Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	S	N	A	S	A	L	G	R	N	G	V	H	D	F	I	L	V	R	A	T	A	I	V	L	T	L	Y	I	I	Y	M	V	G	F	F	A	T	S	G	E	L	T	Y	E	V	W	I	G	F	F	A	S	A	F	T	K	V	F
Secondary structure
SS confidence
Disorder		?	?	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.
Sequence		T	L	L	A	L	F	S	I	L	I	H	A	W	I	G	M	W	Q	V	L	T	D	Y	V	K	P	L	A	L	R	L	M	L	Q	L	V	I	V	V	A	L	V	V	Y	V	I	Y	G	F	V	V	V	W	G	V
Secondary structure
SS confidence
Disorder																																																						?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1nek chain D Region: 3 - 115 Aligned: 113 Modelled: 113 Confidence: 100.0% Identity: 100% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 2bs2 chain C domain 1 Region: 3 - 114 Aligned: 112 Modelled: 112 Confidence: 99.3% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Fumarate reductase respiratory complex cytochrome b subunit, FrdC Phyre2 PDB 1nek chain C Region: 12 - 111 Aligned: 100 Modelled: 100 Confidence: 99.0% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1zp0 chain D Region: 8 - 111 Aligned: 85 Modelled: 88 Confidence: 99.0% Identity: 14% PDB header:oxidoreductase Chain: D: PDB Molecule:small cytochrome binding protein; PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone Phyre2 PDB 1yq3 chain C Region: 13 - 107 Aligned: 95 Modelled: 95 Confidence: 98.5% Identity: 16% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 1kf6 chain C Region: 14 - 72 Aligned: 59 Modelled: 59 Confidence: 96.4% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1kf6 chain D Region: 21 - 107 Aligned: 87 Modelled: 87 Confidence: 95.6% Identity: 20% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1kcf chain A domain 1 Region: 4 - 21 Aligned: 18 Modelled: 18 Confidence: 10.6% Identity: 33% Fold: LEM/SAP HeH motif Superfamily: SAP domain Family: SAP domain Phyre2 PDB 2do5 chain A Region: 7 - 23 Aligned: 17 Modelled: 17 Confidence: 10.4% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:splicing factor 3b subunit 2; PDBTitle: solution structure of the sap domain of human splicing2 factor 3b subunit 2 Phyre2 PDB 3da4 chain B Region: 80 - 106 Aligned: 27 Modelled: 27 Confidence: 10.2% Identity: 30% PDB header:antibiotic Chain: B: PDB Molecule:colicin-m; PDBTitle: crystal structure of colicin m, a novel phosphatase2 specifically imported by escherichia coli Phyre2 PDB 2gzd chain C Region: 80 - 92 Aligned: 13 Modelled: 12 Confidence: 8.1% Identity: 38% PDB header:protein transport Chain: C: PDB Molecule:rab11 family-interacting protein 2; PDBTitle: crystal structure of rab11 in complex with rab11-fip2 Phyre2 PDB 1y8o chain A domain 1 Region: 65 - 84 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 5% Fold: Bromodomain-like Superfamily: alpha-ketoacid dehydrogenase kinase, N-terminal domain Family: alpha-ketoacid dehydrogenase kinase, N-terminal domain Phyre2 PDB 3mvn chain A Region: 79 - 96 Aligned: 18 Modelled: 18 Confidence: 6.3% Identity: 22% PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo- PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp Phyre2 PDB 2eyq chain A domain 6 Region: 81 - 94 Aligned: 14 Modelled: 14 Confidence: 5.4% Identity: 21% Fold: TRCF domain-like Superfamily: TRCF domain-like Family: TRCF domain Phyre2 1 d1nekd_ 2 d2bs2c1 3 d1nekc_ 4 c1zp0D_ 5 c1yq3C_ 6 d1kf6c_ 7 d1kf6d_ 8 d1kcfa1 9 c2do5A_ 10 c3da4B_ 11 c2gzdC_ 12 d1y8oa1 13 c3mvnA_ 14 d2eyqa6

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1nekd_ 100.0 100 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 2 d2bs2c1 99.3 11 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC 3 d1nekc_ 99.0 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 4 c1zp0D_ 99.0 14 PDB header:oxidoreductase Chain: D: PDB Molecule:small cytochrome binding protein; PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone 5 c1yq3C_ 98.5 16 PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone 6 d1kf6c_ 96.4 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 7 d1kf6d_ 95.6 20 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 8 d1kcfa1 10.6 33 Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain 9 c2do5A_ 10.4 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:splicing factor 3b subunit 2; PDBTitle: solution structure of the sap domain of human splicing2 factor 3b subunit 2 10 c3da4B_ 10.2 30 PDB header:antibiotic Chain: B: PDB Molecule:colicin-m; PDBTitle: crystal structure of colicin m, a novel phosphatase2 specifically imported by escherichia coli 11 c2gzdC_ 8.1 38 PDB header:protein transport Chain: C: PDB Molecule:rab11 family-interacting protein 2; PDBTitle: crystal structure of rab11 in complex with rab11-fip2 12 d1y8oa1 6.8 5 Fold:Bromodomain-like Superfamily:alpha-ketoacid dehydrogenase kinase, N-terminal domain Family:alpha-ketoacid dehydrogenase kinase, N-terminal domain 13 c3mvnA_ 6.3 22 PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo- PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp 14 d2eyqa6 5.4 21 Fold:TRCF domain-like Superfamily:TRCF domain-like Family:TRCF domain

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0