I-TASSER results

I-TASSER results for job id Rv0875c

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

Input Sequence in FASTA format

>protein (162 residues)
MKRGVATLPVILVILLSVAAGAGAWLLVRGHGPQQPEISAYSHGHLTRVGPYLYCNVVDL
DDCQTPQAQGELPVSERYPVQLSVPEVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTI
PTVDPQRGRLTGIVVQLLTLVVDHSGELRDVPHAEWSVRLIF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKRGVATLPVILVILLSVAAGAGAWLLVRGHGPQQPEISAYSHGHLTRVGPYLYCNVVDLDDCQTPQAQGELPVSERYPVQLSVPEVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTIPTVDPQRGRLTGIVVQLLTLVVDHSGELRDVPHAEWSVRLIF
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCEEEEHCCEEEHCCCCCCCCCCCCCCEEEHCCCCCEEEEHCCHHHHCCCEEEEEEEHCCCCCEEEEHCCCCCEEEEEHCCCCCCCCEEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEHC
Conf.Score	985468999999999999999999986478999986899999996899976788657888888899985688679996799986877755895899999689998678876998679999868999985899999854578769998577766899999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKRGVATLPVILVILLSVAAGAGAWLLVRGHGPQQPEISAYSHGHLTRVGPYLYCNVVDLDDCQTPQAQGELPVSERYPVQLSVPEVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTIPTVDPQRGRLTGIVVQLLTLVVDHSGELRDVPHAEWSVRLIF
Prediction	643402111113333213221111132355566530302021446324021221031452761547753250405773503040364027241301201324744554314474333130333658523020111322222316745544233022103336
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCEEEEHCCEEEHCCCCCCCCCCCCCCEEEHCCCCCEEEEHCCHHHHCCCEEEEEEEHCCCCCEEEEHCCCCCEEEEEHCCCCCCCCEEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEHC
MKRGVATLPVILVILLSVAAGAGAWLLVRGHGPQQPEISAYSHGHLTRVGPYLYCNVVDLDDCQTPQAQGELPVSERYPVQLSVPEVISRAPWRLLQVYQDPANTTSTLFRPDTRLAVTIPTVDPQRGRLTGIVVQLLTLVVDHSGELRDVPHAEWSVRLIF

4uicA

0.14

1.00

0.76

MUSTER

VNQYVSKVTDAFKAELQKAAQDAKAAYEAALTPKVESVSAIDSTKVTFTKPVDKATAIPLKGTETKLYPKSVEVSESLTATVTLYDTLVDGKTYTVVTLKDTAGTSTNEFTYNKPVPASITFNFNKLPEDSAVDLTKYVTVKDAAGNVIKSGFELEFTSSEK

4mjgA

0.14

0.13

0.96

0.73

dPPAS

ERVSIEEYISRQLPEISSVAVPVAAETGGELTVGLPYVQVCGTGDTQGYRVVGYTTVAPSS--FERLEKLVTENKPDWAVAVQVDKQIDRDA-TRGIQLIDNYGGLVEFKFSEDSIAVRSRSADPGQFVLPSVEEGHVTISDNTNPDLHPVPTLTTGA----

4ld1A1

0.11

0.06

0.55

0.71

wdPPAS

-------------------------------LPDGGRLVVFPNGTRKELSA--------------DGQTVKVMFFNGD-VKHTMP----DQR----VIYYYAEAQTTHITYPDGMEVLQFP--NNQ------TEKHFPKEITFPDQTVKTL-----------

4uicA

0.14

0.99

0.75

wMUSTER

VNQYVSKVTDAFKAELQKAAQDAKAAYEAALTPKVESVSAIDSTFKVTFKPVDKATAIPLKGTETKLYPKSVEVSESLTATVTLYDTLVDGKTYTVVTLKDTAGTSTNEFTYNKPVPASITFNFNKLPEDSAVDLTKYVTVKDAAGNVIKSGF-ELEFTSSE

4kmqA1

0.11

0.07

0.64

0.65

wPPAS

------------------------------------------DGEY---SPYGDDDLYTVQPTESPRDP-----KAGEDVILNIPIENGQDVWVEWTKNGVAQENVTAAYDYNSGWKADLGKFE------KGDEITYTTKGSTNGGT--AYESGPFTFYVT-

2micA

0.09

0.02

0.20

0.92

dPPAS2

LIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ---------------------------------------------------------------------------------------------------------------------------------

5ag8A

0.10

0.08

0.77

0.81

PPAS

-------------------------------VPTKMQVTAPANISASAQTFEVACDYNGIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGNKVTVIKDVKVEGKPYTVAVSGKT-----ITVESPAAGLTIFDMNGR--RVATAKNRMVFEA

1yocB

0.10

0.09

0.88

0.89

Env-PPAS

MSQMMQMYQQVGPAQFSAMIGQFAPYFASIA----PQFVELRPGYAEVTFPKRR-EVLNHIGTVHAIALCNAELAAGTMTDASIPA---GHRWIPRGMTVEYLA------KATGDVRAVADGSQIDWQAT--GNLVVPVVAYVDD---KPVFRAEITMYVSQ

1vw1A

0.11

0.98

0.72

MUSTER

GNIEPASLAMPEYLKRYYNLSDEELSQFIGKASNFGQQEYSNNQLITPVVNVKVYRITREYTTNAYQMDVELFPFGGENYRLDYKKNFYNASYLSIKL-NDKRELVRTEGAPQVNIEYSANITLNTADISQP--FEIGLTRVLPSGS-WAYAAAKFTVEEYN

5ag8A

0.09

0.07

0.76

0.73

dPPAS

----------------------------------VPTKMQVTAPANISASAQTFEVACDYNGASDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTIKDVKVEGKPYTVAVS-----GKTITVESPAAGLTIFDMNGRRVATAKNRMVFEAQN

(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=-4.21

Estimated TM-score = 0.27±0.08

Estimated RMSD = 15.0±3.5Å

Download Model 2

C-score=-4.52

Download Model 3

C-score=-4.61

Download Model 4

C-score=-3.46

Download Model 5

C-score=-4.98

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	3mk7A	0.485	5.19	0.047	0.809
2	3ayfA	0.482	5.15	0.086	0.809
3	2qe8A	0.479	4.49	0.057	0.765
4	2eceA	0.478	5.08	0.085	0.809
5	2yevA	0.476	4.85	0.043	0.747
6	4maeA	0.475	4.99	0.025	0.821
7	2d0vA	0.473	5.07	0.037	0.821
8	4xydA	0.472	5.28	0.063	0.784
9	1xmeA	0.468	4.79	0.055	0.747
10	2sliA	0.468	4.60	0.030	0.753

(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	3gl6A	ZN	Rep, Mult	55,63
2	0.06	3	1v0zD	UUU	Rep, Mult	17,96,108,136,137,138,139
3	0.04	2	1lshB	UPL	Rep, Mult	135,156
4	0.04	2	3mflB	DHY	Rep, Mult	51,52
5	0.04	2	1brrC	ARC	Rep, Mult	19,38,55
6	0.04	2	3jcuD	CLA	Rep, Mult	8,11,15
7	0.02	1	5l1gB	GYB	Rep, Mult	16,17
8	0.02	1	2hj6L	PS2	Rep, Mult	15,72
9	0.02	1	3zevA	GLY	Rep, Mult	2,127
10	0.02	1	2w4yA	CA	Rep, Mult	100,101
11	0.02	1	1dxoA	DQN	Rep, Mult	93,146
12	0.02	1	2cmlD	MAN	Rep, Mult	80,82,95,98
13	0.02	1	4ev6E	MG	Rep, Mult	20,136
14	0.02	1	4pr9B	PIO	Rep, Mult	2,3
15	0.02	1	1w20D	UUU	Rep, Mult	95,96,116,118,119
16	0.02	1	2cmlC	ZMR	Rep, Mult	89,91,92,113,114,115,116
17	0.02	1	1w20C	SIA	Rep, Mult	42,47,49,95,96
18	0.02	1	2cmlB	UUU	Rep, Mult	36,37,38,81,82,83

	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	1yiqA	0.436	5.32	0.038	0.759	1.1.99.-	NA
2	0.060	2cmlC	0.465	4.74	0.056	0.765	3.2.1.18	56,111
3	0.060	1occA	0.460	4.98	0.050	0.753	1.9.3.1	NA
4	0.060	1lrwA	0.469	5.09	0.050	0.827	1.1.99.8	NA
5	0.060	2d0vA	0.473	5.07	0.037	0.821	1.1.99.8	NA
6	0.060	1y9mA	0.441	4.86	0.076	0.741	3.2.1.80	NA
7	0.060	1m56A	0.454	4.58	0.044	0.710	1.9.3.1	NA
8	0.060	1ingA	0.460	4.95	0.049	0.778	3.2.1.18	NA
9	0.060	1pjxA	0.436	4.75	0.051	0.716	3.1.8.2	37
10	0.060	3dvaA	0.442	4.99	0.063	0.722	1.2.4.1	153
11	0.060	1w6sC	0.448	5.16	0.057	0.790	1.1.99.8	NA
12	0.060	2htrA	0.461	4.93	0.028	0.784	3.2.1.18	NA
13	0.060	2h2nA	0.438	5.09	0.069	0.765	3.6.1.6	39,72
14	0.060	1sliA	0.455	4.74	0.043	0.759	4.2.2.15,3.2.1.18	NA
15	0.060	3beqB	0.454	4.96	0.055	0.778	3.2.1.18	58
16	0.060	1kv9A	0.444	5.15	0.057	0.765	1.1.99.-	NA
17	0.060	3kf5A	0.442	4.85	0.044	0.728	3.2.1.26	NA
18	0.060	1w85C	0.433	4.94	0.057	0.716	1.2.4.1	NA
19	0.060	1ncaN	0.456	5.03	0.049	0.772	3.2.1.18	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	0.20	0.364	5.05	0.06	0.62	1l0qA	GO:0016020 GO:0016021
1	0.07	0.487	5.14	0.05	0.81	5djqA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
2	0.07	0.476	4.90	0.07	0.77	3eh3A	GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
3	0.07	0.476	4.85	0.04	0.75	2yevA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
4	0.07	0.472	5.28	0.06	0.78	4xydA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
5	0.07	0.464	5.18	0.09	0.76	3o0rB	GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
6	0.06	0.405	6.01	0.03	0.78	1flgA	GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
7	0.06	0.295	5.00	0.07	0.46	1qleA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
8	0.06	0.378	5.08	0.05	0.65	4l40A	GO:0005506 GO:0016705 GO:0020037 GO:0046872 GO:0055114
9	0.06	0.381	5.04	0.04	0.60	3ollA	GO:0000122 GO:0001046 GO:0001541 GO:0001662 GO:0003677 GO:0003700 GO:0003707 GO:0003713 GO:0004879 GO:0005496 GO:0005576 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005886 GO:0005929 GO:0006351 GO:0006355 GO:0006367 GO:0007165 GO:0007267 GO:0007611 GO:0008144 GO:0008270 GO:0008289 GO:0008584 GO:0008585 GO:0009414 GO:0009725 GO:0014070 GO:0014823 GO:0017085 GO:0019899 GO:0021549 GO:0021764 GO:0021854 GO:0030284 GO:0030308 GO:0030518 GO:0030520 GO:0030850 GO:0031667 GO:0032355 GO:0032993 GO:0033574 GO:0033595 GO:0034056 GO:0035690 GO:0038052 GO:0042493 GO:0042562 GO:0042975 GO:0043005 GO:0043025 GO:0043065 GO:0043204 GO:0043401 GO:0043523 GO:0043565 GO:0043627 GO:0044752 GO:0044849 GO:0045471 GO:0045742 GO:0045893 GO:0045909 GO:0045944 GO:0046872 GO:0048019 GO:0048471 GO:0048521 GO:0048662 GO:0050680 GO:0051091 GO:0060009 GO:0060011 GO:0060548 GO:0070374 GO:0071259 GO:0071392 GO:0071407 GO:0071548 GO:1900116 GO:1901215 GO:1902074 GO:1903924 GO:1903925 GO:1990239 GO:2000252 GO:2000378
10	0.06	0.478	5.08	0.09	0.81	2eceA	GO:0008430
11	0.06	0.323	5.45	0.04	0.57	3dbkA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872
12	0.06	0.306	5.45	0.02	0.56	3qq5A	GO:0005525
13	0.06	0.276	5.48	0.06	0.51	2ebfX	GO:0001907 GO:0004620 GO:0005543 GO:0005576 GO:0005737 GO:0016020 GO:0016021 GO:0020002 GO:0033644 GO:1990216
14	0.06	0.320	5.48	0.09	0.60	4htaA	GO:0005634 GO:0005737 GO:0005829 GO:0009640 GO:0009704 GO:0016787 GO:0080167
15	0.06	0.482	5.15	0.09	0.81	3ayfA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
16	0.06	0.329	5.85	0.06	0.64	3ilfA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0042597
17	0.06	0.309	4.82	0.04	0.49	2vcvA	GO:0004364 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0016740 GO:0070062 GO:1901687
18	0.06	0.334	5.48	0.06	0.63	3cb3A	GO:0003824 GO:0008152 GO:0008867 GO:0009063 GO:0016829 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0046906	GO:0016676	GO:0015002	GO:0015078
GO-Score	0.47	0.47	0.47	0.47	0.47
Biological Processes	GO:0045333	GO:0015992	GO:0098662	GO:0016310	GO:0046034
GO-Score	0.47	0.47	0.47	0.37	0.37
Cellular Component	GO:0016021	GO:0071944
GO-Score	0.39	0.37

(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.