extradom.txt
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UniProt - Swiss-Prot Protein Knowledgebase
SIB Swiss Institute of Bioinformatics; Geneva, Switzerland
European Bioinformatics Institute (EBI); Hinxton, United Kingdom
Protein Information Resource (PIR); Washington DC, USA
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Description: Nomenclature of extracellular domains
Name: extradom.txt
Release: 2013_05 of 01-May-2013
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Nomenclature proposal for domains (or modules) found mainly in extracellular
proteins of higher eukaryotes.
The content of this document has been approved by the participants of the
International Workshop on Sequence, Structure, Function and Evolution of
Extracellular protein Modules (Sep. 24-28 1994, Margretetrop, Sweden) and
has been published as a special poster in TIBS:
Bork P., Bairoch A.
Extracellular protein modules: a proposed nomenclature.
Trends Biochem. Sci. 20:Special poster supplement TIBSC02(1995).
All inquiries about extracellular protein modules should be sent by email
to:
bork@embl-heidelberg.de
Graphical reprentations of the modular structure of extracellular proteins
is available from the following WWW page:
http://www.bork.embl-heidelberg.de/Modules/extra.html
A graphical reprentation of the document you are currently reading is
available as:
http://www.bork.embl-heidelberg.de/Modules/01-nomenclature.gif
Some useful references:
[ 1] Baron M., Norman D.G., Campbell I.D.
Trends Biochem. Sci. 16:13-17(1991).
[ 2] Bork P.
FEBS Lett. 286:47-54(1991).
[ 3] Bork P.
Curr. Opin. Struct. Biol. 2:413-421(1992).
[ 4] Doolittle R.F., Bork P.
Sci. Am. 269:50-56(1993).
[ 5] Patthy L.
Curr. Opin. Struct. Biol. 1:351-361(1991).
___________ _________________________________ __ ____ _____ _____________________________ _________
Abbrev. Full name 3D Size Nb Swiss-Prot domain name PROSITE
5C 2C (aa) Cys entry
___________ _________________________________ __ ____ _____ _____________________________ _________
ANATO AT Anaphylatoxin + 70 6 Anaphylatoxin-like PDOC00906
APPLE AP Apple - 90 4 Apple PDOC00376
C1Q CQ Complement C1q C-terminal + 140 0-3 C1q PDOC00857
CADHE CA Cadherin + 110 0 Cadherin PDOC00205
CCP CP CCP (Sushi) (SCR) + 70 4 Sushi PDOC50923
CLECT CL C-type lectin (CTL) + 130 4/6 C-type lectin PDOC00537
COL4C C4 Collagen IV NC1 - 110 6 collagen IV NC1 PDOC51403
COLFI CF Fibrillar collagens C-terminal - 240 8 Fibrillar collagen C-terminal
CTCK CK C-terminal cystine knot + 90 6/11 CTCK PDOC00912
CUB CU CUB + 110 2/4 CUB PDOC00908
CYSTA CY Cystatin-like + 100 0-4 Cystatin
CYTR CR Cytokine receptor N-terminal + 90 4/6 Cytokine receptors N-T PDOC00214
DSL DS DSL + 50 6 DSL PDOC51051
EGF EG EGF-like + 40 6 EGF-like PDOC00021
FA58A FA Coagulation factors 5/8 type A + 330 2-4 F5/8 type A
FA58C FC Coagulation factors 5/8 type C - 150 0-2 F5/8 type C PDOC00988
FBG FG Fibrinogen beta/gamma C-terminal + 250 4 Fibrinogen C-terminal PDOC00445
FIMAC FM Factor I/MAC proteins C6/7 - 70 8/12 FIMAC
FN1 F1 Fibronectin type-I + 40 4 Fibronectin type-I PDOC00965
FN2 F2 Fibronectin type-II + 60 4 Fibronectin type-II PDOC00022
FN3 F3 Fibronectin type-III + 90 0 Fibronectin type-III PDOC50853
FOLLI FS Follistatin-like + 50 10 Follistatin-like
FTC FT Factor C - 110 4 Factor C
FURIN FU Furin-like Cys-rich - 170 26 FU
FZ FZ Frizzled + 120 10 FZ PDOC50038
GLA GA Gamma-carboxy-glutamate domain + 60 2 Gla PDOC00011
HEMOP HX Hemopexin-like + 60 0-2 Hemopexin-like PDOC00023
IBPNT IB IGFBP/CTGF N-terminal - 70 12 IGFBP N-terminal PDOC00194
IGSF IG Immunoglobulin "superfamily" + 100 0-6 Ig-like PDOC50835
IGC1 I1 Immunoglobulin C1 + 100 0-6 Ig-like C1-type PDOC50835
IGC2 I2 Immunoglobulin C2 + 100 0-6 Ig-like C2-type PDOC50835
IGV IV Immunoglobulin V + 100 0-6 Ig-like V-type PDOC50835
KAZAL KL Kazal-like inhibitor + 50 6 Kazal-like PDOC00254
KRING KR Kringle + 80 6 Kringle PDOC00020
KUNIT KU BPTI/Kunitz-like inhibitor + 60 4/6 BPTI/Kunitz inhibitor PDOC00252
LAMD4 L4 Laminin domain IV (B-type) - 190 0 Laminin IV type B PDOC51115
LAMEG LE Laminin EGF-like + 50 8 Laminin EGF-like PDOC00961
LAMG LG Laminin G-like (A-type module) - 190 0-4 Laminin G-like PDOC50025
LAMNT LN Laminin N-terminal (domain VI) - 250 4/6 Laminin N-terminal PDOC51117
LDLRA LA LDL-receptor class A + 40 6 LDL-receptor class A PDOC00929
LDLRB LY LDL-receptor class B - 50 0 LDL-receptor class B PDOC51120
LINK LK Link (Hyaluronan-binding) + 100 4 Link PDOC00955
LRR LR Leucine-rich repeat + 25 0 LRR
LRRC LC LRR C-flank - 60 4 LRR C-flank
LRRN LP LRR preceeding domain (N-flank) - 40 2/4 LRR N-flank
LY6UP LU Ly6 antigen/uPA receptor + 70 8/10 UPAR/Ly6 PDOC00756
MACPF MA MAC proteins/perforin - 250 8 MACPF
MAM MM MAM - 170 4 MAM PDOC00604
NOTLI NL Lin-12/Notch - 30 6 LNR PDOC50258
NTR NT Netrin (C345C) + 130 6 Netrin PDOC50189
PDOM PD P-type (Trefoil) (TFF) + 50 6 P-type PDOC00024
PKD PK PKD1-like + 80 0 PKD PDOC50093
SAPOA SA Saposin-like type A - 30 4 Saposin A-type PDOC51110
SAPOB SB Saposin-like type B - 80 6 Saposin B-type PDOC50015
SEA SE SEA - 80 0 SEA PDOC50024
SOMAB SO Somatomedin B - 40 8 Somatomedin-B like PDOC00453
SRCR SR Scavenger receptor Cys-rich + 110 6 SRCR PDOC00348
TB TB TGF-beta binding + 70 8 TB PDOC51364
THYG1 TY Thyroglobulin type-I - 50 6/8 Thyroglobulin type-I PDOC00377
TNFRC TR TNF family receptors Cys-rich + 40 6/8 TNFR-Cys PDOC00561
TSPC TC Thrombospondin (TSP) C-terminal - 220 1 TSP C-terminal PDOC51236
TSPN TN Thrombospondin (TSP) N-terminal - 210 2/4 TSP N-terminal
TSP1 T1 Thrombospondin (TSP) type-I (TSR) - 60 4/6 TSP type-1 PDOC50092
VWFA VA von Willebrand factor type A + 200 0-2 VWFA PDOC50234
VWFB VB von Willebrand factor type B - 30 8 VWFB
VWFC VC von Willebrand factor type C - 110 10 VWFC PDOC00928
VWFD VD von Willebrand factor type D - 350 28-32 VWFD PDOC51233
WAP WA WAP (4-disulfide core) + 50 8 WAP PDOC00026
ZONAP ZP Zona pellucida domain - 310 8/10 ZP PDOC00577
Notes:
- The two-character abbreviations should only be used for "cartoon"
representation of the domain structure of extracellular proteins
- The five-character abbreviations are intended for use in the text,
abstract and non-cartoon figures of articles.
Some additional two-character abbreviations which can be used in
cartoon representations of proteins:
AN Ankyrin repeat
C2 C2 domain
CC Coiled-coil region
CH Calponin homology domain
CO Collagen-type region
DG Diacylglycerol/phorbol ester binding domain
EF EF-hand calcium binding loop
KH KH domain
PH PH domain
PZ PDZ domain
S2 SH2 domain
S3 SH3 domain
SI Signal sequence
TM Transmembrane region
TP TPR repeat
Codes for frequently occuring enzyme modules:
[2.7.11.-] Serine/threonine protein kinase
[2.7.10.-] Tyrosine protein kinase
[3.4.21.-] Trypsin-type serine protease
[3.4.24.-] Zinc metallopeptidase
[3.1.3.48] Tyrosine protein phosphatase
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