I-TASSER results

I-TASSER results for job id Rv1593c

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

Input Sequence in FASTA format

>protein (236 residues)
MAHGSTAHEVLAVVFQVRGVGMSRGAAKPQLNVLLWQRAKEPQRGAWSLPGGRLRNDEDM
TSSVRRQLAEKVDLRELAHLEQLAVFSDPHRLPGIRMIASTYLGVVPSPATPELPADTRW
HPVSSLPPMAFDHGPMVTHARTRLIAKMSYTNIGFALAPKEFALSTLRDIYGAALGYQVD
ATNLQRVLARRRVITQTGTIAQSGRSGGRPAALYRFTDSQLRVTDEFAALRPPGQL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAHGSTAHEVLAVVFQVRGVGMSRGAAKPQLNVLLWQRAKEPQRGAWSLPGGRLRNDEDMTSSVRRQLAEKVDLRELAHLEQLAVFSDPHRLPGIRMIASTYLGVVPSPATPELPADTRWHPVSSLPPMAFDHGPMVTHARTRLIAKMSYTNIGFALAPKEFALSTLRDIYGAALGYQVDATNLQRVLARRRVITQTGTIAQSGRSGGRPAALYRFTDSQLRVTDEFAALRPPGQL
Prediction	CCCCCCCCEEEEEEEEHCCEEEEHCCCCCCEEEEEEEHCCCCCCCCEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEEEHCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEHCCCEHCCCCCCCCCCEEEHCCHHHHHCCCCCCCCCCCCCC
Conf.Score	99998765556899997554677656788669999985899989965588855899988999999999999899886544565546888778995799999987557777765544557887365565566489999999999999998575788878987889999999999969888988999999976986876965457888999864565787886446788777898889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAHGSTAHEVLAVVFQVRGVGMSRGAAKPQLNVLLWQRAKEPQRGAWSLPGGRLRNDEDMTSSVRRQLAEKVDLRELAHLEQLAVFSDPHRLPGIRMIASTYLGVVPSPATPELPADTRWHPVSSLPPMAFDHGPMVTHARTRLIAKMSYTNIGFALAPKEFALSTLRDIYGAALGYQVDATNLQRVLARRRVITQTGTIAQSGRSGGRPAALYRFTDSQLRVTDEFAALRPPGQL
Prediction	67464231200000010302011221557401000020544224320000012334433112001000243051542430321233431322442000000101224434244322201002034033332433400420042024205234102510465020530240011016461345203320473610351453466665432102003035731541562231335568
	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                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEEEEEEEEHCCEEEEHCCCCCCEEEEEEEHCCCCCCCCEHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEEEHCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEHCCCEHCCCCCCCCCCEEEHCCHHHHHCCCCCCCCCCCCCC
MAHGSTAHEVLAVVFQVRGVGMSRGAAKPQLNVLLWQRAKEPQRGAWSLPGGRLRNDEDMTSSVRRQLAEKVDLRELAHLEQLAVFSDPHRLPGIRMIASTYLGVVPSPATPELPADTRWHPVSSLPPMAFDHGPMVTHARTRLIAKMSYTNIGFALAPKEFALSTLRDIYGAALGYQVDATNLQRVLARRRVITQTGTIAQSGRSGGRPAALYRFTDSQLRVTDEFAALRPPGQL

3gz6A

0.29

0.26

0.89

2.78

MUSTER

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDCDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQASVSDVKWWPLADVMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASY-------RFLRNL

3gz6A

0.28

0.25

0.90

3.31

dPPAS

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASYRFLRNLE------

3gz6A

0.28

0.25

0.90

4.46

wdPPAS

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQAQIASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASYRFLRNLE------

3gz6A

0.30

0.26

0.89

3.38

wMUSTER

L------LTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDCDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQASVSDVKWWPLADVMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASY-------RFLRNL

3gz6A

0.30

0.26

0.89

4.61

wPPAS

L------LTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACIASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASY-------RFLRNL

3gz6A

0.28

0.25

0.90

5.67

dPPAS2

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASYRFLRNLE------

3gz6A

0.29

0.26

0.89

3.96

PPAS

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQACQASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASY-------RFLRNL

3gz6A

0.29

0.26

0.89

4.62

Env-PPAS

-----QLLTVDAVLFTYHD---------QQLKVLLVQRSNHPFLGLWGLPGGFIDEDESLEQTVLRKLAEKTAVV-PPYIEQLCTVGNNSRDARGWSVTVCYTALMSYQIQIASVSDVKWWPLADQMPLAFDHLQLIEQARERLTQKALYSLVPGFALSEPFTLPELQHVHEVLLGKPIQGKSFRRRVEQADLLIDTGLKRTE---RGRPANLYCLKPDTASY-------RFLRNL

2fb1C

0.30

0.27

0.88

2.57

MUSTER

SSNPTFYLGIDCIIFGFN----------GEISLLLLKRNFEPA-GEWSL-GGFVQKDESVDDAAKRVLAELTGLENV--YEQVGAFGAIDRDPGERVVSIAYYALININEYDRELHNAYWVNINELPALIFDHPEVDKAREK---QKASVEPIGFNLLPKLFTLSQLQSLYEAIYGE-PDKRNFRKRVAE-DFIEKTDKIDKLG--SKRGAALYKFNGKAYRKDPKFKL-------

2fb1C

0.30

0.27

0.89

3.04

dPPAS

SSNPTFYLGIDCIIFGFNE---------GEISLLLLKRNFEPA-GEWSL-GGFVQKDESVDDAAKRVLAELTGLENV--YEQVGAFGAIDRDPGERVVSIAYYALININEYDVQKHNAYWVNINELPALIFDHPEVDKAREK---QKASVEPIGFNLLPKLFTLSQLQSLYEAIYGE-PDKRNFRKRVAE-DFIEKTDKIDKLG--SKRGAALYKFNGKAYRKDPKFKL-------

(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 3 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=0.73

Estimated TM-score = 0.81±0.09

Estimated RMSD = 4.2±2.8Å

Download Model 2

C-score=-1.26

Download Model 3

C-score=-1.26

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	3gz6A	0.869	1.12	0.297	0.898
2	2fb1C	0.772	2.53	0.316	0.881
3	2fmlA	0.724	2.19	0.259	0.814
4	3i9xA	0.550	2.00	0.259	0.606
5	3fjyB	0.528	4.18	0.096	0.695
6	2r5wB	0.501	2.35	0.256	0.564
7	1x51A	0.500	2.66	0.152	0.576
8	1u20A	0.499	2.68	0.105	0.585
9	2qjoB	0.499	2.18	0.244	0.555
10	1qvjA	0.498	3.43	0.112	0.602

(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	0.22	10	3gz8D	APR	Rep, Mult	9,11,38,40,52,53,71,91,92,94,99,133
2	0.15	8	2a8rA	POP	Rep, Mult	11,38,51,52,53,67,71
3	0.11	4	3gz6B	QNA	Rep, Mult	165,182,185,203,207,208,209,211,212
4	0.06	4	2a8tB	UUU	Rep, Mult	11,37,38,49,51,52,53,67,71,99,130,132,133,136
5	0.05	2	3gz6A	QNA	Rep, Mult	180,182,183,186,187,190,209,210,233,234
6	0.05	3	2a8sA	MN	Rep, Mult	51,67,70,71
7	0.02	1	3i9x0	III	Rep, Mult	4,5,7,8,54,56,57,59,60,85,87,89,98,100

	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	0.208	2yvmA	0.476	3.02	0.142	0.568	3.6.1.-	38
2	0.111	1xsbA	0.494	3.09	0.126	0.602	3.6.1.17	NA
3	0.067	2w4eA	0.463	2.77	0.132	0.542	3.6.1.13	38
4	0.060	2j5wA	0.404	6.39	0.049	0.737	1.16.3.1	NA
5	0.060	1h16A	0.420	5.71	0.062	0.708	2.3.1.54	NA
6	0.060	2jfgA	0.393	5.56	0.052	0.657	6.3.2.9	NA
7	0.060	3ff6A	0.407	5.85	0.046	0.708	6.4.1.2,6.3.4.14	NA
8	0.060	1q33A	0.500	3.38	0.112	0.602	3.6.1.13	8,51
9	0.060	1hx3B	0.469	3.10	0.118	0.572	5.3.3.2	70
10	0.060	1v8mA	0.459	3.08	0.132	0.547	3.6.1.13	38,73
11	0.060	2gb5A	0.444	2.83	0.113	0.525	3.6.1.22	7,52,58
12	0.060	2pflA	0.417	5.74	0.057	0.703	2.3.1.54	137,142
13	0.060	1gqyB	0.400	5.56	0.051	0.657	6.3.2.8	NA
14	0.060	2a6tA	0.485	2.84	0.124	0.576	3.6.1.30	70
15	0.060	3hyqA	0.454	2.90	0.124	0.547	5.3.3.2	NA
16	0.060	2q9pA	0.420	2.64	0.136	0.487	3.6.1.52	NA
17	0.060	1gqqA	0.300	6.10	0.046	0.534	6.3.2.8	NA
18	0.060	2qb7A	0.391	5.51	0.022	0.652	3.6.1.11	NA
19	0.060	1mx9D	0.392	6.10	0.037	0.699	3.1.1.1	NA
20	0.060	2pnyA	0.464	3.36	0.081	0.589	5.3.3.2	37
21	0.060	2ewbA	0.402	5.47	0.029	0.657	3.4.11.1,3.4.11.5	NA
22	0.060	1b0pA	0.412	6.15	0.069	0.712	1.2.7.1	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	0.41	0.796	2.60	0.31	0.92	5bs6D	GO:0016787
1	0.37	0.869	1.12	0.30	0.90	3gz6A	GO:0016787
2	0.32	0.735	2.20	0.26	0.83	2fmlA	GO:0016787
3	0.22	0.480	2.70	0.26	0.56	3gg6A	GO:0000287 GO:0005829 GO:0009117 GO:0016787 GO:0034656 GO:0044715 GO:0044716 GO:0044717 GO:0046057 GO:0046067 GO:0046712 GO:0046872
4	0.21	0.527	1.72	0.33	0.56	3gz8C	GO:0016787
5	0.20	0.454	2.32	0.20	0.52	3o8sA
6	0.17	0.550	2.00	0.26	0.61	3i9xA	GO:0016787
7	0.17	0.471	3.01	0.18	0.55	2yyhA	GO:0016787
8	0.13	0.468	3.45	0.12	0.60	2kdvA	GO:0005737 GO:0006402 GO:0016787 GO:0016818 GO:0034353 GO:0046872 GO:0050779
9	0.12	0.470	3.04	0.17	0.57	5bonA	GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
10	0.12	0.470	2.34	0.13	0.53	3dkuA	GO:0016787
11	0.11	0.477	3.17	0.14	0.58	3f13B	GO:0016787
12	0.08	0.464	3.20	0.15	0.56	1su2A	GO:0000166 GO:0005524 GO:0016787
13	0.08	0.485	2.58	0.15	0.56	3q4iA	GO:0016787
14	0.07	0.529	4.05	0.10	0.69	3fjyB	GO:0016787
15	0.07	0.506	3.97	0.10	0.64	3fjyA	GO:0016787
16	0.07	0.493	2.93	0.13	0.59	1xsaA	GO:0000166 GO:0000302 GO:0004081 GO:0005525 GO:0005739 GO:0005759 GO:0006139 GO:0006915 GO:0008796 GO:0008803 GO:0016787
17	0.07	0.479	3.27	0.12	0.58	2qkmB	GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
18	0.07	0.480	2.60	0.16	0.55	1k2eA	GO:0016787
19	0.07	0.461	2.89	0.13	0.55	3fcmB	GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0017110
GO-Score	0.45	0.45
Biological Processes	GO:0046056	GO:0044282	GO:0046066	GO:0009181	GO:0009184	GO:0009154	GO:0046710	GO:0009155	GO:1901069
GO-Score	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45
Cellular Component	GO:0044444
GO-Score	0.45

(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.