C-I-TASSER CIT623

C-I-TASSER results for CIT623

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>JCVISYN3A_0602 (420 residues)
MGNNEFIFEPLKEYDKYQEKNLNIIKEYFDNLIATSKVDIEENKQQVIKINKKQAELNKS
NFNLKKLRIWFITNIVLICLTGVLGAAFIYSLVTYPTYKWYEVLVCVIDLILFIVFILIH
FLVINKKKKEALNAKDKQQAELNQLIEIGLEQTKSLRELIKIGTKNKLLTLTMPFIHLNR
HLGLNKLNKLIDEYGFLNSSSDDTKTTVYVKSGTINNNYFLLTKDYSYEIVKKTYHGSLT
ISWTESYTDSNGNWKTVTKTQVLTASVTKPFVQFSDFSKICFATDLSPNLEFYRKPQQID
KLSEKEKVKLEKQIEKELKKYSQKNINFTPLSNTKFESFWSCFDRNNEREFRLLFTPLAQ
NNLVQLVQDHNKSFGDDYHMLKENKLIIFATEKLNEITFMIMKINISIIVLNIYKIIFIV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MGNNEFIFEPLKEYDKYQEKNLNIIKEYFDNLIATSKVDIEENKQQVIKINKKQAELNKSNFNLKKLRIWFITNIVLICLTGVLGAAFIYSLVTYPTYKWYEVLVCVIDLILFIVFILIHFLVINKKKKEALNAKDKQQAELNQLIEIGLEQTKSLRELIKIGTKNKLLTLTMPFIHLNRHLGLNKLNKLIDEYGFLNSSSDDTKTTVYVKSGTINNNYFLLTKDYSYEIVKKTYHGSLTISWTESYTDSNGNWKTVTKTQVLTASVTKPFVQFSDFSKICFATDLSPNLEFYRKPQQIDKLSEKEKVKLEKQIEKELKKYSQKNINFTPLSNTKFESFWSCFDRNNEREFRLLFTPLAQNNLVQLVQDHNKSFGDDYHMLKENKLIIFATEKLNEITFMIMKINISIIVLNIYKIIFIV
Prediction	CCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCCCCCCHHHHHHHHHHHCCCCCCCCCCCSSSSSSSSSSCCCCSSSSSSSSSSSSSSSSSSSSSSSSSSSSSCCCCCSSSSSSSSSSSSSSSCCCCCCCCCCSSSSSCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCSSSSCCCCSSSSCHHHHHHHHHHHHHCSSSSSSSSSSSSSSSC
Confidence	984267632588889999999999999999999994899899999999999999999876666667889999999999999999999999753123542356689999999999999999986422378999999999999999999999999999998736589999997521310241105489999999748532367886047887644771980899843123774478872599999999975899678999889999999569864235635897045687617870687511157678999999988888888740898310254367887611256524677787168889999999985688998752664245435642124556666653110477765311345639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MGNNEFIFEPLKEYDKYQEKNLNIIKEYFDNLIATSKVDIEENKQQVIKINKKQAELNKSNFNLKKLRIWFITNIVLICLTGVLGAAFIYSLVTYPTYKWYEVLVCVIDLILFIVFILIHFLVINKKKKEALNAKDKQQAELNQLIEIGLEQTKSLRELIKIGTKNKLLTLTMPFIHLNRHLGLNKLNKLIDEYGFLNSSSDDTKTTVYVKSGTINNNYFLLTKDYSYEIVKKTYHGSLTISWTESYTDSNGNWKTVTKTQVLTASVTKPFVQFSDFSKICFATDLSPNLEFYRKPQQIDKLSEKEKVKLEKQIEKELKKYSQKNINFTPLSNTKFESFWSCFDRNNEREFRLLFTPLAQNNLVQLVQDHNKSFGDDYHMLKENKLIIFATEKLNEITFMIMKINISIIVLNIYKIIFIV
Prediction	665254114016405503540362045104500750614264036105403531642553443233110020000212232322221100010324413101000000111011213321102123424413543552454154026301530420240043501340043003302024303362044007503123454444320210211212400000013112412444142423030224334453543334333202020332112136311000003102303112426515514653244115434550342346613034112440321021233534320100001201630241034474511220212343201202152044031103403000000101210013
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted contact map used in C-I-TASSER simulation

C-I-TASSER simulation is guided by consensus contact map (upper left triangle) derived based on confidence scores of TripletRes (lower right triangle), ResTriplet, ResPRE, and NeBcon. In the contact map, the axes mark the residue indexes along the sequence, while each dot represents a residue pair with predicted contact. No dot is close to the diagonal, because C-I-TASSER does not consider contacts for residue pairs separated by <6 residues.

Top 10 threading templates used by C-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380                 400                 420

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCCCCCCHHHHHHHHHHHCCCCCCCCCCCSSSSSSSSSSCCCCSSSSSSSSSSSSSSSSSSSSSSSSSSSSSCCCCCSSSSSSSSSSSSSSSCCCCCCCCCCSSSSSCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCSSSSCCCCSSSSCHHHHHHHHHHHHHCSSSSSSSSSSSSSSSC
MGNNEFIFEPLKEYDKYQEKNLNIIKEYFDNLIATSKVDIEENKQQVIKINKKQAELNKSNFNLKKLRIWFITNIVLICLTGVLGAAFIYSLVTYPTYKWYEVLVCVIDLILFIVFILIHFLVINKKKKEALNAKDKQQAELNQLIEIGLEQTKSLRELIKIGTKNKLLTLTMPFIHLNRHLGLNKLNKLIDEYGFLNSSSDDTKTTVYVKSGTINNNYFLLTKDYSYEIVKKTYHGSLTISWTESYTDSNGNWKTVTKTQVLTASVTKPFVQFSDFSKICFATDLSPNLEFYRKPQQIDKLSEKEKVKLEKQIEKELKKYSQKNINFTPLSNTKFESFWSCFDRNNEREFRLLFTPLAQNNLVQLVQDHNKSFGDDYHMLKENKLIIFATEKLNEITFMIMKINISIIVLNIYKIIFIV

6ezvX

0.08

0.07

2.63

1.00

Neff-PPAS

--QLNPTQQTTQSAFLATTVITAQCHAILNTQFTPPTVKPDWFDDLSKKLDSAKLVAKQWIDDLGPQVSASIPSSVINFDATFQASIDAIHELYKADPTASGKNTTVQQASQIMTALSSQVSGIEATVKGMNKELSDWGVKMQAAHDDLVNGATNIQKTIID------LQTDIESMNNAIDNNRAAIEKLNKDLVYAQVAVGV---------------------------------GIFMLVAGVALTVATAGTAAAVSGGIAAVGAAGV----------------------------TWGVLQNQIDDDYDSIAQEQKQKAEDQQQIIALQGLSNASSAVVSAIETSTSVLSDFETVFGNELDDVVTKLNNG-ASMQSIIMEKVMSDAAKNEWDDAVELAKQLASAKIAIETKELAPAV

6ezvX

0.05

0.04

1.92

1.31

PROSPECTOR2

-TQLNPTQQTTQSAFLATTVITAQCHAILNTQFTPPTVKPDWFDDLSKKLDSAKLVAKQIDDLGPQVSASIPSSVINFDATFQASIDAIHELYKADPTASGKDNTTVQQASQIMTALSSQVSGIEATVKGMNKELSDWGVKMQAAHDDLVNGATNIQKTIIDLQTDESMNNAIDNN-------RAAIEKLNKDLVYAQVAVGVG----------------------------------IFMLVAGVALTVATAGTAAAVSGGIAAVGAAGV-------------------------------TWGVLQNQIDDDYDSIAQEQKQKAEDQQQIIALQGLSNASSAVVSAIETSTSVLSDFETTWTVFGNELDDNGASMQSIIMEKVMSDAAKNEWDDAVELAKQLASAKIAIETKELAPAV

4k1pA

0.10

0.08

2.81

0.84

SPARKS-K

-----IAPNTLSNSIRMLGSQSPLIQAYGLVILQQPDIAMSSLTNHQKFAKANVREWIDEYNPKLIDLNQEMMRYSIRFNSYYSKLYELAGNINEDE--------------QSKADFTNAYGKLQLQVQSIQENMEQDLLELNRFKTVLDKDSNNLSIKADEAIKTLDIVKLREDIKRIQGEIQAELTTILNR----PQEIIK-----------------------------------------------------------GSINIGKQVFTITKTIDFVSIGTLS---------NEIVNAADSQTREAALRIQQKQKELLPLIQKLSQTEAEFVEDQVSSFTELIDRQITTLETKVLNNNMIQIQKNVEEGTYTDSLLQKHFNQIKKVSDEMNKQTNQFEDYNVEVH-----------

2vddA

0.12

0.10

3.51

0.99

FFAS-3D

RLSNPELRKSAADRDAAFEKINEARSPLLPQLGTSASLQLTQDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQ--------KEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANELTARNNLDNAVEQLRQITGNYYVNALLKEA---EKRNLSLLQARLSQDLAREQIRQAQ-----------DGHL---PTL------------DLTASTGISDTSYSQYDDSNMGQNKVGLSFS------LPIYQ---------------------GGMVNSQVKQAQYNFVGASEQLESAHRS------VVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGFSVGTETIVDVLD-------ATTTLYNAKQELANARYNYLILNIKSAL---

6grjG

0.09

0.04

1.45

0.27

HHpred

-STKAQWLRQLSVIKEQATEYQRLSSDTRLVINNNLISNFQGNSKVQGVLAQLNGDIDKVNAAIDGAIA----GIVAGGLLVIGGAFVT--AIGA----VADFVTTSTPVVIGGVVAGAGITAGAIVLHNSLGARQDLYQKRSSLNSEV----LIATQIGGYKGLQVQAQNAVTAATQ-SNALTSDLGSLITD-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

4jspB

0.12

4.21

0.77

MUSTER

YGHWPDVNEALVEGVKAIDTWLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRLIYPLTVASTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPLKETSFNQAYGRDLMEAQEWCRKYMKSKDLTQAWDLYYHVFRRISKQLPQLTSELQYVSPKLLMCRDLELAVPGTYDNQPIIRIQSIAPSLQVIT---SKQRPRKLTLMGSNGHEFVFLLKQLFGLVNTRKNLSIQRYAVIPLSTNSGPHCDTIRDYREKKKILLNIEHRIMLRMAPDYDHLTLMQHAVNNTAGDDLAKLLWLKSPSVWFDRRTNYTSLAVMSMVGYILGLGDRHPSNLMLDRLSKILHIDFGDCFEVAMTREKFPEKIFRLMLTNAMEVT

2av8A

0.11

0.05

1.64

0.76

CNFpred

------ETIHSRSFTHIIRNIVNDPSVVFDDIVTNE--QIQKRAEGISSYYDELIEMTSY-ELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELEGNAKIIRLIARDEALHLTGTQHMLNLLRSGPEMAEIAEECKQECYDLFVQAAQQEDWADYLFRDGSNKDILCQYV------EYITNIRMQAVG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

6o58K

0.14

0.05

1.71

0.58

HHsearch-2

NDLRDLSHENAATLNDVKTLVQ--------QL--YTTLCIEQHRELIERLEDLKEQLAPLEKEIKAEKRTTLVLWGG--LAYMATQFGILARLTWWEYSWD-IMEPVTYFITYGSAMAMYFVMTRQ-EYVYPEARDFDLEKYNQLKDAIAQAEMDLKRLRDPLQVH--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

6d03E

0.07

2.84

0.99

Neff-PPAS

---KRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERISKLIDSEYFITESNNIISQSEETLKLAEDVYDTLYPHLEINEFKKDYDNNVEDLRESIIYIQSYVSSIKSAYRYNVLEKDSVESKQKNIPANSNAQKKVDELLSIIDSISYSNFSVAENFQKMKDYYKEIEKLKIKILQLIEAIKKYQQHVEELI--------

3hd7B

0.16

0.03

1.11

0.54

HHsearch

LSEIETRHSEIIK---LEN-SIRELHDMFAMLVESQGERIEYNVEAVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGI-IIASTIGGI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 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 and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 5 final models from C-I-TASSER

Click to view	Rank^a	Download	C-score^b	Estimated TM-score^c	Estimated RMSD^c
	1	model1.pdb.gz	-3.00	0.38±0.13	14.3±3.8Å
	2	model2.pdb.gz	-3.00
	3	model3.pdb.gz	-3.15
	4	model4.pdb.gz	-4.16
	5	model5.pdb.gz	-4.49

(a)	C-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.
(b)	The model confidence is quantitatified by C-score, calculated based on significance of threading template alignments and convergence of C-I-TASSER simulations. C-score is typically in the range of [-5, 2], with higher C-score signifies higher model confidence.
(c)	Model TM-score and RMSD are estimated based on C-score and protein length for the first model.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6ezvX	0.80	1.59	0.074	0.838	model1_6ezvX.pdb.gz
2	6w08A	0.73	3.08	0.080	0.824	model1_6w08A.pdb.gz
3	6w1wA	0.67	3.61	0.093	0.790	model1_6w1wA.pdb.gz
4	4k1pA	0.66	3.57	0.066	0.779	model1_4k1pA.pdb.gz
5	5j65A	0.62	4.20	0.076	0.779	model1_5j65A.pdb.gz
6	2nrjA	0.59	3.78	0.063	0.717	model1_2nrjA.pdb.gz
7	6grjG	0.50	3.20	0.034	0.567	model1_6grjG.pdb.gz
8	3nvaA	0.27	7.25	0.047	0.464	model1_3nvaA.pdb.gz
9	4hpvA	0.25	6.95	0.039	0.414	model1_4hpvA.pdb.gz
10	3itbD1	0.24	6.06	0.030	0.352	model1_3itbD1.pdb.gz

(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 Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0005524	0.12	ATP binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009405	0.14	pathogenesis

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0016021	0.83	integral component of membrane
GO:0016020	0.83	membrane
GO:0044464	0.67	cell part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2ohyB	0.346	5.79	0.056	0.486	5.4.3.6	NA
2	0.060	1i1iP	0.324	6.82	0.034	0.512	3.4.24.16	NA
3	0.060	1h2aL	0.366	6.83	0.049	0.583	1.12.2.1	193
4	0.060	1frvB	0.389	5.44	0.043	0.533	1.12.2.1	193
5	0.060	2nyfA	0.337	5.91	0.034	0.483	4.3.1.5	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (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.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1xu3A	0.363	5.43	0.036	0.495	0.20	BML	complex1.pdb.gz	11,13,14,17
	2	0.01	1xvdA	0.366	5.80	0.036	0.514	0.30	FPN	complex2.pdb.gz	9,194,195

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Chengxin Zhang, S M Mortuza, Baoji He, Yanting Wang, and Yang Zhang. "Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12." Proteins: Structure, Function, and Bioinformatics (2017). doi: 10.1002/prot.25414