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python-biopython  1.60
Public Member Functions
test_prodoc.TestProdocRead Class Reference

List of all members.

Public Member Functions

def test_read_pdoc00100
def test_read_pdoc00113
def test_read_pdoc00144
def test_read_pdoc00149
def test_read_pdoc00340
def test_read_pdoc00424
def test_read_pdoc00472
def test_read_pdoc00640
def test_read_pdoc00787
def test_read_pdoc0933

Detailed Description

Definition at line 14 of file test_prodoc.py.


Member Function Documentation

Definition at line 16 of file test_prodoc.py.

00016 
00017     def test_read_pdoc00100(self):
00018         "Reading Prodoc record PDOC00100"
00019         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00100.txt')
00020         handle = open(filename)
00021         record = Prodoc.read(handle)
00022         handle.close()
00023 
00024         self.assertEqual(record.accession, "PDOC00100")
00025         self.assertEqual(len(record.prosite_refs), 4)
00026         self.assertEqual(record.prosite_refs[0], ("PS00107", "PROTEIN_KINASE_ATP"))
00027         self.assertEqual(record.prosite_refs[1], ("PS00108", "PROTEIN_KINASE_ST"))
00028         self.assertEqual(record.prosite_refs[2], ("PS00109", "PROTEIN_KINASE_TYR"))
00029         self.assertEqual(record.prosite_refs[3], ("PS50011", "PROTEIN_KINASE_DOM"))
00030         self.assertEqual(record.text, """\
00031 ******************************************
00032 * Protein kinases signatures and profile *
00033 ******************************************
00034 
00035 Eukaryotic  protein kinases [1 to 5]  are  enzymes  that   belong  to  a  very
00036 extensive family of  proteins which share a conserved catalytic core common to
00037 both serine/threonine and  tyrosine protein kinases.  There  are  a  number of
00038 conserved regions in the catalytic domain of protein kinases. We have selected
00039 two of these regions to build signature patterns.  The  first region, which is
00040 located in the N-terminal extremity of the catalytic domain, is a glycine-rich
00041 stretch of residues in the vicinity  of a lysine residue, which has been shown
00042 to be involved in ATP binding.   The second  region,  which is  located in the
00043 central part of the  catalytic  domain,  contains  a  conserved  aspartic acid
00044 residue  which is important for the catalytic activity  of  the enzyme [6]; we
00045 have derived  two signature patterns for that region: one specific for serine/
00046 threonine kinases  and  the  other  for  tyrosine kinases. We also developed a
00047 profile which is based on the alignment in [1] and covers the entire catalytic
00048 domain.
00049 
00050 -Consensus pattern: [LIV]-G-{P}-G-{P}-[FYWMGSTNH]-[SGA]-{PW}-[LIVCAT]-{PD}-x-
00051                     [GSTACLIVMFY]-x(5,18)-[LIVMFYWCSTAR]-[AIVP]-[LIVMFAGCKR]-K
00052                     [K binds ATP]
00053 -Sequences known to belong to this class detected by the pattern: the majority
00054  of known  protein  kinases  but it fails to find a number of them, especially
00055  viral kinases  which  are  quite  divergent in this region and are completely
00056  missed by this pattern.
00057 -Other sequence(s) detected in Swiss-Prot: 42.
00058 
00059 -Consensus pattern: [LIVMFYC]-x-[HY]-x-D-[LIVMFY]-K-x(2)-N-[LIVMFYCT](3)
00060                     [D is an active site residue]
00061 -Sequences known to belong to this class detected by the pattern: Most serine/
00062  threonine  specific protein  kinases  with  10 exceptions (half of them viral
00063  kinases) and  also  Epstein-Barr  virus BGLF4 and Drosophila ninaC which have
00064  respectively Ser and Arg instead of the conserved Lys and which are therefore
00065  detected by the tyrosine kinase specific pattern described below.
00066 -Other sequence(s) detected in Swiss-Prot: 1.
00067 
00068 -Consensus pattern: [LIVMFYC]-{A}-[HY]-x-D-[LIVMFY]-[RSTAC]-{D}-{PF}-N-
00069                     [LIVMFYC](3)
00070                     [D is an active site residue]
00071 -Sequences known to belong to this class detected by the pattern: ALL tyrosine
00072  specific protein  kinases  with  the  exception of human ERBB3 and mouse blk.
00073  This pattern    will    also    detect    most    bacterial    aminoglycoside
00074  phosphotransferases [8,9]  and  herpesviruses ganciclovir kinases [10]; which
00075  are proteins structurally and evolutionary related to protein kinases.
00076 -Other sequence(s) detected in Swiss-Prot: 17.
00077 
00078 -Sequences known to belong to this class detected by the profile: ALL,  except
00079  for three  viral  kinases.  This  profile  also  detects  receptor  guanylate
00080  cyclases (see   <PDOC00430>)  and  2-5A-dependent  ribonucleases.    Sequence
00081  similarities between  these  two  families  and the eukaryotic protein kinase
00082  family have been noticed before. It also detects Arabidopsis thaliana kinase-
00083  like protein TMKL1 which seems to have lost its catalytic activity.
00084 -Other sequence(s) detected in Swiss-Prot: 4.
00085 
00086 -Note: If a protein  analyzed  includes the two protein kinase signatures, the
00087  probability of it being a protein kinase is close to 100%
00088 -Note: Eukaryotic-type protein  kinases  have  also  been found in prokaryotes
00089  such as Myxococcus xanthus [11] and Yersinia pseudotuberculosis.
00090 -Note: The  patterns  shown  above has been updated since their publication in
00091  [7].
00092 
00093 -Expert(s) to contact by email:
00094            Hunter T.; hunter@salk-sc2.sdsc.edu
00095            Quinn A.M.; quinn@biomed.med.yale.edu
00096 
00097 -Last update: April 2006 / Pattern revised.
00098 
00099 """)
00100 
00101         self.assertEqual(len(record.references), 11)
00102         self.assertEqual(record.references[ 0].number, "1")
00103         self.assertEqual(record.references[ 0].authors, "Hanks S.K., Hunter T.")
00104         self.assertEqual(record.references[ 0].citation, """\
00105 "Protein kinases 6. The eukaryotic protein kinase superfamily: kinase
00106 (catalytic) domain structure and classification."
00107 FASEB J. 9:576-596(1995).
00108 PubMed=7768349""")
00109         self.assertEqual(record.references[ 1].number, "2")
00110         self.assertEqual(record.references[ 1].authors, "Hunter T.")
00111         self.assertEqual(record.references[ 1].citation, """\
00112 "Protein kinase classification."
00113 Methods Enzymol. 200:3-37(1991).
00114 PubMed=1835513""")
00115         self.assertEqual(record.references[ 2].number, "3")
00116         self.assertEqual(record.references[ 2].authors, "Hanks S.K., Quinn A.M.")
00117         self.assertEqual(record.references[ 2].citation, """\
00118 "Protein kinase catalytic domain sequence database: identification of
00119 conserved features of primary structure and classification of family
00120 members."
00121 Methods Enzymol. 200:38-62(1991).
00122 PubMed=1956325""")
00123         self.assertEqual(record.references[ 3].number, "4")
00124         self.assertEqual(record.references[ 3].authors, "Hanks S.K.")
00125         self.assertEqual(record.references[ 3].citation, 'Curr. Opin. Struct. Biol. 1:369-383(1991).')
00126         self.assertEqual(record.references[ 4].number, "5")
00127         self.assertEqual(record.references[ 4].authors, "Hanks S.K., Quinn A.M., Hunter T.")
00128         self.assertEqual(record.references[ 4].citation, """\
00129 "The protein kinase family: conserved features and deduced phylogeny
00130 of the catalytic domains."
00131 Science 241:42-52(1988).
00132 PubMed=3291115""")
00133         self.assertEqual(record.references[ 5].number, "6")
00134         self.assertEqual(record.references[ 5].authors, "Knighton D.R., Zheng J.H., Ten Eyck L.F., Ashford V.A., Xuong N.-H., Taylor S.S., Sowadski J.M.")
00135         self.assertEqual(record.references[ 5].citation, """\
00136 "Crystal structure of the catalytic subunit of cyclic adenosine
00137 monophosphate-dependent protein kinase."
00138 Science 253:407-414(1991).
00139 PubMed=1862342""")
00140         self.assertEqual(record.references[ 6].number, "7")
00141         self.assertEqual(record.references[ 6].authors, "Bairoch A., Claverie J.-M.")
00142         self.assertEqual(record.references[ 6].citation, """\
00143 "Sequence patterns in protein kinases."
00144 Nature 331:22-22(1988).
00145 PubMed=3340146; DOI=10.1038/331022a0""")
00146         self.assertEqual(record.references[ 7].number, "8")
00147         self.assertEqual(record.references[ 7].authors, "Benner S.")
00148         self.assertEqual(record.references[ 7].citation, 'Nature 329:21-21(1987).')
00149         self.assertEqual(record.references[ 8].number, "9")
00150         self.assertEqual(record.references[ 8].authors, "Kirby R.")
00151         self.assertEqual(record.references[ 8].citation, """\
00152 "Evolutionary origin of aminoglycoside phosphotransferase resistance
00153 genes."
00154 J. Mol. Evol. 30:489-492(1990).
00155 PubMed=2165531""")
00156         self.assertEqual(record.references[ 9].number, "10")
00157         self.assertEqual(record.references[ 9].authors, "Littler E., Stuart A.D., Chee M.S.")
00158         self.assertEqual(record.references[ 9].citation, 'Nature 358:160-162(1992).')
00159         self.assertEqual(record.references[10].number, "11")
00160         self.assertEqual(record.references[10].authors, "Munoz-Dorado J., Inouye S., Inouye M.")
00161         self.assertEqual(record.references[10].citation, 'Cell 67:995-1006(1991).')

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Definition at line 162 of file test_prodoc.py.

00162 
00163     def test_read_pdoc00113(self):
00164         "Reading Prodoc record PDOC00113"
00165         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00113.txt')
00166         handle = open(filename)
00167         record = Prodoc.read(handle)
00168         handle.close()
00169 
00170         self.assertEqual(record.accession, "PDOC00113")
00171         self.assertEqual(len(record.prosite_refs), 1)
00172         self.assertEqual(record.prosite_refs[0], ("PS00123", "ALKALINE_PHOSPHATASE"))
00173         self.assertEqual(record.text, """\
00174 ************************************
00175 * Alkaline phosphatase active site *
00176 ************************************
00177 
00178 Alkaline phosphatase (EC 3.1.3.1) (ALP) [1] is a zinc and magnesium-containing
00179 metalloenzyme  which hydrolyzes phosphate esters, optimally at high pH.  It is
00180 found in nearly  all living organisms,  with the exception of some plants.  In
00181 Escherichia coli, ALP (gene phoA) is found in the periplasmic space.  In yeast
00182 it (gene  PHO8)  is  found  in  lysosome-like vacuoles and in mammals, it is a
00183 glycoprotein attached to the membrane by a GPI-anchor.
00184 
00185 In mammals, four different isozymes are currently known [2]. Three of them are
00186 tissue-specific:  the  placental,  placental-like (germ cell)   and intestinal
00187 isozymes.  The fourth form is  tissue non-specific and was previously known as
00188 the liver/bone/kidney isozyme.
00189 
00190 Streptomyces' species  involved  in  the  synthesis  of  streptomycin (SM), an
00191 antibiotic, express  a  phosphatase (EC 3.1.3.39) (gene strK) which is  highly
00192 related to ALP.   It specifically cleaves  both  streptomycin-6-phosphate and,
00193 more slowly, streptomycin-3"-phosphate.
00194 
00195 A serine is involved   in the catalytic activity of ALP. The region around the
00196 active site serine is relatively well conserved and can be used as a signature
00197 pattern.
00198 
00199 -Consensus pattern: [IV]-x-D-S-[GAS]-[GASC]-[GAST]-[GA]-T
00200                     [S is the active site residue]
00201 -Sequences known to belong to this class detected by the pattern: ALL.
00202 -Other sequence(s) detected in Swiss-Prot: 3.
00203 -Last update: June 1994 / Text revised.
00204 
00205 """)
00206 
00207         self.assertEqual(len(record.references), 3)
00208         self.assertEqual(record.references[ 0].number, "1")
00209         self.assertEqual(record.references[ 0].authors, "Trowsdale J., Martin D., Bicknell D., Campbell I.")
00210         self.assertEqual(record.references[ 0].citation, """\
00211 "Alkaline phosphatases."
00212 Biochem. Soc. Trans. 18:178-180(1990).
00213 PubMed=2379681""")
00214         self.assertEqual(record.references[ 1].number, "2")
00215         self.assertEqual(record.references[ 1].authors, "Manes T., Glade K., Ziomek C.A., Millan J.L.")
00216         self.assertEqual(record.references[ 1].citation, """\
00217 "Genomic structure and comparison of mouse tissue-specific alkaline
00218 phosphatase genes."
00219 Genomics 8:541-554(1990).
00220 PubMed=2286375""")
00221         self.assertEqual(record.references[ 2].number, "3")
00222         self.assertEqual(record.references[ 2].authors, "Mansouri K., Piepersberg W.")
00223         self.assertEqual(record.references[ 2].citation, """\
00224 "Genetics of streptomycin production in Streptomyces griseus:
00225 nucleotide sequence of five genes, strFGHIK, including a phosphatase
00226 gene."
00227 Mol. Gen. Genet. 228:459-469(1991).
00228 PubMed=1654502""")

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Definition at line 229 of file test_prodoc.py.

00229 
00230     def test_read_pdoc00144(self):
00231         "Reading Prodoc record PDOC00144"
00232         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00144.txt')
00233         handle = open(filename)
00234         record = Prodoc.read(handle)
00235         handle.close()
00236 
00237         self.assertEqual(record.accession, "PDOC00144")
00238         self.assertEqual(len(record.prosite_refs), 2)
00239         self.assertEqual(record.prosite_refs[0], ("PS00159", "ALDOLASE_KDPG_KHG_1"))
00240         self.assertEqual(record.prosite_refs[1], ("PS00160", "ALDOLASE_KDPG_KHG_2"))
00241         self.assertEqual(record.text, """\
00242 *************************************************
00243 * KDPG and KHG aldolases active site signatures *
00244 *************************************************
00245 
00246 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16)  (KHG-aldolase)  catalyzes the
00247 interconversion of  4-hydroxy-2-oxoglutarate  into  pyruvate  and  glyoxylate.
00248 Phospho-2-dehydro-3-deoxygluconate  aldolase   (EC 4.1.2.14)   (KDPG-aldolase)
00249 catalyzes the interconversion of  6-phospho-2-dehydro-3-deoxy-D-gluconate into
00250 pyruvate and glyceraldehyde 3-phosphate.
00251 
00252 These two enzymes are structurally and functionally related [1]. They are both
00253 homotrimeric proteins of approximately 220 amino-acid residues. They are class
00254 I aldolases whose catalytic mechanism involves  the formation of a Schiff-base
00255 intermediate  between  the  substrate  and the epsilon-amino group of a lysine
00256 residue. In both enzymes, an arginine is required for catalytic activity.
00257 
00258 We developed  two signature patterns for these enzymes. The first one contains
00259 the active  site  arginine  and the second, the lysine involved in the Schiff-
00260 base formation.
00261 
00262 -Consensus pattern: G-[LIVM]-x(3)-E-[LIV]-T-[LF]-R
00263                     [R is the active site residue]
00264 -Sequences known to belong to this class detected by the pattern: ALL,  except
00265  for Bacillus  subtilis  KDPG-aldolase  which  has  Thr  instead of Arg in the
00266  active site.
00267 -Other sequence(s) detected in Swiss-Prot: NONE.
00268 
00269 -Consensus pattern: G-x(3)-[LIVMF]-K-[LF]-F-P-[SA]-x(3)-G
00270                     [K is involved in Schiff-base formation]
00271 -Sequences known to belong to this class detected by the pattern: ALL.
00272 -Other sequence(s) detected in Swiss-Prot: NONE.
00273 
00274 -Last update: November 1997 / Patterns and text revised.
00275 
00276 """)
00277 
00278         self.assertEqual(len(record.references), 1)
00279         self.assertEqual(record.references[ 0].number, "1")
00280         self.assertEqual(record.references[ 0].authors, "Vlahos C.J., Dekker E.E.")
00281         self.assertEqual(record.references[ 0].citation, """\
00282 "The complete amino acid sequence and identification of the
00283 active-site arginine peptide of Escherichia coli
00284 2-keto-4-hydroxyglutarate aldolase."
00285 J. Biol. Chem. 263:11683-11691(1988).
00286 PubMed=3136164""")

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Definition at line 287 of file test_prodoc.py.

00287 
00288     def test_read_pdoc00149(self):
00289         "Reading Prodoc record PDOC00149"
00290         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00149.txt')
00291         handle = open(filename)
00292         record = Prodoc.read(handle)
00293         handle.close()
00294 
00295         self.assertEqual(record.accession, "PDOC00149")
00296         self.assertEqual(len(record.prosite_refs), 1)
00297         self.assertEqual(record.prosite_refs[0], ("PS00165", "DEHYDRATASE_SER_THR"))
00298         self.assertEqual(record.text, """\
00299 *********************************************************************
00300 * Serine/threonine dehydratases pyridoxal-phosphate attachment site *
00301 *********************************************************************
00302 
00303 Serine and threonine  dehydratases [1,2]  are  functionally  and  structurally
00304 related pyridoxal-phosphate dependent enzymes:
00305 
00306  - L-serine dehydratase (EC 4.3.1.17) and D-serine  dehydratase  (EC 4.3.1.18)
00307    catalyze the dehydratation of L-serine (respectively D-serine) into ammonia
00308    and pyruvate.
00309  - Threonine dehydratase  (EC 4.3.1.19) (TDH) catalyzes  the  dehydratation of
00310    threonine into  alpha-ketobutarate  and  ammonia.  In Escherichia coli  and
00311    other microorganisms,  two  classes  of  TDH  are  known  to  exist. One is
00312    involved in  the  biosynthesis of isoleucine, the other in hydroxamino acid
00313    catabolism.
00314 
00315 Threonine synthase  (EC 4.2.3.1) is  also  a  pyridoxal-phosphate  enzyme,  it
00316 catalyzes the  transformation of  homoserine-phosphate into threonine.  It has
00317 been shown [3] that  threonine  synthase  is  distantly related to the serine/
00318 threonine dehydratases.
00319 
00320 In all these enzymes, the pyridoxal-phosphate group is  attached  to a  lysine
00321 residue.  The sequence around  this residue is sufficiently conserved to allow
00322 the derivation  of  a  pattern  specific  to serine/threonine dehydratases and
00323 threonine synthases.
00324 
00325 -Consensus pattern: [DESH]-x(4,5)-[STVG]-{EVKD}-[AS]-[FYI]-K-[DLIFSA]-[RLVMF]-
00326                     [GA]-[LIVMGA]
00327                     [The K is the pyridoxal-P attachment site]
00328 -Sequences known to belong to this class detected by the pattern: ALL.
00329 -Other sequence(s) detected in Swiss-Prot: 17.
00330 
00331 -Note: Some   bacterial L-serine dehydratases - such as those from Escherichia
00332  coli - are iron-sulfur proteins [4] and do not belong to this family.
00333 
00334 -Last update: December 2004 / Pattern and text revised.
00335 
00336 """)
00337 
00338         self.assertEqual(len(record.references), 4)
00339         self.assertEqual(record.references[ 0].number, "1")
00340         self.assertEqual(record.references[ 0].authors, "Ogawa H., Gomi T., Konishi K., Date T., Nakashima H., Nose K., Matsuda Y., Peraino C., Pitot H.C., Fujioka M.")
00341         self.assertEqual(record.references[ 0].citation, """\
00342 "Human liver serine dehydratase. cDNA cloning and sequence homology
00343 with hydroxyamino acid dehydratases from other sources."
00344 J. Biol. Chem. 264:15818-15823(1989).
00345 PubMed=2674117""")
00346         self.assertEqual(record.references[ 1].number, "2")
00347         self.assertEqual(record.references[ 1].authors, "Datta P., Goss T.J., Omnaas J.R., Patil R.V.")
00348         self.assertEqual(record.references[ 1].citation, """\
00349 "Covalent structure of biodegradative threonine dehydratase of
00350 Escherichia coli: homology with other dehydratases."
00351 Proc. Natl. Acad. Sci. U.S.A. 84:393-397(1987).
00352 PubMed=3540965""")
00353         self.assertEqual(record.references[ 2].number, "3")
00354         self.assertEqual(record.references[ 2].authors, "Parsot C.")
00355         self.assertEqual(record.references[ 2].citation, """\
00356 "Evolution of biosynthetic pathways: a common ancestor for threonine
00357 synthase, threonine dehydratase and D-serine dehydratase."
00358 EMBO J. 5:3013-3019(1986).
00359 PubMed=3098560""")
00360         self.assertEqual(record.references[ 3].number, "4")
00361         self.assertEqual(record.references[ 3].authors, "Grabowski R., Hofmeister A.E.M., Buckel W.")
00362         self.assertEqual(record.references[ 3].citation, """\
00363 "Bacterial L-serine dehydratases: a new family of enzymes containing
00364 iron-sulfur clusters."
00365 Trends Biochem. Sci. 18:297-300(1993).
00366 PubMed=8236444""")

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Definition at line 367 of file test_prodoc.py.

00367 
00368     def test_read_pdoc00340(self):
00369         "Reading Prodoc record PDOC00340"
00370         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00340.txt')
00371         handle = open(filename)
00372         record = Prodoc.read(handle)
00373         handle.close()
00374 
00375         self.assertEqual(record.accession, "PDOC00340")
00376         self.assertEqual(len(record.prosite_refs), 3)
00377         self.assertEqual(record.prosite_refs[0], ("PS00406", "ACTINS_1"))
00378         self.assertEqual(record.prosite_refs[1], ("PS00432", "ACTINS_2"))
00379         self.assertEqual(record.prosite_refs[2], ("PS01132", "ACTINS_ACT_LIKE"))
00380         self.assertEqual(record.text, """\
00381 *********************
00382 * Actins signatures *
00383 *********************
00384 
00385 Actins [1 to 4] are highly conserved contractile  proteins that are present in
00386 all eukaryotic cells. In vertebrates there are three groups of actin isoforms:
00387 alpha, beta and gamma.  The alpha actins are found in muscle tissues and are a
00388 major constituent of the contractile apparatus.  The beta and gamma actins co-
00389 exists in most cell  types as  components of the cytoskeleton and as mediators
00390 of internal cell motility.  In plants [5]  there  are  many isoforms which are
00391 probably involved  in  a  variety of  functions such as cytoplasmic streaming,
00392 cell shape determination,  tip growth,  graviperception, cell wall deposition,
00393 etc.
00394 
00395 Actin exists either in a monomeric form (G-actin) or in a polymerized form (F-
00396 actin). Each actin monomer  can  bind a molecule of ATP;  when  polymerization
00397 occurs, the ATP is hydrolyzed.
00398 
00399 Actin is a protein of from 374 to 379 amino acid  residues.  The  structure of
00400 actin has been highly conserved in the course of evolution.
00401 
00402 Recently some  divergent  actin-like  proteins have been identified in several
00403 species. These proteins are:
00404 
00405  - Centractin  (actin-RPV)  from mammals, fungi (yeast ACT5, Neurospora crassa
00406    ro-4) and  Pneumocystis  carinii  (actin-II).  Centractin  seems  to  be  a
00407    component of  a  multi-subunit  centrosomal complex involved in microtubule
00408    based vesicle motility. This subfamily is also known as ARP1.
00409  - ARP2  subfamily  which  includes  chicken ACTL, yeast ACT2, Drosophila 14D,
00410    C.elegans actC.
00411  - ARP3  subfamily  which includes actin 2 from mammals, Drosophila 66B, yeast
00412    ACT4 and fission yeast act2.
00413  - ARP4  subfamily  which includes yeast ACT3 and Drosophila 13E.
00414 
00415 We developed  three  signature  patterns. The first two are specific to actins
00416 and span  positions  54 to 64 and 357 to 365. The last signature picks up both
00417 actins and  the actin-like proteins and corresponds to positions 106 to 118 in
00418 actins.
00419 
00420 -Consensus pattern: [FY]-[LIV]-[GV]-[DE]-E-[ARV]-[QLAH]-x(1,2)-[RKQ](2)-[GD]
00421 -Sequences known to belong to this class detected by the pattern: ALL,  except
00422  for the actin-like proteins and 10 actins.
00423 -Other sequence(s) detected in Swiss-Prot: NONE.
00424 
00425 -Consensus pattern: W-[IVC]-[STAK]-[RK]-x-[DE]-Y-[DNE]-[DE]
00426 -Sequences known to belong to this class detected by the pattern: ALL,  except
00427  for the actin-like proteins and 9 actins.
00428 -Other sequence(s) detected in Swiss-Prot: NONE.
00429 
00430 -Consensus pattern: [LM]-[LIVMA]-T-E-[GAPQ]-x-[LIVMFYWHQPK]-[NS]-[PSTAQ]-x(2)-
00431                     N-[KR]
00432 -Sequences known to belong to this class detected by the pattern: ALL,  except
00433  for 5 actins.
00434 -Other sequence(s) detected in Swiss-Prot: NONE.
00435 
00436 -Last update: December 2004 / Patterns and text revised.
00437 
00438 """)
00439 
00440         self.assertEqual(len(record.references), 5)
00441         self.assertEqual(record.references[ 0].number, "1")
00442         self.assertEqual(record.references[ 0].authors, "Sheterline P., Clayton J., Sparrow J.C.")
00443         self.assertEqual(record.references[ 0].citation, '(In) Actins, 3rd Edition, Academic Press Ltd, London, (1996).')
00444         self.assertEqual(record.references[ 1].number, "2")
00445         self.assertEqual(record.references[ 1].authors, "Pollard T.D., Cooper J.A.")
00446         self.assertEqual(record.references[ 1].citation, 'Annu. Rev. Biochem. 55:987-1036(1986).')
00447         self.assertEqual(record.references[ 2].number, "3")
00448         self.assertEqual(record.references[ 2].authors, "Pollard T.D.")
00449         self.assertEqual(record.references[ 2].citation, """\
00450 "Actin."
00451 Curr. Opin. Cell Biol. 2:33-40(1990).
00452 PubMed=2183841""")
00453         self.assertEqual(record.references[ 3].number, "4")
00454         self.assertEqual(record.references[ 3].authors, "Rubenstein P.A.")
00455         self.assertEqual(record.references[ 3].citation, """\
00456 "The functional importance of multiple actin isoforms."
00457 BioEssays 12:309-315(1990).
00458 PubMed=2203335""")
00459         self.assertEqual(record.references[ 4].number, "5")
00460         self.assertEqual(record.references[ 4].authors, "Meagher R.B., McLean B.G.")
00461         self.assertEqual(record.references[ 4].citation, 'Cell Motil. Cytoskeleton 16:164-166(1990).')

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Definition at line 462 of file test_prodoc.py.

00462 
00463     def test_read_pdoc00424(self):
00464         "Reading Prodoc record PDOC00424"
00465         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00424.txt',)
00466         handle = open(filename)
00467         record = Prodoc.read(handle)
00468         handle.close()
00469 
00470         self.assertEqual(record.accession, "PDOC00424")
00471         self.assertEqual(len(record.prosite_refs), 1)
00472         self.assertEqual(record.prosite_refs[0], ("PS00488", "PAL_HISTIDASE"))
00473         self.assertEqual(record.text, """\
00474 **********************************************************
00475 * Phenylalanine and histidine ammonia-lyases active site *
00476 **********************************************************
00477 
00478 Phenylalanine ammonia-lyase (EC 4.3.1.5) (PAL) is  a  key  enzyme of plant and
00479 fungi  phenylpropanoid  metabolism  which is involved in the biosynthesis of a
00480 wide  variety  of secondary metabolites such  as  flavanoids,   furanocoumarin
00481 phytoalexins and  cell  wall  components.  These compounds have many important
00482 roles in plants during normal growth and in responses to environmental stress.
00483 PAL catalyzes  the  removal  of  an  ammonia  group from phenylalanine to form
00484 trans-cinnamate.
00485 
00486 Histidine ammonia-lyase (EC 4.3.1.3) (histidase)  catalyzes  the first step in
00487 histidine degradation, the removal of  an  ammonia  group  from  histidine  to
00488 produce urocanic acid.
00489 
00490 The two types of enzymes are functionally and  structurally related [1].  They
00491 are the only enzymes  which are known to have the modified amino acid dehydro-
00492 alanine (DHA) in their active site. A serine residue has been shown [2,3,4] to
00493 be the  precursor  of  this  essential electrophilic moiety. The region around
00494 this active  site  residue  is  well  conserved and can be used as a signature
00495 pattern.
00496 
00497 -Consensus pattern: [GS]-[STG]-[LIVM]-[STG]-[SAC]-S-G-[DH]-L-x-[PN]-L-[SA]-
00498                     x(2,3)-[SAGVTL]
00499                     [S is the active site residue]
00500 -Sequences known to belong to this class detected by the pattern: ALL.
00501 -Other sequence(s) detected in Swiss-Prot: NONE.
00502 -Last update: April 2006 / Pattern revised.
00503 
00504 """)
00505 
00506         self.assertEqual(len(record.references), 4)
00507         self.assertEqual(record.references[ 0].number, "1")
00508         self.assertEqual(record.references[ 0].authors, "Taylor R.G., Lambert M.A., Sexsmith E., Sadler S.J., Ray P.N., Mahuran D.J., McInnes R.R.")
00509         self.assertEqual(record.references[ 0].citation, """\
00510 "Cloning and expression of rat histidase. Homology to two bacterial
00511 histidases and four phenylalanine ammonia-lyases."
00512 J. Biol. Chem. 265:18192-18199(1990).
00513 PubMed=2120224""")
00514         self.assertEqual(record.references[ 1].number, "2")
00515         self.assertEqual(record.references[ 1].authors, "Langer M., Reck G., Reed J., Retey J.")
00516         self.assertEqual(record.references[ 1].citation, """\
00517 "Identification of serine-143 as the most likely precursor of
00518 dehydroalanine in the active site of histidine ammonia-lyase. A study
00519 of the overexpressed enzyme by site-directed mutagenesis."
00520 Biochemistry 33:6462-6467(1994).
00521 PubMed=8204579""")
00522         self.assertEqual(record.references[ 2].number, "3")
00523         self.assertEqual(record.references[ 2].authors, "Schuster B., Retey J.")
00524         self.assertEqual(record.references[ 2].citation, """\
00525 "Serine-202 is the putative precursor of the active site
00526 dehydroalanine of phenylalanine ammonia lyase. Site-directed
00527 mutagenesis studies on the enzyme from parsley (Petroselinum crispum
00528 L.)."
00529 FEBS Lett. 349:252-254(1994).
00530 PubMed=8050576""")
00531         self.assertEqual(record.references[ 3].number, "4")
00532         self.assertEqual(record.references[ 3].authors, "Taylor R.G., McInnes R.R.")
00533         self.assertEqual(record.references[ 3].citation, """\
00534 "Site-directed mutagenesis of conserved serines in rat histidase.
00535 Identification of serine 254 as an essential active site residue."
00536 J. Biol. Chem. 269:27473-27477(1994).
00537 PubMed=7961661""")

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Definition at line 538 of file test_prodoc.py.

00538 
00539     def test_read_pdoc00472(self):
00540         "Reading Prodoc record PDOC00472"
00541         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00472.txt')
00542         handle = open(filename)
00543         record = Prodoc.read(handle)
00544         handle.close()
00545 
00546         self.assertEqual(record.accession, "PDOC00472")
00547         self.assertEqual(len(record.prosite_refs), 1)
00548         self.assertEqual(record.prosite_refs[0], ("PS00546", "CYSTEINE_SWITCH"))
00549         self.assertEqual(record.text, """\
00550 *****************************
00551 * Matrixins cysteine switch *
00552 *****************************
00553 
00554 Mammalian extracellular matrix metalloproteinases (EC 3.4.24.-), also known as
00555 matrixins [1] (see <PDOC00129>), are zinc-dependent enzymes. They are secreted
00556 by cells  in an inactive form (zymogen) that differs from the mature enzyme by
00557 the presence  of  an  N-terminal propeptide. A highly conserved octapeptide is
00558 found two  residues  downstream  of the C-terminal end of the propeptide. This
00559 region has been shown to be  involved  in  autoinhibition  of matrixins [2,3];
00560 a cysteine  within the octapeptide chelates  the  active  site  zinc ion, thus
00561 inhibiting the  enzyme.  This  region has been called the 'cysteine switch' or
00562 'autoinhibitor region'.
00563 
00564 A cysteine switch has been found in the following zinc proteases:
00565 
00566  - MMP-1 (EC 3.4.24.7) (interstitial collagenase).
00567  - MMP-2 (EC 3.4.24.24) (72 Kd gelatinase).
00568  - MMP-3 (EC 3.4.24.17) (stromelysin-1).
00569  - MMP-7 (EC 3.4.24.23) (matrilysin).
00570  - MMP-8 (EC 3.4.24.34) (neutrophil collagenase).
00571  - MMP-9 (EC 3.4.24.35) (92 Kd gelatinase).
00572  - MMP-10 (EC 3.4.24.22) (stromelysin-2).
00573  - MMP-11 (EC 3.4.24.-) (stromelysin-3).
00574  - MMP-12 (EC 3.4.24.65) (macrophage metalloelastase).
00575  - MMP-13 (EC 3.4.24.-) (collagenase 3).
00576  - MMP-14 (EC 3.4.24.-) (membrane-type matrix metalliproteinase 1).
00577  - MMP-15 (EC 3.4.24.-) (membrane-type matrix metalliproteinase 2).
00578  - MMP-16 (EC 3.4.24.-) (membrane-type matrix metalliproteinase 3).
00579  - Sea urchin hatching enzyme (EC 3.4.24.12) (envelysin) [4].
00580  - Chlamydomonas reinhardtii gamete lytic enzyme (GLE) [5].
00581 
00582 -Consensus pattern: P-R-C-[GN]-x-P-[DR]-[LIVSAPKQ]
00583                     [C chelates the zinc ion]
00584 -Sequences known to belong to this class detected by the pattern: ALL,  except
00585  for cat MMP-7 and mouse MMP-11.
00586 -Other sequence(s) detected in Swiss-Prot: NONE.
00587 -Last update: November 1997 / Pattern and text revised.
00588 
00589 """)
00590 
00591         self.assertEqual(len(record.references), 5)
00592         self.assertEqual(record.references[ 0].number, "1")
00593         self.assertEqual(record.references[ 0].authors, "Woessner J.F. Jr.")
00594         self.assertEqual(record.references[ 0].citation, """\
00595 "Matrix metalloproteinases and their inhibitors in connective tissue
00596 remodeling."
00597 FASEB J. 5:2145-2154(1991).
00598 PubMed=1850705""")
00599         self.assertEqual(record.references[ 1].number, "2")
00600         self.assertEqual(record.references[ 1].authors, "Sanchez-Lopez R., Nicholson R., Gesnel M.C., Matrisian L.M., Breathnach R.")
00601         self.assertEqual(record.references[ 1].citation, 'J. Biol. Chem. 263:11892-11899(1988).')
00602         self.assertEqual(record.references[ 2].number, "3")
00603         self.assertEqual(record.references[ 2].authors, "Park A.J., Matrisian L.M., Kells A.F., Pearson R., Yuan Z.Y., Navre M.")
00604         self.assertEqual(record.references[ 2].citation, """\
00605 "Mutational analysis of the transin (rat stromelysin) autoinhibitor
00606 region demonstrates a role for residues surrounding the 'cysteine
00607 switch'."
00608 J. Biol. Chem. 266:1584-1590(1991).
00609 PubMed=1988438""")
00610         self.assertEqual(record.references[ 3].number, "4")
00611         self.assertEqual(record.references[ 3].authors, "Lepage T., Gache C.")
00612         self.assertEqual(record.references[ 3].citation, """\
00613 "Early expression of a collagenase-like hatching enzyme gene in the
00614 sea urchin embryo."
00615 EMBO J. 9:3003-3012(1990).
00616 PubMed=2167841""")
00617         self.assertEqual(record.references[ 4].number, "5")
00618         self.assertEqual(record.references[ 4].authors, "Kinoshita T., Fukuzawa H., Shimada T., Saito T., Matsuda Y.")
00619         self.assertEqual(record.references[ 4].citation, """\
00620 "Primary structure and expression of a gamete lytic enzyme in
00621 Chlamydomonas reinhardtii: similarity of functional domains to matrix
00622 metalloproteases."
00623 Proc. Natl. Acad. Sci. U.S.A. 89:4693-4697(1992).
00624 PubMed=1584806""")

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Definition at line 625 of file test_prodoc.py.

00625 
00626     def test_read_pdoc00640(self):
00627         "Reading Prodoc record PDOC00640"
00628         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00640.txt',)
00629         handle = open(filename)
00630         record = Prodoc.read(handle)
00631         handle.close()
00632 
00633         self.assertEqual(record.accession, "PDOC00640")
00634         self.assertEqual(len(record.prosite_refs), 1)
00635         self.assertEqual(record.prosite_refs[0], ("PS00812", "GLYCOSYL_HYDROL_F8"))
00636         self.assertEqual(record.text, """\
00637 ******************************************
00638 * Glycosyl hydrolases family 8 signature *
00639 ******************************************
00640 
00641 The microbial degradation  of cellulose and  xylans requires  several types of
00642 enzymes such as endoglucanases (EC 3.2.1.4),  cellobiohydrolases (EC 3.2.1.91)
00643 (exoglucanases), or xylanases (EC 3.2.1.8) [1,2].  Fungi and bacteria produces
00644 a spectrum of cellulolytic  enzymes (cellulases)  and  xylanases which, on the
00645 basis of sequence similarities,  can be classified into families. One of these
00646 families is known as the cellulase family D [3] or as  the glycosyl hydrolases
00647 family 8  [4,E1].  The  enzymes  which  are  currently known to belong to this
00648 family are listed below.
00649 
00650  - Acetobacter xylinum endonuclease cmcAX.
00651  - Bacillus strain KSM-330 acidic endonuclease K (Endo-K).
00652  - Cellulomonas josui endoglucanase 2 (celB).
00653  - Cellulomonas uda endoglucanase.
00654  - Clostridium cellulolyticum endoglucanases C (celcCC).
00655  - Clostridium thermocellum endoglucanases A (celA).
00656  - Erwinia chrysanthemi minor endoglucanase y (celY).
00657  - Bacillus circulans beta-glucanase (EC 3.2.1.73).
00658  - Escherichia coli hypothetical protein yhjM.
00659 
00660 The most conserved region in  these enzymes is  a stretch of about 20 residues
00661 that contains  two conserved aspartate. The first asparatate is thought [5] to
00662 act as the nucleophile in the catalytic mechanism. We have used this region as
00663 a signature pattern.
00664 
00665 -Consensus pattern: A-[ST]-D-[AG]-D-x(2)-[IM]-A-x-[SA]-[LIVM]-[LIVMG]-x-A-
00666                     x(3)-[FW]
00667                     [The first D is an active site residue]
00668 -Sequences known to belong to this class detected by the pattern: ALL.
00669 -Other sequence(s) detected in Swiss-Prot: NONE.
00670 
00671 -Expert(s) to contact by email:
00672            Henrissat B.; bernie@afmb.cnrs-mrs.fr
00673 
00674 -Last update: November 1997 / Text revised.
00675 
00676 """)
00677 
00678         self.assertEqual(len(record.references), 6)
00679         self.assertEqual(record.references[ 0].number, "1")
00680         self.assertEqual(record.references[ 0].authors, "Beguin P.")
00681         self.assertEqual(record.references[ 0].citation, """\
00682 "Molecular biology of cellulose degradation."
00683 Annu. Rev. Microbiol. 44:219-248(1990).
00684 PubMed=2252383; DOI=10.1146/annurev.mi.44.100190.001251""")
00685         self.assertEqual(record.references[ 1].number, "2")
00686         self.assertEqual(record.references[ 1].authors, "Gilkes N.R., Henrissat B., Kilburn D.G., Miller R.C. Jr., Warren R.A.J.")
00687         self.assertEqual(record.references[ 1].citation, """\
00688 "Domains in microbial beta-1, 4-glycanases: sequence conservation,
00689 function, and enzyme families."
00690 Microbiol. Rev. 55:303-315(1991).
00691 PubMed=1886523""")
00692         self.assertEqual(record.references[ 2].number, "3")
00693         self.assertEqual(record.references[ 2].authors, "Henrissat B., Claeyssens M., Tomme P., Lemesle L., Mornon J.-P.")
00694         self.assertEqual(record.references[ 2].citation, """\
00695 "Cellulase families revealed by hydrophobic cluster analysis."
00696 Gene 81:83-95(1989).
00697 PubMed=2806912""")
00698         self.assertEqual(record.references[ 3].number, "4")
00699         self.assertEqual(record.references[ 3].authors, "Henrissat B.")
00700         self.assertEqual(record.references[ 3].citation, """\
00701 "A classification of glycosyl hydrolases based on amino acid sequence
00702 similarities."
00703 Biochem. J. 280:309-316(1991).
00704 PubMed=1747104""")
00705         self.assertEqual(record.references[ 4].number, "5")
00706         self.assertEqual(record.references[ 4].authors, "Alzari P.M., Souchon H., Dominguez R.")
00707         self.assertEqual(record.references[ 4].citation, """\
00708 "The crystal structure of endoglucanase CelA, a family 8 glycosyl
00709 hydrolase from Clostridium thermocellum."
00710 Structure 4:265-275(1996).
00711 PubMed=8805535""")
00712         self.assertEqual(record.references[ 5].number, "E1")
00713         self.assertEqual(record.references[ 5].authors, "")
00714         self.assertEqual(record.references[ 5].citation, 'http://www.expasy.org/cgi-bin/lists?glycosid.txt')

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Definition at line 715 of file test_prodoc.py.

00715 
00716     def test_read_pdoc00787(self):
00717         "Reading Prodoc record PDOC00787"
00718         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00787.txt')
00719         handle = open(filename)
00720         record = Prodoc.read(handle)
00721         handle.close()
00722 
00723         self.assertEqual(record.accession, "PDOC00787")
00724         self.assertEqual(len(record.prosite_refs), 1)
00725         self.assertEqual(record.prosite_refs[0], ("PS01027", "GLYCOSYL_HYDROL_F39"))
00726         self.assertEqual(record.text, """\
00727 ******************************************************
00728 * Glycosyl hydrolases family 39 putative active site *
00729 ******************************************************
00730 
00731 It has  been  shown  [1,E1]  that  the  following  glycosyl  hydrolases can be
00732 classified into a single family on the basis of sequence similarities:
00733 
00734  - Mammalian lysosomal alpha-L-iduronidase (EC 3.2.1.76).
00735  - Caldocellum  saccharolyticum  and  Thermoanaerobacter saccharolyticum beta-
00736    xylosidase (EC 3.2.1.37) (gene xynB).
00737 
00738 The best  conserved  regions  in  these  enzymes is  located in the N-terminal
00739 section. It   contains  a  glutamic  acid  residue  which,  on  the  basis  of
00740 similarities with other  families of glycosyl hydrolases [2], probably acts as
00741 the proton donor in the catalytic mechanism. We use this region as a signature
00742 pattern.
00743 
00744 -Consensus pattern: W-x-F-E-x-W-N-E-P-[DN]
00745                     [The second E may be the active site residue]
00746 -Sequences known to belong to this class detected by the pattern: ALL.
00747 -Other sequence(s) detected in Swiss-Prot: NONE.
00748 
00749 -Expert(s) to contact by email:
00750            Henrissat B.; bernie@afmb.cnrs-mrs.fr
00751 
00752 -Last update: May 2004 / Text revised.
00753 
00754 """)
00755 
00756         self.assertEqual(len(record.references), 3)
00757         self.assertEqual(record.references[ 0].number, "1")
00758         self.assertEqual(record.references[ 0].authors, "Henrissat B., Bairoch A.")
00759         self.assertEqual(record.references[ 0].citation, """\
00760 "New families in the classification of glycosyl hydrolases based on
00761 amino acid sequence similarities."
00762 Biochem. J. 293:781-788(1993).
00763 PubMed=8352747""")
00764         self.assertEqual(record.references[ 1].number, "2")
00765         self.assertEqual(record.references[ 1].authors, "Henrissat B., Callebaut I., Fabrega S., Lehn P., Mornon J.-P., Davies G.")
00766         self.assertEqual(record.references[ 1].citation, """\
00767 "Conserved catalytic machinery and the prediction of a common fold for
00768 several families of glycosyl hydrolases."
00769 Proc. Natl. Acad. Sci. U.S.A. 92:7090-7094(1995).
00770 PubMed=7624375""")
00771         self.assertEqual(record.references[ 2].number, "E1")
00772         self.assertEqual(record.references[ 2].authors, '')
00773         self.assertEqual(record.references[ 2].citation, "http://www.expasy.org/cgi-bin/lists?glycosid.txt")

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Definition at line 774 of file test_prodoc.py.

00774 
00775     def test_read_pdoc0933(self):
00776         "Reading Prodoc record PDOC00933"
00777         filename = os.path.join( 'Prosite', 'Doc', 'pdoc00933.txt')
00778         handle = open(filename)
00779         record = Prodoc.read(handle)
00780         handle.close()
00781 
00782         self.assertEqual(record.accession, "PDOC00933")
00783         self.assertEqual(len(record.prosite_refs), 1)
00784         self.assertEqual(record.prosite_refs[0], ("PS01213", "GLOBIN_FAM_2"))
00785         self.assertEqual(record.text, """\
00786 **********************************************
00787 * Protozoan/cyanobacterial globins signature *
00788 **********************************************
00789 
00790 Globins are heme-containing  proteins involved in  binding and/or transporting
00791 oxygen [1]. Almost all globins belong to a large family (see <PDOC00793>), the
00792 only exceptions  are  the  following proteins which form a family of their own
00793 [2,3,4]:
00794 
00795  - Monomeric  hemoglobins  from the protozoan Paramecium caudatum, Tetrahymena
00796    pyriformis and Tetrahymena thermophila.
00797  - Cyanoglobins  from  the  cyanobacteria Nostoc commune and Synechocystis PCC
00798    6803.
00799  - Globins  LI637  and  LI410  from  the chloroplast of the alga Chlamydomonas
00800    eugametos.
00801  - Mycobacterium tuberculosis globins glbN and glbO.
00802 
00803 These proteins  contain a conserved histidine which could be involved in heme-
00804 binding. As a signature pattern, we use a conserved region that ends with this
00805 residue.
00806 
00807 -Consensus pattern: F-[LF]-x(4)-[GE]-G-[PAT]-x(2)-[YW]-x-[GSE]-[KRQAE]-x(1,5)-
00808                     [LIVM]-x(3)-H
00809                     [The H may be a heme ligand]
00810 -Sequences known to belong to this class detected by the pattern: ALL.
00811 -Other sequence(s) detected in Swiss-Prot: NONE.
00812 -Last update: April 2006 / Pattern revised.
00813 
00814 """)
00815 
00816         self.assertEqual(len(record.references), 4)
00817         self.assertEqual(record.references[ 0].number, "1")
00818         self.assertEqual(record.references[ 0].authors, "Concise Encyclopedia Biochemistry, Second Edition, Walter de Gruyter, Berlin New-York (1988).")
00819         self.assertEqual(record.references[ 0].citation, '')
00820         self.assertEqual(record.references[ 1].number, "2")
00821         self.assertEqual(record.references[ 1].authors, "Takagi T.")
00822         self.assertEqual(record.references[ 1].citation, 'Curr. Opin. Struct. Biol. 3:413-418(1993).')
00823         self.assertEqual(record.references[ 2].number, "3")
00824         self.assertEqual(record.references[ 2].authors, "Couture M., Chamberland H., St-Pierre B., Lafontaine J., Guertin M.")
00825         self.assertEqual(record.references[ 2].citation, """\
00826 "Nuclear genes encoding chloroplast hemoglobins in the unicellular
00827 green alga Chlamydomonas eugametos."
00828 Mol. Gen. Genet. 243:185-197(1994).
00829 PubMed=8177215""")
00830         self.assertEqual(record.references[ 3].number, "4")
00831         self.assertEqual(record.references[ 3].authors, "Couture M., Das T.K., Savard P.Y., Ouellet Y., Wittenberg J.B., Wittenberg B.A., Rousseau D.L., Guertin M.")
00832         self.assertEqual(record.references[ 3].citation, """\
00833 "Structural investigations of the hemoglobin of the cyanobacterium
00834 Synechocystis PCC6803 reveal a unique distal heme pocket."
00835 Eur. J. Biochem. 267:4770-4780(2000).
00836 PubMed=10903511""")

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The documentation for this class was generated from the following file: