Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	N	Y	Y	D	I	T	L	A	L	A	G	I	C	Q	S	A	R	L	V	Q	Q	L	A	H	Q	G	H	C	D	A	D	A	L	H	V	S	L	N	S	I	I	D	M	N	P	S	S	T	L	A	V	F	G	G	S	E	A
Secondary structure
SS confidence
Disorder		?	?	?	?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	L	R	V	G	L	E	T	L	L	G	V	L	N	A	S	S	R	Q	G	L	N	A	E	L	T	R	Y	T	L	S	L	M	V	L	E	R	K	L	S	S	A	K	G	A	L	D	T	L	G	N	R	I	N	G	L	Q	R	Q	L
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?	?	?	?	?																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		E	H	F	D	L	Q	S	E	T	L	M	S	A	M	A	A	I	Y	V	D	V	I	S	P	L	G	P	R	I	Q	V	T	G	S	P	A	V	L	Q	S	P	Q	V	Q	A	K	V	R	A	T	L	L	A	G	I	R	A	A	V	L
Secondary structure
SS confidence
Disorder																										?	?			?					?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.
Sequence		W	H	Q	V	G	G	G	R	L	Q	L	M	F	S	R	N	R	L	T	T	Q	A	K	Q	I	L	A	H	L	T	P	E	L
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 1sdi chain A Region: 2 - 213 Aligned: 212 Modelled: 212 Confidence: 100.0% Identity: 100% Fold: YcfC-like Superfamily: YcfC-like Family: YcfC-like Phyre2 PDB 2xr1 chain A Region: 127 - 167 Aligned: 41 Modelled: 41 Confidence: 39.1% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:cleavage and polyadenylation specificity factor 100 kd PDBTitle: dimeric archaeal cleavage and polyadenylation specificity2 factor with n-terminal kh domains (kh-cpsf) from methanosarcina3 mazei Phyre2 PDB 2gej chain A Region: 97 - 152 Aligned: 50 Modelled: 51 Confidence: 33.1% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol mannosyltransferase (pima); PDBTitle: crystal structure of phosphatidylinositol mannosyltransferase (pima)2 from mycobacterium smegmatis in complex with gdp-man Phyre2 PDB 2ycb chain A Region: 127 - 167 Aligned: 41 Modelled: 41 Confidence: 30.0% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:cleavage and polyadenylation specificity factor; PDBTitle: structure of the archaeal beta-casp protein with n-terminal2 kh domains from methanothermobacter thermautotrophicus Phyre2 PDB 2rdc chain A Region: 86 - 178 Aligned: 87 Modelled: 93 Confidence: 27.0% Identity: 22% PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution Phyre2 PDB 3af5 chain A Region: 139 - 167 Aligned: 29 Modelled: 29 Confidence: 22.9% Identity: 34% PDB header:hydrolase Chain: A: PDB Molecule:putative uncharacterized protein ph1404; PDBTitle: the crystal structure of an archaeal cpsf subunit, ph1404 from2 pyrococcus horikoshii Phyre2 PDB 2fge chain A domain 1 Region: 59 - 159 Aligned: 99 Modelled: 101 Confidence: 21.5% Identity: 17% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: MPP-like Phyre2 PDB 2k1v chain B Region: 175 - 189 Aligned: 13 Modelled: 15 Confidence: 15.7% Identity: 46% PDB header:hormone Chain: B: PDB Molecule:relaxin-3; PDBTitle: r3/i5 relaxin chimera Phyre2 PDB 2rpa chain A Region: 9 - 33 Aligned: 25 Modelled: 25 Confidence: 15.1% Identity: 28% PDB header:hydrolase Chain: A: PDB Molecule:katanin p60 atpase-containing subunit a1; PDBTitle: the solution structure of n-terminal domain of microtubule severing2 enzyme Phyre2 PDB 3fxd chain D Region: 134 - 144 Aligned: 11 Modelled: 11 Confidence: 14.0% Identity: 36% PDB header:unknown function Chain: D: PDB Molecule:protein icmr; PDBTitle: crystal structure of interacting domains of icmr and icmq Phyre2 PDB 3cx3 chain A Region: 104 - 157 Aligned: 54 Modelled: 54 Confidence: 11.7% Identity: 7% PDB header:metal binding protein Chain: A: PDB Molecule:lipoprotein; PDBTitle: crystal structure analysis of the streptococcus pneumoniae2 adcaii protein Phyre2 PDB 3mzk chain C Region: 160 - 193 Aligned: 34 Modelled: 34 Confidence: 11.7% Identity: 18% PDB header:protein transport Chain: C: PDB Molecule:protein transport protein sec16; PDBTitle: sec13/sec16 complex, s.cerevisiae Phyre2 PDB 2rms chain B Region: 9 - 17 Aligned: 9 Modelled: 9 Confidence: 11.6% Identity: 56% PDB header:transcription Chain: B: PDB Molecule:msin3a-binding protein; PDBTitle: solution structure of the msin3a pah1-sap25 sid complex Phyre2 PDB 2xdj chain F Region: 92 - 140 Aligned: 49 Modelled: 48 Confidence: 10.4% Identity: 22% PDB header:unknown function Chain: F: PDB Molecule:uncharacterized protein ybgf; PDBTitle: crystal structure of the n-terminal domain of e.coli ybgf Phyre2 PDB 2h8b chain B Region: 180 - 189 Aligned: 10 Modelled: 10 Confidence: 9.8% Identity: 40% PDB header:hormone/growth factor Chain: B: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 Phyre2 PDB 2ogw chain B Region: 103 - 157 Aligned: 55 Modelled: 55 Confidence: 9.0% Identity: 13% PDB header:transport protein Chain: B: PDB Molecule:high-affinity zinc uptake system protein znua PDBTitle: structure of abc type zinc transporter from e. coli Phyre2 PDB 2r5u chain D Region: 80 - 140 Aligned: 50 Modelled: 61 Confidence: 8.9% Identity: 20% PDB header:hydrolase Chain: D: PDB Molecule:replicative dna helicase; PDBTitle: crystal structure of the n-terminal domain of dnab helicase from2 mycobacterium tuberculosis Phyre2 PDB 2juf chain A Region: 179 - 189 Aligned: 11 Modelled: 11 Confidence: 8.5% Identity: 27% PDB header:gene regulation Chain: A: PDB Molecule:p53-associated parkin-like cytoplasmic protein; PDBTitle: nmr solution structure of parc cph domain. nesg target2 hr3443b/sgc-toronto Phyre2 PDB 1qi9 chain A Region: 27 - 54 Aligned: 28 Modelled: 28 Confidence: 8.3% Identity: 29% Fold: Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily: Acid phosphatase/Vanadium-dependent haloperoxidase Family: Haloperoxidase (bromoperoxidase) Phyre2 PDB 2fhd chain A Region: 178 - 187 Aligned: 10 Modelled: 10 Confidence: 8.3% Identity: 20% PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains Phyre2 1 d1sdia_ 2 c2xr1A_ 3 c2gejA_ 4 c2ycbA_ 5 c2rdcA_ 6 c3af5A_ 7 d2fgea1 8 c2k1vB_ 9 c2rpaA_ 10 c3fxdD_ 11 c3cx3A_ 12 c3mzkC_ 13 c2rmsB_ 14 c2xdjF_ 15 c2h8bB_ 16 c2ogwB_ 17 c2r5uD_ 18 c2jufA_ 19 d1qi9a_ 20 c2fhdA_ 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

Detailed template information

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

1 d1sdia_ 100.0 100 Fold:YcfC-like Superfamily:YcfC-like Family:YcfC-like 2 c2xr1A_ 39.1 20 PDB header:hydrolase Chain: A: PDB Molecule:cleavage and polyadenylation specificity factor 100 kd PDBTitle: dimeric archaeal cleavage and polyadenylation specificity2 factor with n-terminal kh domains (kh-cpsf) from methanosarcina3 mazei 3 c2gejA_ 33.1 12 PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol mannosyltransferase (pima); PDBTitle: crystal structure of phosphatidylinositol mannosyltransferase (pima)2 from mycobacterium smegmatis in complex with gdp-man 4 c2ycbA_ 30.0 15 PDB header:hydrolase Chain: A: PDB Molecule:cleavage and polyadenylation specificity factor; PDBTitle: structure of the archaeal beta-casp protein with n-terminal2 kh domains from methanothermobacter thermautotrophicus 5 c2rdcA_ 27.0 22 PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution 6 c3af5A_ 22.9 34 PDB header:hydrolase Chain: A: PDB Molecule:putative uncharacterized protein ph1404; PDBTitle: the crystal structure of an archaeal cpsf subunit, ph1404 from2 pyrococcus horikoshii 7 d2fgea1 21.5 17 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:MPP-like 8 c2k1vB_ 15.7 46 PDB header:hormone Chain: B: PDB Molecule:relaxin-3; PDBTitle: r3/i5 relaxin chimera 9 c2rpaA_ 15.1 28 PDB header:hydrolase Chain: A: PDB Molecule:katanin p60 atpase-containing subunit a1; PDBTitle: the solution structure of n-terminal domain of microtubule severing2 enzyme 10 c3fxdD_ 14.0 36 PDB header:unknown function Chain: D: PDB Molecule:protein icmr; PDBTitle: crystal structure of interacting domains of icmr and icmq 11 c3cx3A_ 11.7 7 PDB header:metal binding protein Chain: A: PDB Molecule:lipoprotein; PDBTitle: crystal structure analysis of the streptococcus pneumoniae2 adcaii protein 12 c3mzkC_ 11.7 18 PDB header:protein transport Chain: C: PDB Molecule:protein transport protein sec16; PDBTitle: sec13/sec16 complex, s.cerevisiae 13 c2rmsB_ 11.6 56 PDB header:transcription Chain: B: PDB Molecule:msin3a-binding protein; PDBTitle: solution structure of the msin3a pah1-sap25 sid complex 14 c2xdjF_ 10.4 22 PDB header:unknown function Chain: F: PDB Molecule:uncharacterized protein ybgf; PDBTitle: crystal structure of the n-terminal domain of e.coli ybgf 15 c2h8bB_ 9.8 40 PDB header:hormone/growth factor Chain: B: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 16 c2ogwB_ 9.0 13 PDB header:transport protein Chain: B: PDB Molecule:high-affinity zinc uptake system protein znua PDBTitle: structure of abc type zinc transporter from e. coli 17 c2r5uD_ 8.9 20 PDB header:hydrolase Chain: D: PDB Molecule:replicative dna helicase; PDBTitle: crystal structure of the n-terminal domain of dnab helicase from2 mycobacterium tuberculosis 18 c2jufA_ 8.5 27 PDB header:gene regulation Chain: A: PDB Molecule:p53-associated parkin-like cytoplasmic protein; PDBTitle: nmr solution structure of parc cph domain. nesg target2 hr3443b/sgc-toronto 19 d1qi9a_ 8.3 29 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 20 c2fhdA_ 8.3 20 PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains 21 c3h25A_ not modelled 8.2 32 PDB header:replication/dna Chain: A: PDB Molecule:replication protein b; PDBTitle: crystal structure of the catalytic domain of primase repb' in complex2 with initiator dna 22 c3hgkE_ not modelled 8.2 20 PDB header:transferase Chain: E: PDB Molecule:effector protein hopab2; PDBTitle: crystal structure of effect protein avrptob complexed with2 kinase pto 23 d2jnga1 not modelled 7.9 27 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:CPH domain 24 d1qhba_ not modelled 7.7 18 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 25 d1vkea_ not modelled 7.6 13 Fold:AhpD-like Superfamily:AhpD-like Family:CMD-like 26 d1up8a_ not modelled 7.5 14 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 27 c2o1eB_ not modelled 7.5 11 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:ycdh; PDBTitle: crystal structure of the metal-dependent lipoprotein ycdh2 from bacillus subtilis, northeast structural genomics3 target sr583 28 d1u7ka_ not modelled 7.2 33 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 29 d2jeka1 not modelled 7.1 20 Fold:Rv1873-like Superfamily:Rv1873-like Family:Rv1873-like 30 c1yv0T_ not modelled 7.0 27 PDB header:contractile protein Chain: T: PDB Molecule:troponin t, fast skeletal muscle isoforms; PDBTitle: crystal structure of skeletal muscle troponin in the ca2+-2 free state 31 c1xouA_ not modelled 7.0 24 PDB header:structural protein/chaperone Chain: A: PDB Molecule:espa; PDBTitle: crystal structure of the cesa-espa complex 32 d1xoua_ not modelled 7.0 24 Fold:EspA/CesA-like Superfamily:EspA/CesA-like Family:EspA-like 33 d2v7qi1 not modelled 6.7 60 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Epsilon subunit of mitochondrial F1F0-ATP synthase Family:Epsilon subunit of mitochondrial F1F0-ATP synthase 34 c2w9zA_ not modelled 6.5 17 PDB header:transferase Chain: A: PDB Molecule:g1/s-specific cyclin-d1; PDBTitle: crystal structure of cdk4 in complex with a d-type cyclin 35 c3nrhA_ not modelled 6.4 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bf1032; PDBTitle: crystal structure of protein bf1032 from bacteroides fragilis,2 northeast structural genomics consortium target bfr309 36 d1jwea_ not modelled 6.2 18 Fold:N-terminal domain of DnaB helicase Superfamily:N-terminal domain of DnaB helicase Family:N-terminal domain of DnaB helicase 37 c1cosA_ not modelled 6.2 29 PDB header:alpha-helical bundle Chain: A: PDB Molecule:coiled serine; PDBTitle: crystal structure of a synthetic triple-stranded alpha-2 helical bundle 38 c1cosB_ not modelled 6.2 29 PDB header:alpha-helical bundle Chain: B: PDB Molecule:coiled serine; PDBTitle: crystal structure of a synthetic triple-stranded alpha-2 helical bundle 39 c1cosC_ not modelled 6.2 29 PDB header:alpha-helical bundle Chain: C: PDB Molecule:coiled serine; PDBTitle: crystal structure of a synthetic triple-stranded alpha-2 helical bundle 40 c3imoC_ not modelled 6.1 21 PDB header:unknown function Chain: C: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass14 41 d1hula_ not modelled 5.7 19 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 42 c2f59B_ not modelled 5.5 20 PDB header:transferase Chain: B: PDB Molecule:6,7-dimethyl-8-ribityllumazine synthase 1; PDBTitle: lumazine synthase ribh1 from brucella abortus (gene bruab1_0785,2 swiss-prot entry q57dy1) complexed with inhibitor 5-nitro-6-(d-3 ribitylamino)-2,4(1h,3h) pyrimidinedione 43 d1b8za_ not modelled 5.5 14 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 44 d2bs2b2 not modelled 5.4 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin domains from multidomain proteins 45 c3dlaD_ not modelled 5.3 19 PDB header:ligase Chain: D: PDB Molecule:glutamine-dependent nad(+) synthetase; PDBTitle: x-ray crystal structure of glutamine-dependent nad+ synthetase from2 mycobacterium tuberculosis bound to naad+ and don 46 c3c4vB_ not modelled 5.2 14 PDB header:transferase Chain: B: PDB Molecule:predicted glycosyltransferases; PDBTitle: structure of the retaining glycosyltransferase msha:the2 first step in mycothiol biosynthesis. organism:3 corynebacterium glutamicum : complex with udp and 1l-ins-1-4 p. 47 c3lk2B_ not modelled 5.0 18 PDB header:protein binding Chain: B: PDB Molecule:f-actin-capping protein subunit beta isoforms 1 and 2; PDBTitle: crystal structure of capz bound to the uncapping motif from carmil

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