Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

alpha superhelicesrepeating alpha-helix hairpins form a superhelix

alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain

alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix

beta barrelssingle beta-sheet folded upon itself to form a barrel

beta meanderssingle beta-sheet with mainly meander topology

beta sandwichestwo beta-sheets stacked together to form a sandwich

beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain

beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander

a+b two layersone alpha-helix layer and one beta-sheet layer

X: Tautomerase/MIF-like

X: Uncharacterized protein BTH I2711

X: Peptidase inhibitors family I69

X: Asparaginal-tRNA synthetase N-terminal domain

X: Flagellar hook protein FlgE D0 domain

X: Curli production assembly/transport component CsgF

X: Anti-LPS factor/recA domain

X: Obg GTP-binding protein C-terminal domain-like

X: Ribosomal protein L9 C-domain

X: Urease, gamma-subunit

X: C-terminal domain of nonstructural protein nsp4

X: Putative heterocyst differentiation inhibitor NpR1517

X: Head-to-tail joining protein W, gpW

X: XkdW-like

X: Hypothetical protein MTH677

X: GTF2I-like repeat

X: Ribosomal protein L35p

X: Archaea-specific ribosomal protein L46a

X: PB2 C-terminal domain-like

X: Peptidoglycan deacetylase N-terminal noncatalytic region

X: ERH-like

X: ssDNA binding protein VirE2

X: N-terminal a+b domain in urocanase (Pfam 01175)

X: CbiD-like (Pfam 01888) N-terminal domain

X: Prion-like

X: gp120 inner domain

X: Ribosomal protein L31e-like

X: SSHS domain

X: MTH1598-like

X: Reverse ferredoxin

X: Tetrapyrrole methylase C-terminal domain-like

X: ImmE5-like

X: Polycystin-mucolipin domain

X: UvrB-binding domain of UvrA

X: FAM3 superfamily

X: a+b domain in Ribosomal protein L1

X: Photosystem I subunit PsaD

X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase

X: uncharacterized protein YP_926445.1

X: Insertion domain in phosphocholine transferase AnkX

X: HPr-like

X: EcoKMcrA modification binding domain

X: Allophycocyanin linker chain (domain)

X: Small outer capsid protein (Soc)

X: GYF/BRK domain-like

X: Pesticin N-terminal domain

X: Uncharacterized protein Q2S0R5

X: Tombusvirus P19 core protein, VP19

X: YjbQ-like (Pfam 01894)

X: SSo0622-like (Pfam 02676)

X: MTHFR SAM-binding regulatory domain

X: barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes

X: Uncharacterized protein yibL

X: L9 N-domain-like

X: NosL/MerB-like

X: DUF2233 N-terminal domain

X: DNA helicase UvsW N-terminal a+b domain-related

X: EKC/KEOPS complex subunit GON7

X: Putative acetamidase tm0119 C-terminal domain

X: Csm1 ferredoxin-like domain

X: Uncharacterized protein VC_0899

X: ferredoxin-like domain in VP1

X: Seb1 domain 2

X: protein PCC1

X: HLTF protein HIRAN domain

X: Cof C2 cap domain

X: N-terminal domain of vibrio phospholipase

X: Alpha-beta plaits

X: DNA Mimic Protein Arn

X: Ribosomal protein L22e

X: 60S ribosomal export protein NMD3 a+b domain

X: uncharacterized protein lpg1496 N-terminal domain

X: ferredoxin-like domain in flagellar biosynthesis protein flhA

X: Uncharacterized protein VC_A0919

X: PHP14-like

X: N-terminal domain of chitin biosynthesis protein CHS6

X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit

X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit

X: Translation initiation factor eIF4e and phosphothreonine lyase

X: uncharacterized protein SAMEA2273162_06031

X: Ribosomal protein L30p/L7e

X: Insertion domain in 60S ribosomal protein rpP0 (L10P)

X: a+b domain in PB2

X: tRNA pseudouridine synthase TruD insertion domain

X: Barrel domain in dedicator of cytokinesis protein 9

X: YcgL/NE1680-like

X: L,D-transpeptidase C-terminal domain

X: Oxalate Biosynthetic Component A (ObcA) insertion domains

X: GP2-like

X: SdbC C-terminal domain

X: Formate dehydrogenase/DMSO reductase, domain 1

X: 4Fe-4S ferredoxin

X: Diedel

X: Uncharacterized protein MXAN_0049

X: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

H: LuxS, MPP, ThrRS/AlaRS common domain

T: LuxS/MPP-like metallohydrolase

F: Peptidase_M16,Peptidase_M16_C

F: PQQ_syn_pqqF_N_2

F: PqqF-like_C_4

F: Peptidase_M16

F: PqqF_C_3

F: Peptidase_M16_M

F: PreP_C

F: M16C_assoc

F: LuxS

Representatives:

e1j98A1[A:4-157] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: ZN ; X-RAY DIFFRACTION 1.20Å

e2fqtA1[A:4-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-RIBOSYLHOMOCYSTEINE LYASE ; ligands: CO,H1D,SO4 ; X-RAY DIFFRACTION 1.79Å

e1jqwA1[A:8-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Autoinducer-2 production protein luxS ; ligands: HCS,ZN ; X-RAY DIFFRACTION 2.3Å

e1j6xA1[A:5-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 2.38Å

e2fqoA1[A:4-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-RIBOSYLHOMOCYSTEINE LYASE ; ligands: CO,HYI,SO4 ; X-RAY DIFFRACTION 1.87Å

e1jviA1[A:4-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Autoinducer-2 production protein luxS ; ligands: HCS,RHC,SO4,ZN ; X-RAY DIFFRACTION 2.2Å

e1ie0A1[A:4-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: GOL,ZN ; X-RAY DIFFRACTION 1.6Å

e1j6xB1[B:5-151] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 2.38Å

e1vgxA1[A:8-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-ribosylhomocysteinase ; ligands: ZN ; X-RAY DIFFRACTION 1.90Å

e1vjeB1[B:7-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Autoinducer-2 production protein LuxS ; ligands: MSE,ZN ; X-RAY DIFFRACTION 1.64Å

e1vjeA1[A:8-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Autoinducer-2 production protein LuxS ; ligands: MSE,ZN ; X-RAY DIFFRACTION 1.64Å

e1innB1[B:7-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 1.80Å

e1vgxB1[B:6-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-ribosylhomocysteinase ; ligands: ZN ; X-RAY DIFFRACTION 1.90Å

e1vh2A1[A:7-158] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-RIBOSYLHOMOCYSTEINASE ; ligands: ZN ; X-RAY DIFFRACTION 2.0Å

e1joeB1[B:9-156] Image Pymol Jmol Links: PDB, SCOP, CATH

AUTOINDUCER-2 PRODUCTION PROTEIN ; ligands: HG,ZN ; X-RAY DIFFRACTION 2.30Å

e1joeA1[A:9-156] Image Pymol Jmol Links: PDB, SCOP, CATH

AUTOINDUCER-2 PRODUCTION PROTEIN ; ligands: HG,ZN ; X-RAY DIFFRACTION 2.30Å

e1joeC1[C:9-156] Image Pymol Jmol Links: PDB, SCOP, CATH

AUTOINDUCER-2 PRODUCTION PROTEIN ; ligands: HG,ZN ; X-RAY DIFFRACTION 2.30Å

e1joeD1[D:9-156] Image Pymol Jmol Links: PDB, SCOP, CATH

AUTOINDUCER-2 PRODUCTION PROTEIN ; ligands: HG,ZN ; X-RAY DIFFRACTION 2.30Å

e1j6vA1[A:7-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: ZN ; X-RAY DIFFRACTION 2.10Å

e1innA1[A:6-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 1.80Å

e1j6wB1[B:3-162] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 2.10Å

e1yclA1[A:4-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-ribosylhomocysteinase ; ligands: CO,KRI,SO4 ; X-RAY DIFFRACTION 1.8Å

e4xchA1[A:12-160] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e4xchB1[B:12-160] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e4xchC1[C:12-160] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e4xchD1[D:12-160] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e5e68B1[B:3-174] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: MET,PAV,ZN ; X-RAY DIFFRACTION 1.58Å

e5v2wA1[A:3-169] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 2.30Å

e5v2wB1[B:3-174] Image Pymol Jmol Links: PDB, SCOP, CATH

S-ribosylhomocysteine lyase ; ligands: ZN ; X-RAY DIFFRACTION 2.30Å

e1j6wA1[A:3-163] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AUTOINDUCER-2 PRODUCTION PROTEIN LUXS ; ligands: MET,ZN ; X-RAY DIFFRACTION 2.10Å

F: Peptidase_M16_C

PF05193 CL0094

F: Peptidase_M16_C,Peptidase_M16_M

PF05193 PF16187

F: Peptidase_M16_C,M16C_assoc

PF05193 PF08367

F: Unmapped domains

Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.

T: ThrRS/AlaRS editing domain

X: Glutamine synthetase-like

X: Cytoplasmic domain of BfpC

X: Ribosomal protein L5

X: hypothetical protein TA0743

X: DCoH-like

X: Prokaryotic AspRS, insert domain

X: Thymidylate synthase-complementing protein Thy1

X: Chorismate synthase, AroC

X: a+b domain in type II DNA topoisomerase

X: TRCF domain

X: Homing endonucleases-like

X: Endonuclease PI-TkoII domain IV

X: C-terminal domain in some PLP-dependent transferases

X: BtrG-like (Pfam 03674)

X: Glucose permease domain IIB-like

X: Putative oxidoreductase

X: Hedgehog/DD-peptidase

X: RRF/tRNA synthetase additional domain-like

X: AFV1-102

X: N-terminal subdomain in UbiD middle domain

X: Dodecin subunit-like

X: Tp47 lipoprotein N-terminal domain

X: DLC

X: Factor H binding protein B (FhbB)

X: ClpS-like

contains a HTH motif

X: R3H domain-like

X: hydrogenase expression protein-like

X: Chromosome partition protein mukE N-terminal domain

X: Ribosomal protein S8, C-terminal domain

X: IF3-like

X: BLIP-like

X: yfeY-like

X: Ribosomal protein S16

X: Ribosomal protein S19

X: RPB5-like RNA polymerase subunit

X: Subtilisin inhibitor

X: Putative lipoprotein CPF_1278-related

X: The spindle assembly checkpoint protein mad2

X: C-terminal functional domain of REDD1

X: MesJ substrate recognition domain-like

X: AMMECR1-like

X: THUMP domain-like

X: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase

X: C-terminal domain in a functionally unknown conserved protein

X: Spliceosomal helicase Aquarius insert domain

X: Integrin beta tail domain

X: NSFL1 (p97 ATPase) cofactor p47, SEP domain

X: Hypothetical protein Yml108w

X: a+b domain in YebC-like proteins

X: Nqo5-like

X: Baseplate structural protein gp6 C-terminal domain III

X: T-fold

X: Ribonuclease PH domain 2-like

X: Rrs1

X: MotY N-terminal domain

X: ssDNA-binding transcriptional regulator domain-like

X: N-terminal domain of effector protein PipB2

X: Bacterial protein-export protein SecB

X: mRNA decapping enzyme DcpS N-terminal domain

X: PipX

X: uncharacterized protein PA1076

X: Immunity protein NMB0503

X: Uncharacterized protein MK0293 C-terminal domain

X: Hypothetical protein TM0160

X: Methane monooxygenase hydroxylase, MmoD

X: dsRBD-like

X: C-terminal domain in RNA helicases

X: C-P lyase subunit PhnG

X: Beta domain of DivIB/FtsQ

X: Giardia Dicer N-terminal domain

X: FlaG-like

X: NMB0488-like

X: Enolase-N/ribosomal protein

X: Serine/threonine-protein kinase GCN2 C-terminal domain

X: Carboxyl terminal domain of human deltex 3-like

X: a+b domain in Capz

X: Bacterial conjugation factor PsiB

X: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523)

X: Ribosomal protein L6

X: OsmC-like

X: hypothetical protein RUMGNA_01148-related

X: GerBC protein

X: Insertion domain of carboxypeptidase dacD

X: Alpha-lytic protease prodomain-like

X: Transactivation domain (TAD) of FoxM1

X: DNA polymerase D large subunit DP2 N-terminal domain

X: amino-terminal domain of OmpATb

X: DNA mismatch repair protein MutL dimerization subdomain

X: TrkA C-terminal domain-like

X: putative secreted protein PA3611

X: Uncharacterized protein yciN

X: hypothetical protein DESPIG_00776

X: RumA insert domain

X: Sex pheromone staph-cAM373

X: TolA/TonB C-terminal domain

X: Chorismate lyase

X: hypothetical protein TTHB210

X: Chromosomal protein MC1

X: DNA topoisomerase I domain

X: DNA-binding protein Tfx

X: FYSH domain

X: DNA-binding domain

X: Domain 2 in immunoglobulin A protease

X: CI-2 family of serine protease inhibitors-like

X: DNA clamp

X: Cdc48 domain 2-like

X: Ribosomal protein S5 domain 2-like

X: Proteasome assembling chaperone 3 (PAC3)-related

X: MocoBD/DmpA-related

X: Thioesterase/thiol ester dehydrase-isomerase-like

X: beta-Grasp

X: beta-grasp domain in anthrax protective antigen

X: GTP-binding protein lepA C-terminal domain-like

X: ubiquitin-binding domain from PLAA

X: C-terminal domain of OAT (ornithine acetyltransferase)

X: Central kinetochore subunit CHL4 C-terminal domain

X: Cas3 C-terminal domain

X: POZ domain

X: uncharacterized protein Svir_20580

X: Uncharacterized protein PA1075

X: Microbial ribonucleases-like

X: C-terminal domain of CdiA toxin

X: Yeast killer toxin-like

X: N-terminal domain of alcaligin biosynthesis protein C

X: Uncharacterized protein yohN

X: C-terminal domain in CigR

X: RelE-like

X: Nuclease domain of PRRSV nonstructural protein Nsp1

X: Uncharacterized protein Atu1219

X: PX domain

X: Cpn0803

X: Shew3726-like

X: Ornithine cyclodeaminase-like enzymes dimerization domain

X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related

X: TBP-like

X: Recombination-associated protein rdgC

X: Putative lipoprotein LppA

X: hypothetical protein BPSL2088

X: Uncharacterized Protein Rru_A0810

X: Lp2179-like

X: Sm-Like archaeal protein Smap3, C-terminal domain

X: Cystatin-like

X: Csd3 N-terminal domain

X: RNase inhibitor Dip

X: hypotheical protein Lreu_0056

X: Uncharacterized protein YPO2434

X: hypothetical protein SAV0303

X: PH1570-like

X: N-terminal a+b domain in DNA primase core

X: AF0104/ALDC/Ptd012-like

X: Cellular targeting domain in sucrose synthase-1

X: LEE-encoded effector EspG N-terminal domain-related

X: LEE-encoded effector EspG C-terminal domain-related

X: RIP/Polo-box domain

X: DUF4479

X: a+b domain in carbohydrate phosphatases

X: OxsB N-terminal domain

X: SpoVG-like

X: Uncharacterized protein gp49

X: FKBP-like

X: Heparin lyase I insertion domain

X: Domain in small RNA methyltransferase HEN1

X: N-terminal domain in xanthine dehydrogenase

X: Sterol carrier protein-like

X: Fragilysin-3 prodomain-like

X: RNA bacteriophage capsid protein

X: UBC-like

X: FYR domain

X: Kinetochore globular domain-like

X: Ribonuclease Rh-like

X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like

X: a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes

X: Hypothetical protein YjiA, C-terminal domain

X: SRP9/14-like

X: Cell wall binding protein cwp8 domain 2

X: TTHA1528-like

X: Paratox

X: Uncharacterized protein ATC0905

X: MHC antigen-recognition domain

X: BH3703-like

X: Acidic mitochondrial matrix protein p32-like

X: Hypothetical Protein Vc0508

X: Nuclease AFV1-157

X: SH2

X: Ribosome-associated factor Y

X: Integron cassette protein VCH_CASS14

X: Virion infectivity factor Vif

X: Uncharacterized protein TGAM_1934

X: Uncharacterized protein EF_1977

X: Uncharacterized protein Rv3902c

X: Type III secretory system chaperone-like

X: N-terminal domain of PprA

X: TEN domain of telomerase reverse transcriptase

X: NAP-like

X: PG1388-like

X: BPSL1050

X: BACOVA_05496-like

X: Meander beta sheet domain in fatty acid synthase subunit beta

X: Omega-3 polyunsaturated fatty acid synthase subunit PfaD N-terminal domain

X: XisI-like

X: YehR-like

X: SMI1/KNR4-like

X: YkuJ-like

X: A hypothetical protein from Neisseria gonorrhoeae

X: Middle domain of ribosomal protein S2-related protein

X: Nitrogen fixation protein

X: Insertion domain in adenylylcyclase toxin (the edema factor)

X: Thymidylate synthase/dCMP hydroxymethylase

X: C-terminal domain of FliK

X: Pili subunits

X: Bacteriochlorophyll A protein

X: Chalcone isomerase

X: Cytochrome P460

X: Heme-binding protein A (HasA)

X: N-terminal domain of colicin N

X: Mago nashi protein

X: WGR domain

X: Escherichia coli HybE

X: FAD-linked reductases, C-terminal domain-like

X: Hypothetical virulence protein

X: putative RnfG subunit of electron transport complex

X: RPL28

X: AMPKBI-like

X: Probable 30S ribosomal protein PSRP-3

X: FwdE/GAPDH domain-like

X: N-terminal domain of DC-UbP

X: a functionally unknown protein from Leptospirillum sp. Group II UBA

X: 40S ribosomal protein rpS21 (S21e)

X: Alr2454 protein

X: C-terminal domain in putative protease YP_001302526.1

X: a+b domain in heme oxygenase

X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2

X: PafA/Dop C-terminal domain

X: Glycoprotein E3

X: Nonstructural protein 7 alpha

X: Laminaripentaose-producing beta-1,3-glucanase insertion domain

X: uncharacterised protein rbstp2171

X: DNA polymerase III C-terminal domain

X: XPD arch domain

X: putative cell adhesion protein BACOVA_01548 insertion domain

X: Salmon anemia virus nucleoprotein N-terminal domain

X: ESX-1 secretion system protein eccB1 linker domains

X: Lon-like protease MtaLonC helical domain

X: Photosystem II antenna protein PsbB insertion domain

X: Ribosomal protein L11/L12e N-terminal domain-like

X: Hypothetical protein Q4D059

X: N-terminal domain of spumavirus gag protein

X: Meiosis-expressed gene 1 protein

X: Hypothetical protein TA0938

X: Domain 1 of outer membrane lipoprotein Wza

X: C-terminal domain of bypass of forespore C, BofC

X: DUF3222-like

X: DUF1107-like

X: DUF960-like

X: Phage tail assembly chaperone

X: TT1592-like

X: Pro-domain of Hemolysin hlyA

X: KS-MAT linker domain in fatty acid synthase

X: Dimerization domain of erythronate-4-phosphate dehydrogenase PdxB

X: a+b domain in platelet binding protein GspB

X: Uncharacterized virus protein A-100

X: Hypothetical protein RPA3313

a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers

a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers

a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers

a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain

a/b barrelsrepeating beta-alpha units form a barrel

a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers

mixed a+b and a/balpha and beta domain consists of both a+b and a/b regions

few secondary structure elementsstabilized by cofactors or disulfides

extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes

special