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<html>
<TITLE>Definition of SwissProt Format</TITLE>
<!-- Changed by: Astrid Reinhardt, 7-Feb-1996 -->
<body bgcolor=#ffffff alink=#d9d919 vlink=#994499 link=#aa00aa >
<CENTER>
<H1>
<B>
2. CONVENTIONS USED IN THE DATA BANK
</B>
</H1>
</CENTER>
<br>
<BR>
The following sections describes the general conventions used in SWISS-<br>
PROT to achieve uniformity of presentation. Experienced users of the<br>
EMBL Database can skip these sections and directly refer to Appendix C,<br>
which lists the minor differences in format between the two data<br>
collections.<br>
<H2> 2.1 General structure of the data bank<br></H2>
The SWISS-PROT protein sequence data bank is composed of sequence<br>
entries. Each entry corresponds to a single contiguous sequence as<br>
contributed to the bank or reported in the literature. In some cases,<br>
entries have been assembled from several papers that report overlapping<br>
sequence regions. Conversely, a single paper can provide data for<br>
several entries, e.g. when related sequences from different organisms<br>
are reported.<br>
<br>
References to positions within a sequence are made using sequential<br>
numbering, beginning with 1 at the N-terminal end of the sequence.<br>
<br>
Except for initiator N-terminal methionine residues, which are not<br>
included in a sequence when their absence from the mature sequence has<br>
been proven, the sequence data correspond to the precursor form of a<br>
protein before post-translational modifications and processing.<br>
<br>
<br>
<br>
2.2 Classes of data<br>
<br>
In order to attempt to make data available to users as quickly as<br>
possible after publication, SWISS-PROT entries may be released before<br>
all their details are finalized. The concept of data classes gives the<br>
user some idea of the areas in which the data still require further<br>
work. The class of each entry is indicated on the first (ID) line of<br>
the entry. At present two classes are supported:<br>
<br>
STANDARD : Data which are complete to the standards laid down by<br>
the SWISS-PROT data bank.<br>
<br>
PRELIMINARY: Data for which only the sequence and bibliographic<br>
information have been submitted to thorough checks.<br>
<br>
<br>
2.3 Structure of a sequence entry<br>
<br>
The entries in the SWISS-PROT data bank are structured so as to be<br>
usable by human readers as well as by computer programs. The<br>
explanations, descriptions, classifications and other comments are in<br>
ordinary English. Wherever possible, symbols familiar to biochemists,<br>
protein chemists and molecular biologists are used.<br>
<br>
Each sequence entry is composed of lines. Different types of lines,<br>
each with their own format, are used to record the various data which<br>
make up the entry. A sample sequence entry is shown in the next three<br>
pages.<br>
<br>
ID TNFA_HUMAN STANDARD; PRT; 233 AA.<br>
AC P01375;<br>
DT 21-JUL-1986 (REL. 01, CREATED)<br>
DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)<br>
DT 01-FEB-1995 (REL. 31, LAST ANNOTATION UPDATE)<br>
DE TUMOR NECROSIS FACTOR PRECURSOR (TNF-ALPHA) (CACHECTIN).<br>
GN TNFA.<br>
OS HOMO SAPIENS (HUMAN).<br>
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA;<br>
OC EUTHERIA; PRIMATES.<br>
RN [1]<br>
RP SEQUENCE FROM N.A.<br>
RX MEDLINE; 87217060.<br>
RA NEDOSPASOV S.A., SHAKHOV A.N., TURETSKAYA R.L., METT V.A.,<br>
RA AZIZOV M.M., GEORGIEV G.P., KOROBKO V.G., DOBRYNIN V.N.,<br>
RA FILIPPOV S.A., BYSTROV N.S., BOLDYREVA E.F., CHUVPILO S.A.,<br>
RA CHUMAKOV A.M., SHINGAROVA L.N., OVCHINNIKOV Y.A.;<br>
RL COLD SPRING HARB. SYMP. QUANT. BIOL. 51:611-624(1986).<br>
RN [2]<br>
RP SEQUENCE FROM N.A.<br>
RX MEDLINE; 85086244.<br>
RA PENNICA D., NEDWIN G.E., HAYFLICK J.S., SEEBURG P.H., DERYNCK R.,<br>
RA PALLADINO M.A., KOHR W.J., AGGARWAL B.B., GOEDDEL D.V.;<br>
RL NATURE 312:724-729(1984).<br>
RN [3]<br>
RP SEQUENCE FROM N.A.<br>
RX MEDLINE; 85137898.<br>
RA SHIRAI T., YAMAGUCHI H., ITO H., TODD C.W., WALLACE R.B.;<br>
RL NATURE 313:803-806(1985).<br>
RN [4]<br>
RP SEQUENCE FROM N.A.<br>
RX MEDLINE; 86016093.<br>
RA NEDWIN G.E., NAYLOR S.L., SAKAGUCHI A.Y., SMITH D.H.,<br>
RA JARRETT-NEDWIN J., PENNICA D., GOEDDEL D.V., GRAY P.W.;<br>
RL NUCLEIC ACIDS RES. 13:6361-6373(1985).<br>
RN [5]<br>
RP SEQUENCE FROM N.A.<br>
RX MEDLINE; 85142190.<br>
RA WANG A.M., CREASEY A.A., LADNER M.B., LIN L.S., STRICKLER J.,<br>
RA VAN ARSDELL J.N., YAMAMOTO R., MARK D.F.;<br>
RL SCIENCE 228:149-154(1985).<br>
RN [6]<br>
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).<br>
RX MEDLINE; 90008932.<br>
RA ECK M.J., SPRANG S.R.;<br>
RL J. BIOL. CHEM. 264:17595-17605(1989).<br>
RN [7]<br>
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).<br>
RX MEDLINE; 91193276.<br>
RA JONES E.Y., STUART D.I., WALKER N.P.;<br>
RL J. CELL SCI. SUPPL. 13:11-18(1990).<br>
RN [8]<br>
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).<br>
RX MEDLINE; 90008932.<br>
RA ECK M.J., SPRANG S.R.;<br>
RL J. BIOL. CHEM. 264:17595-17605(1989).<br>
RN [9]<br>
RP MUTAGENESIS.<br>
RX MEDLINE; 91184128.<br>
RA OSTADE X.V., TAVERNIER J., PRANGE T., FIERS W.;<br>
RL EMBO J. 10:827-836(1991).<br>
RN [10]<br>
RP MYRISTOYLATION.<br>
RX MEDLINE; 93018820.<br>
RA STEVENSON F.T., BURSTEN S.L., LOCKSLEY R.M., LOVETT D.H.;<br>
RL J. EXP. MED. 176:1053-1062(1992).<br>
CC -!- FUNCTION: CYTOKINE WITH A WIDE VARIETY OF FUNCTIONS: IT CAN<br>
CC CAUSE CYTOLYSIS OF CERTAIN TUMOR CELL LINES, IT IS IMPLICATED<br>
CC IN THE INDUCTION OF CACHEXIA, IT IS A POTENT PYROGEN CAUSING<br>
CC FEVER BY DIRECT ACTION OR BY STIMULATION OF IL-1 SECRETION, IT<br>
CC CAN STIMULATE CELL PROLIFERATION & INDUCE CELL DIFFERENTIATION<br>
CC UNDER CERTAIN CONDITIONS.<br>
CC -!- SUBUNIT: HOMOTRIMER.<br>
CC -!- SUBCELLULAR LOCATION: TYPE II MEMBRANE PROTEIN. ALSO EXISTS AS<br>
CC AN EXTRACELLULAR SOLUBLE FORM.<br>
CC -!- PTM: THE SOLUBLE FORM DERIVES FROM THE MEMBRANE FORM BY<br>
CC PROTEOLYTIC PROCESSING.<br>
CC -!- DISEASE: CACHEXIA ACCOMPANIES A VARIETY OF DISEASES, INCLUDING<br>
CC CANCER AND INFECTION, AND IS CHARACTERIZED BY GENERAL ILL<br>
CC HEALTH AND MALNUTRITION.<br>
CC -!- SIMILARITY: BELONGS TO THE TUMOR NECROSIS FACTOR FAMILY.<br>
DR EMBL; X02910; HSTNFA.<br>
DR EMBL; M16441; HSTNFAB.<br>
DR EMBL; X01394; HSTNFR.<br>
DR EMBL; M10988; HSTNFAA.<br>
DR PIR; B23784; QWHUN.<br>
DR PIR; A44189; A44189.<br>
DR PDB; 1TNF; 15-JAN-91.<br>
DR PDB; 2TUN; 31-JAN-94.<br>
DR MIM; 191160; 11TH EDITION.<br>
DR PROSITE; PS00251; TNF.<br>
KW CYTOKINE; CYTOTOXIN; TRANSMEMBRANE; GLYCOPROTEIN; SIGNAL-ANCHOR;<br>
KW MYRISTYLATION; 3D-STRUCTURE.<br>
FT PROPEP 1 76<br>
FT CHAIN 77 233 TUMOR NECROSIS FACTOR.<br>
FT TRANSMEM 36 56 SIGNAL-ANCHOR (TYPE-II PROTEIN).<br>
FT LIPID 19 19 MYRISTATE.<br>
FT LIPID 20 20 MYRISTATE.<br>
FT DISULFID 145 177<br>
FT MUTAGEN 108 108 R->W: BIOLOGICALLY INACTIVE.<br>
FT MUTAGEN 112 112 L->F: BIOLOGICALLY INACTIVE.<br>
FT MUTAGEN 162 162 S->F: BIOLOGICALLY INACTIVE.<br>
FT MUTAGEN 167 167 V->A,D: BIOLOGICALLY INACTIVE.<br>
FT MUTAGEN 222 222 E->K: BIOLOGICALLY INACTIVE.<br>
FT CONFLICT 63 63 F -> S (IN REF. 5).<br>
FT STRAND 89 93<br>
FT TURN 99 100<br>
FT TURN 109 110<br>
FT STRAND 112 113<br>
FT TURN 115 116<br>
FT STRAND 118 119<br>
FT STRAND 124 125<br>
FT STRAND 130 143<br>
FT STRAND 152 159<br>
FT STRAND 166 170<br>
FT STRAND 173 174<br>
FT TURN 183 184<br>
FT STRAND 189 202<br>
FT TURN 204 205<br>
FT STRAND 207 212<br>
FT HELIX 215 217<br>
FT STRAND 218 218<br>
FT STRAND 227 232<br>
SQ SEQUENCE 233 AA; 25644 MW; 279986 CN;<br>
MSTESMIRDV ELAEEALPKK TGGPQGSRRC LFLSLFSFLI VAGATTLFCL LHFGVIGPQR<br>
EEFPRDLSLI SPLAQAVRSS SRTPSDKPVA HVVANPQAEG QLQWLNRRAN ALLANGVELR<br>
DNQLVVPSEG LYLIYSQVLF KGQGCPSTHV LLTHTISRIA VSYQTKVNLL SAIKSPCQRE<br>
TPEGAEAKPW YEPIYLGGVF QLEKGDRLSA EINRPDYLDF AESGQVYFGI IAL<br>
//<br>
<br>
<br>
Each line begins with a two-character line code, which indicates the<br>
type of data contained in the line. The current line types and line<br>
codes and the order in which they appear in an entry, are shown below:<br>
<br>
ID - Identification.<br>
AC - Accession number(s).<br>
DT - Date.<br>
DE - Description.<br>
GN - Gene name(s).<br>
OS - Organism species.<br>
OG - Organelle.<br>
OC - Organism classification.<br>
RN - Reference number.<br>
RP - Reference position.<br>
RC - Reference comments.<br>
RX - Reference cross-references.<br>
RA - Reference authors.<br>
RL - Reference location.<br>
CC - Comments or notes.<br>
DR - Database cross-references.<br>
KW - Keywords.<br>
FT - Feature table data.<br>
SQ - Sequence header.<br>
- (blanks) sequence data.<br>
// - Termination line.<br>
<br>
<br>
Some entries do not contain all of the line types, and some line types<br>
occur many times in a single entry. Each entry must begin with an<br>
identification line (ID) and end with a terminator line (//). In<br>
addition the following line types are always present in an entry: AC<br>
(once), DT (3 times), DE (1 or more), OS (1 or more), OC (1 or more),<br>
RN (1 or more), RP (1 or more), RA (1 or more), RL (1 or more), SQ<br>
(once), and at least one sequence data line. The other line types (GN,<br>
OG, RC, RM, CC, DR, KW and FT) are optional.<br>
<br>
A detailed description of each line type is given in the next section<br>
of this document.<br>
<br>
It must be noted that all SWISS-PROT line types exist in the EMBL<br>
Database. A description of the format differences between the SWISS-<br>
PROT and EMBL data banks is given in Appendix C of this document.<br>
<br>
The two-character line type code which begins each line is always<br>
followed by three blanks, so that the actual information begins with<br>
the sixth character. Information is not extended beyond character<br>
position 75.<br>
<br>
<br>
3. THE DIFFERENT LINE TYPES<br>
<br>
<br>
3.1 The ID line<br>
<br>
The ID (IDentification) line is always the first line of an entry. The<br>
general form of the ID line is:<br>
<br>
ID ENTRY_NAME DATA_CLASS; MOLECULE_TYPE; SEQUENCE_LENGTH.<br>
<br>
3.1.1 Entry Name<br>
<br>
The first item on the ID line is the entry name of the sequence. This<br>
name is a useful means of identifying a sequence. The entry name<br>
consists of up to ten uppercase alphanumeric characters.<br>
<br>
SWISS-PROT uses a general purpose naming convention which can be<br>
symbolized as X_Y, where<br>
<br>
X is a mnemonic code of at most 4 alphanumeric characters representing<br>
the protein name. Examples: B2MG is for Beta-2-microglobulin, HBA is<br>
for Hemoglobin alpha chain and INS is for Insulin.<br>
<br>
The `_' sign serves as a separator.<br>
<br>
Y is a mnemonic species identification code of at most 5 alphanumeric<br>
characters representing the biological source of the protein. This<br>
code is generally made of the first three letters of the genus and<br>
the first two letters of the species. Examples: PSEPU is for<br>
Pseudomonas putida and NAJNI is for Naja nivea.<br>
<br>
However, for species commonly encountered in the data bank, self-<br>
explanatory codes are used. There are 16 of those codes. They are:<br>
BOVIN for Bovine, CHICK for Chicken, ECOLI for Escherichia coli,<br>
HORSE for Horse, HUMAN for Human, MAIZE for Maize (Zea mays) , MOUSE<br>
for Mouse, PEA for Garden pea (Pisum sativum), PIG for Pig, RABIT<br>
for Rabbit, RAT for Rat, SHEEP for Sheep, SOYBN for Soybean (Glycine<br>
max), TOBAC for Common tobacco (Nicotina tabacum), WHEAT for Wheat<br>
(Triticum aestivum), YEAST for Baker's yeast (Saccharomyces<br>
cerevisiae).<br>
<br>
As it was not possible to apply the above rules to viruses, they<br>
were given arbitrary, but generally easy to remember, identification<br>
codes. In some cases it was not possible to assign a definitive code<br>
to a species. In these cases a temporary code was chosen.<br>
<br>
Examples of complete protein sequence entry names are: RL1_ECOLI for<br>
ribosomal protein L1 from Escherichia coli, FER_HALHA for ferredoxin<br>
from Halobacterium halobium.<br>
<br>
The name of all the presently defined species identification codes are<br>
listed in the SWISS-PROT document file SPECLIST.TXT.<br>
<br>
<br>
3.1.2 Data class<br>
<br>
The second item on the ID line indicates the data class of the entry<br>
(see section 2.2).<br>
<br>
3.1.3 Molecule type<br>
<br>
The third item on the ID line is a three letter code which indicates<br>
the type of molecule of the entry: in SWISS-PROT it is PRT (for<br>
PRoTein).<br>
<br>
3.1.4 Length of the molecule<br>
<br>
The fourth and last item of the ID line is the length of the molecule,<br>
which is the total number of amino acids in the sequence. This number<br>
includes the positions reported to be present but which have not been<br>
determined (coded as `X'). The length is followed by the letter code AA<br>
(Amino Acids).<br>
<br>
3.1.5 Examples of identification lines<br>
<br>
Two examples of ID lines are shown below:<br>
<br>
ID CYC_BOVIN STANDARD; PRT; 104 AA.<br>
ID GIA2_GIALA PRELIMINARY; PRT; 296 AA.<br>
<br>
<br>
3.2 The AC line<br>
<br>
The AC (ACcession number) line lists the accession numbers associated<br>
with an entry. An example of an accession number line is shown below:<br>
<br>
AC P00321; P05348;<br>
<br>
The accession numbers are separated by semicolons and the list is<br>
terminated by a semicolon. If necessary, more then one AC line will be<br>
used. Most SWISS-PROT sequence entries currently have only one<br>
accession number.<br>
<br>
The purpose of accession numbers is to provide a stable way of<br>
identifying entries from release to release. It is sometimes necessary<br>
for reasons of consistency to change the names of the entries, for<br>
example, to ensure that related entries have similar names. However, an<br>
accession number is always conserved, and therefore allows unambiguous<br>
citation of SWISS-PROT entries.<br>
<br>
Researchers who wish to cite entries in their publications should<br>
always cite the first accession number.<br>
<br>
Entries will have more than one accession number if they have been<br>
merged or split. For example, when two entries are merged into one, a<br>
new accession number goes at the start of the AC line, and those from<br>
the merged entries are listed after this one. Similarly, if an existing<br>
entry is split into two or more entries (a rare occurrence), the<br>
original accession number list is retained in all the derived entries.<br>
<br>
An accession number is dropped only when the data to which it was<br>
assigned have been completely removed from the data bank.<br>
<br>
<br>
<br>
3.3 The DT line<br>
<br>
The DT (DaTe) lines show the date of entry or last modification of the<br>
sequence entry. The format of the DT lines is:<br>
<br>
DT DD-MMM-YEAR (REL. XX, COMMENT)<br>
<br>
where `DD' is the day, `MMM' the month, `YEAR' the year, and `XX' the<br>
SWISS-PROT release number. The comment portion of the line indicates<br>
the action taken on that date. There are ALWAYS three DT lines in each<br>
entry, each of them is associated with a specific comment:<br>
<br>
- The first DT line indicates when the entry first appeared in the<br>
data bank. The associated comment is `CREATED'.<br>
- The second DT line indicates when the sequence data was last<br>
modified. The associated comment is `LAST SEQUENCE UPDATE'.<br>
- The third DT line indicates when any data other then the sequence<br>
was last modified. The associated comment is `LAST ANNOTATION<br>
UPDATE'.<br>
<br>
Example of a block of DT lines:<br>
<br>
DT 01-JAN-1988 (REL. 06, CREATED)<br>
DT 01-JUL-1989 (REL. 11, LAST SEQUENCE UPDATE)<br>
DT 01-AUG-1992 (REL. 23, LAST ANNOTATION UPDATE)<br>
<br>
<br>
3.4 The DE line<br>
<br>
The DE (DEscription) lines contain general descriptive information<br>
about the sequence stored. This information is generally sufficient to<br>
identify the sequence precisely. The format of the DE lines is:<br>
<br>
DE DESCRIPTION.<br>
<br>
The description is given in ordinary English and is free-format. In<br>
some cases, more than one DE line is required; in this case, the text<br>
is divided only between words and only the last DE line is terminated<br>
by a period.<br>
<br>
When the complete sequence was not determined the last information<br>
given on the DE lines will be `(FRAGMENT)' or `(FRAGMENTS)'.<br>
<br>
Two examples of description lines are given here:<br>
<br>
DE NADH DEHYDROGENASE (EC 1.6.99.3).<br>
<br>
DE LYSOPINE DEHYDROGENASE (EC 1.5.1.16) (OCTOPINE SYNTHASE)<br>
DE (LYSOPINE SYNTHASE) (FRAGMENT).<br>
<br>
<br>
<br>
3.5 The GN line<br>
<br>
The GN (Gene Name) line contains the name(s) of the gene(s) that encode<br>
for the stored protein sequence. The format of the GN line is:<br>
<br>
GN NAME1[ AND|OR NAME2...].<br>
<br>
Examples:<br>
<br>
GN ALB.<br>
GN REX-1.<br>
<br>
It often occurs that more than one gene name has been assigned to an<br>
individual locus. In that case all the synonyms will be listed. The<br>
word `OR' separates the different designations. The first name in the<br>
list is assumed to be the most correct (or most current) designation.<br>
Example:<br>
<br>
GN HNS OR DRDX OR OSMZ OR BGLY.<br>
<br>
In a few cases, multiple genes encode for an identical protein<br>
sequence. In that case all the different gene names will be listed. The<br>
word `AND' separates the designations. Example:<br>
<br>
GN CECA1 AND CECA2.<br>
<br>
In very rare cases `AND' and `OR' can both be present. In that case<br>
parenthesis are used as shown in the following example:<br>
<br>
GN GVPA AND (GVPB OR GVPA2).<br>
<br>
<br>
<br>
3.6 The KW line<br>
<br>
The KW (KeyWord) lines provide information which can be used to<br>
generate cross-reference indexes of the sequence entries based on<br>
functional, structural, or other categories. The keywords chosen for<br>
each entry serve as a subject reference for the sequence. Often several<br>
KW lines are necessary for a single entry. The format of the KW lines<br>
is:<br>
<br>
KW KEYWORD[; KEYWORD...].<br>
<br>
More than one keyword may be listed on each KW line; the keywords are<br>
separated by semicolons, and the last keyword is followed by a period.<br>
Keywords may consist of more than one word (they may contain blanks),<br>
but are never split between lines. An example of a KW line is:<br>
<br>
KW EYE LENS PROTEIN; ACETYLATION.<br>
<br>
The order of the keywords is not significant. The above example could<br>
also have been written:<br>
<br>
KW ACETYLATION; EYE LENS PROTEIN.<br>
<br>
<br>
<br>
3.7 The OS line<br>
<br>
The OS (Organism Species) line specifies the organism(s) which was the<br>
source of the stored sequence. In the rare case where all the species<br>
information will not fit on a single line more than one OS line is<br>
used. The last OS line is terminated by a period.<br>
<br>
The species designation consists, in most cases, of the Latin genus and<br>
species designation followed by the English name (in parentheses). For<br>
viruses, only the common English name is given. In cases where a<br>
protein sequence is identical in more then one species the OS line(s)<br>
will list the names of all those species.<br>
<br>
Examples of OS lines are shown here:<br>
<br>
OS ESCHERICHIA COLI.<br>
OS HOMO SAPIENS (HUMAN).<br>
OS ROUS SARCOMA VIRUS (STRAIN SCHMIDT-RUPPIN).<br>
OS NAJA NAJA (INDIAN COBRA), AND NAJA NIVEA (CAPE COBRA).<br>
<br>
<br>
<br>
3.8 The OG line<br>
<br>
The OG (OrGanelle) lines indicate if the gene coding for a protein<br>
originates from the mitochondria, the chloroplast, a cyanelle, or a<br>
plasmid. The format of the OG line is:<br>
<br>
OG CHLOROPLAST.<br>
OG CYANELLE.<br>
OG MITOCHONDRION.<br>
OG PLASMID name.<br>
<br>
Where 'name' is the name of the plasmid.<br>
<br>
<br>
3.9 The OC line<br>
<br>
The OC (Organism Classification) lines contain the taxonomic<br>
classification of the source organism. The classification is listed<br>
top-down as nodes in a taxonomic tree in which the most general<br>
grouping is given first. The classification may be distributed over<br>
several OC lines, but nodes are not split or hyphenated between lines.<br>
The individual items are separated by semicolons and the list is<br>
terminated by a period. The format of the OC lines is:<br>
<br>
OC NODE[; NODE...].<br>
<br>
For example the classification lines for a human sequence would be:<br>
<br>
OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA;<br>
OC EUTHERIA; PRIMATES.<br>
<br>
<br>
3.10 The reference (RN, RP, RC, RX, RA, RL) lines<br>
<br>
These lines comprise the literature citations within SWISS-PROT. The<br>
citations indicate the papers from which the data has been abstracted.<br>
The reference lines for a given citation occur in a block, and are<br>
always in the order RN, RP, RC, RM, RA, RL. Within each such reference<br>
block the RN and RP lines occur once, the RC line occurs zero or more<br>
times, the RM line occurs zero or once, and the RA and RL lines each<br>
occur one or more times. If several references are given, there will be<br>
a reference block for each.<br>
<br>
An example of a complete reference is:<br>
<br>
RN [1]<br>
RP SEQUENCE FROM N.A., AND SEQUENCE OF 1-15.<br>
RC STRAIN=SPRAGUE-DAWLEY; TISSUE=LIVER;<br>
RM 91002678<br>
RA CHAN Y.-L., PAZ V., OLVERA J., WOOL I.G.;<br>
RL BIOCHIM. BIOPHYS. ACTA 1050:69-73(1990).<br>
<br>
The formats of the individual lines are explained below.<br>
<br>
3.10.1 The RN line<br>
<br>
The RN (Reference Number) line gives a sequential number to each<br>
reference citation in an entry. This number is used to indicate the<br>
reference in comments and feature table notes. The format of the RN<br>
line is:<br>
<br>
RN [N]<br>
<br>
where N denotes the nth reference for this entry. The reference number<br>
is always enclosed in square brackets.<br>
<br>
3.10.2 The RP line<br>
<br>
The RP (Reference Position) line describes the extent of the work<br>
carried out by the authors of the reference cited. The format of the RP<br>
line is:<br>
<br>
RP COMMENT.<br>
<br>
Typical examples of RP lines are shown below:<br>
<br>
RP SEQUENCE FROM N.A.<br>
RP SEQUENCE FROM N.A., AND SEQUENCE OF 12-35.<br>
RP SEQUENCE OF 34-56; 67-73 AND 123-345, AND DISULFIDE BONDS.<br>
RP REVISIONS TO 67-89.<br>
RP STRUCTURE BY NMR.<br>
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).<br>
RP CHARACTERIZATION.<br>
RP MUTAGENESIS OF TYR-56.<br>
RP REVIEW.<br>
RP VARIANT ALA-58.<br>
RP VARIANTS XLI LEU-341; ARG-372 AND TYR-446.<br>
<br>
<br>
<br>
3.10.3 The RC line<br>
<br>
The RC (Reference Comment) lines are optional lines which are used to<br>
store comments relevant to the reference cited. The format of the RC<br>
line is:<br>
<br>
RC TOKEN1=TEXT; TOKEN2=TEXT; .....<br>
<br>
Where the currently defined tokens are:<br>
<br>
PLASMID<br>
SPECIES<br>
STRAIN<br>
TISSUE<br>
TRANSPOSON<br>
<br>
The `SPECIES' token is only used when an entry describes a sequence<br>
which is identical in more than one species; similarly the `PLASMID' is<br>
only used if an entry describes a sequence identical in more than one<br>
plasmid.<br>
<br>
An example of an RC line is:<br>
<br>
RC STRAIN=SPRAGUE-DAWLEY; TISSUE=LIVER;<br>
3.10.4 The RX line<br>
<br>
The RX (Reference cross-reference) line is an optional line which is<br>
used to indicate the identifier assigned to a specific reference in a<br>
bibliographic database. The format of the RX line is:<br>
<br>
RX BIBLIOGRAPHIC_DATABASE_NAME; IDENTIFIER.<br>
<br>
where the valid bibliographic database names and their associated<br>
identifier are:<br>
<br>
Name: MEDLINE<br>
Database: Medline from the National Library of Medicine (NLM)<br>
Identifier: Eight digit Medline Unique Identifier (UID)<br>
<br>
Example of RX line:<br>
<br>
RX MEDLINE; 91002678.<br>
<br>
3.10.5 The RA line<br>
<br>
The RA (Reference Author) lines list the authors of the paper (or other<br>
work) cited. All of the authors are included, and are listed in the<br>
order given in the paper. The names are listed surname first followed<br>
by a blank followed by initial(s) with periods. The authors' names are<br>
separated by commas and terminated by a semicolon. Author names are not<br>
split between lines. An example of the use of RA lines is shown below:<br>
<br>
RA YANOFSKY C., PLATT T., CRAWFORD I.P., NICHOLS B.P., CHRISTIE G.E.,<br>
RA HOROWITZ H., VAN CLEEMPUT M., WU A.M.;<br>
<br>
As many RA lines as necessary are included for each reference.<br>
<br>
3.10.6 The RL line<br>
<br>
The RL (Reference Location) lines contain the conventional citation<br>
information for the reference. In general, the RL lines alone are<br>
sufficient to find the paper in question.<br>
<br>
a) Journal citations<br>
<br>
The RL line for a journal citation includes the journal abbreviation,<br>
the volume number, the page range, and the year. The format for such a<br>
RL line is:<br>
<br>
RL JOURNAL VOL:PP-PP(YEAR).<br>
<br>
Journal names are abbreviated according to the conventions used by the<br>
National Library of Medicine (NLM) and are based on the existing ISO<br>
and ANSI standards. A list of the abbreviations currently in use is<br>
given in the SWISS-PROT document file JOURLIST.TXT.<br>
<br>
<br>
An example of an RL line is:<br>
<br>
RL J. MOL. BIOL. 168:321-331(1983).<br>
<br>
When a reference is made to a paper which is `in press' at the time<br>
when the data bank is released, the page range, and eventually the<br>
volume number are indicated as '0' (zero). An example of a RL line of<br>
such type is shown here:<br>
<br>
RL NUCLEIC ACIDS RES. 22:0-0(1994).<br>
<br>
b) Book citations<br>
<br>
A variation of the RL line format is used for papers found in books or<br>
other similar publications, which are cited as shown below:<br>
<br>
RL (IN) THE ENZYMES, 3RD ED., VOL.11, PART A, BOYER P.D., ED.,<br>
RL PP.397-547, ACADEMIC PRESS, NEW YORK, (1975).<br>
<br>
The first RL line contains the designation `(IN)', which indicates that<br>
this is a book reference. These citations generally include the<br>
following information: the title of the book, the name of the<br>
editor(s), the page range, the publisher name, the city where it is<br>
published, and the year of publication (which is always shown between<br>
parenthesis).<br>
<br>
c) Unpublished results<br>
<br>
RL lines for unpublished results follows the format shown in the<br>
following example:<br>
<br>
RL UNPUBLISHED RESULTS, CITED BY:<br>
RL ULRICH E.L., KROGMANN D.W., MARKLEY J.L.;<br>
RL J. BIOL. CHEM. 257:9356-9364(1982).<br>
<br>
d) Unpublished observations<br>
<br>
For unpublished observations the format of the RL line is:<br>
<br>
RL UNPUBLISHED OBSERVATIONS (MMM-YEAR).<br>
<br>
Where `MMM' is the month and `YEAR' is the year.<br>
<br>
We use the `unpublished observations' RL line to cite communications by<br>
scientists to SWISS-PROT of unpublished information concerning various<br>
aspects of a sequence entry.<br>
<br>
e) Thesis<br>
<br>
For Ph.D. theses the format of the RL line is:<br>
<br>
RL THESIS (YEAR), INSTITUTION_NAME, COUNTRY.<br>
<br>
<br>
An example of such a line is given here:<br>
<br>
RL THESIS (1972), GEORGE WASHINGTON UNIVERSITY, U.S.A.<br>
<br>
f) Patent applications<br>
<br>
For patent applications the format of the RL line is:<br>
<br>
RL PATENT NUMBER PAT_NUMB, DD-MMM-YYYY.<br>
<br>
Where `PAT_NUMB' is the international publication number of the patent,<br>
`DD' is the day, `MMM' is the month and `YEAR' is the year.<br>
<br>
g) Submissions<br>
<br>
The final form that an RL line can take is that used for submissions.<br>
The format of such a RL line is:<br>
<br>
RL SUBMITTED (MMM-YEAR) TO DATABASE_NAME.<br>
<br>
Where `MMM' is the month, `YEAR' is the year and `DATABASE_NAME' is one<br>
of the following:<br>
<br>
EMBL/GENBANK/DDBJ DATA BANKS<br>
THE SWISS-PROT DATA BANK<br>
THE ECOSEQ DATA BANK<br>
THE HIV DATA BANK<br>
THE MIM DATA BANK<br>
THE NEWAT DATA BANK<br>
THE PDB DATA BANK<br>
THE PIR DATA BANK<br>
<br>
Two examples of submission RL lines are given here:<br>
<br>
RL SUBMITTED (APR-1994) TO EMBL/GENBANK/DDBJ DATA BANKS.<br>
RL SUBMITTED (FEB-1995) TO THE SWISS-PROT DATA BANK.<br>
<br>
<br>
3.11 The DR line<br>
<br>
3.11.1 Definition<br>
<br>
The DR (Database cross-Reference) lines are used as pointers to<br>
information related to SWISS-PROT entries and found in data collections<br>
other than SWISS-PROT.<br>
<br>
For example, if the X-ray crystallographic atomic coordinates of a<br>
sequence are stored in the Brookhaven Protein Data Bank (PDB) there<br>
will be DR line(s) pointing to the corresponding entri(es) in that data<br>
bank. For a sequence translated from a nucleotide sequence there can be<br>
DR lines pointing to entries in the EMBL or Genbank data banks which<br>
correspond to the DNA or RNA sequence(s) from which it was translated.<br>
<br>
The format of the DR line is:<br>
<br>
DR DATA_BANK_IDENTIFIER; PRIMARY_IDENTIFIER; SECONDARY_IDENTIFIER.<br>
<br>
<br>
3.11.2 Data bank identifier<br>
<br>
The first item on the DR line, the data bank identifier, is the<br>
abbreviated name of the data collection to which reference is made. The<br>
currently defined data bank identifiers are the following:<br>
<br>
EMBL Nucleotide sequence database of EMBL (EBI)<br>
DICTYDB Dictyostelium discoideum genome database<br>
ECO2DBASE Escherichia coli gene-protein database (2D gel<br>
spots) (ECO2DBASE)<br>
ECOGENE Escherichia coli K12 genome database (EcoGene)<br>
FLYBASE Drosophila genome database (FlyBase)<br>
GCRDB G-protein--coupled receptor database (GCRDb)<br>
HIV HIV sequence database<br>
HSSP Homology-derived secondary structure of proteins<br>
database (HSSP).<br>
LISTA Yeast (Saccharomyces cerevisiae) genome<br>
database (LISTA)<br>
MAIZEDB Maize genome database (MaizeDB)<br>
MIM Mendelian Inheritance in Man Database (MIM)<br>
PDB Brookhaven Protein Data Bank (PDB)<br>
PIR Protein sequence database of the Protein<br>
Information Resource (PIR)<br>
PROSITE PROSITE dictionary of sites and patterns in<br>
proteins<br>
REBASE Restriction enzyme database (REBASE)<br>
AARHUS/GHENT-2DPAGE Human keratinocyte 2D gel protein database from<br>
Aarhus and Ghent universities<br>
SGD Saccharomyces Genome Database (SGD)<br>
STYGENE Salmonella typhimurium LT2 genome database<br>
(StyGene)<br>
SUBTILIST Bacillus subtilis 168 genome database (SubtiList)<br>
SWISS-2DPAGE Human 2D Gel Protein Database from the University<br>
of Geneva (SWISS-2DPAGE)<br>
TRANSFAC Transcription factor database (Transfac)<br>
WORMPEP Caenorhabditis elegans genome sequencing project<br>
protein database (Wormpep)<br>
YEPD Yeast electrophoresis protein database (YEPD)<br>
<br>
<br>
3.11.3 The primary identifier<br>
<br>
The second item on the DR line, the primary identifier, is an<br>
unambiguous pointer to the information entry in the data bank to which<br>
reference is being made.<br>
<br>
- For an EMBL, DictyDb, EcoGene, FlyBase, GCRDb, HIV, LISTA, PIR,<br>
PROSITE, SGD, StyGene, SubtiList, SWISS-2DPAGE or Transfac reference<br>
the primary identifier is the first accession number (also called<br>
the Unique Identifier in some data banks) of the entry to which<br>
reference is being made.<br>
- For a MIM reference the primary identifier is the catalog number of<br>
the disease (or phenotype).<br>
- For a PDB or REBASE reference the primary identifier is the entry<br>
name.<br>
- For an AARHUS/GHENT-2DPAGE, ECO2DBASE or YEPD reference the primary<br>
identifier is the protein spot alphanumeric designation.<br>
- For a WormPep reference the primary identifier is the cosmid-derived<br>
name given to that protein by the C.elegans genome sequencing<br>
project.<br>
- For a MaizeDB reference the primary identifier is the "Gene-product"<br>
accession ID.<br>
- For a HSSP reference the primary identifier is the accession number<br>
of a SWISS-PROT entry cross-referenced to a PDB entry whose<br>
structure is expected to be similar to that of the entry in which<br>
the HSSP cross-reference is present.<br>
<br>
<br>
3.11.4 The secondary identifier<br>
<br>
The third and last item on the DR line, the secondary identifier, is<br>
used to complement the information given by the first identifier.<br>
<br>
- For an EMBL, GenBank, HIV, PIR or PROSITE reference the secondary<br>
identifier is the entry's name.<br>
- For a PDB reference the secondary identifier is the most recent date<br>
on which PDB revised the entry (last `REVDAT' record).<br>
- For a DictyDb, EcoGene, FlyBase, LISTA, SGD, StyGene or SubtiList<br>
reference the secondary identifier is the gene designation. If the<br>
gene designation is not available a dash "-" is used.<br>
For a MIM, REBASE, or ECO2DBASE reference the secondary identifier<br>
is the latest release number or edition of the database that has<br>
been used to derive the cross-reference.<br>
- For a SWISS-2DPAGE reference the secondary identifier is the species<br>
of origin.<br>
- For an AARHUS/GHENT-2DPAGE reference the secondary identifier is<br>
either `IEF' (for isoelectric focusing) or `NEPHGE' (for non-<br>
equilibrium pH gradient electrophoresis).<br>
- For a WormPep reference the secondary identifier is a number<br>
attributed by the C.elegans genome sequencing project to that<br>
protein.<br>
- For a GCRDb, MaizeDB, Transfac or YEPD reference the secondary<br>
identifier is not defined and a dash "-" is stored in that field.<br>
- For a HSSP reference the secondary identifier is the entry name of<br>
the PDB structure related to that of the entry in which the HSSP<br>
cross-reference is present.<br>
<br>
<br>
Examples of complete DR lines are shown here:<br>
<br>
DR AARHUS/GHENT-2DPAGE; 8006; IEF.<br>
DR DICTYDB; DD01047; MYOA.<br>
DR EMBL; X01704; GMNOD23.<br>
DR ECO2DBASE; G052.0; 6TH EDITION.<br>
DR ECOGENE; EG10054; ARAC.<br>
DR FLYBASE; FBGN0000055; ADH.<br>
DR GCRDB; GCR_0087; -.<br>
DR HIV; K02013; NEF$BRU.<br>
DR HSSP; P00438; 1DOB.<br>
DR LISTA; SC00018; ACT1.<br>
DR MAIZEDB; 25342; -.<br>
DR MIM; 249900; 11TH EDITION.<br>
DR PDB; 3ADK; 16-APR-88.<br>
DR PIR; A02768; R5EC7.<br>
DR PROSITE; PS00021; KRINGLE.<br>
DR REBASE; BSURI; RELEASE 9410.<br>
DR SGD; L0000008; AAR2.<br>
DR STYGENE; SG10312; PROV.<br>
DR SUBTILIST; BG10774; OPPD.<br>
DR SWISS-2DPAGE; P10599; HUMAN.<br>
DR TRANSFAC; T00141; -.<br>
DR WORMPEP; ZK637.7; CE00437.<br>
DR YEPD; 4270; -.<br>
<br>
<br>
3.12 The FT line<br>
<br>
The FT (Feature Table) lines provide a precise but simple means for the<br>
annotation of the sequence data. The table describes regions or sites<br>
of interest in the sequence. In general the feature table lists post-<br>
translational modifications, binding sites, enzyme active sites, local<br>
secondary structure or other characteristics reported in the cited<br>
references. Sequence conflicts between references are also included in<br>
the feature table. The feature table is updated when more becomes known<br>
about a given sequence.<br>
<br>
The FT lines have a fixed format. The column numbers allocated to each<br>
of the data items within each FT line are shown in the following table<br>
(column numbers not referred to in the table are always occupied by<br>
blanks):<br>
<br>
+---------------+-----------------------+<br>
| Columns | Data item |<br>
+---------------+-----------------------+<br>
| 1- 2 | FT |<br>
| 6-13 | Key name |<br>
| 15-20 | `FROM' endpoint |<br>
| 22-27 | `TO' endpoint |<br>
| 35-75 | Description |<br>
+---------------+-----------------------+<br>
<br>
The key name and the endpoints are always on a single line, but the<br>
description may require continuation. For this purpose, the next line<br>
contains blanks in the key, the `FROM', and the `TO' columns positions,<br>
and the description is continued in its normal position. Thus a blank<br>
key always denotes a continuation of the previous description.<br>
<br>
An example of a feature table is shown below:<br>
<br>
FT NON_TER 1 1<br>
FT PEPTIDE 1 9 ARG-VASOPRESSIN.<br>
FT PEPTIDE 13 107 NEUROPHYSIN 2.<br>
FT PEPTIDE 109 147 COPEPTIN.<br>
FT DISULFID 1 6<br>
FT MOD_RES 9 9 AMIDATION (ACTIVE ARG-VASOPRESSIN).<br>
FT CONFLICT 102 102 D -> S (IN REF. 2).<br>
FT CONFLICT 105 105 MISSING (IN REF. 3).<br>
FT CARBOHYD 114 114<br>
<br>
The first item on each FT line is the key name, which is a fixed<br>
abbreviation (up to 8 characters) with a defined meaning. A list of the<br>
currently defined key names can be found in Appendix A of this<br>
document.<br>
<br>
Following the key name are the `FROM' and `TO' endpoint specifications.<br>
These fields designate (inclusively) the endpoints of the feature named<br>
in the key field. In general, these fields simply contain residue<br>
numbers indicating positions in the sequence as listed. Note that these<br>
positions are always specified assuming a numbering of the listed<br>
sequence from 1 to n; this numbering is not necessarily the same as<br>
that used in the original reference(s). The following should be noted<br>
in interpreting these endpoints:<br>
<br>
- If the `FROM' and `TO' specifications are equal, the feature<br>
indicated consists of the single amino acid at that position.<br>
<br>
- When a feature is known to extend beyond the end(s) of the sequenced<br>
region, the endpoint specification will be preceded by < for<br>
features which continue to the left end (N-terminal direction) or by<br>
> for features which continue to the right end (C-terminal<br>
direction).<br>
<br>
- Unknown endpoints are denoted by `?'.<br>
<br>
See also the notes concerning each of the key names in the appendix A.<br>
<br>
The remaining portion of the FT line is a description which contains<br>
additional information about the feature. For example, for a residue<br>
post-translational modification (key MOD_RES) the chemical nature of<br>
that modification is given, while for a sequence variation (key<br>
VARIANT) the nature of the variation is indicated. This portion of the<br>
line is generally in free form, and may be continued on additional<br>
lines when necessary.<br>
<br>
<br>
3.13 The SQ line<br>
<br>
The SQ (SeQuence header) line marks the beginning of the sequence data<br>
and gives a quick summary of its content. The format of the SQ line is:<br>
<br>
SQ SEQUENCE XXXX AA; XXXXX MW; XXXXX CN;<br>
<br>
The line contains the length of the sequence in amino-acids (AA)<br>
followed by the molecular weight (MW) rounded to the nearest gram and a<br>
checking number (CN) as defined in the following reference:<br>
<br>
Bairoch A.<br>
Biochem. J. 203:527-528(1982).<br>
<br>
An example of an SQ line is shown here:<br>
<br>
SQ SEQUENCE 104 AA; 11530 MW; 54319 CN;<br>
<br>
The information in the SQ line can be used as a check on accuracy or<br>
for statistical purposes. The word `SEQUENCE' is present solely for<br>