LOMETS results for example

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

Input Sequence in FASTA format

>protein (123 residues)
FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVH
IDSTERRIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFE
EFL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTERRIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL
Prediction	CHHHHHHHCCCSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCSSSSSSSSCSSSSSSCCCCCCHHHHHHHHHHHCCCCSSSCCCCSSSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHC
Conf.Score	868989875989999997997999999976987489998767578987889999677999987887674999999999779978985688899975799865775577789999999999769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTERRIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL
Prediction	645404521444030303645404020343444010203304566654111010332134053365621540053046216504316524003024414034531524231053035106626
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact and Distance Map Used in LOMETS

Contact Map

Distance Map

LOMETS threading is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact and distance maps, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map a color scale represents a distance of 1-20+ angstroms. No dot is close to the diagonal in the contact map, because LOMETS does not consider contacts for residue pairs separated by <4 residues.

Predicted Domain Information by FUpred

Contact Map

Scoring Map

LOMETS uses FUpred and ThreaDom to predict the domain boundary for the target protein. Where ThreaDom is used for homologous target and FUpred is used for non-homologous target. The domain prediction result is shown in the predicted contact map (left) and the FUscore for continuous/discontinuous domain are also shown (right).

Domain partition by LOMETS and Individual Domain Threading/Modeling Results

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	example-D1	1-66	66		FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTER
2	example-D2	67-123	57		RIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL

Modeling the target as 2 domain protein. Click the Domain column or image, you can go into the individual page to check the individual domain threading/modeling results.

Top 10 Assembled Templates by LOMETS

Rank

CMO

MAE

ID1

ID2

Cov

Norm.
Zscore

Download
Alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

Sec.Str.
Sol.Acc.
Seq

CHHHHHHHCCCSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCSSSSSSSSCSSSSSSCCCCCCHHHHHHHHHHHCCCCSSSCCCCSSSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHC
645404521444030303645404020343444010203304566654111010332134053365621540053046216504316524003024414034531524231053035106626
FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTERRIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL

0.608

1.664

0.20

0.98

1.60

LOMETS-Assemble

LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEINVYKRGTMVVRENVLFISPVP-SIVEQFVQTLEKGFSDIKVEDTGHIVLLQEETLIQITHIICDNMLRVRLRDLVLK--

0.586

1.885

0.21

0.20

0.95

1.60

LOMETS-Assemble

LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEINVYKRGTMVVRENVLFISPVP-AIVNKVAEMARERGYTVDT---TDGAKIIFWVLVRAIRIFSEAEYLNLGIELLEK--

0.599

1.715

0.19

0.98

1.60

LOMETS-Assemble

LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEINVYKRGTMVVRENVLFISPVP-SIPVEQFVQTLEKHSDIKVETAGHIVLLQEATLIQDSTIICDNDLRVRLRDLVLKF-

0.571

1.847

0.16

0.15

0.94

1.60

LOMETS-Assemble

LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDYKRGTMVVRENVLFISPVP-TA-LRVYSHLKSVH-CVQHLP-DGSVTVE-SVLLQAALVSWTEELGSLTSLLKKG--

0.552

1.876

0.18

0.98

1.60

LOMETS-Assemble

LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDYKRGTMVVRENVLFISPVP-IPVEQFVQTLEKHGFSDIVEDTGHIVLLQEAETLIQSTCDNDEMLRVRLRDLVLKF-

0.574

1.750

0.20

0.98

1.60

LOMETS-Assemble

GTTKMVSLLNHSLNVTTKDGRTFVGQLLAFDGFMNLVLSDCQEYEKRMLGLVILRGFIVSLSVQG-IPVEQFVQTLEKHFSDIKVEDKGHIVLLQEATLIQIEICDNDEMLRVRLRDLVLKF-

0.562

1.868

0.14

0.98

1.60

LOMETS-Assemble

GTTKMVSLLNHSLNVTTKDGRTFVGQLLAFDGFMNLVLSDCQEYEKRMLGLVILRGFIVSLSVQG-ETALRVYSHLKSVLDHCVQHLPDGSVTVESVLLQAAALVSWDEELGSFLTSLLKGL-

0.577

1.917

0.15

0.98

1.20

LOMETS-Assemble

PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYMVNRLETILLSNNVAMLVPGG-NIETESRQFIENKNYSIQSIGPMLRVVFTRLATVDQYLTGANRSLGQELADHLFET-

0.577

1.917

0.15

0.98

1.20

LOMETS-Assemble

PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYMVNRLETILLSNNVAMLVPGG-NIETESRQFIENKNYSIQSIGPMLRVVFTRLATVDQYLTGANRSLGQELADHLFET-

0.534

1.829

0.18

0.98

1.20

LOMETS-Assemble

PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYMVNRLETILLSNNVAMLVPGG-IPVEQFVQTLEKHFSDIKVEDTGHIVLLQELIQIEEDSCDNDEMLRVRLRDLVLKF-

(a)	Templates are ranked in descending order of the following score: score(i,j)=conf(i)·Z(i,j)/Z₀(i)+seqid(i,j), where Z(i,j) is the Z-score of j-th template; Z₀(i) is the Z-score cutoff for defining good/bad templates for the i-th server; conf(i) is the confidence which is defined as the average TM-score to the natives of all predictions calculated from a large-scale benchmark test; and seqid(i,j) is the sequence identity to query of j-th template. (See here for details)
(b)	CMO is the contact map overlap score, calculated from the number of overlapping contacts between the predicted contact map and the contact map derived from the aligned template, then normalized by the number of predicted contacts.
(c)	MAE is the mean absolute error between the predicted distance map and the distance map derived from the aligned template.
(d)	ID1 is the number of template residues identical to query divided by the number of aligned residues.
(e)	ID2 is the number of template residues identical to query divided by the query sequence length.
(f)	Cov is equal to the number of aligned template residues divided by the query sequence length.
(g)	Norm. Zscore is the normalized Z-score of the threading alignments. A normalized Z-score ≥1 means a good alignment.
(h)	Download Alignment list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.
(i)	Sec.Str. is predicted secondary structure, with H, S and C representing helix, strand, and coil, respectively.
(j)	Sol.Acc. is predicted solvent accessibility, where values range from 0 (buried residue) to 8 (highly exposed residue)

Top 10 Full-chain Threading Templates Identified by LOMETS

Rank

PDB
Hit

RCSB
Link

CMO

MAE

ID1

ID2

Cov

Norm.
Zscore

Download
Alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

Sec.Str.
Sol.Acc.
Seq

CHHHHHHHCCCSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSSCCCCSSSSSSSSCSSSSSSCCCCCCHHHHHHHHHHHCCCCSSSCCCCSSSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHC
645404521444030303645404020343444010203304566654111010332134053365621540053046216504316524003024414034531524231053035106626
FVAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTERRIDREFAKQAEKIFPGVKYIEETNVVLIGDKVRVSEIGVEGVGPVAERAKRLFEEFL

5mkl11

5mkl

0.349

3.250

0.24

0.21

0.87

1.24

HHpred

PLKSLKTALNKIVLVKLKNGEEYVGRLEQSDGTMNLVLKDCTEDPVAKYGRVLIRSNILFISIDYESIMENPLKSLKTALNKVLVKSDGTMNLVLKDCTEYREGTDP----------------

6ppnB

6ppn

0.435

1.947

0.25

0.17

0.68

1.60

SparksX

FYSFFKTLIDTEVTVELKNDMSIRGILKSVDQFLNVKLENISVVDAAAVKDLFIRSVVRYVHMSSAYVDILLADACRRDLANNK---------------------------------------

3jcr2

3jcr

0.386

2.244

0.28

0.18

0.65

1.32

HHsearch

FYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTHMLSVKNCFIRSVVRYVQLPADEVDQLLQDAARKEA-------------------------------------------

5nrll

5nrl

0.454

2.064

0.18

0.14

0.76

1.31

MUSTER

LVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLIASLQYINIRNTIRQIILPDSLNLDSLLVDQKQLNSLRRSANKRP-----------RRGL------------------

6ppnB

6ppn

0.444

2.199

0.26

0.16

0.63

1.12

FFAS3D

-YSFFKTLIDTEVTVELKNDMSIRGILKSVDQFLNVKLENISVVDASKVKDLFIRGVVRYVHMSSAYVDTILLADACRR--------------------------------------------

6v4xC

6v4x

0.426

2.196

0.23

0.15

0.66

1.22

HHpred

LIILLQGLQGRVTTVDLRDESVAHGRIDNVDAFMNIRLAKVTYGHQVKLDDLFVTRNVRYVHIPDD-VNSTIEQQLQIIHRV-----------------------------------------

5mkl11

5mkl

0.522

2.415

0.21

1.00

1.56

SparksX

PLKSLKTALNKIVLVKLKNGEEYVGRLEQSDGTMNLVLKDCTEYREGKYGRVLIRSNILFISIDYESIIENPLKSLKTALNKVLVKLKNGEEYVGRLEQSDGTMNLVLKDCTEYREGTSDPVA

6ppnD

6ppn

0.448

2.107

0.22

0.14

0.64

1.29

HHsearch

PLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTKFFRLPECYIRNNIKYLRIQDEVLSVAKQQAQQRE--------------------------------------------

4m77A

4m77

0.398

2.325

0.20

0.13

0.65

1.18

MUSTER

---TLKDYLNKRVVIILVDGESLIASLNGFDKNTNLFLTNVFNRISFISKAQLLRSEIALVGLIDAENDDSLIENEHVIWEKV----------------------------------------

4c8qB

4c8q

0.383

2.427

0.28

0.18

0.63

1.09

FFAS3D

-FSFFKTLVDQEVVVELKNDIEIKGTLQSVDQFLNLKLDNISCTDEKKVRNIFIRGSTVRYVYLNKNVDTNLLQDATRR--------------------------------------------

(a)	Templates are ranked in descending order of the following score: score(i,j)=conf(i)·Z(i,j)/Z₀(i)+seqid(i,j), where Z(i,j) is the Z-score of j-th template of i-th server; Z₀(i) is the Z-score cutoff for defining good/bad templates for the i-th server; conf(i) is the confidence of i-th server which is defined as the average TM-score to the natives of all predictions calculated from a large-scale benchmark test; and seqid(i,j) is the sequence identity to query of j-th template of i-th server. (See here for details)
(b)	PDB Hit is the PDB of the specific domain/chain aligned to the query.
(c)	RCSB Link is the RCSB PDB link of the full-length protein.
(d)	CMO is the contact map overlap score, calculated from the number of overlapping contacts between the predicted contact map and the contact map derived from the aligned template, then normalized by the number of predicted contacts.
(e)	MAE is the mean absolute error between the predicted distance map and the distance map derived from the aligned template.
(f)	ID1 is the number of template residues identical to query divided by the number of aligned residues.
(g)	ID2 is the number of template residues identical to query divided by the query sequence length.
(h)	Cov is equal to the number of aligned template residues divided by the query sequence length.
(i)	Norm. Zscore is the normalized Z-score of the threading alignments. A normalized Z-score ≥1 means a good alignment.
(j)	Download Alignment list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.
(k)	Sec.Str. is predicted secondary structure, with H, S and C representing helix, strand, and coil, respectively.
(l)	Sol.Acc. is predicted solvent accessibility, where values range from 0 (buried residue) to 8 (highly exposed residue)
(m)	Images of the top 10 PDB hits are listed below, together with the threading programs used to detect them:

5mkl
HHpred,SparksX

6ppn
SparksX,FFAS3D

3jcr
HHsearch

5nrl
MUSTER

6v4x
HHpred

6ppn
HHsearch

4m77
MUSTER

4c8q
FFAS3D

Full-Length Models

LOMETS uses L-BFGS to construct full-length models guided by the distance restraints predicted by DeepPotential and calculated from top detected templates.
By dragging your mouse on the images, you can rotate and zoom the structure.

Download Model 1
Download Model 2
Download Model 3
Download Model 4
Download Model 5

Proteins with similar structure

LOMETS uses the TM-align structural alignment program to match the first 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 model.
Due to the structural similarity, these proteins often have similar functions to the target.

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

Rank	RCSB Link	TM-score	RMSD^a	IDEN^a	Cov.	Download PDB	Download FASTA
1	1m5q	0.627	3.64	0.779	0.91	1m5qY	1m5qY
2	4c8q	0.511	2.46	0.297	0.60	4c8qD	4c8qD
3	1it7	0.511	4.36	0.069	0.82	1it7A	1it7A
4	4ci7	0.51	4.27	0.08	0.81	4ci7A	4ci7A
5	1i8f	0.505	1.05	0.212	0.53	1i8fF	1i8fF
6	3jcr	0.503	1.14	0.197	0.53	3jcr7	3jcr7
7	6ppn	0.502	1.96	0.176	0.55	6ppnH	6ppnH
8	3cw1	0.5	1.72	0.314	0.56	3cw12	3cw12
9	3jcr	0.499	2.01	0.246	0.56	3jcr4	3jcr4
10	6pzk	0.498	4.16	0.049	0.83	6pzkA	6pzkA

(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 the length of the query protein.
(f)	Download PDB provides the structure of the aligned model and template.
(g)	Download FASTA provides the fasta format and full-length alignment of model and template. Shows alignment for potential ligand binding pockets and GO/EC terms.

Function Annotation for Proteins with Similar Structure

(a)	PDB Hit is the PDB of the specific domain/chain aligned to Model 1
(b)	RCSB Link is the RCSB PDB link of the full-length protein.
(c)	Gene Ontology (GO) term and Enzyme Commission (EC) number list the function annotations for structurally aligned proteins, as collected by BioLiP database.
(d)	Ligand lists known binding ligands for each aligned protein, as collected by BioLiP database.
(e)	Binding Site Residues lists the known binding residues for each ligand as collected by BioLiP database. The residue numbering is based on the specfic domain/chain numbering and highlighted residues means they are present in the alignment with Model 1. Note: Listed binding residues may not be representative of the full ligand binding pocket and may be part of a complex with another protein chain/domain. Also, for a single ligand, one template may have multiple binding sites.

Rank	PDB Hit	RCSB Link	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Enzyme_Commission (EC)_number	Ligand	Binding site residues
1	1m5qY	1m5q		GO:0000398	GO:0005732
2	4c8qD	4c8q		GO:0006396,GO:0000398,GO:0000956
3	1it7A	1it7	GO:0003723,GO:0016763,GO:0016757,GO:0046872,GO:0016740	GO:0006400,GO:0008033		2.4.2.48	ZN MG GUN	C274 C276 C279 H302 A523 V526 M561 I562 F564 Q565 D90 S93 F94 D125 P127 Q164 G190 G191 V193 F224
4	4ci7A	4ci7	GO:0008234	GO:0006508		3.4.22.15	CA	L298 E407 K419 N446
5	1i8fF	1i8f
6	3jcr7	3jcr	GO:0003723,GO:0005515,GO:0017070	GO:0000398,GO:0000956,GO:0006397,GO:0008380,GO:0043928	GO:0071004,GO:0005689,GO:0071013,GO:0005688,GO:1990726,GO:0005634,GO:0005681,GO:0046540,GO:0071005,GO:0120115,GO:0005654,GO:0005829
7	6ppnH	6ppn					NUC	H30 T31 T32 N33 R61 G62 E63
8	3cw12	3cw1	GO:0003723,GO:0005515	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0006369,GO:0008334,GO:0051170	GO:0005732,GO:0005681,GO:0005685,GO:0071013,GO:0005634,GO:0005737,GO:0005829,GO:0005683,GO:0005687,GO:0005689,GO:0030532,GO:0034709,GO:0034715,GO:0034719,GO:0046540,GO:0071005,GO:0071007,GO:0005654
9	3jcr4	3jcr	GO:0003723,GO:0017070,GO:0005515,GO:0042731	GO:0006396,GO:0000398,GO:0000956,GO:0000387,GO:0033962,GO:0006397,GO:0008380,GO:0043928	GO:0000932,GO:0005688,GO:0005634,GO:0005681,GO:0043005,GO:0005829,GO:0016020,GO:0032991,GO:0046540,GO:0071005,GO:0120115,GO:0005654
10	6pzkA	6pzk					III	R424 R460 R463

Function Predictions from COFACTOR with LOMETS Structural Analogues and Templates

Protein functions in LOMETS3 are predicted by the modified COFACTOR pipeline, which adds the LOMETS3 threading templates associated with structure analogues as templates in COFACTOR structure-based pipelines. Function predictions include Gene Ontology (GO), Enzyme Commission (EC), and ligand binding sites, where GO is further categorized into three sub-aspects of molecular function (MF), biological process (BP) and cellular component (CC).

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0003676	0.94	nucleic acid binding
GO:0003723	0.83	RNA 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:0009987	0.99	cellular process
GO:0071704	0.98	organic substance metabolic process
GO:0044238	0.98	primary metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0006807	0.96	nitrogen compound metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0034641	0.95	cellular nitrogen compound metabolic process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0006139	0.91	nucleobase-containing compound metabolic process
GO:0016070	0.88	RNA metabolic process
GO:0016071	0.77	mRNA metabolic process
GO:0009058	0.72	biosynthetic process
GO:0044249	0.71	cellular biosynthetic process
GO:0006396	0.71	RNA processing
GO:1901576	0.67	organic substance biosynthetic process
GO:0000377	0.67	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0044271	0.65	cellular nitrogen compound biosynthetic process
GO:0009059	0.57	macromolecule biosynthetic process
GO:0034645	0.55	cellular macromolecule biosynthetic process

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:0030529	1.00	intracellular ribonucleoprotein complex
GO:0044446	0.94	intracellular organelle part
GO:0097525	0.93	spliceosomal snRNP complex
GO:0044444	0.90	cytoplasmic part
GO:0043229	0.90	intracellular organelle
GO:0097526	0.89	spliceosomal tri-snRNP complex
GO:0005681	0.86	spliceosomal complex
GO:0005634	0.76	nucleus
GO:0071013	0.72	catalytic step 2 spliceosome
GO:0046540	0.70	U4/U6 x U5 tri-snRNP complex
GO:0043234	0.69	protein complex
GO:0043232	0.65	intracellular non-membrane-bounded organelle
GO:0005737	0.65	cytoplasm
GO:0005685	0.65	U1 snRNP
GO:0005687	0.63	U4 snRNP
GO:0071010	0.61	prespliceosome
GO:0005684	0.61	U2-type spliceosomal complex
GO:0005686	0.59	U2 snRNP
GO:0005682	0.59	U5 snRNP
GO:0005829	0.56	cytosol
GO:0071011	0.50	precatalytic spliceosome
GO:0005689	0.50	U12-type spliceosomal complex

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	2gl6A	0.438	3.59	0.067	0.650	2.7.3.2	NA
2	0.060	1qh3A	0.444	4.35	0.085	0.780	3.1.2.6	NA
3	0.060	2g8eA	0.355	5.35	0.058	0.740	3.4.22.52	NA
4	0.060	2c91A	0.426	4.08	0.061	0.683	1.-.-.-	8,10
5	0.060	3dopB	0.390	4.54	0.089	0.658	1.3.1.3	52

	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.09	1lnxD	0.498	1.05	0.215	0.528	0.58	URI	complex1.pdb.gz	10,13,37
2	0.03	1m8vH	0.476	1.34	0.266	0.520	0.57	RQA	complex2.pdb.gz	29,30,31
3	0.03	1lnxG	0.500	1.01	0.215	0.528	0.58	URI	complex3.pdb.gz	9,10,13,49,50,51,52
4	0.01	2voyK	0.125	0.86	0.048	0.130	0.58	III	complex4.pdb.gz	7,12,13

	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.

Top Templates and Function Annotation from Component Threading Programs

LOMETS combines templates from multiple individual threading programs, as listed in the following tables.

(a)	Templates are ranked in descending order of normalized Z-score, as explained by (i) below.
(b)	PDB Hit is the PDB of the specific domain/chain aligned to the query.
(c)	RCSB Link is the RCSB PDB link of the full-length protein.
(d)	CMO is the contact map overlap score, calculated from the number of overlapping contacts between the predicted contact map and the contact map derived from the aligned template, then normalized by the number of predicted contacts.
(e)	MAE is the mean absolute error between the predicted distance map and the distance map derived from the aligned template.
(f)	ID1 is the number of template residues identical to query divided by the number of aligned residues.
(g)	ID2 is the number of template residues identical to query divided by the query sequence length.
(h)	Cov is equal to the number of aligned template residues divided by the query sequence length.
(i)	Norm. Zscore is the normalized Z-score of the threading alignments. A normalized Z-score ≥1 means a good alignment.
(j)	Download PDB provides the structure of the aligned region for each template.
(k)	Download FASTA provides the fasta format and full-length alignment of model and template. Shows alignment for potential ligand binding pockets and GO/EC terms.
(l)	Gene Ontology (GO) term and Enzyme Commission (EC) number list the function annotations for template proteins, as collected by BioLiP database.
(m)	Ligand lists known binding ligands for each template protein, as collected by BioLiP database.
(n)	Binding Site Residues lists the known binding residues for each ligand as collected by BioLiP database. The residue numbering is based on the template PDB numbering and highlighted residues means they are aligned with the query sequence. Note: Listed binding residues may not be representative of the full ligand binding pocket and may be part of a complex with another protein chain/domain. Also, for a single ligand, one template may have multiple binding sites.

Templates from Hybrid-CEthreader

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	5mkl14	5mkl	0.506	2.428	0.20	0.20	1.29	0.75	template_1	template_1
2	5mkl11	5mkl	0.478	2.481	0.18	0.18	1.21	0.70	template_2	template_2
3	1d3bL	1d3b	0.451	2.559	0.12	0.07	0.73	0.66	template_3	template_3
4	5uz5K	5uz5	0.448	2.188	0.17	0.14	1.01	0.66	template_4	template_4	GO:0003723,GO:0005515,GO:0003674	GO:0000398,GO:0006397,GO:0008380	GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005634
5	6ppnD	6ppn	0.448	2.094	0.24	0.15	0.72	0.66	template_5	template_5				NUC	Y35 N37 R62 N64
6	6ppnB	6ppn	0.441	1.985	0.25	0.17	0.76	0.64	template_6	template_6				NUC	F35 L36 N37 R63 G64 S65
7	6v4xC	6v4x	0.444	2.131	0.22	0.16	0.93	0.64	template_7	template_7				NUC NUC	K8 I12 R34 D35 F49 R62 R77 R80 V7 K8 T11 I12 E14 N15 R105 K110
8	5nrll	5nrl	0.451	2.120	0.17	0.13	0.80	0.64	template_8	template_8	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
9	5nrld	5nrl	0.438	2.223	0.23	0.14	0.67	0.62	template_9	template_9	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004
10	6ppnH	6ppn	0.432	2.342	0.15	0.11	0.76	0.62	template_10	template_10				NUC	H30 T31 T32 N33 R61 G62 E63

Templates from SparksX

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	6ppnB	6ppn	0.435	1.947	0.25	0.17	0.76	1.60	template_1	template_1				NUC	F35 L36 N37 R63 G64 S65
2	5mkl11	5mkl	0.522	2.415	0.21	0.21	1.21	1.56	template_2	template_2
3	5nrll	5nrl	0.448	2.109	0.17	0.13	0.80	1.49	template_3	template_3	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
4	5mkl14	5mkl	0.534	2.396	0.21	0.21	1.29	1.47	template_4	template_4
5	4c8qB	4c8q	0.401	2.067	0.26	0.18	0.85	1.45	template_5	template_5	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005730,GO:0005732	CO	E28 R78 Y79
6	6ppnD	6ppn	0.444	2.362	0.25	0.16	0.72	1.41	template_6	template_6				NUC	Y35 N37 R62 N64
7	3jb9E	3jb9	0.417	2.170	0.17	0.13	0.80	1.33	template_7	template_7	GO:0003723,GO:0003674	GO:0000395,GO:0000398,GO:0006397,GO:0008380	GO:0005634,GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005681,GO:0005829,GO:0071014	NUC	G1 T2 A29 F30 G32 F33 M34 N35 R58 G59 E60
8	5mkiA	5mki	0.407	2.859	0.24	0.12	0.57	1.28	template_8	template_8	GO:0003723
9	5mkl15	5mkl	0.432	2.669	0.32	0.18	0.73	1.28	template_9	template_9
10	6ppnH	6ppn	0.426	2.331	0.15	0.11	0.76	1.28	template_10	template_10				NUC	H30 T31 T32 N33 R61 G62 E63

Templates from CEthreader

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	5mkl14	5mkl	0.534	2.394	0.20	0.20	1.29	0.62	template_1	template_1
2	5mkl11	5mkl	0.534	2.366	0.24	0.24	1.21	0.61	template_2	template_2
3	1d3bL	1d3b	0.451	2.559	0.12	0.07	0.73	0.49	template_3	template_3
4	6ppnD	6ppn	0.448	2.094	0.24	0.15	0.72	0.49	template_4	template_4				NUC	Y35 N37 R62 N64
5	5uz5K	5uz5	0.448	2.188	0.17	0.14	1.01	0.49	template_5	template_5	GO:0003723,GO:0005515,GO:0003674	GO:0000398,GO:0006397,GO:0008380	GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005634
6	5nrll	5nrl	0.454	2.054	0.20	0.15	0.80	0.49	template_6	template_6	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
7	6ppnB	6ppn	0.441	1.985	0.25	0.17	0.76	0.48	template_7	template_7				NUC	F35 L36 N37 R63 G64 S65
8	6v4xC	6v4x	0.444	2.131	0.22	0.16	0.93	0.48	template_8	template_8				NUC NUC	K8 I12 R34 D35 F49 R62 R77 R80 V7 K8 T11 I12 E14 N15 R105 K110
9	5nrld	5nrl	0.438	2.223	0.23	0.14	0.67	0.48	template_9	template_9	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004
10	6ppnH	6ppn	0.432	2.342	0.15	0.11	0.76	0.48	template_10	template_10				NUC	H30 T31 T32 N33 R61 G62 E63

Templates from HHsearch

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	3jcr2	3jcr	0.386	2.244	0.28	0.18	0.73	1.32	template_1	template_1	GO:0003723,GO:0005515,GO:0017160,GO:0017070	GO:0006397,GO:0000398,GO:0008380,GO:0043928	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0071005,GO:0120115,GO:0005654,GO:0005829
2	6ppnD	6ppn	0.448	2.107	0.22	0.14	0.72	1.29	template_2	template_2				NUC	Y35 N37 R62 N64
3	5mkl11	5mkl	0.457	2.253	0.24	0.22	1.21	1.29	template_3	template_3
4	6ppnB	6ppn	0.435	1.975	0.25	0.17	0.76	1.29	template_4	template_4				NUC	F35 L36 N37 R63 G64 S65
5	4c8qB	4c8q	0.401	1.968	0.24	0.16	0.85	1.29	template_5	template_5	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005730,GO:0005732	CO	E28 R78 Y79
6	3swnA	3swn	0.417	2.645	0.16	0.09	0.62	1.25	template_6	template_6	GO:0003723,GO:0005515,GO:0008266	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0045292,GO:1905323	GO:0005688,GO:0046540,GO:1990726,GO:0005634,GO:0005681,GO:0005730,GO:0005732,GO:0005697,GO:0120115	ZN	E46 E55 H57
7	5nrll	5nrl	0.448	2.060	0.20	0.15	0.80	1.25	template_7	template_7	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
8	4c8qE	4c8q	0.389	2.775	0.16	0.09	0.67	1.25	template_8	template_8	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398,GO:0000956	GO:0005688,GO:0046540,GO:1990726,GO:0005634,GO:0005681,GO:0005730,GO:0005732
9	5mqfg	5mqf	0.420	2.321	0.19	0.11	0.67	1.25	template_9	template_9	GO:0003723,GO:1990446,GO:0005515	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0000245,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0005654,GO:0030532
10	1jbmA	1jbm	0.414	2.581	0.26	0.15	0.63	1.23	template_10	template_10		GO:0000398	GO:0005732

Templates from MapAlign

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Enzyme_Commission (EC)_number	Ligand	Binding site residues
1	5mkl14	5mkl	0.599	2.130	0.21	0.20	1.29	0.95	template_1	template_1
2	5mkl11	5mkl	0.583	2.282	0.23	0.22	1.21	0.89	template_2	template_2
3	4xi6A	4xi6	0.506	2.853	0.11	0.10	2.95	0.66	template_3	template_3	GO:0008270,GO:0004842,GO:0046872	GO:0016567		2.3.2.27	ZN ZN	C79 C82 C103 C106 C94 C97 H112 H116
4	5ohqA	5ohq	0.503	2.809	0.12	0.10	0.89	0.66	template_4	template_4		GO:0006357,GO:0032784
5	3dlmA	3dlm	0.491	2.334	0.11	0.09	1.69	0.63	template_5	template_5				2.1.1.43
6	5uz5K	5uz5	0.481	2.511	0.20	0.15	1.01	0.63	template_6	template_6	GO:0003723,GO:0005515,GO:0003674	GO:0000398,GO:0006397,GO:0008380	GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005634
7	7abi7	7abi	0.491	3.156	0.05	0.04	1.92	0.63	template_7	template_7
8	2ckkA	2ckk	0.491	3.003	0.06	0.05	0.98	0.61	template_8	template_8
9	6ppnD	6ppn	0.463	2.572	0.23	0.15	0.72	0.58	template_9	template_9					NUC	Y35 N37 R62 N64
10	7oqcb	7oqc	0.466	2.167	0.19	0.15	0.98	0.58	template_10	template_10

Templates from MUSTER

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	5nrll	5nrl	0.454	2.064	0.18	0.14	0.80	1.31	template_1	template_1	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
2	4m77A	4m77	0.398	2.325	0.20	0.13	0.67	1.18	template_2	template_2	GO:0003723,GO:0005515	GO:0000398,GO:0016070,GO:0006397,GO:0008380,GO:0006364,GO:0008033	GO:0005688,GO:0046540,GO:0005634,GO:0005681,GO:0005737,GO:0005730
3	5mqfg	5mqf	0.426	2.374	0.20	0.12	0.67	1.15	template_3	template_3	GO:0003723,GO:1990446,GO:0005515	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0000245,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0005654,GO:0030532
4	5ganl	5gan	0.373	2.207	0.22	0.15	0.74	1.14	template_4	template_4	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532	NUC	K2 K8 K9 R11 K20 S33 P34 Q35 N37 R61 G62 N63 R66 L79 D82 Q83
5	4c8qB	4c8q	0.401	2.067	0.26	0.18	0.85	1.13	template_5	template_5	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005730,GO:0005732	CO	E28 R78 Y79
6	5mqfe	5mqf	0.407	2.303	0.20	0.12	0.68	1.11	template_6	template_6	GO:0003723,GO:0071209,GO:0070034,GO:1990446,GO:0019899,GO:0005515,GO:0071208	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0006479,GO:0006369,GO:0008334,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0005654,GO:0005683,GO:0005697,GO:0016604,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0030532
7	3jb9D	3jb9	0.407	2.077	0.18	0.13	0.78	1.09	template_7	template_7	GO:0003755,GO:0003723,GO:0005515,GO:0003729	GO:0000413,GO:0006457,GO:0000395,GO:0006396,GO:0000387,GO:0006397,GO:0008380	GO:0005681,GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0071004,GO:0005634,GO:0046540,GO:0071014	NUC	N35 N37 R61 G62 K81 P84 R96
8	4c8qD	4c8q	0.417	2.271	0.31	0.19	0.66	1.07	template_8	template_8		GO:0006396,GO:0000398,GO:0000956
9	5nrld	5nrl	0.438	2.286	0.21	0.13	0.67	1.07	template_9	template_9	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004
10	5mkl11	5mkl	0.485	2.469	0.23	0.23	1.21	1.06	template_10	template_10

Templates from MRFsearch

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	3jcr2	3jcr	0.377	2.401	0.26	0.16	0.73	0.42	template_1	template_1	GO:0003723,GO:0005515,GO:0017160,GO:0017070	GO:0006397,GO:0000398,GO:0008380,GO:0043928	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0071005,GO:0120115,GO:0005654,GO:0005829
2	6v4xC	6v4x	0.441	2.277	0.24	0.15	0.93	0.40	template_2	template_2				NUC NUC	K8 I12 R34 D35 F49 R62 R77 R80 V7 K8 T11 I12 E14 N15 R105 K110
3	5ganl	5gan	0.383	2.281	0.23	0.15	0.74	0.40	template_3	template_3	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532	NUC	K2 K8 K9 R11 K20 S33 P34 Q35 N37 R61 G62 N63 R66 L79 D82 Q83
4	5nrll	5nrl	0.451	2.236	0.23	0.15	0.80	0.40	template_4	template_4	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
5	4c8qB	4c8q	0.398	2.180	0.26	0.16	0.85	0.40	template_5	template_5	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005730,GO:0005732	CO	E28 R78 Y79
6	5mkl11	5mkl	0.457	2.197	0.25	0.20	1.21	0.40	template_6	template_6
7	6ppnB	6ppn	0.432	2.186	0.24	0.15	0.76	0.38	template_7	template_7				NUC	F35 L36 N37 R63 G64 S65
8	6ppnD	6ppn	0.441	2.233	0.25	0.15	0.72	0.38	template_8	template_8				NUC	Y35 N37 R62 N64
9	5mkl14	5mkl	0.466	2.203	0.24	0.20	1.29	0.37	template_9	template_9
10	5mqfg	5mqf	0.426	2.355	0.21	0.12	0.67	0.35	template_10	template_10	GO:0003723,GO:1990446,GO:0005515	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0000245,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0005654,GO:0030532

Templates from DisCovER

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	6ppnD	6ppn	0.432	2.597	0.26	0.14	0.72	0.70	template_1	template_1				NUC	Y35 N37 R62 N64
2	5nrll	5nrl	0.438	2.538	0.21	0.13	0.80	0.61	template_2	template_2	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
3	3jb9E	3jb9	0.410	2.675	0.22	0.11	0.80	0.61	template_3	template_3	GO:0003723,GO:0003674	GO:0000395,GO:0000398,GO:0006397,GO:0008380	GO:0005634,GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005681,GO:0005829,GO:0071014	NUC	G1 T2 A29 F30 G32 F33 M34 N35 R58 G59 E60
4	1m8vA	1m8v	0.407	3.030	0.27	0.13	0.59	0.61	template_4	template_4				NUC NUC NUC U	R3 L5 D6 H9 G32 Y33 D34 A1 R3 D34 H36 H36 N38 R62 D64
5	4c8qF	4c8q	0.392	2.981	0.30	0.15	0.63	0.59	template_5	template_5	GO:0003723,GO:0005515	GO:0000398,GO:0030490,GO:0006397,GO:0008380,GO:0006364,GO:0008033	GO:0005732,GO:0000932,GO:0005688,GO:0005730,GO:0046540,GO:0005634,GO:0005681,GO:0005737,GO:1990726
6	1i5lC	1i5l	0.401	3.102	0.27	0.13	0.60	0.59	template_6	template_6				URI	H37 N39 R63 G64 D65
7	6ppnB	6ppn	0.420	2.331	0.24	0.15	0.76	0.59	template_7	template_7				NUC	F35 L36 N37 R63 G64 S65
8	5mkiA	5mki	0.407	3.031	0.23	0.11	0.57	0.58	template_8	template_8	GO:0003723
9	5nrld	5nrl	0.435	2.510	0.22	0.12	0.67	0.57	template_9	template_9	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004
10	5mkl12	5mkl	0.423	2.639	0.31	0.17	0.64	0.57	template_10	template_10

Templates from FFAS3D

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	6ppnB	6ppn	0.444	2.199	0.26	0.16	0.76	1.12	template_1	template_1				NUC	F35 L36 N37 R63 G64 S65
2	4c8qB	4c8q	0.383	2.427	0.28	0.18	0.85	1.09	template_2	template_2	GO:0003723,GO:0005515	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0000398	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005730,GO:0005732	CO	E28 R78 Y79
3	6ppnD	6ppn	0.426	2.507	0.24	0.15	0.72	1.08	template_3	template_3				NUC	Y35 N37 R62 N64
4	5nrll	5nrl	0.423	2.513	0.18	0.11	0.80	1.06	template_4	template_4	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
5	3jcr2	3jcr	0.377	2.486	0.29	0.19	0.73	1.02	template_5	template_5	GO:0003723,GO:0005515,GO:0017160,GO:0017070	GO:0006397,GO:0000398,GO:0008380,GO:0043928	GO:0000932,GO:0005688,GO:0046540,GO:1990726,GO:0071013,GO:0005634,GO:0005681,GO:0071005,GO:0120115,GO:0005654,GO:0005829
6	5mkl15	5mkl	0.398	3.061	0.30	0.16	0.73	0.99	template_6	template_6
7	5mqfe	5mqf	0.370	2.934	0.19	0.11	0.68	0.99	template_7	template_7	GO:0003723,GO:0071209,GO:0070034,GO:1990446,GO:0019899,GO:0005515,GO:0071208	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0006479,GO:0006369,GO:0008334,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0005654,GO:0005683,GO:0005697,GO:0016604,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0030532
8	5mqfg	5mqf	0.404	2.606	0.18	0.11	0.67	0.99	template_8	template_8	GO:0003723,GO:1990446,GO:0005515	GO:0000398,GO:0000387,GO:0006397,GO:0008380,GO:0000245,GO:0051170	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0034709,GO:0046540,GO:0071005,GO:0071007,GO:0005654,GO:0030532
9	5gann	5gan	0.377	2.966	0.19	0.11	0.67	0.98	template_9	template_9	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004	NUC	N1 S36 N38 R62 G63 S64
10	5nrld	5nrl	0.407	2.871	0.19	0.11	0.67	0.98	template_10	template_10	GO:0003723,GO:0005515,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005737,GO:0046540,GO:0071004

Templates from EigenThreader

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	5uz5K	5uz5	0.444	2.364	0.18	0.14	1.01	0.75	template_1	template_1	GO:0003723,GO:0005515,GO:0003674	GO:0000398,GO:0006397,GO:0008380	GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005634
2	1pzdA	1pzd	0.389	2.675	0.08	0.07	2.20	0.73	template_2	template_2	GO:0005198	GO:0006886,GO:0016192	GO:0030117,GO:0030126
3	5nrll	5nrl	0.494	2.388	0.18	0.13	0.80	0.73	template_3	template_3	GO:0003723,GO:0003729	GO:0000387,GO:0006397,GO:0008380,GO:0000398	GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0005634,GO:0005829,GO:0046540,GO:0071004,GO:0030532
4	5mkl11	5mkl	0.522	2.180	0.22	0.19	1.21	0.73	template_4	template_4
5	4m75A	4m75	0.438	2.466	0.14	0.11	1.08	0.73	template_5	template_5		GO:0000956
6	4a53A	4a53	0.327	2.946	0.14	0.11	1.02	0.73	template_6	template_6	GO:0003729	GO:0031087
7	5mkl14	5mkl	0.500	2.300	0.18	0.16	1.29	0.72	template_7	template_7
8	3jb9E	3jb9	0.346	2.574	0.15	0.11	0.80	0.70	template_8	template_8	GO:0003723,GO:0003674	GO:0000395,GO:0000398,GO:0006397,GO:0008380	GO:0005634,GO:0005737,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071004,GO:0005687,GO:0071013,GO:0005681,GO:0005829,GO:0071014	NUC	G1 T2 A29 F30 G32 F33 M34 N35 R58 G59 E60
9	7oqcb	7oqc	0.429	2.607	0.16	0.12	0.98	0.70	template_9	template_9
10	3jb9D	3jb9	0.435	2.436	0.18	0.13	0.78	0.67	template_10	template_10	GO:0003755,GO:0003723,GO:0005515,GO:0003729	GO:0000413,GO:0006457,GO:0000395,GO:0006396,GO:0000387,GO:0006397,GO:0008380	GO:0005681,GO:0005686,GO:0005685,GO:0000243,GO:0005682,GO:0005687,GO:0005689,GO:0034715,GO:0034719,GO:0071013,GO:0071004,GO:0005634,GO:0046540,GO:0071014	NUC	N35 N37 R61 G62 K81 P84 R96

Templates from HHpred

Rank	PDB Hit	RCSB Link	CMO	MAE	ID1	ID2	Cov	Norm. Zscore	Download PDB	Download FASTA	Gene_Ontology_(GO)_term (Molecular_Function)	Gene_Ontology_(GO)_term (Biological_Process)	Gene_Ontology_(GO)_term (Cellular_Componenet)	Ligand	Binding site residues
1	5mkl11	5mkl	0.349	3.250	0.24	0.21	1.21	1.24	template_1	template_1
2	6v4xC	6v4x	0.426	2.196	0.23	0.15	0.93	1.22	template_2	template_2				NUC NUC	K8 I12 R34 D35 F49 R62 R77 R80 V7 K8 T11 I12 E14 N15 R105 K110
3	4gouA1	4gou	0.028	39.121	0.17	0.02	0.63	0.23	template_3	template_3	GO:0005515,GO:0005089	GO:0035023
4	1y96A	1y96	0.404	2.880	0.22	0.14	0.70	1.19	template_4	template_4		GO:0000245	GO:0005634
5	3swnA	3swn	0.417	2.645	0.16	0.09	0.62	1.22	template_5	template_5	GO:0003723,GO:0005515,GO:0008266	GO:0006397,GO:0008380,GO:0006364,GO:0008033,GO:0045292,GO:1905323	GO:0005688,GO:0046540,GO:1990726,GO:0005634,GO:0005681,GO:0005730,GO:0005732,GO:0005697,GO:0120115	ZN	E46 E55 H57
6	2fwkA	2fwk	0.410	2.695	0.16	0.09	0.63	1.34	template_6	template_6
7	1m8vA	1m8v	0.435	2.705	0.27	0.14	0.59	1.20	template_7	template_7				NUC NUC NUC U	R3 L5 D6 H9 G32 Y33 D34 A1 R3 D34 H36 H36 N38 R62 D64
8	3cw1C	3cw1	0.383	2.866	0.17	0.09	0.72	1.21	template_8	template_8	GO:0005515,GO:0003723	GO:0008380,GO:0000398,GO:0000387,GO:0006397,GO:0000245,GO:0051170	GO:0030532,GO:0005686,GO:0005685,GO:0005682,GO:0046540,GO:0071013,GO:0005634,GO:0005681,GO:0005737,GO:0005829,GO:0070062,GO:0005687,GO:0005689,GO:0034709,GO:0034715,GO:0034719,GO:0071005,GO:0071007,GO:0005654
9	5mkiA	5mki	0.407	2.934	0.24	0.12	0.57	1.25	template_9	template_9	GO:0003723
10	5ganr	5gan	0.377	2.773	0.18	0.10	0.56	1.21	template_10	template_10	GO:0003723,GO:0005515,GO:0003674	GO:0006397,GO:0008380,GO:0000398	GO:0071004,GO:0005689,GO:0071013,GO:0005686,GO:0005685,GO:0005682,GO:0005687,GO:0034719,GO:0043186,GO:0005634,GO:0005681,GO:0046540	NUC	N19 L35 N36 R57 G58

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

References:
1.	W Zheng, Q Wuyun, X Zhou, Y Li, P Freddolino, Y Zhang. LOMETS3: Integrating deep-learning and profile-alignment for advanced protein template recognition and function annotation. in preparation, (2021)
2.	W Zheng, C Zhang, Q Wuyun, R Pearce, Y Li, Y Zhang. LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research, 47: W429-W436 (2019).
3.	S Wu, Y Zhang. LOMETS: A local meta-threading-server for protein structure prediction. Nucleic Acids Research, 35: 3375-3382 (2007).