Computer Methods for Macromolecular Sequence Analysis

712 Pages·1996·10.706 MB·English

by  Doolittle R., Abelson J., Simon M.

Preface
Volume 381 of Methods in Enzymology dealing with the computer
analysis of protein and nucleic acid sequences has proved very popular with
molecular biologists and biochemists. Computers and computer programs
evolve rapidly, however, and can become outmoded very quickly. As a
result, there was pressure to issue an updated volume that covers much
the same general subject areas.
Like the earlier volume, this one is divided into several sections, the
first of which deals with databases and some aspects related to their hold-
ings. Also, there have been some relocations of major databases. GenBank
is now centered at the National Center for Biotechnology Information
(NCBI) at the National Library of Medicine in Bethesda, Maryland, and
the EMBL Database has relocated to the European Bioinformatics Institute
(EBI) at a site just outside Cambridge, England. More than ever, of course,
geographic location is becoming moot, thanks to the World Wide Web
(WWW) and extended hyperlink access.
There is some new vocabulary in this volume that did not appear in
Volume 183. The use of neural nets, for example, is discussed in several
places, including chapters dealing with the classification of sequences, on
the one hand, and with predicting secondary structure, on the other. The
kinds of databases are also changing. For instance, it has been found that
the fragmentary data known as Expressed Sequence Tags (EST) are ex-
tremely useful.
Searching newly determined sequences remains the first order of busi-
ness. More often than not, a simple search of a new sequence provides
both functional and structural information. New pattern searching programs
have greatly extended the power of this approach so that very distant
relatives of well-characterized families can be identified.
The multiple alignment of protein sequences continues to have a promi-
nent role in protein characterization. Whether the sequences are of the
"same" protein from different organisms or are paralogs that have resulted
from gene duplications, the alignment problems are the same. Interestingly,
the most popular algorithms have not changed much, but the amino acid
substitution tables that support them have. This is chiefly the result of there
being so much comparative data in the current databases that empirical
measures of relationships can be obtained by simply tallying the occurrences
of the amino acids in blocks of obviously aligned sequences. As discussed
in Chapter 6 by Henikoff and Henikoff, these BLOSUM tables have been
remarkably effective.
xiii
xiv ECAFERP
Among their many uses, multiple alignments are used to construct
profiles for more sensitive searching than is possible by single-searching.
They are also used in the consensus mode for better predictions of secondary
structure and for three-dimensional searches. And, of course, they are used
in the construction of phylogenetic trees.
Recent advances have led to some changes in emphasis in some of the
sections. Most of the chapters focus on protein sequences, even though the
vast majority of those are determined by DNA sequencing. Accordingly,
a section on RNA folding that appeared in the earlier volume has been
dropped, and instead a number of chapters that relate to the secondary
structure and three-dimensional aspects of proteins have been added.
Indeed, three-dimensional searching is following the course of sequence
searching a decade ago. As a new protein structure is characterized, the
first matter of general interest is to determine whether the fold resembles
that of any that were reported previously. The remarkable thing is that not
only are most new structures falling into well-defined families, but often
there is no hint in advance on the basis of either structure or function. The
problems associated with structure searching are similar to those experi-
enced by sequence searchers in the past: a burgeoning data bank (PDB is the
Protein Data Bank), choices of search programs, and, finally, the problem of
judgment on how significant a resemblance may be. Many of these problems
are addressed in Section V of this volume.
As with Volume 183, authors were encouraged to make their programs
or databases available to readers. Many chapters make reference to a
WWW home page or an Internet email address from which additional
information can be extracted.
Finally, I thank all the authors who wrote such interesting and informa-
tive chapters under a very strict and compressed timetable. Academic Press,
and especially our editor, Shirley Light, outdid themselves in getting the
manuscripts through the publication process in record time. As in the case
of the previous volume dealing with this topic, I must also acknowledge
that the task could not have been accomplished without the help of my
assistant, Karen Anderson. Her relentless but always gentle prodding of
authors to produce manuscripts and her remarkable organizational skills
that kept the courier traffic flowing in the right direction were indispensable.
LLESSUR F. ELTTILOOD
Contributors to Volume 266
Article numbers are in parentheses following the names of contributors.
Affiliations listed are current.
NEHPETS F. ALTSCHUL (27), National retneC JEAN-MICHEL CLAVERIE (14), Laboratory of
for Biotechnology Information, National Structural and Genetic Information, E.P.
Library of ,enicideM National Institutes of 91--Centre National ed al Recherche Sci-
,htlaeH Bethesda, Maryland 49802 ,euqifitne 20431 ,elliesraM ecnarF
PATRICK ARGOS (8), European Molecular MARC DELARUE (40), Immunologie -rutcurtS
Biology Laboratory, 69117 ,grebledieH ela Institut ,ruetsaP 51057 Paris, ecnarF
Germany RUSSELL F. DOOLITrLE (21), Center for Mo-
MARCELLA ATFIMONELLI (17), Dipartimento ralucel Genetics, University of ,ainrofilaC
ed Biochimica e Biologia ,eraloceloM -inU naS Diego, La Jolla, California 39029
dtisrev di Bari, 70125 Bari, Italy DAVID EISENBERG (35), Department of
WINONA C. BARKER (3, 4), National Biomedi- Chemistry and Biochemistry and DOE
lac hcraeseR Foundation, Washington, Dis- Laboratory of larutcurtS Biology and Mo-
tcirt of Columbia 20007 ralucel Medicine, University of ,ainrofilaC
Los Angeles, Los Angeles, ainrofilaC 42009
GEOFFREY J. BARTON (29), Laboratory of
Molecular Biophysics, University of Ox- JONATHAN A. EPSTEIN (10), National retneC
ford, Oxford OX1 3QU, United Kingdom for Biotechnology Information, National
Library of ,enicideM National Institutes of
PEER BORK (11), European Molecular Biol-
,htlaeH Bethesda, Maryland 49802
ogy Laboratory, D-69012 ,grebledieH Ger-
",ynam and Max-Delbriick-Center for THURE ETZOLD (8), European Molecular
Molecular ,enicideM Department of Bioin- Biology Laboratory, 69117 ,grebledieH
formatics, D-13122 Berlin-Buch, Germany ynamreG
JAMES U. BOWIE (35), Department of -simehC SCOTt FEDERHEN (33), National Center for
yrt and Biochemistry and DOE Laboratory Biotechnology Information, National Li-
of Structural Biology and Molecular Medi- brary of Science, National Institutes of
,enic University of ,ainrofilaC Los Angeles, ,htlaeH Bethesda, Maryland 49802
Los Angeles, California 59009 JOSEPH NIETSNESLEF (24), Department of -eG
STEVEN E. BRENNER (37), Medical hcraeseR ,sciten University of Washington, ,elttaeS
Washington 59189
Council Centre Laboratories of Molecular
Biology, Cambridge 2BC 2QH, United DA-FEI FENG (20, Center for Molecular -eG
Kingdom ,sciten University of ,ainrofilaC naS ,ogeiD
La Jolla, California 39029
GRAHAM N. CAMERON (1), European Molec-
ular Biology Laboratory Outstation--the JEAN GARNIER (32), Unit~ ed Bioinformat-
European Bioinformatics Institute, Hinx- ique Biotechnologies, INRA, 25387 Jouy-
ton, Cambridge CBIO 1RQ, United ,sasoJ-ne Paris, ecnarF
Kingdom DAVID G. GEORGE (3, 4), National Biomedi-
CYRUS CHOTHIA (37), Medical Research lac hcraeseR Foundation, Washington, Dis-
Council Centre Laboratories of Molecular trict of Columbia 20007
Biology and Cambridge ertneC for Protein JEAN-FRANfO~S GIBRAT (32), ~tinU ed Bioin-
Engineering, Cambridge 2BC 2QH, formatique Biotechnologies, INRA, 25387
detinU Kingdom ,sasoJ-ne-yuoJ Paris, ecnarF
ix
X CONTRIBUTORS TO VOLUME 266
TOBY J. GIBSON (11, 22), European raluceloM for Biotechnology, University of Turku,
Biology Laboratory, 69012 ,grebledieH 12502-NIF Turku, Finland
ynamreG JONATHAN A. KANS (10), National retneC for
WARREN GISH (27), Department of ,sciteneG Biotechnology Information, National Li-
notgnihsaW ytisrevinU School of ,enicideM brary of Medicine, National Institutes of
.tS Louis, Missouri 80136 ,htlaeH Bethesda, Maryland 49802
MICHAEL GRIBSKOV (13), naS Diego Super- ANTHONY R. KERLAVAGE (2), ehT Institute
computer ,retneC La ,alloJ California 39029 for Genomic Research, ,grubsrehtiaG
XUN Gu (26), Human Genetics ,retneC Sph, Maryland 05802
ytisrevinU of ,saxeT Houston, Texas 52277 EUGENE V. KOONIN (18), National retneC for
DANIEL GUSFIELD (28), Computer Science Biotechnology Information, National Li-
Department, University of ,ainrofilaC brary of Medicine, National Institutes of
Davis, Davis, California 61659 ,htlaeH Bethesda, Maryland 49802
ROBERT A. L. HARPER (1), European -celoM ERIC S. LANDER (19), Whitehead Institute for
ular Biology Laboratory Outstation--the Biomedical Research and Department of
European Bioinformatics Institute, Hinx- Biology, Massachusetts Institute of Tech-
ton, Cambridge CBIO 1RQ, United nology, ,egdirbmaC sttesuhcassaM 24120
Kingdom WEN-HSIUNG L1 (26), Human Genetics -neC
JOTUN HEIN (23), Department of Ecology and ,ret Sph, Health Science ,retneC ytisrevinU
,sciteneG Institute of Biological ,secneicS of ,saxeT Houston, Texas 52277
Aarhus University, DK-8000 Aarhus, CRAIG D. LIVINGSTONE (29), Genomics Sup-
Denmark port Group, SmithKline Beecham Pharma-
JORJA G. HEN1KOFF (6), Fred Hutchinson ,slacituec New sreitnorF ecneicS Park, Har-
recnaC Research ,retneC Seattle, Washing- low, Essex CM19 5AW, United Kingdom
ton 40189 ANDREI LUPAS (30), Abteilung Molukulare
STEVEN VVOKINEH (6), Howard Hughes -ideM Strukturbiologie, Max-Planck-Institut fiir
lac Institute, Fred Hutchinson Cancer -eR ,eimehcoiB 25128-D ,deirsnitraM Germany
hcraes ,retneC ,elttaeS Washington 40189 THOMAS L. MADDEN (9), National retneC for
DESMOND G. HIGGINS (22), European -celoM Biotechnology Information, National Li-
ular Biology Laboratory Outstation--the brary of Medicine, National Institutes of
European Bioinformatics Institute, Hinx- ,htlaeH Bethesda, Maryland 49802
ton, Cambridge CBIO 1RQ, United ALEX C. W. MAY (34), Department of -latsyrC
Kingdom ,yhpargol Birkbeck ,egelloC University of
LIISA HOLM (39), European Molecular Biol- London, London WC1E 7HX, United
ogy Laboratory Outstation--the European Kingdom
Bioinformatics Institute, Hinxton, Cam- RICHARD J. MURAL (16), Biology ,noisiviD
egdirb CBIO 1RQ, United Kingdom Oak Ridge National Laboratory, Oak
TIMOTHY J. P. HUBBARD (37), Medical Re- ,egdiR eessenneT 13873
hcraes Council ertneC Laboratories of Mo- ALEXEY G. MURZ1N (37), Medical hcraeseR
ralucel Biology and Cambridge Centre for Council Centre Laboratories of raluceloM
nietorP ,gnireenignE Cambridge CB2 2Q ,H Biology and Cambridge ertneC for Protein
detinU Kingdom Engineering, Cambridge 2BC 2QH,
Lois T. HUNT (3), National Biomedical Re- detinU Kingdom
hcraes Foundation, Washington, District of HITOMI OHKAWA (10), National Center for
Columbia 20007 Biotechnology Information, National Li-
MARK S. NOSNHOJ (34), Molecular Modelling brary of Medicine, National Institutes of
and Biocomputing Group, Turku Center ,htlaeH Bethesda, Maryland 49802
CONTRIBUTORS TO VOLUME 266 xi
CHRISTINE A. ORENGO (36), Department of NARUYA SAITOU (25), Laboratorv of Evolu-
Biochemistry and Molecular Biology, -inU tionary ,sciteneG National Institute of -eG
ytisrev ,egelloC London WC1E 6BT, En- netics, Mishima-shi, Shizuoka-ken, ,114
dnalg napaJ
JOHN P. OVER1NGTON (34), Computational CHRIS SANDER (39), European Molecular Bi-
,yrtsimehC Pfizer Central ,hcraeseR Sand- ology Laboratory Outstation--the Euro-
,hciw Kent CT13 9NJ, United Kingdom pean Bioinformatics Institute, Hinxton.
egdirbmaC CBIO 1RQ, United Kingdom
LASZLO PATTHY (12), Institute of Enzymol-
,ygo Biological hcraeseR ,retneC nairagnuH GREGORY D. SCHULER (10), National retneC
Academy of Sciences, Budapest ,3111-H for Biotechnology Information, National
yragnuH Library of ,enicideM National Institutes of
,htlaeH ,adsehteB Maryland 49802
WILLIAM R. PEARSON (15), Department of
,yrtsimehcoiB ytisrevinU of ,ainigriV -rahC BENNY SHOMER (1), European Molecular -iB
oh)gy Laboratory Outstation--the Euro-
,ellivsettol Virginia 80922
pean Bioinformatics Institute, Hinxton,
GRAZIANO PESOLE (17), Dipartimento id Bio-
egdirbmaC CBIO IRQ, United Kingdom
acimihc e Biologia ,eraloceloM JttisrevinU
RODGER STADEN (7), Medical Research
di Bari, 52107 Bari, Italy
Council Centre Laboratories of radtceloM
FRIEDHELM PFEIFFER (4), Martinsried Insti-
Biology, Cambridge 2BC 2QH, United
tute for Protein Sequences, Max Planck
Kingdom
Institute for Biochemistry, Martinsried
P. STELLING (28), Computer Science -trapeD
,25128 Germany
ment, University of California, Davis,
OLIV1ER POCH (40), RPU 2009 ud Centre -aN ,sivaD California 61659
tional ed al ehcrehceR ,euqifitneicS I.B.M.C.
JENS K~ABLVOTS (23), Department of ygolocE
ud Centre National ed al Recherche -neicS
and Genetics, Institute of Biological Sci-
,euqifit 67084 ,gruobsartS ecnarF
,secne Aarhus University, DK-8000 Aar-
BARRY ROBSON (32), Dirac Foundation, Bio- hus, Denmark
informatics Laboratory, Royal yranireteV MARK BASIL SLLEDNIWS (38), Department of
,egelloC University of London, London Molecular Design, Institute for Drug Dis-
NW10TU, United Kingdom Trevoc ,hcraeseR Yamanouchi -uecamrahP
MICHAEL A. RODIONOV (34), Molecular tical Company, Ltd., Tsukuba 305, Japan
Modelling and Biocomputing Group, ROMAN L. TATUSOV (9, 18), National retneC
Turku ertneC for Biotechnology, ytisrevinU of Biotechnology Information, National Li-
of Turku, FIN-20521 Turku, Finland; and brary of Medicine, National Institutes of
Institute of Bioorganic Chemistry, Belarus ,htlaeH Bethesda, Maryland 49802
Academy of ,secneicS Minsk-141, Republic WILLIAM R. TAYLOR (20, 36), Division of
of Belarus 141022 Mathematical Biology, National Institute
BURKHARD ROST (31), Protein Design ,puorG for Medical ,hcraeseR London NW7 lAA,
European Molecular Biology Laboratory, detinU Kingdom
21096 ,grebledieH Germany JUL1E D. THOMPSON (22), European Molecu-
KENNETH E. RUDD (18), National Center for ral Biology Laboratory, 69012 Heidel-
Biotechnology Information, National Li- ,greb Germany
brary of Medicine, National "setutitsnI of EDWARD C. UBERBACHER (16), Computer
,htlaeH Bethesda, Maryland 49802 secneicS and Mathematics Division, Oak
CECILIA SACCONE (17), Dipartmento id Bio- Ridge National Laboratory, Oak ,egdiR
acimihc e Biologia Moleculare, t~tisrevinU eessenneT 13873
id Bari and Centro di Studio sui Mitocondri ANATOLY ULYANOV (8), European raluceloM
e Metabolismo Energetico, CNR, 52107 Biology Laboratory, 69117 ,grebledieH
,iraB Italy ynamreG
xii CONTRIBUTORS TO VOLUME 266
STELLA VERETNIK (13), San Diego Supercom- YING Xu (16), Computer secneicS and -ehtaM
puter ,retneC La Jolla, California 39029 scitam Division, Oak Ridge National Labo-
OWEN WHITE (2), ehT Institute for Genomic ,yrotar Oak Ridge, Tennessee 13873
,hcraeseR ,grubsrehtiaG Maryland 05802
TAu-Mu YI (19), Whitehead Institute for Bio-
MATrmAS SNNAMLIW (35), European -celoM medical Research and Department of Biol-
ular Biology Laboratory, 69001 Heidel- ,ygo sttesuhcassaM Institute of ,ygolonhceT
,greb Germany ,egdirbmaC sttesuhcassaM 24120
JOHN C. WooTroN (33), National Center for
JINGHUI ZHANG (9), National retneC for Bio-
Biotechnology Information, National Li-
technology Information, National Library
brary of Medicine, National Institutes of
of ,enicideM National Institutes of ,htlaeH
,htlaeH Bethesda, Maryland 49802
,adsehteB Maryland 29802
CATHY H. Wu (5), Departments of -loimedipE
ogy and Biomathematics, University of KAM ZHANG (35), Division of Basic ,secneicS
Texas Health Center at Tyler, Tyler, Fred Hutchinson Cancer Center, ,elttaeS
Texas 01757 Washington 40189
1 NAEPORUE SCITAMROFNIOIB ETUTITSNI 3
1 Information Services of the European
Bioinformaties Institute
yB YNNEB ,REMOHS TREBOR A. L. ,REPRAH
and MAHARG N. NOREMAC
Introduction
The European Bioinformatics Institute (EBI) was established in Sep-
tember 1994 as a new outstation of the European Molecular Biology Labo-
ratories (EMBL). The new outstation is located at Hinxton Hall, Cam-
bridgeshire, United Kingdom. Its main tasks are management of databases
for molecular biology, bioinformatics services, and research and develop-
ment in these fields)
The move of the bioinformatics services from the EMBL headquarters
in Heidelberg, Germany, to the EBI had various implications, including
considerable expansion in the computer power and the number of staff.
The computers are used for management of the principal databases, and
for providing network servers. The outstation provides excellent communi-
cations channels to the scientific and research community throughout Eu-
rope, and a specialized user support group ensures that all the services are
properly maintained and functional.
Various new services (which will be reviewed in this chapter) have been
established, and this has been due to the fact that there has been an increase
in both computational power and manpower at the EBI. The inspiration
for these new services has come from the various research and development
(R&D) teams now operating at the EBI, who do research on managing
sequence databases and studying the interrelationships between various
kinds of data. The main thrust of this work is to provide novel ways to
access the data and to provide interfaces that are intuitive and easy to use
for the EBI user community.
This chapter is divided into two sections. The first section is devoted
to describing the various current and future databases and resources that
are being developed in-house, and the second section describes the various
interfaces and network connections that EBI provides for the scientific
community globally. A glossary is provided at the end of this chapter that
gives a brief description of common terms.
t D. B. Emmert, P. J. Stoehr, G. Stoesser, and G. N. Cameron, Nucleic Acids Res. 22,
3445 (1994).
Copyright © 1996 by Academic Press, Inc.
METHODS IN ENZYMOLOGY, VOL. 266 All rights of reproduction in any form reserved.
4 DATABASES AND RESOURCES 11
EBI Databases and Resources
EMBL Nucleotide Sequence Database
The EMBL Nucleotide Sequence Database is a comprehensive database
of DNA and RNA sequences either collected from the scientific literature
and patent applications or submitted directly from researchers and sequenc-
ing groups. 2 The database is produced in a collaboration between the
EMBL, GenBank (Washington DC, USA), and the DNA Data Bank of
Japan (DDBJ, Mishima, Japan). Each entry that is created at any of these
databases is automatically exchanged between the other two databases.
This allows almost complete synchronization between the databases.
Currently, there is a %57 annual growth rate of the nucleotide sequence
database. The total number of entries and bases for different taxonomic
divisions can be seen in Table I. With further technological advancements,
the rate of growth of the databases will increase even more.
The nucleotide database is maintained in the relational database man-
agement system (RDBMS) ORACLE, running on a DEC Alpha VMS
cluster. Each entry in the database is assigned an accession number, which
is a permanent unique identifier. The entry is represented externally as an
ASCII "flat file." The flat file (see Fig. )1 is composed of lines beginning
with a two-character tag and followed by an associated text. The header
information ("annotation") is followed by the sequence itself. The sequence
entry ends with the unique identifier "//." Table II summarizes the meaning
of the two-character line tags.
The EBI maintains a very high level of quality assurance of the sequence
data in the EMBL database. Each new entry is carefully reviewed by a
team of annotators, and, when necessary, direct communication with the
submitting author is initiated to clarify ambiguities. Rapid data turnaround
is essential; we guarantee to process well-formed submissions within 1 week,
although in practice entries are created within 2-3 days after receipt.
Development of the next generation of the sequence database is one
of the R&D group activities. This group concentrates on various means of
ensuring database integrity and developing state-of-the-art implementa-
tions of the data. The latest release (Release 45, December 1995) contains
622,566 entries, comprising 427,620,278 nucleotides.
SWISS-PROT Protein Sequence Database
The SWISS-PROT Protein Sequence Database is a database of protein
sequences? This database is produced and maintained in a collaboration
2 C. M. Rice, R. Fuchs, D. G. Higgins, P. J. Stoehr, and G. N. Cameron, Nucleic Acids Res.
21, 2967 (1993).
3 A. Bairoch and B. Boeckmann, Nucleic Acid Res. 22, 3578 (1994).
1
EUROPEAN BIOINFORMATICS INSTITUTE 5
TABLE I
NUMBERS OF ENTRIES AND BASES NI EMBL
NUCLEOTIDE SEQUENCE DATABASE a ACCORDING
TO TAXONOMIC DIVISION
noisiviD b Entries Nucleotides
egahpoiretcaB 6601 714,394,1
TSE 123,526 39,332,522
ignuF 8420 19,940,449
setarbetrevnI 13,831 27,610,495
sellenagrO 5918 452,463,9
Other slammam 2726 513,679,6
Other setarbetrev 1407 226,441,8
stnalP 11,105 14,145,431
setamirP 35,290 36,665,648
setoyrakorP 21,427 37,074,154
stnedoR 23,626 26,850,022
STS 2327 774,882,2
citehtnyS 7958 482,592,4
deifissalcnU 2806 036,775,3
sesuriV 21,496 24,801,066
latotbuS 303,206 262,559,786
Other patents 6866 360,705,2
latoT 309,892 265,066,849
" Data era total numbers of entries dna sesab
ni eht EMBL editoelcun database at eht emit
of gnizeerf eht database for gnidliub esaeleR
.24
b EST, desserpxE sequence tags; ,STS
ecneuqes tagged .setis
between Dr. Amos Bairoch from the University of Geneva and the EBI.
The data in SWISS-PROT arise from several sources; they are derived from
translations of sequences from the EMBL Nucleotide Sequence Database,
adapted from the Protein Identification Resource (PIR) collection, ex-
tracted from the literature, and directly submitted by researchers. The
database contains high-quality annotation, is nonredundant, and is cross-
referenced to several other databases, notably the EMBL nucleotide Se-
quence Database, PROSITE pattern database, and Protein Data Bank
(PDB). The latest release (Release 32, November 1995) contained 49,340
sequence entries comprising 17,385,503 amino acids abstracted from
43,056 references.
As in the nucleotide sequence database, SWISS-PROT entries are rep-
resented externally as an ASCII flat file. The main difference between both
flat files is in the feature table, which in SWISS-PROT describes the
ID standard; IliA; PRO; 1636 BP.
XX
AC Zi1747; S35943;
XX
Dr 28-FEB-1992 (Rel. 31, Created)
Dr 30-JUN-1993 (Rel. 36, Last tlcdated, Version )6
XX
DE C.symbiost~ gdh gene encodir~ glutamate dehydrogermse.
XX
KW 9dz gene; glut6m~te dehydrogenase.
OS Clostridi~ symbiostm
OC Prokaryota; Bacteria; Firmicutes; I~zdospore-forming rods and cocci;
OC Bacillaceae; Clostridiu~.
XX
~N 1
RP 1-1636
RX M~3LINE; 92267007.
RA Teller J.K., Smith R.J., McPhersc~ M.J., Ehgel P.C., Guest J.R. ;
RT "qhe glutan~te dehydrogerkmse gene of Clostridit~n symbios~n.
RT Cloning by polymarase chain reactic~l, sequence analysis and
RT over-expressic~ in Escherichia coll.";
RL Eur. J. Bioc/le~. 206:151-159(1992).
XX
RN 2
RP 1-1636
RA Teller J.K. ;
RT
RL Suhnitted (26-FEB-1992) to the 194BL/GenBank/EfB/ databases.
RL Teller J.K., University of Sheffield, Molecular Biology and
RL Biotechnology, Western Bank, Sheffield, ihited ~ , SI0 2L~
XX
m SWISS-PROT; P24295; EHE2_CLOSY.
ZX
FH Key Locati(xl/Quali fiers
FH
FT ecrt%os i..1636
FF / organm~= "C lostridiu~ symbiosum"
FT /clcne="pC~516"
FT RBS 189.. 194
5T / citation= 1
FT CDS 204..1556
FT /gene= "~dg"
F? /EC_nunber:-" .i 4. i. 2"
F? /product: "Glutamate Dehydrogenase"
FT /evidence=~AL
FT /citaticn= i
FT /note: "pid: g49280"
SQ Sequence 1636 BP; 474 A; 329 C; 416 G; 417 T; 0 other;
aacgtcgatc gtgcacgttt gcgctgtaac aattataatg ctaattcaat ttc3cttatat 60
aaQtgaaatg cgttataata aaaccag~c agaaaatttc acaas~cat agat~ 120
< ..... >
aagaccggca gctattattt aataacaatt gcataagcgg ttgtctg~t gattggggct 1620
gctgcattaa gtatat 1636
//