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Table 1.   List of extracellular Pfam-A domain families

Description

Smart name

Pfam name

Pfam ID

Amyloid A4

A4_EXTRA

APP_N

PF02177

Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family

AAI

Tryp_alpha_amyl

PF00234

Serum albumin

ALBUMIN

Serum_albumin

PF00273

Vitamin D binding protein, domain III

-

VitD-bind_III

PF09164

Ami_2

Ami_2

Amidase_2

PF01510

Ami_3

Ami_3

Amidase_3

PF01520

Anaphylatoxin homologous domain

ANATO

ANATO

PF01821

Adhesion-associated domain present in MUC4 and other proteins

AMOP

AMOP

PF03782

APPLE domain

APPLE

PAN_1

PF00024

PAN-like domain

-

PAN_2

PF08276

PAN-like domain

-

PAN_3

PF08277

PAN domain

-

PAN_4

PF14295

Bulb-type mannose-specific lectin

B_lectin

B_lectin

PF01453

Bowman-Birk type proteinase inhibitor

BowB

Bowman-Birk_leg

PF00228

BPI/LBP/CETP N-terminal domain

BPI1

LBP_BPI_CETP

PF01273

Complement component C1q domain

C1Q

C1q

PF00386

Netrin C-terminal Domain

C345C

NTR

PF01759

C-terminal tandem repeated domain in type 4 procollagens

C4

C4

PF01413

Cadherin repeats

CA

Cadherin

PF00028

Cadherin-like

-

Cadherin_2

PF08266

Cadherin prodomain like

Cadherin_pro

Cadherin_pro

PF08758

Calcitonin

CALCITONIN

Calc_CGRP_IAPP

PF00214

Cellulose Binding Domain Type IV

CBD_IV

CBM_6

PF03422

Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)

CCP

Sushi

PF00084

CFEM

CFEM

CFEM

PF05730

A domain in the BMP inhibitor chordin and in microbial proteins

CHRD

CHRD

PF07452

Chitin binding domain

ChtBD1

Chitin_bind_1

PF00187

Chitin binding Peritrophin-A domain

-

CBM_14

PF01607

Chitin-binding domain type 2

ChtBD2

CBM_2

PF00553

Carbohydrate binding domain

-

CBM_5_12

PF02839

Clostridial hydrophobic, with a conserved W residue, domain

ChW

ChW

PF07538

CLUSTERIN alpha chain

CLa

Clusterin

PF01093

CLUSTERIN Beta chain

CLb

Clusterin

PF01093

Fibrillar collagens C-terminal domain

COLFI

COLFI

PF01410

Corticotropin-releasing factor

CRF

CRF

PF00473

Granulocyte-macrophage colony-simulating factor (GM-CSF)

CSF2

GM_CSF

PF01109

Somatotropin hormone family

-

Hormone_1

PF00103

Erythropoietin/thrombopoietin

-

EPO_TPO

PF00758

flt3 ligand

-

Flt3_lig

PF02947

Interferin gamma

-

IFN-gamma

PF00714

Interleukin 11

-

IL11

PF07400

Interleukin-12 alpha subunit

-

IL12

PF03039

Interleukin-13

-

IL13

PF03487

Interleukin 22 IL-10-related T-cell-derived-inducible factor

-

IL22

PF14565

Interleukin-3

-

IL3

PF02059

Interleukin 34

-

IL34

PF15036

Interleukin 5

-

IL5

PF02025

Leptin

-

Leptin

PF02024

Leukemia inhibitory factor

LIF_OSM

LIF_OSM

PF01291

Plethodontid receptivity factor PRF

-

PRF

PF06875

Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein

CUB

CUB

PF00431

Defensin/corticostatin family

DEFSN

Defensin_beta

PF00711

Homologues of snake disintegrins

DISIN

Disintegrin

PF00200

DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function

DM4_12

DM4_12

PF07841

Cysteine-rich domain currently specific to Drosophila

DM6

DUF1431

PF07248

Possible catecholamine-binding domain present in a variety of eukaryotic proteins

DoH

DOMON

PF03351

Delta serrate ligand

DSL

DSL

PF01414

Epidermal growth factor-like domain

EGF

EGF

PF00008

Calcium-binding EGF-like domain

EGF_CA

EGF_CA

PF07645

Laminin-type epidermal growth factor-like domain

EGF_Lam

Laminin_EGF

PF00053

Coagulation Factor Xa inhibitory site

-

FXa_inhibition

PF14670

Follistatin/Osteonectin-like EGF domain

-

FOLN

PF09289

Complement Clr-like EGF-like

-

cEGF

PF12662

EGF-like domain

-

EGF_2

PF07974

EGF domain

-

EGF_3

PF12947

Human growth factor-like EGF

-

hEGF

PF12661

Thrombomodulin like fifth domain, EGF-like

-

Tme5_EGF_like

PF09064

Endothelin

END

Endothelin

PF00322

Ependymins

EPEND

Ependymin

PF00811

Ephrin receptor ligand binding domain

EPH_lbd

Ephrin_lbd

PF01404

F5/8 type C domain

 

F5_F8_type_C

PF00754

Four repeated domains in the Fasciclin I family of proteins, present in many other contexts

FAS1

Fasciclin

PF02469

Fibrinogen-related domains (FReDs)

FBG

Fibrinogen_C

PF00147

Fungal-type cellulose-binding domain

fCBD

CBM_1

PF00734

Fibronectin type 1 domain

FN1

fn1

PF00039

Fibronectin type 2 domain

FN2

fn2

PF00040

Frizzled

FRI

Fz

PF01392

Furin-like repeats

FU

Furin-like

PF00757

Growth factor receptor domain IV

 

GF_recep_IV

PF14843

G2 nidogen domain and fibulin

G2F

G2F

PF07474

Gastrin / cholecystokinin / caerulein family

GASTRIN

Gastrin

PF00918

Glycoprotein hormone alpha chain homologues

GHA

Hormone_6

PF00236

Glycoprotein hormone beta chain homologues

GHB

Cys_knot

PF00007

Coagulin

-

Coagulin

PF02035

DAN domain

-

DAN

PF03045

Noggin

-

Noggin

PF05806

Sclerostin (SOST)

-

Sclerostin

PF05463

Domain containing Gla (gamma-carboxyglutamate) residues

GLA

Gla

PF00594

Glucagon like hormones

GLUCA

Hormone_2

PF00123

Glycosyl hydrolase family 10

Glyco_10

Glyco_hydro_10

PF00331

Glyco_18

Glyco_18

Glyco_hydro_18

PF00704

Glycosyl hydrolases family 25

Glyco_25

Glyco_hydro_25

PF01183

Glycosyl hydrolases family 32

Glyco_32

Glyco_hydro_32

PF00251

G-protein-coupled receptor proteolytic site domain

GPS

GPS

PF01825

Granulin

GRAN

Granulin

PF00396

Hint (Hedgehog/Intein) domain C-terminal region

HintC

Hint

PF01079

Hint (Hedgehog/Intein) domain N-terminal region

HintN

Hint

PF01079

Domain present in hormone receptors

HormR

HRM

PF02793

Hemopexin-like repeats

HX

Hemopexin

PF00045

Hydrophobins

HYDRO

Hydrophobin

PF01185

Insulin growth factor-binding protein homologues

IB

IGFBP

PF00219

Interferon alpha, beta and delta

IFabd

Interferon

PF00143

Interleukin-10 family

IL10

IL10

PF00726

Interleukin-2 family

IL2

IL2

PF00715

Interleukins 4 and 13

IL4_13

IL4

PF00727

Interleukin-6 homologues

IL6

IL6

PF00489

Interleukin-7 and interleukin-9 family

IL7

IL7

PF01415

Insulin / insulin-like growth factor / relaxin family

IlGF

Insulin

PF00049

Nematode insulin-related peptide beta type

-

Ins_beta

PF03488

Integrin beta subunits (N-terminal portion of extracellular region)

INB

Integrin_beta

PF00362

Integrin alpha (beta-propellor repeats)

Int_alpha

Integrin_alpha

PF00357

Kazal type serine protease inhibitors

KAZAL

Kazal_1

PF00050

Kazal type serine protease inhibitors

KAZAL

Kazal_2

PF07648

Knottins

Knot1

Defensin_2

PF01097

Plant self-incompatibility response (SCRL) protein

-

SCRL

PF06876

S locus-related glycoprotein 1 binding pollen coat protein (SLR1-BP)

-

SLR1-BP

PF07333

Ergtoxin family

-

Toxin_17

PF08086

Scorpion short toxin, BmKK2

-

Toxin_2

PF00451

Scorpion toxin-like domain

-

Toxin_3

PF00537

Potassium channel toxin

-

Toxin_38

PF14866

Scorpion short toxin

-

Toxin_5

PF05294

Antifungal peptide termicin

-

Toxin_37

PF11415

Kringle domain

KR

Kringle

PF00051

BPTI/Kunitz family of serine protease inhibitors

KU

Kunitz_BPTI

PF00014

Laminin B domain

LamB

Laminin_B

PF00052

Laminin G domain

LamG

Laminin_G_1

PF00054

Laminin N-terminal domain (domain VI)

LamNT

Laminin_N

PF00055

LCCL

LCCL

LCCL

PF03815

Low-density lipoprotein receptor domain class A

LDLa

Ldl_recept_a

PF00057

Leukemia inhibitory factor

LIF_OSM

LIF_OSM

PF01291

Link (Hyaluronan-binding)

LINK

Xlink

PF00193

Lipoprotein N-terminal Domain

LPD_N

Vitellogenin_N

PF01347

Ly-6 antigen / uPA receptor -like domain

LU

UPAR_LY6

PF00021

Low-density lipoprotein-receptor YWTD domain

LY

Ldl_recept_b

PF00058

Alpha-lactalbumin / lysozyme C

LYZ1

Lys

PF00062

Lysozyme subfamily 2

LYZ2

Glucosaminidase

PF01832

Membrane-attack complex / perforin

MACPF

MACPF

PF01823

Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

MAM

MAM

PF00629

Domain involved in innate immunity and lipid metabolism

ML

E1_DerP2_DerF2

PF02221

NEAr Transporter domain

NEAT

NEAT

PF05031

Nerve growth factor (NGF or beta-NGF)

NGF

NGF

PF00243

Neurohypophysial hormones

NH

Hormone_5

PF00184

Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

NIDO

NIDO

PF06119

Domain found in Notch and Lin-12

NL

Notch

PF00066

Neuromedin U

NMU

NMU

PF02070

Tissue inhibitor of metalloproteinase family

NTR

TIMP

PF00965

DNA/RNA non-specific endonuclease*

NUC

Endonuclease_NS

PF01223

Olfactomedin-like domains

OLF

OLF

PF02191

Osteopontin

OSTEO

Osteopontin

PF00865

Phospholipase A2

PA2c

Phospholip_A2_1

PF00068

Pancreatic hormones / neuropeptide F / peptide YY family

PAH

Hormone_3

PF00159

Bacterial periplasmic substrate-binding proteins

PBPb

SBP_bac_3

PF00497

Bacterial extracellular solute-binding protein

-

SBP_bac_1

PF01547

Bacterial extracellular solute-binding protein

-

SBP_bac_11

PF13531

Bacterial extracellular solute-binding proteins, family 5 Middle

-

SBP_bac_5

PF00496

Bacterial extracellular solute-binding protein

-

SBP_bac_6

PF13343

Bacterial extracellular solute-binding protein, family 7

-

SBP_bac_7

PF03480

Bacterial extracellular solute-binding protein

-

SBP_bac_8

PF13416

P or trefoil or TFF domain

PD

Trefoil

PF00088

Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family

PDGF

PDGF

PF00341

Papain family cysteine protease

Pept_C1

Peptidase_C1

PF00112

Insect pheromone/odorant binding protein domains

PhBP

PBP_GOBP

PF01395

Repeats in polycystic kidney disease 1 (PKD1) and other proteins

PKD

PKD

PF00801

Major prion protein

PRP

Prion

PF00377

Paramecium Surface Antigen Repeat

PSA

Paramecium_SA

PF01508

Domain found in Plexins, Semaphorins and Integrins

PSI

PSI

PF01437

Plant trypsin inhibitors

PTI

Squash

PF00299

Pentraxin / C-reactive protein / pentaxin family

PTX

Pentaxin

PF00354

Pancreatic ribonuclease

RNAse_Pc

RnaseA

PF00074

Serum amyloid A proteins

SAA

SAA

PF00277

Saposin/surfactant protein-B A-type DOMAIN

SAPA

SapA

PF02199

Saposin (B) Domains

SapB

SapB_1

PF05184

Saposin (B) Domains

SapB

SapB_2

PF03489

SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains

SCP

SCP

PF00188

Intercrine alpha family (small cytokine C-X-C) (chemokine CXC)

SCY

IL8

PF00048

Domain found in sea urchin sperm protein, enterokinase, agrin

SEA

SEA

PF01390

Semaphorin domain

Sema

Sema

PF01403

ShK toxin domain

ShKT

ShTK

PF01549

Crisp

-

Crisp

PF08562

Somatomedin B -like domains

SO

Somatomedin_B

PF01033

Scavenger receptor Cys-rich

SR

SRCR

PF00530

Hepsin, SRCR

-

Hepsin-SRCR

PF09272

Scavenger receptor cysteine-rich domain

-

SRCR_2

PF15494

Soybean trypsin inhibitor (Kunitz) family of protease inhibitors

STI

Kunitz_legume

PF00197

Transforming growth factor-beta (TGF-beta) family

TGFB

TGF_beta

PF00019

Thaumatin family

THN

Thaumatin

PF00314

Tachykinin family

TK

Tachykinin

PF02202

Tumour necrosis factor family

TNF

TNF

PF00229

Tumor necrosis factor receptor / nerve growth factor receptor repeats

TNFR

TNFR_c6

PF00020

Transferrin

TR_FER

Transferrin

PF00405

Transthyretin

TR_THY

Transthyretin

PF00576

Trypsin-like serine protease

Tryp_SPc

Trypsin

PF00089

Thrombospondin type 1 repeats

TSP1

TSP_1

PF00090

Thyroglobulin type I repeats

TY

Thyroglobulin_1

PF00086

Uteroglobin

UTG

Uteroglobin

PF01099

Allergen Fel d I-B chain

-

Feld-I_B

PF09252

von Willebrand factor (vWF) type C domain

VWC

VWC

PF00093

Beta-microseminoprotein

-

PSP94

PF05825

von Willebrand factor (vWF) type D domain

VWD

VWD

PF00094

Four-disulfide core domains

WAP

WAP

PF00095

Wnt-inhibitory factor-1 like domain

WIF

WIF

PF02019

Found in Wnt-1

WNT1

wnt

PF00110

Present in yeast cell wall integrity and stress response component proteins

WSC

WSC

PF01822

Zinc-dependent metalloprotease

ZnMc

Peptidase_M10

PF00413

Zona pellucida (ZP) domain

ZP

Zona_pellucida

PF00100

ADAM-TS Spacer 1

-

ADAM_spacer1

PF05986

Animal haem peroxidase

-

An_peroxidase

PF03098

Antistasin

-

Antistasin

PF02822

Copper type II ascorbate-dependent monooxygenase, C-terminal domain

-

Cu2_monoox_C

PF03712

Copper type II ascorbate-dependent monooxygenase, N-terminal domain

-

Cu2_monooxygen

PF01082

Laminin Domain I

-

Laminin_I

PF06008

Laminin Domain II

-

Laminin_II

PF06009

Laminin G domain

-

Laminin_G_2

PF02210

Class I Histocompatibility antigen, domains alpha 1 and 2

-

MHC_I

PF00129

Class II histocompatibility antigen, beta domain

MHC_II_beta

MHC_II_beta

PF00969

Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2

-

MHC_I_2

PF14586

Class II histocompatibility antigen, alpha domain

MHC_II_alpha

MHC_II_alpha

PF00993

Agrin NtA domain

-

NtA

PF03146

Reprolysin (M12B) family zinc metalloprotease

-

Reprolysin

PF01421

*Highlighted extracellular domain families found to be multilocale.

 

Table 2.   List of intracellular Pfam-A signaling domain families

Description

Smart name

Pfam name

Pfam ID

14-3-3 homologues

14_3_3

14-3-3

PF00244

Actin depolymerisation factor/cofilin -like domains

ADF

Cofilin_ADF

PF00241

Ankyrin repeats

ANK

Ank

PF00023

Ankyrin repeats (3 copies)*

-

Ank_2

PF12796

Ankyrin repeat*

-

Ank_3

PF13606

Ankyrin repeats (many copies)*

-

Ank_4

PF13637

Ankyrin repeats (many copies)*

-

Ank_5

PF13857

ARF-like small GTPases; ARF, ADP-ribosylation factor

ARF

Arf

PF00025

Putative GTP-ase activating proteins for the small GTPase, ARF

ArfGap

ArfGap

PF01412

Band 4.1 homologues

B41

Band_41

PF00373

Cytochrome b-561 / ferric reductase transmembrane domain

B561

Cytochrom_B561

PF03188

Bulb-type mannose-specific lectin

B_lectin

B_lectin

PF01453

BAG domains, present in regulator of Hsp70 proteins

BAG

BAG

PF02179

BH4 Bcl-2 homology region 4

BH4

BH4

PF02180

Bruton's tyrosine kinase Cys-rich motif

BTK

BTK

PF00779

Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains)

C1

C1_1

PF00130

C1 domain*

-

C1_2

PF03107

C1-like domain*

-

C1_3

PF07649

TFIIH C1-like domain*

-

C1_4

PF07975

Calponin homology domain

CH

CH

PF00307

Two component signalling adaptor domain

CheW

CheW

PF01584

Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2

CNH

CNH

PF00780

Cyclic nucleotide-monophosphate binding domain

cNMP

cNMP_binding

PF00027

Cold shock protein domain

CSP

CSD

PF00313

Cullin

CULLIN

Cullin

PF00888

Adenylyl- / guanylyl cyclase, catalytic domain

CYCc

Guanylate_cyc

PF00211

Diacylglycerol kinase accessory domain (presumed)

DAGKa

DAGK_acc

PF00609

Diacylglycerol kinase catalytic domain (presumed)

DAGKc

DAGK_cat

PF00781

Domain present in Dishevelled and axin

DAX

DIX

PF00778

Death effector domain

DED

DED

PF01335

Domain found in Dishevelled, Egl-10, and Pleckstrin

DEP

DEP

PF00610

Dual specificity phosphatase, catalytic domain

DSPc

DSPc

PF00782

Domain of Unknown Function with GGDEF motif

DUF1

GGDEF

PF00990

Domain of Unknown Function 2

DUF2

EAL

PF00563

Dynamin, GTPase

DYNc

Dynamin_N

PF00350

Epsin N-terminal homology (ENTH) domain

ENTH

ENTH

PF01417

A Receptor for Ubiquitination Targets

FBOX

F-box

PF00646

 

 

FBA

PF04300

Fes/CIP4 homology domain

FCH

FCH

PF00611

Contains two conserved F residues

FF

FF

PF01846

Formin Homology 2 Domain

FH2

FH2

PF02181

Forkhead associated domain

FHA

FHA

PF00498

Protein present in Fab1, YOTB, Vac1, and EEA1

FYVE

FYVE

PF01363

FYVE-type zinc finger*

-

FYVE_2

PF02318

Growth-Arrest-Specific Protein 2 Domain

GAS2

GAS2

PF02187

Dynamin GTPase effector domain

GED

GED

PF02212

G protein gamma subunit-like motifs

GGL

G-gamma

PF00631

LGN motif, putative GEFs specific for G-alpha GTPases

GoLoco

GoLoco

PF02188

Domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins*

GRAM

GRAM

PF02893

Guanylate kinase homologues

GuKc

Guanylate_kin

PF00625

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain

HAMP

HAMP

PF00672

Histidine kinase-like ATPases

HATPase_c

HATPase_c

PF02518

Domain Homologous to E6-AP Carboxyl Terminus with*

HECTc

HECT

PF00632

His Kinase A (phosphoacceptor) domain

HisKA

HisKA

PF00512

Histidine kinase*

-

HisKA_2

PF07568

Histidine kinase*

-

HisKA_3

PF07730

Histidine Phosphotransfer domain

HPT

Hpt

PF01627

Rho effector or protein kinase C-related kinase homology region 1 homologues

Hr1

HR1

PF02185

I/LWEQ domain*

ILWEQ

I_LWEQ

PF01608

Inositol polyphosphate phosphatase, catalytic domain homologues

IPPc

Exo_endo_phos

PF03372

Short calmodulin-binding motif containing conserved Ile and Gln residues

IQ

IQ

PF00612

Immunoreceptor tyrosine-based activation motif

ITAM

ITAM

PF02189

Kinesin motor, catalytic domain. ATPase

KISc

Kinesin

PF00225

Domain in receptor targeting proteins Lin-2 and Lin-7*

L27

L27

PF02828

Zinc-binding domain present in Lin-11, Isl-1, Mec-3*

LIM

LIM

PF00412

Low molecular weight phosphatase family

LMWPc

LMWPc

PF01451

Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer)

MA

MCPsignal

PF00015

Myosin

MYSc

Myosin_head

PF00063

Domain in Myosin and Kinesin Tails

MyTH4

MyTH4

PF00784

NEUZ

NEUZ

Neuralized

PF07177

PAS domain*

PAS

PAS

PF00989

P21-Rho-binding domain*

PBD

PBD

PF00786

Pleckstrin homology domain

PH

PH

PF00169

Phosphoinositide 3-kinase, region postulated to contain C2 domain*

PI3K_C2

PI3K_C2

PF00792

PI3-kinase family, p85-binding domain*

PI3K_p85B

PI3K_p85B

PF02192

PI3-kinase family, Ras-binding domain*

PI3K_rbd

PI3K_rbd

PF00794

Phosphoinositide 3-kinase family, accessory domain (PIK domain)*

PI3Ka

PI3Ka

PF00613

Phosphoinositide 3-kinase, catalytic domain*

PI3Kc

PI3_PI4_kinase

PF00454

Phosphatidylinositol phosphate kinases*

PIPKc

PIP5K

PF01504

Cytoplasmic phospholipase A2, catalytic subunit

PLAc

PLA2_B

PF01735

Phospholipase C, catalytic domain (part); domain X

PLCXc

PI-PLC-X

PF00388

Phospholipase C, catalytic domain (part); domain Y

PLCYc

PI-PLC-Y

PF00387

Phospholipase D. Active site motifs

PLDc

PLDc

PF00614

Serine/threonine phosphatases, family 2C, catalytic domain

PP2Cc

PP2C

PF00481

Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain*

PTB

PID

PF00640

Phosphotyrosine-binding domain (IRS1-like)

PTBI

IRS

PF02174

Protein tyrosine phosphatase, catalytic domain*

PTPc

Y_phosphatase

PF00102

Protein tyrosine phosphatase, catalytic domain motif*

PTPc_motif

Y_phosphatase

PF00102

PhoX homologous domain, present in p47phox and p40phox

PX

PX

PF00787

Domain associated with PX domains

PXA

PXA

PF02194

Ras association (RalGDS/AF-6) domain

RA

RA

PF00788

Ran-binding domain*

RanBD

Ran_BP1

PF00638

Ras subfamily of RAS small GTPases

RAS

Ras

PF00071

GTPase-activator protein for Ras-like GTPases

RasGAP

RasGAP

PF00616

Guanine nucleotide exchange factor for Ras-like small GTPases

RasGEF

RasGEF

PF00617

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif

RasGEFN

RasGEF_N

PF00618

Raf-like Ras-binding domain

RBD

RBD

PF02196

Regulator of G protein signalling domain

RGS

RGS

PF00615

GTPase-activator protein for Rho-like GTPases

RhoGAP

RhoGAP

PF00620

Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases

RhoGEF

RhoGEF

PF00621

RIIalpha, Regulatory subunit portion of type II PKA R-subunit

RIIa

RIIa

PF02197

RIO-like kinase

RIO

RIO1

PF01163

Extension to Ser/Thr-type protein kinases

S_TK_X

Pkinase_C

PF00433

Serine/Threonine protein kinases, catalytic domain

S_TKc

Pkinase

PF00069

Sterile alpha motif

SAM

SAM_1

PF00536

Sterile alpha motif*

SAM

SAM_2

PF07647

Sec7 domain*

Sec7

Sec7

PF01369

Src homology 2 domains*

SH2

SH2

PF00017

Suppressors of cytokine signalling

SOCS

SOCS_box

PF07525

Spectrin repeats

SPEC

Spectrin

PF00435

In StAR and phosphatidylcholine transfer protein*

START

START

PF01852

Protein kinase; unclassified specificity*

STYKc

Pkinase

PF00069

Helical region found in SNAREs

t_SNARE

SNARE

PF05739

Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

TBC

RabGAP-TBC

PF00566

Metallochaperone-like domain

TRASH

YHS

PF04945

Tyrosine kinase, catalytic domain

TyrKc

Pkinase

PF00069

Ubiquitin associated domain

UBA

UBA

PF00627

Ubiquitin associated domain

-

UBA_2

PF08587

Fungal ubiquitin-associated domain

-

UBA_3

PF09288

UBA-like domain

-

UBA_4

PF14555

Ubiquitin homologues

UBQ

ubiquitin

PF00240

Ubiquitin-like domain

-

Ubiquitin_2

PF14560

Ubiquitin-like domain

-

Ubiquitin_3

PF14836

Domain present in ubiquitin-regulatory proteins

UBX

UBX

PF00789

Domain present in VPS-27, Hrs and STAM

VHS

VHS

PF00790

Domain present in VPS9

VPS9

VPS9

PF02204

WD40 repeats*

WD40

WD40

PF00400

WASP homology region 1

WH1

WH1

PF00568

Wiskott Aldrich syndrome homology region 2

WH2

WH2

PF02205

Domain with 2 conserved Trp (W) residues*

WW

WW

PF00397

A20-like zinc fingers*

ZnF_A20

zf-A20

PF01754

Zinc-binding domain, present in Dystrophin, CREB-binding protein

ZnF_ZZ

ZZ

PF00569

Domain present in ZO-1 and Unc5-like netrin receptors

ZU5

ZU5

PF00791

*Highlighted intracellular signaling domain families found to be multilocale.

 

 

Table 3.   List of nuclear Pfam-A domain families

Description

Smart name

Pfam name

Pfam ID

3'-5' exonuclease

35EXOc

DNA_pol_A_exo1

PF01612

DNA polymerase family B, exonuclease domain

-

DNA_pol_B_exo1

PF03104

5'-3' exonuclease*

53EXOc

5_3_exonuc

PF01367

tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)*

ADEAMc

A_deamin

PF02137

DNA-binding domain in plant proteins such as APETALA2 and EREBPs

AP2

AP2

PF00847

Bromo adjacent homology domain

BAH

BAH

PF01426

Basic domain in HLH proteins of MYOD family

BASIC

Basic

PF01586

B-Box-type zinc finger*

BBOX

zf-B_box

PF00643

BCL (B-Cell lymphoma); contains BH1, BH2 regions*

BCL

Bcl-2

PF00452

Breast cancer carboxy-terminal domain

BRCT

BRCT

PF00533

BRIGHT, ARID (A/T-rich interaction domain) domain

BRIGHT

ARID

PF01388

Domain in transcription and CHROMO domain helicases

BRK

BRK

PF07533

Basic region leucin zipper

BRLZ

bZIP

PF00170

Bromo domain

BROMO

Bromodomain

PF00439

Domain in transcription factors and synapse-associated proteins

BSD

BSD

PF03909

Bromodomain transcription factors and PHD domain containing proteins

BTP

Bromo_TP

PF07524

CCAAT-Binding transcription Factor

CBF

CBFB_NFYA

PF02045

Chromatin organization modifier domain

CHROMO

Chromo

PF00385

Catalytic domain of ctd-like phosphatases*

CPDc

NIF

PF03031

Copper-Fist

Cu_Fist

Copper-fist

PF00649

Domain in different transcription and chromosome remodeling factors

DDT

DDT

PF02791

DEAD-like helicases superfamily

DEXDc

SNF2_N

PF00176

Doublesex DNA-binding motif

DM

DM

PF00751

Double-stranded RNA binding motif*

DSRM

dsrm

PF00035

Domain A in dwarfin family proteins*

DWA

MH1

PF03165

Domain B in dwarfin family proteins*

DWB

MH2

PF03166

Domain in DSRM or ZnF_C2H2 domain containing proteins

DZF

DZF

PF07528

Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5*

eIF5C

W2

PF02020

Endonuclease III

ENDO3c

HhH-GPD

PF00730

Erythroblast transformation specific domain*

ETS

Ets

PF00178

FORKHEAD

FH

Fork_head

PF00250

"FY-rich" domain, C-terminal region

FYRC

FYRC

PF05965

"FY-rich" domain, N-terminal region

FYRN

FYRN

PF05964

Domain in histone families 1 and 5

H15

Linker_histone

PF00538

Histone 2A

H2A

Histone

PF00125

Histone H2B

H2B

Histone

PF00125

Histone H3

H3

Histone

PF00125

Histone H4

H4

Histone

PF00125

Homeobox associated leucin zipper

HALZ

HALZ

PF02183

Helicase superfamily c-terminal domain

HELICc

Helicase_C

PF00271

Helix-hairpin-helix DNA-binding motif class 1

HhH1

HHH

PF00633

High mobility group

HMG

HMG_box

PF00505

Domain in high mobilty group proteins HMG14 and HMG 17

HMG17

HMG14_17

PF01101

HNH nucleases

HNHc

HNH

PF01844

Domain in histone-like proteins of HNS family

HNS

Histone_HNS

PF00816

Ligand binding domain of hormone receptors

HOLI

Hormone_recep

PF00104

Helicase and RNase D C-terminal

HRDC

HRDC

PF00570

Domain in helicases and associated with SANT domains

HSA

HSA

PF07529

Interferon regulatory factor*

IRF

IRF

PF00605

A domain family that is part of the cupin metalloenzyme superfamily

JmjC

JmjC

PF02373

Small domain found in the jumonji family of transcription factors

JmjN

JmjN

PF02375

In nuclear membrane-associated proteins

LEM

LEM

PF03020

Ligase N family

LIGANc

DNA_ligase_aden

PF01653

Domain in DAP-5, eIF4G, MA-3 and other proteins*

MA3

MA3

PF02847

MADS

MADS

SRF-TF

PF00319

Methyl-CpG binding domain

MBD

MBD

PF01429

Minichromosome maintenance proteins

MCM

MCM

PF00493

ATPase domain of DNA mismatch repair MUTS family

MUTSac

MutS_V

PF00488

Orange domain

ORANGE

Hairy_orange

PF07527

Paired Box domain

PAX

PAX

PF00292

PHD zinc finger

PHD

PHD

PF00628

Short conserved domain in transcriptional regulators

Plus3

Plus-3

PF03126

DNA polymerase type-B family

POLBc

DNA_pol_B

PF00136

A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins

POP4

UPF0086

PF01868

Found in Pit-Oct-Unc transcription factors

POU

Pou

PF00157

Domain associated with HOX domains

POX

POX

PF07526

N-terminal to some SET domains

PreSET

Pre-SET

PF05033

Proline-rich domain in spliceosome associated proteins

PSP

PSP

PF04046

DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria

PUR

PurA

PF04845

Ribonuclease III family*

RIBOc

Ribonuclease_3

PF00636

DNA-directed RNA-polymerase II subunit

RPOL4c

RNA_pol_Rpb4

PF03874

RNA polymerase subunit 8

RPOL8c

RNA_pol_Rpb8

PF03870

RNA polymerase subunit 9

RPOL9

RNA_POL_M_15KD

PF02150

RNA polymerase I subunit A N-terminus

RPOLA_N

RNA_pol_Rpb1_2

PF00623

RNA polymerase subunit CX

RPOLCX

DNA_RNApol_7kD

PF03604

RPR

RPR

CTD_bind

PF04818

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation

SAP

SAP

PF02037

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

SET

SET

PF00856

Found in Skp1 protein family*

Skp1

Skp1

PF01466

snRNP Sm proteins

Sm

LSM

PF01423

SET and RING finger associated domain

SRA

SAD_SRA

PF02182

STE like transcription factors

STE

STE

PF02200

Domain first found in the mice T locus (Brachyury) protein

TBOX

T-box

PF00907

TEA domain

TEA

TEA

PF01285

Transcription initiation factor IIE

TFIIE

TFIIE_alpha

PF02002

Domain in the central regions of transcription elongation factor S-II (and elsewhere)

TFS2M

TFIIS_M

PF07500

Bacterial DNA topoisomerase I DNA-binding domain

TOP1Ac

Topoisom_bac

PF01131

Bacterial DNA topoisomeraes I ATP-binding domain

TOP1Bc

Topoisom_bac

PF01131

DNA Topoisomerase I (eukaryota)

TOPEUc

Topoisom_I

PF01028

TOPRIM

TOPRIM

Toprim

PF01751

Toprim-like

-

Toprim_2

PF13155

Toprim domain

-

Toprim_3

PF13362

Toprim domain

-

Toprim_4

PF13662

Xeroderma pigmentosum G I-region

XPGI

XPG_I

PF00867

Xeroderma pigmentosum G N-region

XPGN

XPG_N

PF00752

Z-DNA-binding domain in adenosine deaminases

Zalpha

z-alpha

PF02295

BED zinc finger

ZnF_BED

zf-BED

PF02892

C2C2 Zinc finger

ZnF_C2C2

TFIIS_C

PF01096

Zinc finger

ZnF_C2H2

zf-C2H2

PF00096

C4 zinc finger in nuclear hormone receptors

ZnF_C4

zf-C4

PF00105

Zinc finger

ZnF_CHCC

zf-CHC2

PF01807

Zinc finger in DBF-like proteins

ZnF_DBF

zf-DBF

PF07535

Zinc finger binding to DNA consensus sequence [AT]GATA[AG]

ZnF_GATA

GATA

PF00320

Plant mutator transposase zinc finger

ZnF_PMZ

SWIM

PF04434

*Highlighted nuclear domain families found to be multilocale.