I-TASSER results

I-TASSER results for job id Rv1628c

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

Input Sequence in FASTA format

>protein (163 residues)
MPEVTREEPAIDGWFTTDKAGNPHLLGGKCPQCGTYVFPPRADNCPNPACGSDTLESVGL
STRGKLWSYTENRYAPPPPYPAPDPFEPFAVAAVELADEGLIVLGKVVDGTLAADLKVGM
EMELTTMPLFADDDGVQRIVYAWRIPSRAGDDAERSDAEERRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPEVTREEPAIDGWFTTDKAGNPHLLGGKCPQCGTYVFPPRADNCPNPACGSDTLESVGLSTRGKLWSYTENRYAPPPPYPAPDPFEPFAVAAVELADEGLIVLGKVVDGTLAADLKVGMEMELTTMPLFADDDGVQRIVYAWRIPSRAGDDAERSDAEERRR
Prediction	CCCCCCCCCCCCCCHHHHHHHCCCEEEEHCCCCCEEEHCCCCCCCCCCCCCCCCCEEEHCCCEEEEEEEEEEHCCCCCCCCCCCCCCCEEEEEEEHCCCCCEEEEEHCCCCCHHHCCCCEEEEEEEEEEEHCCCCCEEEEEEEEHCCCCCCCCCCCCHHHCCC
Conf.Score	9988788998776567777765968999858999699599887788988888885899849969999999987589998777767898799999968999589998747888777778867999999856579985788878987889988766787566579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPEVTREEPAIDGWFTTDKAGNPHLLGGKCPQCGTYVFPPRADNCPNPACGSDTLESVGLSTRGKLWSYTENRYAPPPPYPAPDPFEPFAVAAVELADEGLIVLGKVVDGTLAADLKVGMEMELTTMPLFADDDGVQRIVYAWRIPSRAGDDAERSDAEERRR
Prediction	7673554323353231141175240103215612422012325313323032651432504450202000011243444244465331100000104743120102015435274041425030203514447523422122021256576565564665458
	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

CCCCCCCCCCCCCCHHHHHHHCCCEEEEHCCCCCEEEHCCCCCCCCCCCCCCCCCEEEHCCCEEEEEEEEEEHCCCCCCCCCCCCCCCEEEEEEEHCCCCCEEEEEHCCCCCHHHCCCCEEEEEEEEEEEHCCCCCEEEEEEEEHCCCCCCCCCCCCHHHCCC
MPEVTREEPAIDGWFTTDKAGNPHLLGGKCPQCGTYVFPPRADNCPNPACGSDTLESVGLSTRGKLWSYTENRYAPPPPYPAPDPFEPFAVAAVELADEGLIVLGKVVDGTLAADLKVGMEMELTTMPLFADDDGVQRIVYAWRIPSRAGDDAERSDAEERRR

3irbA

0.17

0.13

0.76

2.10

MUSTER

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSF-----QWPLRVKVD----------------------

3irbA

0.16

0.12

0.76

3.63

dPPAS

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPNIEGGLLCYAEGN-----VKVGAKAKILSF-----QWPLRVKVD----------------------

3irbA

0.17

0.13

0.74

4.09

wdPPAS

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSYC---EHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSFRVKVD-------------------------------

3irbA

0.17

0.13

0.76

2.55

wMUSTER

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSF-----QWPLRVKVD----------------------

3irbA

0.17

0.12

0.74

3.60

wPPAS

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRF-PNIEGGLLCYA----EGNVKVGAKAKILSFRVKVD-------------------------------

3irbA

0.17

0.13

0.74

11.72

dPPAS2

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSFRVKVD-------------------------------

3irbA

0.17

0.13

0.74

3.00

PPAS

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSFRVKVD-------------------------------

3irbA

0.16

0.12

0.76

3.74

Env-PPAS

VEAEREYTVGPAGEQFFNGLKQNKIIGSKCSKCGRIFVPARSY---CEHCFVKIENYVEINDEAYVDSYTIIYNDD----EGNKLAQPVYIALIRFPN-IEGGLLCYAEG----NVKVGAKAKILSFQWP--------LRVKVD-------------------

4tmdA

0.13

0.12

0.94

0.72

MUSTER

FGPVSEVAPTGIDPKLLSPQKLPEGVKFEPADCAKFAEGQQFP----PGLQGNMAATAAEGEGNRFIVMAVETSEPVPLSDPGDE------KRVKFLGTGARGQVDVVESPQIDDARVGTHRIIQTMRTGELYNDNYMVIVTANPLVLPDKPVAKVDTERARE

4r5oA4

0.08

0.06

0.67

1.12

dPPAS

----------------------------------QPAKGPYHSSPTIGVASETENIIYLVSTDGAIYKYILGDSDSLKAPFIAAESGVSITAPLQLNQQSGELYVTYTEERKD-----------ESKIVVYSKDGKVLHTVDCGESVPSQILFNN--------

(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=-0.80

Estimated TM-score = 0.61±0.14

Estimated RMSD = 6.6±4.0Å

Download Model 2

C-score=-2.15

Download Model 3

C-score=-1.29

Download Model 4

C-score=-3.23

Download Model 5

C-score=-3.06

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	3irbA	0.680	2.12	0.177	0.761
2	2wp8J	0.441	4.87	0.029	0.742
3	3go5A	0.439	4.26	0.050	0.675
4	4gopC	0.438	4.37	0.056	0.656
5	3ja84	0.436	4.32	0.073	0.656
6	3ja83	0.431	4.18	0.037	0.650
7	3kf8A	0.428	5.05	0.047	0.712
8	3ja87	0.428	4.06	0.129	0.632
9	1l1oC	0.427	4.08	0.025	0.614
10	1yrzA	0.426	5.29	0.045	0.779

(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	0.66	19	1e31A	ZN	Rep, Mult	30,33,47,50

	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	1d8yA	0.378	5.86	0.033	0.749	2.7.7.7	25
2	0.060	1e5mA	0.394	5.53	0.048	0.712	2.3.1.179	NA
3	0.060	2ckzB	0.413	3.91	0.026	0.607	2.7.7.6	67
4	0.060	2uvnA	0.386	5.18	0.086	0.669	1.14.-.-	NA
5	0.060	2ecfA	0.397	5.37	0.076	0.736	3.4.14.5	68,115
6	0.060	1kasA	0.400	5.67	0.048	0.724	2.3.1.179	111
7	0.060	1b3nA	0.389	5.33	0.034	0.681	2.3.1.179,2.3.1.41	NA
8	0.060	2r93G	0.385	3.98	0.051	0.571	2.7.7.6	123
9	0.060	1txgB	0.390	5.14	0.041	0.656	1.1.1.94	139
10	0.060	2zsgA	0.401	4.84	0.028	0.681	3.4.11.9	NA
11	0.060	3dfjA	0.320	5.55	0.082	0.595	3.4.21.-	24,105
12	0.060	3l24A	0.389	5.05	0.079	0.693	3.1.8.2,3.4.13.9,3.1.8.1	NA
13	0.060	1k9aB	0.388	4.07	0.043	0.583	2.7.10.2,2.7.1.112	115
14	0.060	2wk5A	0.382	4.98	0.067	0.656	2.4.2.4	NA
15	0.060	3d7uA	0.284	5.46	0.040	0.540	2.7.10.2	63
16	0.060	3hkzQ	0.401	3.95	0.039	0.589	2.7.7.6	89
17	0.060	1txgA	0.394	4.98	0.048	0.675	1.1.1.94	NA
18	0.060	1wqlA	0.396	4.57	0.025	0.638	1.14.12.-	NA
19	0.060	2c9hA	0.312	5.53	0.052	0.589	2.3.1.41	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	0.36	0.681	2.04	0.17	0.76	3irbA	GO:0046872
1	0.06	0.427	4.08	0.03	0.61	1l1oC	GO:0000082 GO:0000722 GO:0000723 GO:0000724 GO:0000784 GO:0003676 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005654 GO:0005662 GO:0006260 GO:0006261 GO:0006281 GO:0006283 GO:0006284 GO:0006289 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006297 GO:0006298 GO:0006310 GO:0006974 GO:0016605 GO:0016925 GO:0019985 GO:0033683 GO:0036297 GO:0042276 GO:0042769 GO:0046872 GO:0070987 GO:1900034 GO:1901796
2	0.06	0.429	5.23	0.04	0.77	4ifdJ	GO:0000049 GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0006364 GO:0016075 GO:0016787 GO:0043628 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071035 GO:0071038 GO:0071039 GO:0071042 GO:0071051 GO:0090502
3	0.06	0.401	5.23	0.05	0.72	4pmwA	GO:0000175 GO:0000176 GO:0000177 GO:0000287 GO:0000291 GO:0000932 GO:0003723 GO:0004518 GO:0004527 GO:0004540 GO:0005737 GO:0006364 GO:0006402 GO:0007049 GO:0007067 GO:0008266 GO:0008285 GO:0010587 GO:0016075 GO:0016787 GO:0019827 GO:0034427 GO:0046872 GO:0051301 GO:0051306 GO:0090501 GO:0090503 GO:1990074
4	0.06	0.393	4.34	0.04	0.59	1fguA	GO:0000082 GO:0000722 GO:0000723 GO:0000724 GO:0000784 GO:0003676 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005654 GO:0005662 GO:0006260 GO:0006261 GO:0006281 GO:0006283 GO:0006284 GO:0006289 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006297 GO:0006298 GO:0006310 GO:0006974 GO:0016605 GO:0016925 GO:0019985 GO:0033683 GO:0036297 GO:0042276 GO:0042769 GO:0046872 GO:0070987 GO:1900034 GO:1901796
5	0.06	0.372	4.94	0.02	0.61	2ix1A	GO:0000175 GO:0000178 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004540 GO:0005737 GO:0005829 GO:0006364 GO:0006401 GO:0006402 GO:0008859 GO:0016070 GO:0016787 GO:0090305 GO:0090501 GO:0090503
6	0.06	0.400	4.27	0.07	0.58	3u50C	GO:0003676 GO:0046872
7	0.06	0.362	3.93	0.03	0.52	2k5vA	GO:0003676
8	0.06	0.375	4.30	0.08	0.56	2k50A	GO:0003676 GO:0003677 GO:0006260 GO:0006281 GO:0006974 GO:0046872
9	0.06	0.327	5.55	0.02	0.60	2iqtA	GO:0003824 GO:0004332 GO:0006096 GO:0016829
10	0.06	0.365	4.26	0.04	0.55	1ynxA	GO:0000722 GO:0000724 GO:0000781 GO:0000794 GO:0003676 GO:0003677 GO:0003690 GO:0003697 GO:0005634 GO:0005662 GO:0005737 GO:0005829 GO:0006260 GO:0006265 GO:0006268 GO:0006281 GO:0006289 GO:0006310 GO:0006312 GO:0007004 GO:0007131 GO:0010833 GO:0016567 GO:0030491 GO:0043565 GO:0043934 GO:0045184 GO:0046872
11	0.06	0.324	5.51	0.03	0.61	4ro1B	GO:0000175 GO:0000176 GO:0000177 GO:0000291 GO:0000932 GO:0003723 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006364 GO:0008266 GO:0010587 GO:0016075 GO:0016787 GO:0034427 GO:0046872 GO:0090305 GO:0090503 GO:1990074
12	0.06	0.323	5.35	0.06	0.58	3jbwB	GO:0003677 GO:0003682 GO:0005546 GO:0005547 GO:0005634 GO:0006310 GO:0008270 GO:0016568 GO:0030098 GO:0030183 GO:0033077 GO:0033151 GO:0035064 GO:0035091 GO:0043325 GO:0046872 GO:0048534 GO:0048538 GO:0080025
13	0.06	0.312	5.48	0.06	0.60	1frvB	GO:0008901 GO:0016151 GO:0016491 GO:0042597 GO:0046872 GO:0047806 GO:0055114
14	0.06	0.305	5.31	0.05	0.56	4iedC	GO:0008658
15	0.06	0.308	5.16	0.06	0.52	3libA	GO:0000155 GO:0000160 GO:0004871 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0023014
16	0.06	0.300	5.64	0.05	0.59	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
17	0.06	0.313	5.75	0.05	0.62	3ii0C	GO:0003824 GO:0004069 GO:0004609 GO:0005634 GO:0005737 GO:0005739 GO:0005764 GO:0005829 GO:0006094 GO:0006103 GO:0006107 GO:0006114 GO:0006520 GO:0006531 GO:0006532 GO:0006533 GO:0006536 GO:0007219 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0019550 GO:0019551 GO:0030170 GO:0031406 GO:0032869 GO:0042802 GO:0043648 GO:0043679 GO:0047801 GO:0051384 GO:0055089 GO:0070062 GO:0080130
18	0.06	0.307	5.28	0.04	0.55	3li8A	GO:0000155 GO:0000160 GO:0004871 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0023014

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0097159	GO:1901363
GO-Score	0.48	0.35	0.35
Biological Processes	GO:0006283	GO:0000082	GO:0006298	GO:1900034	GO:0006293	GO:0006297	GO:0016925	GO:0000724	GO:0006296	GO:0036297	GO:0070987	GO:0000722	GO:1901796	GO:0006284	GO:0006294	GO:0042276	GO:0006261	GO:0006295	GO:0042769	GO:0071042	GO:0071038	GO:0071051	GO:0090502	GO:0000467	GO:0070481	GO:0071035	GO:0071028	GO:0071039	GO:0070651	GO:0070478	GO:1990074	GO:0008285	GO:0051301	GO:0019827	GO:0051306	GO:0010587
GO-Score	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0043231
GO-Score	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.