Debugging the bug/50-mapped-reactions

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Mapped reactions


50: (rndr4 udpreduct-rxn) (50 B2235  [c] : trdrd + udp --> dudp + h2o  
+ trdox RNDR4)
51: (rndr3 cdpreduct-rxn) (51 B2235  [c] : cdp + trdrd --> dcdp + h2o  
+ trdox RNDR3)
52: (rndr2 gdpreduct-rxn) (52 B2235  [c] : gdp + trdrd --> dgdp + h2o  
+ trdox RNDR2)
53: (rndr2 gdpreduct-rxn) (53 EG10661 nrdB Reduced Thioredoxin + GDP   
=  Thioredoxin Disulfide + dGDP + H_2_O GDPREDUCT-RXN)
54: (RIBabcpp ABC-28-RXN) (54	EG10814	rbsA	ATP + D-ribose_[periplasmic space]_ + H_2_O =ADP + phosphate + D-ribose_[cytosol]_ 	ABC-28-RXN)
55: ("http://www.ecocyc.org/reactions/ribulokin-rxn"="http://gcrg.ucsd.edu/reaction/RBK_L1") (55	EG10053	araB	L-ribulose + ATP  ->  L-ribulose-5-phosphate + ADP	RIBULOKIN-RXN)
59: (abc-24-rxn spmdabcpp) (59 EG10752 potD ATP + spermidine_[periplasmic space]_ + H_2_O =ADP + phosphate + spermidine_[cytosol]_  ABC-24-RXN)
59: (ptrcabcpp abc-25-rxn) (59 EG11632 potI ATP + putrescine_[periplasmic space]_ + H_2_O =ADP + phosphate + putrescine_[cytosol] ABC-25-RXN)
63: (proline--trna-ligase-rxn protrs) (63 B0194  [c] : atp + pro-L + trnapro --> amp + ppi + protrna PROTRS)
64: (abc-26-rxn proabcpp) (64 B2679  atp[c] + h2o[c] + pro-L[p] --> adp[c] + h[c] + pi[c] + pro-L[c] PROabcpp)
66: (chorm chorismatemut-rxn) (66 EG11039 tyrA chorismate  =  prephenate CHORISMATEMUT-RXN)
69: (trans-rxn-32 abc-27-rxn) (69 EG10734 pstS ATP + phosphate_[periplasmic space]_ + H_2_O =ADP + phosphate_[cytosol]_ + phosphate_[cytosol]_  ABC-27-RXN
71: (phenylalanine--trna-ligase-rxn phetrs) (71 B1714  [c] : atp + phe-L + trnaphe --> amp + phetrna + ppi PHETRS)
72: (phemeabcpp trans-rxn0-162) (72 EG12057 ccmC protoheme_[cytosol]_ + ATP + H_2_O =phosphate + ADP + protoheme_[periplasmic space]_  TRANS-RXN0-162)
74: (UDCPDP undecaprenyl-diphosphatase-rxn) (74 EG10705 pgpB  undecaprenyl diphosphate + H_2_O  ->  undecaprenyl phosphate + phosphate UNDECAPRENYL-DIPHOSPHATASE-RXN)
81: (1.8.4.8-rxn papsr) (81 B2762  [c] : paps + trdrd --> (2) h + pap + so3 + trdox PAPSR)
81: (1.8.4.8-rxn papsr) (81 EG10189 cysH PAPS + Reduced Thioredoxin  =  adenosine 3',5'-bisphosphate + SO_3__-2_ + Thioredoxin Disulfide 1.8.4.8-RXN)
84: (ornabcpp abc-37-rxn) (84 B2308  atp[c] + h2o[c] + orn[p] --> adp[c] + h[c] + orn[c] + pi[c] ORNabcpp)
89: (ntptp1 dgtptriphydro-rxn) (89 EG10225 dgt H_2_O + dGTP  ->  PPP_i_ + deoxyguanosine DGTPTRIPHYDRO-RXN)
90: (ntpp10 rxn0-1602) (90 G7530 rdgB dITP + H_2_O  ->  dIMP +  pyrophosphate RXN0-1602)
90: (rxn0-1603 ntpp11) (90 G7530 rdgB XTP + H_2_O  ->  XMP + pyrophosphate RXN0-1603)

93: (ntpp1 rxn0-385) (93 EG10626 mutT dGTP + H_2_O  =  dGMP +  pyrophosphate RXN0-385)
94: (ntp3 rxn0-1021) (94 G7841 yjeQ GTP + H_2_O  =  GDP + phosphate  RXN0-1021)


Unmapped reaction notes

56:

an orthophosphoric monoester subsumes r5p, and an alcohol subsumes rib-D

 56:  COMMENT: "WIDE SPECIFICITY. ALSO CATALYSES TRANSPHOSPHORYLATIONS."
 56:  equivalent to ALKAPHOSPHA-RXN in terms of stoichiometry.  But context
 56	B4055		[p] : h2o + r5p --> pi + rib-D	R5PPpp
 56	EG11934	aphA	H_2_O + an orthophosphoric monoester  =  phosphate + an alcohol	ACID-PHOSPHATASE-RXN

57:

Generic reaction. a sugar phosphate subsumes r5p and a sugar subsumes rib-D

57	B0822		[c] : h2o + r5p --> pi + rib-D	R5PP
57	G6425	ybiV	H_2_O + a sugar phosphate  =  a sugar + phosphate	SUGAR-PHOSPHATASE-RXN

58:

PYDXPP is an orphan enzyme? Closest matches are the following:

 (union (reactions-of-compound 'pyridoxal_phosphate) (reactions-of-compound 'pyridoxal))
 (PMPOXI-RXN PNPOXI-RXN PYRDAMPTRANS-RXN PYRIDOXKIN-RXN PYROXALTRANSAM-RXN)
 EC(48): (intersection (reactions-of-compound 'pyridoxal_phosphate) (reactions-of-compound 'pyridoxal))
 (PYRIDOXKIN-RXN)
 EC(49): (substrates-of-reaction 'pyridoxkin-rxn)
 (PYRIDOXAL ATP ADP PYRIDOXAL_PHOSPHATE)
 58	no-b-gene		[c] : h2o + pydx5p --> pi + pydx	PYDXPP

60:

Generic reaction. an orthophosphoric monoester subsumes thrp, and an alcohol subsumes thr-L.

 60	B4055		[p] : h2o + thrp --> pi + thr-L	PTHRpp
 60	EG11934	aphA	H_2_O + an orthophosphoric monoester  =  phosphate + an alcohol	ACID-PHOSPHATASE-RXN

61:

PSSA_EC According to compound notes, tv org: Hpylori, Ecoli scaled up (50x) of phosphatidylserine with an average 2 fatty acid chain (C1686H3148O100) Checked N JLR

 61	B2585		[c] : (0.02) cdpdag_EC + ser-L <==> cmp + h + (0.02) ps_EC	PSSA_EC
 61	EG10781	pssA	CDP-diacylglycerol + L-serine  =  CMP + L-1-phosphatidylserine	PHOSPHASERSYN-RXN


62:

PSD_EC ps_EC and pe_EC are scaled up (50x)

 62	B4160		[c] : h + (0.02) ps_EC --> co2 + (0.02) pe_EC	PSD_EC
 62	EG10775	psd	L-1-phosphatidylserine  =  L-1-phosphatidyl-ethanolamine + CO_2_	PHOSPHASERDECARB-RXN


65:

ALKAPHOSPHA-RXn subsumes PPTHpp because an orthophosphoric monoester subsumes ppt, and an alcohol subsumes h2.

 65	B0383		[p] : h2o + ppt --> h2 + pi	PPTHpp
 65	EG10727	phoA	an orthophosphoric monoester + H_2_O  =  an alcohol + phosphate	ALKAPHOSPHA-RXN

67:

Update: 2.7.4.1 is a generic reaction. How did iJR904 get PPKr?

 67: PPKr	NIL	polyphosphate kinase	[c] : atp + pi <==> adp + ppi	Update	2.7.4.1	b2501
 67	B2501		[c] : atp + pi <==> adp + ppi	PPKr
 67	EG11510	ppk	long chain polyphosphate + ATP  =  long chain polyphosphate + ADP POLYPHOSPHATE-KINASE-RXN

68:

Update: 2.7.4.1 is a generic reaction. How did iJR904 get PPK2r?

 68: PPK2r	NIL	polyphosphate kinase	[c] : atp + ppi <==> adp + pppi	Update	2.7.4.1	b2501
 68	B2501		[c] : atp + ppi <==> adp + pppi	PPK2r
 68	EG11510	ppk	long chain polyphosphate + ATP  =  long chain polyphosphate + ADP	  POLYPHOSPHATE-KINASE-RXN

70:

The PHYT-RXN only releases 1 phosphate. PHYTSpp releases all 6. Unfortunately, there is no reaction that releases the other 5 reactions down to 0 in EcoCyc. Palsson wins.

 70: Note:  RXN-1001 is a duplicate of PHYT-RXN	
 70	B0980		[p] : (6) h2o + minohp --> inost + (6) pi	PHYTSpp
 70	EG10049	appA	H_2_O + phytate  =  phosphate + D-_myo_-inositol (1,2,3,4,5)-penta_kis_phosphate	6-PHYT-RXN
 70	EG10049	appA	GTP + H_2_O  =  GDP + phosphate	RXN0-1021

73:

(50x) problem again

 73	B1912		[c] : (0.02) cdpdag_EC + glyc3p <==> cmp + h + (0.02) pgp_EC	PGSA_EC
 73	EG10706	pgsA	CDP-diacylglycerol + glycerol-3-phosphate  =  CMP + L-1-phosphatidylglycerol-phosphate	PHOSPHAGLYPSYN-RXN


75:

Glucose-1-phosp subsumes Alpha-D-Glucose!

 75	B0688		[c] : g1p <==> g6p	PGMT
 75	EG12144	pgm	α-D-glucose 1-phosphate  =  α-D-glucose-6-phosphate	PHOSPHOGLUCMUT-RXN
 75	B2690		[c] : g1p <==> g6p	PGMT

76:

(50x) problem again

 76	B3546		[p] : lipa + (0.02) pe_EC --> (0.02) 12dgr_EC + enlipa	PETNTpp
 76	EG12267	eptB	KDO_2_-lipid IV_A_ + Phosphatidylethenolamine  =  1,2-diacylglycerol + phosphatidylethanolamine-KDO_2_-lipidA	RXN0-4581

77:

(50x) problem again

 77	no-b-gene		[c] : cmp + h + (0.02) pe_EC <==> (0.02) 12dgr_EC + cdpea	PEPT_EC
 77 This reaction is closest to ETHANOLAMINEPHOSPHOTRANSFERASE-RXN, but this reaction only exists in MetaCyc, not EcoCyc. An orphan enzyme?

78:

3.6.3.39-RXN subsumes PEabcpp.

 78	B0914		atp[c] + h2o[c] + pe_EC[c] --> adp[c] + h[c] + pe_EC[p] + pi[c]	PEabcpp
 78	EG10613	msbA	a lipopolysaccharide_[cytosol]_ + H_2_O + ATP =a lipopolysaccharide_[out]_ + phosphate + ADP 	3.6.3.39-RXN

79:

Closest to PNKIN-RXN. No EC number. No gene indicates possible orphan enzyme? Where is the evidence?

 79	no-b-gene		[c] : h2o + pdx5p --> pi + pydxn	PDXPP

80:

This is a combination of PDXA-RXN and PDXJ-RXN.

 80	B0052		[c] : dxyl5p + nad + phthr --> co2 + h + (2) h2o + nadh + pdx5p + pi	PDX5PS
 80	EG10691	pdxA	phospho-hydroxy-threonine + NAD_+_  =  1-amino-propan-2-one-3-phosphate + NADH + CO_2_	 PDXA-RXN
 80	B2564		[c] : dxyl5p + nad + phthr --> co2 + h + (2) h2o + nadh + pdx5p + pi	PDX5PS
 80	EG10693	pdxJ	1-amino-propan-2-one-3-phosphate + 1-deoxy-D-xylulose 5-phosphate  =  pyridoxine-5'-phosphate + phosphate + 2 H_2_O	PDXJ-RXN


82:

Another (50x) problem. No gene. orphan enzyme? Same as PHOSPHATIDATE-PHOSPHATASE-RXN in MetaCyc. no evidence.

 82	no-b-gene		[c] : h2o + (0.02) pa_EC --> (0.02) 12dgr_EC + pi	PAPA_EC
 82	no-b-gene		[c] : h2o + (0.02) pa_EC --> (0.02) 12dgr_EC + pi	PAPA_EC


83:

PYRROLINECARBREDUCT-RXN subsumes P5CR, because NAD(P)H is a generic compound.

 83	B0386		[c] : 1pyr5c + (2) h + nadph --> nadp + pro-L	P5CR
 83	EG10769	proC	pyrroline 5-carboxylate + NAD(P)H + H_+_  =  L-proline + NAD(P)_+_	PYRROLINECARBREDUCT-RXN


85:

This is odd. OPPSYN-RXN does not include octaprenyl-diphosphate (octdp) as a substrate, but it mentions it in the comments. OCTDPS seems to combine compounds in OPPSYN-RXN and FPPSYN-RXN.

 85	B3187		[c] : frdp + (5) ipdp --> octdp + (5) ppi	OCTDPS
 85	EG10017	ispB	_trans_-polyisoprenyl_n_-PP + Δ_3_-isopentenyl-PP  =  _trans_-polyisoprenyl_n+1_-PP + pyrophosphate	OPPSYN-RXN

86:

There appears to some correspondence to reactions in the same pathway, but which is not clear: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=ANARESPACC-PWY

 86: 1.7.7.2-RXN contains cytochrome, which is a protein.  It is unclear if these reactions are the same.
 86	B4070		(2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p]	NTRIR4pp
 86	EG11781	nrfA	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 86	B4071		(2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p]	NTRIR4pp
 86	EG11945	nrfB	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 86	B4072		(2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p]	NTRIR4pp
 86	EG11946	nrfC	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 86	B4073		(2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p]	NTRIR4pp
 86	EG11947	nrfD	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN

87:

Cytochrome is *not* the same as quinone.

 87: NOTE  CAS number and KEGG ID for quinone are algorithms.
 87	B4070		(2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c]	NTRIR3pp
 87	EG11781	nrfA	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 87	B4071		(2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c]	NTRIR3pp
 87	EG11945	nrfB	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 87	B4072		(2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c]	NTRIR3pp
 87	EG11946	nrfC	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN
 87	B4073		(2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c]	NTRIR3pp
 87	EG11947	nrfD	NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_  ->  ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O	1.7.7.2-RXN

88:

NITRITEREDUCT-RXN subsumes NTRIR2x because NAD(P)H makes it a generic reaction.

 88	B3365		[c] : (5) h + (3) nadh + no2 --> (2) h2o + (3) nad + nh4	NTRIR2x
 88	EG10653	nirB	3 NAD(P)_+_ + NH(4)OH + H_2_O  ->  3 NAD(P)H + NO_2__-_	NITRITREDUCT-RXN
 88	B3366		[c] : (5) h + (3) nadh + no2 --> (2) h2o + (3) nad + nh4	NTRIR2x
 88	EG10655	nirD	3 NAD(P)_+_ + NH(4)OH + H_2_O  ->  3 NAD(P)H + NO_2__-_	NITRITREDUCT-RXN

91:

RXN0-1041 subsumes NTPP8 becuase a nucleoside triphosphate makes it RXN0-1041 a generic reaction.

 91	B2781		[c] : h2o + utp --> h + ppi + ump	NTPP8
 91	EG10572	mazG	a nucleoside triphosphate + H_2_O  ->  a nucleoside monophosphate + pyrophosphate	RXN0-1041

92:

RXN0-1041 subsumes NTPP7 becuase a nucleoside triphosphate makes it RXN0-1041 a generic reaction.

 92	B2781		[c] : dttp + h2o --> dtmp + h + ppi	NTPP7
 92	EG10572	mazG	a nucleoside triphosphate + H_2_O  ->  a nucleoside monophosphate + pyrophosphate	RXN0-1041

95:

doesn't quite fit into either reaction. dgmp and dgsn are deoxy-ribonucleosides, not ribonucleosides.

 95:  RXN0-3741 subsumes NTD8pp because dgmp is a deoxyribonucleoside monophosphate and dgsn is a deoxyribonucleoside
 95:  b0480 and b4055 have a function in iJR904 that EcoCyc does not.
 95	B0480		[p] : dgmp + h2o --> dgsn + pi	NTD8pp
 95	EG11060	ushA	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN
 95	EG11060	ushA	a UDP-sugar + H_2_O  =  UMP + a sugar-1-phosphate	UDPSUGARHYDRO-RXN
 95	B4055		[p] : dgmp + h2o --> dgsn + pi	NTD8pp
 95	EG11934	aphA	H_2_O + an orthophosphoric monoester  =  phosphate + an alcohol	ACID-PHOSPHATASE-RXN

96:

RXN0-3741 subsumes NTD8 because dgmp is a deoxyribonucleoside monophosphate and dgsn is a deoxyribonucleoside

 96	B2291		[c] : dgmp + h2o --> dgsn + pi	NTD8
 96	G7185	yfbR	a deoxyribonucleoside 5'-monophosphate + H_2_O  ->  a deoxyribonucleoside + phosphate	RXN0-3741
 96	B2744		[c] : dgmp + h2o --> dgsn + pi	NTD8
 96	EG11817	surE	a nucleoside 3'-phosphate + H_2_O  =  a ribonucleoside + phosphate	3-NUCLEOTID-RXN
 96	EG11817	surE	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN

97:

RXN0-3741 subsumes NTD8 because damp is a deoxyribonucleoside monophosphate and dad-2 is a deoxyribonucleoside.

 97:  b0480 and b4055 have a function in iJR904 that EcoCyc does not.
 97	B0480		[p] : damp + h2o --> dad-2 + pi	NTD6pp
 97	EG11060	ushA	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN
 97	EG11060	ushA	a UDP-sugar + H_2_O  =  UMP + a sugar-1-phosphate	UDPSUGARHYDRO-RXN
 97	B4055		[p] : damp + h2o --> dad-2 + pi	NTD6pp
 97	EG11934	aphA	H_2_O + an orthophosphoric monoester  =  phosphate + an alcohol	ACID-PHOSPHATASE-RXN

98:

RXN0-3741 subsumes NTD6pp because damp is a deoxyribonucleoside monophosphate and dad-2 is a deoxyribonucleoside

 98: NOTE:  deoxyribonucleoside monophosphate and a deoxyribonucleoside should be class frames, and should have (damp,dcmp, dtmp, dgmp) and (deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythiamine) respectively as instances.
 98: 5'-NUCLEOTID-RXN is resolved in 100
 98	B2291		[c] : damp + h2o --> dad-2 + pi	NTD6
 98	G7185	yfbR	a deoxyribonucleoside 5'-monophosphate + H_2_O  ->  a deoxyribonucleoside + phosphate	RXN0-3741
 98	B2744		[c] : damp + h2o --> dad-2 + pi	NTD6
 98	EG11817	surE	a nucleoside 3'-phosphate + H_2_O  =  a ribonucleoside + phosphate	3-NUCLEOTID-RXN
 98	EG11817	surE	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN



99:

5'-NUCLEOTID-RXN subsumes NTD4pp because cmp is a ribonucleoside monophosphate and cytd is a ribonucleoside

 99:	NTD4pp	NIL	5'-nucleotidase (CMP)	[p] : cmp + h2o --> cytd + pi	Update	3.1.3.5	( b0480  or  b4055 )
 99	B0480		[p] : cmp + h2o --> cytd + pi	NTD4pp
 99	EG11060	ushA	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN
 99	EG11060	ushA	a UDP-sugar + H_2_O  =  UMP + a sugar-1-phosphate	UDPSUGARHYDRO-RXN
 99	B4055		[p] : cmp + h2o --> cytd + pi	NTD4pp
 99	EG11934	aphA	H_2_O + an orthophosphoric monoester  =  phosphate + an alcohol	ACID-PHOSPHATASE-RXN

100:

5'-NUCLEOTID-RXN subsumes NTD4 because cmp is a ribonucleoside monophosphate and cytd is a ribonucleoside

 100	B2744		[c] : cmp + h2o --> cytd + pi	NTD4
 100	EG11817	surE	a nucleoside 3'-phosphate + H_2_O  =  a ribonucleoside + phosphate	3-NUCLEOTID-RXN
 100	EG11817	surE	a ribonucleoside monophosphate + H_2_O  =  a ribonucleoside + phosphate	5'-NUCLEOTID-RXN