Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	K	T	N	D	W	L	D	F	D	Q	L	A	E	E	K	V	R	D	A	L	K	P	P	S	M	Y	K	V	I	L	V	N	D	D	Y	T	P	M	E	F	V	I	D	V	L	Q	K	F	F	S	Y	D	V	E	R	A	T	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.
Sequence		L	M	L	A	V	H	Y	Q	G	K	A	I	C	G	V	F	T	A	E	V	A	E	T	K	V	A	M	V	N	K	Y	A	R	E	N	E	H	P	L	L	C	T	L	E	K	A
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 1r6o chain C domain 1 Region: 20 - 106 Aligned: 87 Modelled: 87 Confidence: 100.0% Identity: 100% Fold: ClpS-like Superfamily: ClpS-like Family: Adaptor protein ClpS (YljA) Phyre2 PDB 3dnj chain B Region: 26 - 105 Aligned: 80 Modelled: 80 Confidence: 100.0% Identity: 59% PDB header:peptide binding protein Chain: B: PDB Molecule:atp-dependent clp protease adapter protein clps; PDBTitle: the structure of the caulobacter crescentus clps protease2 adaptor protein in complex with a n-end rule peptide Phyre2 PDB 2jwl chain B Region: 2 - 50 Aligned: 49 Modelled: 49 Confidence: 30.9% Identity: 14% PDB header:membrane protein Chain: B: PDB Molecule:protein tolr; PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data Phyre2 PDB 3ge5 chain A Region: 58 - 84 Aligned: 27 Modelled: 26 Confidence: 29.5% Identity: 22% PDB header:oxidoreductase Chain: A: PDB Molecule:putative nad(p)h:fmn oxidoreductase; PDBTitle: crystal structure of a putative nad(p)h:fmn oxidoreductase (pg0310)2 from porphyromonas gingivalis w83 at 1.70 a resolution Phyre2 PDB 2r01 chain A Region: 58 - 84 Aligned: 27 Modelled: 26 Confidence: 21.1% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:nitroreductase family protein; PDBTitle: crystal structure of a putative fmn-dependent nitroreductase (ct0345)2 from chlorobium tepidum tls at 1.15 a resolution Phyre2 PDB 1xdy chain A Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 19.8% Identity: 18% Fold: Oxidoreductase molybdopterin-binding domain Superfamily: Oxidoreductase molybdopterin-binding domain Family: Oxidoreductase molybdopterin-binding domain Phyre2 PDB 1xdy chain C Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 19.4% Identity: 18% PDB header:oxidoreductase Chain: C: PDB Molecule:bacterial sulfite oxidase; PDBTitle: structural and biochemical identification of a novel2 bacterial oxidoreductase, w-containing cofactor Phyre2 PDB 2gia chain A domain 1 Region: 16 - 36 Aligned: 21 Modelled: 21 Confidence: 17.0% Identity: 19% Fold: ssDNA-binding transcriptional regulator domain Superfamily: ssDNA-binding transcriptional regulator domain Family: Guide RNA binding protein gBP Phyre2 PDB 1ogp chain A domain 2 Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 15.9% Identity: 27% Fold: Oxidoreductase molybdopterin-binding domain Superfamily: Oxidoreductase molybdopterin-binding domain Family: Oxidoreductase molybdopterin-binding domain Phyre2 PDB 2bii chain A Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 15.6% Identity: 18% PDB header:oxidoreductase Chain: A: PDB Molecule:nitrate reductase [nadph]; PDBTitle: crystal structure of nitrate-reducing fragment of2 assimilatory nitrate reductase from pichia angusta Phyre2 PDB 1sox chain B Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 15.3% Identity: 18% PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite oxidase; PDBTitle: sulfite oxidase from chicken liver Phyre2 PDB 2bih chain A Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 15.2% Identity: 18% PDB header:oxidoreductase Chain: A: PDB Molecule:nitrate reductase [nadph]; PDBTitle: crystal structure of the molybdenum-containing nitrate2 reducing fragment of pichia angusta assimilatory nitrate3 reductase Phyre2 PDB 2xts chain C Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 14.8% Identity: 18% PDB header:oxidoreductase/electron transport Chain: C: PDB Molecule:sulfite dehydrogenase; PDBTitle: crystal structure of the sulfane dehydrogenase soxcd from paracoccus2 pantotrophus Phyre2 PDB 2bpb chain A Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 14.7% Identity: 27% PDB header:oxidoreductase Chain: A: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit a; PDBTitle: sulfite dehydrogenase from starkeya novella Phyre2 PDB 3etj chain A domain 2 Region: 87 - 105 Aligned: 19 Modelled: 19 Confidence: 14.0% Identity: 16% Fold: PreATP-grasp domain Superfamily: PreATP-grasp domain Family: BC N-terminal domain-like Phyre2 PDB 2gid chain P Region: 16 - 36 Aligned: 21 Modelled: 21 Confidence: 12.9% Identity: 19% PDB header:translation Chain: P: PDB Molecule:mitochondrial rna-binding protein 2; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 Phyre2 PDB 1vkw chain A Region: 58 - 76 Aligned: 19 Modelled: 17 Confidence: 12.6% Identity: 26% Fold: FMN-dependent nitroreductase-like Superfamily: FMN-dependent nitroreductase-like Family: Putative nitroreductase TM1586 Phyre2 PDB 2a9d chain A domain 2 Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 12.4% Identity: 18% Fold: Oxidoreductase molybdopterin-binding domain Superfamily: Oxidoreductase molybdopterin-binding domain Family: Oxidoreductase molybdopterin-binding domain Phyre2 PDB 1ogp chain D Region: 93 - 103 Aligned: 11 Modelled: 11 Confidence: 11.8% Identity: 27% PDB header:oxidoreductase Chain: D: PDB Molecule:sulfite oxidase; PDBTitle: the crystal structure of plant sulfite oxidase provides2 insight into sulfite oxidation in plants and animals Phyre2 PDB 3hj9 chain A Region: 58 - 84 Aligned: 27 Modelled: 27 Confidence: 11.3% Identity: 11% PDB header:oxidoreductase Chain: A: PDB Molecule:oxidoreductase; PDBTitle: crystal structure of a putative nitroreductase (reut_a1228) from2 ralstonia eutropha jmp134 at 2.00 a resolution Phyre2 1 d1r6oc1 2 c3dnjB_ 3 c2jwlB_ 4 c3ge5A_ 5 c2r01A_ 6 d1xdya_ 7 c1xdyC_ 8 d2giaa1 9 d1ogpa2 10 c2biiA_ 11 c1soxB_ 12 c2bihA_ 13 c2xtsC_ 14 c2bpbA_ 15 d3etja2 16 c2gidP_ 17 d1vkwa_ 18 d2a9da2 19 c1ogpD_ 20 c3hj9A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50

Detailed template information

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

1 d1r6oc1 100.0 100 Fold:ClpS-like Superfamily:ClpS-like Family:Adaptor protein ClpS (YljA) 2 c3dnjB_ 100.0 59 PDB header:peptide binding protein Chain: B: PDB Molecule:atp-dependent clp protease adapter protein clps; PDBTitle: the structure of the caulobacter crescentus clps protease2 adaptor protein in complex with a n-end rule peptide 3 c2jwlB_ 30.9 14 PDB header:membrane protein Chain: B: PDB Molecule:protein tolr; PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data 4 c3ge5A_ 29.5 22 PDB header:oxidoreductase Chain: A: PDB Molecule:putative nad(p)h:fmn oxidoreductase; PDBTitle: crystal structure of a putative nad(p)h:fmn oxidoreductase (pg0310)2 from porphyromonas gingivalis w83 at 1.70 a resolution 5 c2r01A_ 21.1 15 PDB header:oxidoreductase Chain: A: PDB Molecule:nitroreductase family protein; PDBTitle: crystal structure of a putative fmn-dependent nitroreductase (ct0345)2 from chlorobium tepidum tls at 1.15 a resolution 6 d1xdya_ 19.8 18 Fold:Oxidoreductase molybdopterin-binding domain Superfamily:Oxidoreductase molybdopterin-binding domain Family:Oxidoreductase molybdopterin-binding domain 7 c1xdyC_ 19.4 18 PDB header:oxidoreductase Chain: C: PDB Molecule:bacterial sulfite oxidase; PDBTitle: structural and biochemical identification of a novel2 bacterial oxidoreductase, w-containing cofactor 8 d2giaa1 17.0 19 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Guide RNA binding protein gBP 9 d1ogpa2 15.9 27 Fold:Oxidoreductase molybdopterin-binding domain Superfamily:Oxidoreductase molybdopterin-binding domain Family:Oxidoreductase molybdopterin-binding domain 10 c2biiA_ 15.6 18 PDB header:oxidoreductase Chain: A: PDB Molecule:nitrate reductase [nadph]; PDBTitle: crystal structure of nitrate-reducing fragment of2 assimilatory nitrate reductase from pichia angusta 11 c1soxB_ 15.3 18 PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite oxidase; PDBTitle: sulfite oxidase from chicken liver 12 c2bihA_ 15.2 18 PDB header:oxidoreductase Chain: A: PDB Molecule:nitrate reductase [nadph]; PDBTitle: crystal structure of the molybdenum-containing nitrate2 reducing fragment of pichia angusta assimilatory nitrate3 reductase 13 c2xtsC_ 14.8 18 PDB header:oxidoreductase/electron transport Chain: C: PDB Molecule:sulfite dehydrogenase; PDBTitle: crystal structure of the sulfane dehydrogenase soxcd from paracoccus2 pantotrophus 14 c2bpbA_ 14.7 27 PDB header:oxidoreductase Chain: A: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit a; PDBTitle: sulfite dehydrogenase from starkeya novella 15 d3etja2 14.0 16 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like 16 c2gidP_ 12.9 19 PDB header:translation Chain: P: PDB Molecule:mitochondrial rna-binding protein 2; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 17 d1vkwa_ 12.6 26 Fold:FMN-dependent nitroreductase-like Superfamily:FMN-dependent nitroreductase-like Family:Putative nitroreductase TM1586 18 d2a9da2 12.4 18 Fold:Oxidoreductase molybdopterin-binding domain Superfamily:Oxidoreductase molybdopterin-binding domain Family:Oxidoreductase molybdopterin-binding domain 19 c1ogpD_ 11.8 27 PDB header:oxidoreductase Chain: D: PDB Molecule:sulfite oxidase; PDBTitle: the crystal structure of plant sulfite oxidase provides2 insight into sulfite oxidation in plants and animals 20 c3hj9A_ 11.3 11 PDB header:oxidoreductase Chain: A: PDB Molecule:oxidoreductase; PDBTitle: crystal structure of a putative nitroreductase (reut_a1228) from2 ralstonia eutropha jmp134 at 2.00 a resolution 21 c2a9dB_ not modelled 10.7 18 PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite oxidase; PDBTitle: crystal structure of recombinant chicken sulfite oxidase with arg at2 residue 161 22 c3koqC_ not modelled 10.6 15 PDB header:oxidoreductase Chain: C: PDB Molecule:nitroreductase family protein; PDBTitle: crystal structure of a nitroreductase family protein (cd3355) from2 clostridium difficile 630 at 1.58 a resolution 23 d1cmga_ not modelled 9.6 10 Fold:EF Hand-like Superfamily:EF-hand Family:Calmodulin-like 24 d1n0yb_ not modelled 9.5 5 Fold:EF Hand-like Superfamily:EF-hand Family:Calmodulin-like 25 d2o8ra3 not modelled 8.9 21 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Polyphosphate kinase C-terminal domain 26 c3of4A_ not modelled 8.5 15 PDB header:oxidoreductase Chain: A: PDB Molecule:nitroreductase; PDBTitle: crystal structure of a fmn/fad- and nad(p)h-dependent nitroreductase2 (nfnb, il2077) from idiomarina loihiensis l2tr at 1.90 a resolution 27 c3g14B_ not modelled 8.4 15 PDB header:oxidoreductase Chain: B: PDB Molecule:nitroreductase family protein; PDBTitle: crystal structure of nitroreductase family protein (yp_877874.1) from2 clostridium novyi nt at 1.75 a resolution 28 c2kgrA_ not modelled 8.3 8 PDB header:protein binding Chain: A: PDB Molecule:intersectin-1; PDBTitle: solution structure of protein itsn1 from homo sapiens.2 northeast structural genomics consortium target hr5524a 29 d1fsha_ not modelled 8.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 30 d1qnaa1 not modelled 7.9 14 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 31 d2d8ca1 not modelled 7.8 24 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 32 d1wzla2 not modelled 7.6 18 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 33 c2islB_ not modelled 7.4 26 PDB header:flavoprotein Chain: B: PDB Molecule:blub; PDBTitle: blub bound to reduced flavin (fmnh2) and molecular oxygen.2 (clear crystal form) 34 c3fiaA_ not modelled 7.3 5 PDB header:protein binding Chain: A: PDB Molecule:intersectin-1; PDBTitle: crystal structure of the eh 1 domain from human intersectin-2 1 protein. northeast structural genomics consortium target3 hr3646e. 35 d1v3fa_ not modelled 6.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 36 c2kc8B_ not modelled 6.6 33 PDB header:toxin/toxin repressor Chain: B: PDB Molecule:antitoxin relb; PDBTitle: structure of e. coli toxin rele (r81a/r83a) mutant in2 complex with antitoxin relbc (k47-l79) peptide 37 c2x2oA_ not modelled 6.6 16 PDB header:flavoprotein Chain: A: PDB Molecule:nrdi protein; PDBTitle: the flavoprotein nrdi from bacillus cereus with the2 initially oxidized fmn cofactor in an intermediate3 radiation reduced state 38 c2xznM_ not modelled 6.6 11 PDB header:ribosome Chain: M: PDB Molecule:rps18e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 39 c3pg8B_ not modelled 6.5 8 PDB header:transferase Chain: B: PDB Molecule:phospho-2-dehydro-3-deoxyheptonate aldolase; PDBTitle: truncated form of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase2 from thermotoga maritima 40 d2jxca1 not modelled 6.5 13 Fold:EF Hand-like Superfamily:EF-hand Family:Eps15 homology domain (EH domain) 41 c3bemA_ not modelled 6.0 19 PDB header:oxidoreductase Chain: A: PDB Molecule:putative nad(p)h nitroreductase ydfn; PDBTitle: crystal structure of putative nitroreductase ydfn (2632848) from2 bacillus subtilis at 1.65 a resolution 42 c2kfhA_ not modelled 6.0 7 PDB header:protein binding Chain: A: PDB Molecule:eh domain-containing protein 1; PDBTitle: structure of the c-terminal domain of ehd1 with fnyestgpftak 43 c3u5zA_ not modelled 6.0 17 PDB header:dna binding protein/dna Chain: A: PDB Molecule:dna polymerase accessory protein 62; PDBTitle: structure of t4 bacteriophage clamp loader bound to the t4 clamp,2 primer-template dna, and atp analog 44 d2frea1 not modelled 5.7 15 Fold:FMN-dependent nitroreductase-like Superfamily:FMN-dependent nitroreductase-like Family:NADH oxidase/flavin reductase 45 c2b1uA_ not modelled 5.7 5 PDB header:metal binding protein Chain: A: PDB Molecule:calmodulin-like protein 5; PDBTitle: solution structure of calmodulin-like skin protein c2 terminal domain 46 d1c07a_ not modelled 5.6 7 Fold:EF Hand-like Superfamily:EF-hand Family:Eps15 homology domain (EH domain) 47 d2i1sa1 not modelled 5.3 18 Fold:MM3350-like Superfamily:MM3350-like Family:MM3350-like 48 d1w4ma_ not modelled 5.2 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 49 c3kwkA_ not modelled 5.2 9 PDB header:oxidoreductase Chain: A: PDB Molecule:putative nadh dehydrogenase/nad(p)h nitroreductase; PDBTitle: crystal structure of putative nadh dehydrogenase/nad(p)h2 nitroreductase (np_809094.1) from bacteroides thetaiotaomicron vpi-3 5482 at 1.54 a resolution 50 d1fi6a_ not modelled 5.1 10 Fold:EF Hand-like Superfamily:EF-hand Family:Eps15 homology domain (EH 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

---

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