	129,133
17	0.02	1	1sezA	TON	Rep, Mult	28,46,98,102

	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	2p0mA	0.513	4.73	0.049	0.800	1.13.11.33	NA
2	0.060	2iukA	0.501	4.83	0.073	0.810	1.13.11.12	NA
3	0.060	2yr4A	0.484	5.54	0.094	0.835	1.13.12.9	143
4	0.060	2j2fA	0.475	4.16	0.014	0.690	1.14.19.2,1.14.99.6	NA
5	0.060	2uw1B	0.449	4.26	0.043	0.675	1.14.99.6	NA
6	0.060	3e6sF	0.498	3.75	0.089	0.675	1.16.3.1	151
7	0.060	1no3A	0.503	4.75	0.057	0.775	1.13.11.12	NA
8	0.060	3ee4A	0.468	4.31	0.074	0.705	1.17.4.1	NA
9	0.060	3bvlF	0.482	3.92	0.059	0.675	1.16.3.1	46,176
10	0.060	1xpmC	0.482	5.27	0.050	0.775	2.3.3.10	NA
11	0.060	1mfrW	0.485	4.10	0.073	0.680	1.16.3.1	9
12	0.060	3kvnX	0.477	5.39	0.043	0.795	3.1.1.1	113
13	0.060	1r03A	0.451	3.73	0.062	0.620	1.16.3.1	151,180
14	0.060	2wlaA	0.477	3.74	0.089	0.640	1.16.3.1	35,37,175
15	0.060	2e9eA	0.480	4.86	0.072	0.745	1.11.1.7	NA
16	0.060	1mhyD	0.544	5.12	0.064	0.875	1.14.13.25	NA
17	0.060	1z7hA	0.470	5.14	0.053	0.775	3.4.24.68	173
18	0.060	2v4wD	0.483	5.75	0.053	0.830	2.3.3.10	8
19	0.060	1eumE	0.494	3.61	0.030	0.670	1.16.3.1	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	0.10	0.659	4.15	0.13	0.93	5i20E	GO:0016020 GO:0016021
1	0.08	0.544	5.12	0.06	0.88	1mhyD	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
2	0.07	0.553	4.10	0.09	0.80	5i20F	GO:0016020 GO:0016021
3	0.07	0.556	4.22	0.05	0.79	4mlbB	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
4	0.07	0.546	4.61	0.08	0.83	3mktA
5	0.07	0.553	4.24	0.06	0.79	3vvpA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
6	0.07	0.541	4.47	0.04	0.79	5c6nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
7	0.07	0.514	4.16	0.07	0.73	4z3nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
8	0.07	0.550	5.39	0.09	0.93	5doqA	GO:0016020 GO:0016021
9	0.06	0.533	5.25	0.10	0.89	1fziA	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
10	0.06	0.496	5.19	0.05	0.81	3dhiA	GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
11	0.06	0.574	5.09	0.06	0.93	5doqB	GO:0016020 GO:0016021 GO:0055114
12	0.06	0.406	5.66	0.04	0.72	4zlfA	GO:0003824 GO:0005975 GO:0030246
13	0.06	0.403	5.85	0.03	0.72	4ffcA	GO:0003824 GO:0003867 GO:0008483 GO:0009448 GO:0016740 GO:0030170
14	0.06	0.388	4.20	0.03	0.56	3eiwA
15	0.06	0.350	4.96	0.07	0.56	1qkiF	GO:0004345 GO:0005536 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005829 GO:0005975 GO:0006006 GO:0006098 GO:0006629 GO:0006695 GO:0006739 GO:0006740 GO:0006749 GO:0009051 GO:0009898 GO:0010734 GO:0014070 GO:0016020 GO:0016491 GO:0019322 GO:0021762 GO:0030246 GO:0032094 GO:0034599 GO:0042802 GO:0042803 GO:0043231 GO:0043249 GO:0043523 GO:0045471 GO:0046390 GO:0050661 GO:0051156 GO:0055114 GO:0070062
16	0.06	0.335	5.58	0.05	0.56	4yprA	GO:0003677 GO:0003824 GO:0006281 GO:0006284 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0019104 GO:0046872 GO:0051536 GO:0051539
17	0.06	0.496	5.40	0.06	0.84	2incA	GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
18	0.06	0.572	4.88	0.06	0.88	2innA	GO:0006725 GO:0016491 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0015049	GO:0015297	GO:0015238
GO-Score	0.08	0.08	0.07	0.07
Biological Processes	GO:0006725	GO:0006730	GO:0055114	GO:0006855
GO-Score	0.08	0.08	0.08	0.07
Cellular Component	GO:0031224
GO-Score	0.34

(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.