I-TASSER results

I-TASSER results for job id Rv0990c

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

Input Sequence in FASTA format

>protein (218 residues)
MAESSLNPSLVSRISAFLRPDWTRTVRARRFAAAGLVMLAGVAALRSNPEDDRSEVVVAA
HDLRPGTALTPGDVRLEKRSATTLPDGSQADLDAVVGSTLASPTRRGEVLTDVRLLGSRL
AESTAGPDARIVPLHLADSALVDLVRVGDVVDVLAAPVTDSPAALRLLATDAIVVLVSAQ
QKAQAADSDRVVLVALPARLANTVAGAALGQTVTLTLH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MAESSLNPSLVSRISAFLRPDWTRTVRARRFAAAGLVMLAGVAALRSNPEDDRSEVVVAAHDLRPGTALTPGDVRLEKRSATTLPDGSQADLDAVVGSTLASPTRRGEVLTDVRLLGSRLAESTAGPDARIVPLHLADSALVDLVRVGDVVDVLAAPVTDSPAALRLLATDAIVVLVSAQQKAQAADSDRVVLVALPARLANTVAGAALGQTVTLTLH
Prediction	CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCCCCEHCCCCCEEEEEHCHHHCCCCCCCCHHHHCCEEEHCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCEEEEEEEHCCCCCCCCEEEEEHCCEEEEHCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHCCEEEEEHC
Conf.Score	98778898656666765688764589999999999999999999855777886589998677899877677657898857776998868998885786875568998666544446776444567998699999767764554679995899999578998865689986979999668878887887768999869999999999986685899989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MAESSLNPSLVSRISAFLRPDWTRTVRARRFAAAGLVMLAGVAALRSNPEDDRSEVVVAAHDLRPGTALTPGDVRLEKRSATTLPDGSQADLDAVVGSTLASPTRRGEVLTDVRLLGSRLAESTAGPDARIVPLHLADSALVDLVRVGDVVDVLAAPVTDSPAALRLLATDAIVVLVSAQQKAQAADSDRVVLVALPARLANTVAGAALGQTVTLTLH
Prediction	76655252422530431333422202100200001003111111123446674140000236054444046730423513572237421442440243304340454330254403454336443454210020414453113204341300000024676553131114503010023555566665320000003372044023115614030104
	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

CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCCCCEHCCCCCEEEEEHCHHHCCCCCCCCHHHHCCEEEHCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCEEEEEEEHCCCCCCCCEEEEEHCCEEEEHCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHHCCEEEEEHC
MAESSLNPSLVSRISAFLRPDWTRTVRARRFAAAGLVMLAGVAALRSNPEDDRSEVVVAAHDLRPGTALTPGDVRLEKRSATTLPDGSQADLDAVVGSTLASPTRRGEVLTDVRLLGSRLAESTAGPDARIVPLHLADSALVDLVRVGDVVDVLAAPVTDSPAALRLLATDAIVVLVSAQQKAQAADSDRVVLVALPARLANTVAGAALGQTVTLTLH

3teeA

0.17

0.14

0.83

0.93

MUSTER

GFSDEVVRSSPNLLPSCEQPAFSMKLWGNVNVVARCANEKRYLQVNVQA---TGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQAWR------------------------VKAGQRVQVIANGEGFSVNAEGQAMNNAQNARVRMTSGQIVSDSDGNILINL-SSSVDKLAAALE---------

3teeA

0.13

0.10

0.72

1.05

dPPAS

-------------------------------QDINAQLTTWFSQRLAGFSDETGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQAWRVKAG-----QRVQVIANGEGF--------SVNAEGQAMNNAAVAQNARVRMTIVSGTVDSDG--------NILINLSSSVDKLAAALE----------

3teeA

0.14

0.10

0.68

1.41

wdPPAS

-------------------------------QDINAQLTTWFSQRLAGFSDETGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQAWRVKA----G-QRVQVIANGEGFS---AVAQNARVRMTSGQ--------IVS-GTVDS------------DGNILINLSSSVDKLAAALE----------

3teeA

0.16

0.12

0.76

1.05

wMUSTER

RSSPNLLPS--EQPAFSMKLWGNVNVVAR--------------RYLQVNVQATGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQAWRVKA----G-QRVQVIANGEGFGQAMNVAQNARVRMTSGQ--------IVS-GTVDS------------DGNILINL-SSSVDKLAAALE---------

3teeA

0.17

0.12

0.72

1.49

wPPAS

LPQPAFSMKLWGNVNVVARANEKRYLQVNVQA--------------------TGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQA----WRVKAG-QRVQVIANGEGF---VAVAQNARVRMTSGQ--------IVS-GTVDS------------DGNILINLSDKLAAALE-------------

3teeA3

0.18

0.06

0.30

2.43

dPPAS2

-----------------------------------------------------GNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQA----------------------------------------------------------------------------------------------------

3teeA

0.17

0.13

0.80

1.36

PPAS

LAGFSDERSSPNLLPSCEQPAFSMKLWGNVNVVARCANEKRYLQVNVQA---TGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQA----WRVKAG-QRVQVIANGEGFS---AVAQNARVRMT-------------SGQIVSGT---------DSDGNILINL-SSSVDKLAAALE---------

3teeA

0.15

0.12

0.82

1.24

Env-PPAS

LAGFSDERSSPNLLPSCEQPAFSMKLWGNVNVVARCANEKRYLQVNVQA---TGNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQAWR----VKAG-QRVQVIANGEGFSNNAAVAQNARVRMTSG-------QIVSG--TVDS------------DGNILINL-SSSVDKLAAALE---------

5c17A

0.09

0.08

0.92

0.71

MUSTER

---KTELKKFYELLLAKLPK---ESVPILRTIFFSIRDESSLINQTGINTKTVQSVVKILAQRQM-IVREADQKIVGALGLSIIPTTNQIHLG---GRTLFAWCAISTLELSTALVADVDIHSRCAYTGEPIEVTVRNGKLAK-TTP-DSTVIWTVPFDSEAPWAGGTCKQIHYFSSVEHANKWKEEHPKLQGEIMTLEQALSFGNELK-KFLS----

3teeA3

0.18

0.06

0.30

0.96

dPPAS

-----------------------------------------------------GNYVAVAAPIARGGKLTPANVTLKRGRLDQLPPRTVLDIRQIQDAVSLRDLAPGQPVQLTMIRQA----------------------------------------------------------------------------------------------------

(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=-3.10

Estimated TM-score = 0.36±0.12

Estimated RMSD = 12.8±4.2Å

Download Model 2

C-score=-4.00

Download Model 3

C-score=-4.41

Download Model 4

C-score=-4.37

Download Model 5

C-score=-4.31

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	3teeA	0.655	3.37	0.140	0.798
2	3frnA	0.487	4.29	0.145	0.661
3	1t6bX	0.440	5.33	0.059	0.729
4	3lq2A	0.421	6.25	0.071	0.794
5	5do7A	0.415	5.72	0.074	0.716
6	3wssA	0.413	6.04	0.064	0.748
7	4zktB	0.411	5.92	0.063	0.739
8	4c4aA	0.410	6.05	0.059	0.761
9	5do7B	0.408	5.80	0.060	0.711
10	5cskA	0.407	6.27	0.075	0.748

(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	0.14	7	4fh2A	MA4	Rep, Mult	131,148,150,193
2	0.06	3	3s4lA	CA	Rep, Mult	192,218
3	0.06	3	2i13B	GOL	Rep, Mult	202,205
4	0.04	2	3tewA	MXE	Rep, Mult	66,67,68,99,101
5	0.02	1	4gosA	BMA	Rep, Mult	171,173
6	0.02	1	1y10C	CA	Rep, Mult	148,149
7	0.02	1	1qgdB	TPP	Rep, Mult	138,142,201,204
8	0.02	1	1t5bA	FMN	Rep, Mult	69,74
9	0.02	1	4dz2A	CA	Rep, Mult	152,153
10	0.02	1	1b0pA	SF4	Rep, Mult	137,143,144,145,146,147,176
11	0.02	1	4ryoA	MPG	Rep, Mult	200,204
12	0.02	1	5d92D	8K6	Rep, Mult	194,204
13	0.02	1	1thzA	326	Rep, Mult	138,195,197,198
14	0.02	1	2o8mB	III	Rep, Mult	40,42

	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	2ocaA	0.375	6.01	0.057	0.670	3.6.4.12	140,199,213
2	0.060	1p4rA	0.402	6.11	0.078	0.734	2.1.2.3,3.5.4.10	NA
3	0.060	1n1hA	0.374	6.13	0.052	0.665	2.7.7.48	217
4	0.060	1z0hB	0.335	6.26	0.036	0.633	3.4.24.69	196
5	0.060	2np0A	0.398	6.21	0.060	0.739	3.4.24.69	NA
6	0.060	1fohC	0.374	5.75	0.052	0.651	1.14.13.7	NA
7	0.060	3ikmD	0.377	6.21	0.054	0.711	2.7.7.7	75
8	0.060	1bglA	0.317	6.49	0.065	0.624	3.2.1.23	NA
9	0.060	1itzA	0.384	6.06	0.056	0.697	2.2.1.1	97,98
10	0.060	1rm6A	0.383	6.22	0.053	0.693	1.3.99.20	NA
11	0.060	1jroB	0.378	6.22	0.075	0.693	1.1.1.204	NA
12	0.060	1br2A	0.356	5.69	0.098	0.615	3.6.1.32	NA
13	0.060	2qtcB	0.425	6.22	0.042	0.794	1.2.4.1	132
14	0.060	1itzB	0.373	5.82	0.107	0.651	2.2.1.1	130,215
15	0.060	1ug9A	0.375	6.23	0.059	0.697	3.2.1.70	77
16	0.060	1jrpB	0.346	6.30	0.046	0.638	1.17.1.4	84,89
17	0.060	1l8aA	0.345	6.23	0.072	0.633	1.2.4.1	NA
18	0.060	2pdaA	0.400	6.06	0.047	0.711	1.2.7.1	203
19	0.060	2dkiA	0.391	5.56	0.039	0.656	1.14.13.23	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	0.30	0.655	3.37	0.14	0.80	3teeA	GO:0042597 GO:0044781
1	0.19	0.487	4.29	0.14	0.66	3frnA
2	0.06	0.382	6.08	0.09	0.71	2e6kA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
3	0.06	0.329	6.36	0.03	0.61	1ay0A	GO:0003824 GO:0004802 GO:0005737 GO:0006098 GO:0008152 GO:0016740 GO:0046872
4	0.06	0.387	6.18	0.07	0.72	3uptA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
5	0.06	0.375	6.01	0.06	0.67	2ocaA	GO:0000166 GO:0003677 GO:0004386 GO:0005524 GO:0016787
6	0.06	0.388	6.39	0.07	0.72	4xeuA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
7	0.06	0.380	6.02	0.04	0.68	4c7vA	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
8	0.06	0.406	5.88	0.08	0.72	4kxwA	GO:0003824 GO:0004802 GO:0005634 GO:0005654 GO:0005777 GO:0005829 GO:0005999 GO:0006098 GO:0008152 GO:0009052 GO:0016740 GO:0031982 GO:0040008 GO:0042803 GO:0043209 GO:0046166 GO:0046872 GO:0048037 GO:0070062
9	0.06	0.337	6.49	0.05	0.64	2j42A	GO:0005576 GO:0009405 GO:0051260
10	0.06	0.384	6.06	0.06	0.70	1itzA	GO:0003824 GO:0004802 GO:0008152 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0016740 GO:0019253 GO:0046872
11	0.06	0.366	6.53	0.04	0.70	2f2hA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0042802 GO:0061634 GO:0080176
12	0.06	0.328	6.07	0.04	0.60	3jcrV	GO:0000245 GO:0000398 GO:0005634 GO:0005654 GO:0005681 GO:0006397 GO:0007049 GO:0008270 GO:0008380 GO:0016579 GO:0036459 GO:0046872 GO:0051301
13	0.06	0.388	6.40	0.06	0.73	1r9jB	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
14	0.06	0.369	6.37	0.06	0.69	3m49A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
15	0.06	0.337	5.70	0.05	0.59	3rimA	GO:0003824 GO:0004802 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0008152 GO:0016740 GO:0040007 GO:0046872
16	0.06	0.334	6.49	0.03	0.65	3s5mA	GO:0003824 GO:0004222 GO:0006508 GO:0008270 GO:0016485 GO:0016787 GO:0020011 GO:0020020 GO:0042540 GO:0046872
17	0.06	0.440	5.54	0.07	0.74	4namA	GO:0000122 GO:0001933 GO:0005576 GO:0005615 GO:0005886 GO:0009405 GO:0010008 GO:0010629 GO:0035897 GO:0042802 GO:0043409 GO:0044533 GO:0046872 GO:0051260 GO:0061136 GO:0097300 GO:1903140
18	0.06	0.319	6.46	0.03	0.62	3s5kA	GO:0003824 GO:0004222 GO:0006508 GO:0008270 GO:0016485 GO:0016787 GO:0020011 GO:0020020 GO:0042540 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0016744	GO:0043169
GO-Score	0.36	0.36
Biological Processes	GO:0044781
GO-Score	0.30
Cellular Component	GO:0042597
GO-Score	0.30

(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.