I-TASSER results

I-TASSER results for job id Rv1871c

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

Input Sequence in FASTA format

>protein (129 residues)
MNAAMNLKREFVHRVQRFVVNPIGRQLPMTMLETIGRKTGQPRRTAVGGRVVDNQFWMVS
EHGEHSDYVYNIKANPAVRVRIGGRWRSGTAYLLPDDDPRQRLRGLPRLNSAGVRAMGTD
LLTIRVDLD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNAAMNLKREFVHRVQRFVVNPIGRQLPMTMLETIGRKTGQPRRTAVGGRVVDNQFWMVSEHGEHSDYVYNIKANPAVRVRIGGRWRSGTAYLLPDDDPRQRLRGLPRLNSAGVRAMGTDLLTIRVDLD
Prediction	CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEHCCCCCCEEEEEEEEEEHCCEEEEEHCCCCCCHHHEHCCCCCEEEEEHCCEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEHCC
Conf.Score	987566788999998464446544568889999958989977889889999699899997699996565433339869999989899999998797568999999887655666665445658988769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNAAMNLKREFVHRVQRFVVNPIGRQLPMTMLETIGRKTGQPRRTAVGGRVVDNQFWMVSEHGEHSDYVYNIKANPAVRVRIGGRWRSGTAYLLPDDDPRQRLRGLPRLNSAGVRAMGTDLLTIRVDLD
Prediction	556255234302430343222323433410102022143444241101214364200000132631300200343350304246643503133246744440044135334322322344312030338
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEHCCCCCCEEEEEEEEEEHCCEEEEEHCCCCCCHHHEHCCCCCEEEEEHCCEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEHCC
MNAAMNLKREFVHRVQRFVVNPIGRQLPMTMLETIGRKTGQPRRTAVGGRVVDNQFWMVSEHGEHSDYVYNIKANPAVRVRIGGRWRSGTAYLLPDDDPRQRLRGLPRLNSAGVRAMGTDLLTIRVDLD

3r5zA

0.19

1.00

2.79

MUSTER

SPSDWARKQVETYENSGGTEGTTLQGKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVWPDYAEYQTKEIPVFVLTPR

3r5zA

0.20

0.99

4.37

dPPAS

PSDWARKQVETYENSGGTEGTTLQ-GKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVWPDYAEYQTKTTREIPVFVL

3r5yA

0.18

0.99

4.67

wdPPAS

PSEWIGNQVAQYEASDGAEAGEFD-GRPLVILTTVGRKTGALRKTPVMRVEHDGRYAVVASQGTHPAWYFNLVADPRAQLRDKDAVLSVVARELAGPERAEWWERAVRAYPTYQEYQDNTRRVLLLEPG

3r5zA

0.19

0.98

3.33

wMUSTER

PSDWARKQVETYENSGGTEGTTL-QGKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVWPDYAEYQTKTT-VFVLTPR

3r5zA

0.21

0.20

0.95

4.11

wPPAS

PSDWARKQVETYENSGGTEGTTL-QGKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVW---PDYAEYQTKTTR---E

3r5zA

0.20

0.19

0.93

8.08

dPPAS2

PSDWARKQVETYENSGGTEGTTLQ-GKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVWPDYAEYQTKT--------T

3r5zA

0.21

0.20

0.95

3.63

PPAS

PSDWARKQVETYENSGGTEGTTL-QGKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVW---PDYAEYQTKTTR---E

3r5zA

0.19

0.99

4.04

Env-PPAS

PSDWARKQVETYENSGGTEGTTL-QGKPVVVLTTKGAKTGKLRKTPLMRVEHNGEYAVVASLGKHPVWYHNIKAEPHVELRDGTEVGDYTAREVTGEEKRVWWERAVEVWPDYAEYQTKEIPVFVLTPR

3r5yA

0.19

1.00

2.74

MUSTER

VPSPSEWIGNQVAQYEASAEAGEFDGRPLVILTTVGRKTGALRKTPVMRVEHDGRYAVVASQGTHPAWYFNLVADPRAQLRDKDAVLSVVARELAGPERAEWWERAVRAYPTYQEYQDNLIPVLLLEPG

3r5yA

0.20

0.99

4.30

dPPAS

PSEWIGNQVAQYEASDGAEAGEFD-GRPLVILTTVGRKTGALRKTPVMRVEHDGRYAVVASQGTHPAWYFNLVADPRAQLRDKDAVLSVVARELAGPERAEWWERAVRAYPTYQEYQDNTRRLIPVLLL

(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=1.09

Estimated TM-score = 0.86±0.07

Estimated RMSD = 2.4±1.8Å

Download Model 2

C-score=-4.82

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.03

Download Model 5

C-score=1.06

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	3r5zA	0.945	1.04	0.180	0.992
2	3r5yA	0.907	1.62	0.180	0.992
3	3h96A	0.766	2.27	0.115	0.946
4	4y9iA	0.750	1.64	0.196	0.830
5	3r5lA	0.698	2.34	0.248	0.806
6	4zkyA	0.682	2.29	0.164	0.798
7	3dnhA1	0.679	2.07	0.115	0.783
8	5bncA1	0.678	2.07	0.107	0.783
9	2arzA	0.675	2.27	0.113	0.791
10	1vl7A	0.669	2.04	0.150	0.783

(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	28	3r5wM	F42	Rep, Mult	29,36,37,38,39,43,45,46,47,48,59,60,61,62,66,67,68,70,71,113
2	0.03	2	2iab0	III	Rep, Mult	29,31,33,34,35,36,37,40,41,42,43,44,46,75,77,79,80,81,86
3	0.03	2	3gasB	UUU	Rep, Mult	59,60,65,66,68,115,116,122
4	0.01	1	2ou5A	FMN	Rep, Mult	32,80,82,87
5	0.01	1	1vl70	III	Rep, Mult	28,29,31,33,35,40,41,42,43,44,46,48,60,65,66,77,79,81,110,114
6	0.01	1	3in6B	FMN	Rep, Mult	54,58,127

	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	1nrgA	0.574	3.08	0.108	0.775	1.4.3.5	NA
2	0.060	1jnwA	0.570	3.23	0.158	0.744	1.4.3.5	44
3	0.060	1rs0A	0.433	4.19	0.019	0.667	3.4.21.47	61
4	0.060	1gvhA	0.468	4.57	0.047	0.752	1.14.12.17	NA
5	0.060	1qtfA	0.454	4.47	0.054	0.705	3.4.21.-	NA
6	0.060	2puxB	0.434	4.65	0.057	0.729	3.4.21.5	NA
7	0.060	2vdcA	0.457	3.88	0.060	0.698	1.4.1.13	NA
8	0.060	1arbA	0.472	3.59	0.038	0.682	3.4.21.50	NA
9	0.060	2ok5A	0.470	4.10	0.036	0.713	3.4.21.47	NA
10	0.060	3rp2A	0.464	4.53	0.100	0.713	3.4.21.-	91,105
11	0.060	1a5iA	0.453	4.56	0.082	0.713	3.4.21.68	NA
12	0.060	1kynB	0.454	4.32	0.178	0.698	3.4.21.20	NA
13	0.060	1mkwK	0.413	4.27	0.043	0.659	3.4.21.5	NA
14	0.060	3lkwA	0.456	3.21	0.021	0.628	3.6.4.13,3.6.1.15,3.4.21.91	NA
15	0.060	1riwB	0.428	4.02	0.075	0.659	3.4.21.5	62
16	0.060	1cqxB	0.461	4.26	0.051	0.721	1.14.12.17	100
17	0.060	1ky9B	0.462	3.87	0.094	0.674	3.4.21.-	NA
18	0.060	2vdcF	0.455	3.97	0.089	0.705	1.4.1.13	NA
19	0.060	1ucyE	0.360	3.41	0.055	0.512	3.4.21.5	53,56

(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	0.47	0.903	1.39	0.17	0.98	3r5yD	GO:0010181 GO:0016491 GO:0055114
1	0.41	0.945	1.04	0.18	0.99	3r5zA	GO:0016491 GO:0055114
2	0.36	0.742	1.64	0.20	0.82	4y9iA	GO:0016491 GO:0055114
3	0.29	0.708	2.32	0.24	0.81	3r5lA	GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
4	0.26	0.797	2.24	0.12	0.98	3h96C	GO:0016491 GO:0055114
5	0.24	0.682	2.29	0.16	0.80	4zkyA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
6	0.22	0.640	2.23	0.14	0.77	2asfA	GO:0004733 GO:0005576 GO:0005618 GO:0010181 GO:0016491 GO:0042823 GO:0055114
7	0.22	0.585	2.96	0.16	0.74	2htdB	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
8	0.21	0.630	2.87	0.18	0.78	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
9	0.21	0.610	2.60	0.15	0.74	5escA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
10	0.20	0.603	3.14	0.17	0.77	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
11	0.19	0.667	2.13	0.10	0.78	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
12	0.16	0.626	2.49	0.16	0.75	2hq9B	GO:0000166 GO:0010181 GO:0016491 GO:0055114
13	0.16	0.602	2.56	0.15	0.76	2hq7B	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
14	0.15	0.669	2.04	0.15	0.78	1vl7A	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
15	0.10	0.570	2.70	0.12	0.73	3dmbA	GO:0010181 GO:0016491 GO:0055114
16	0.06	0.352	5.21	0.01	0.68	1yb5A	GO:0003723 GO:0003730 GO:0003960 GO:0005737 GO:0005829 GO:0007601 GO:0008270 GO:0016491 GO:0042178 GO:0051289 GO:0055114 GO:0070062 GO:0070402 GO:0070404
17	0.06	0.401	4.55	0.04	0.67	3uw1A	GO:0004751 GO:0006098 GO:0009052 GO:0016853
18	0.06	0.294	5.24	0.04	0.57	3ag6A	GO:0000166 GO:0004592 GO:0005524 GO:0005737 GO:0015940 GO:0016874
19	0.06	0.325	5.03	0.05	0.58	3o3fA	GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004523 GO:0005737 GO:0006298 GO:0006401 GO:0016787 GO:0030145 GO:0032299 GO:0043137 GO:0046872 GO:0090305 GO:0090502
20	0.06	0.311	4.73	0.05	0.53	3ct8A	GO:0046872
21	0.06	0.331	4.13	0.06	0.53	3j79M	GO:0003735 GO:0005840 GO:0006412 GO:0022625 GO:0030529 GO:0070180
22	0.06	0.306	4.50	0.06	0.51	2btfP	GO:0003779 GO:0005737 GO:0005856 GO:0030036 GO:0030833 GO:0032233
23	0.06	0.311	4.04	0.05	0.47	1qfwI	GO:0003823
24	0.06	0.252	4.93	0.04	0.47	1fj0A	GO:0009055 GO:0015979 GO:0020037 GO:0046872 GO:0055114
25	0.06	0.285	5.36	0.04	0.57	1tceA	GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001784 GO:0005068 GO:0005088 GO:0005154 GO:0005158 GO:0005159 GO:0005168 GO:0005543 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005886 GO:0007165 GO:0007173 GO:0007176 GO:0007265 GO:0007507 GO:0007568 GO:0008284 GO:0008286 GO:0009636 GO:0010008 GO:0014070 GO:0016032 GO:0016337 GO:0030036 GO:0030182 GO:0030971 GO:0031100 GO:0031175 GO:0031532 GO:0032403 GO:0032868 GO:0032869 GO:0035094 GO:0035556 GO:0036498 GO:0038095 GO:0038128 GO:0040008 GO:0042127 GO:0042542 GO:0043547 GO:0045740 GO:0045907 GO:0046875 GO:0048661 GO:0050900 GO:0051219 GO:0051384 GO:0051721 GO:0070435 GO:0071363
26	0.06	0.254	4.80	0.06	0.45	5dfsA	GO:0005739 GO:0005758 GO:0005829 GO:0006915 GO:0009055 GO:0020037 GO:0045155 GO:0046872 GO:0055114 GO:0070469

Consensus prediction of GO terms

Molecular Function	GO:0016491	GO:0010181	GO:0050662
GO-Score	0.89	0.63	0.58
Biological Processes	GO:0055114
GO-Score	0.89
Cellular Component	GO:0030312	GO:0016020
GO-Score	0.58	0.44

(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.