Alignments for a candidate for metH in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Shewanella oneidensis MR-1

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 200213 SO1030 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__MR1:200213
          Length = 1244

 Score = 1614 bits (4180), Expect = 0.0
 Identities = 815/1238 (65%), Positives = 970/1238 (78%), Gaps = 14/1238 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S  +  +R QL+ RIL+LDG MGTMIQ Y+L EAD+RGERF DW  D+KGNNDLLVL++P
Sbjct: 9    SHTLADIRNQLSTRILILDGAMGTMIQGYKLEEADYRGERFKDWHTDVKGNNDLLVLTQP 68

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
             +I  IH  Y  AGADIIETNTFN+TTIAMADY M+SLSAEIN   A+LAR   D     
Sbjct: 69   HIIKQIHTDYLLAGADIIETNTFNATTIAMADYDMQSLSAEINREGARLAREACDAIEQA 128

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            T  KPRYVAGVLGPTNRT SISPDVNDP FRNI FD LV AY EST+AL+EGGAD+I++E
Sbjct: 129  TG-KPRYVAGVLGPTNRTCSISPDVNDPGFRNIHFDELVTAYCESTRALIEGGADIIMVE 187

Query: 182  TVFDTLNAKAAVFAVKTEFEAL-----GVELPIMISGTITDASGRTLSGQTTEAFYNSLR 236
            T+FDTLNAKAA+FA++T F+ L        LP+MISGTITDASGRTL+GQTTEAFYNSLR
Sbjct: 188  TIFDTLNAKAALFAIETVFDELFGANSPARLPVMISGTITDASGRTLTGQTTEAFYNSLR 247

Query: 237  HAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIR 296
            H + L+ GLNCALGP ELR YV+ELSRIAECYV+AHPNAGLPN FG YD   + MAK I+
Sbjct: 248  HIKPLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMAKVIQ 307

Query: 297  EWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLF 356
            EWA+ G LNI+GGCCG+TP+HI  +  AVE  APR LPEIPVACRL+GLEPL I   +LF
Sbjct: 308  EWAREGMLNIIGGCCGSTPEHIKVIREAVEQFAPRVLPEIPVACRLAGLEPLTIDAQTLF 367

Query: 357  VNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRF 416
            VNVGERTNVTGSAKF +LIKE K+ +ALDVAR+QVE+GAQIIDINMDEGMLD    M +F
Sbjct: 368  VNVGERTNVTGSAKFLKLIKEGKFEQALDVAREQVESGAQIIDINMDEGMLDGVEIMHKF 427

Query: 417  LNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRY 476
            LNLIA EPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSIS+KEG + FI  A L++RY
Sbjct: 428  LNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEKFIEQATLVKRY 487

Query: 477  GAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHN 536
            GAA ++MAFDEQGQADT+ARK+EIC RAY++L ++VGFPPEDIIFDPNIFA+ATGI+EH+
Sbjct: 488  GAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHD 547

Query: 537  NYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGI 596
            NYA DFI A ++IK  LPHA+ISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGI
Sbjct: 548  NYAVDFIDAIKEIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGI 607

Query: 597  VNAGQLAIYDDLPAELRDAVEDVILN-----RRDDGTERLLELAEKYRGSKTDDTANAQQ 651
            VNAGQLAI+DD+  EL+  VE+V+LN        + TE+LLE+AEK+RG  +  +A  + 
Sbjct: 608  VNAGQLAIFDDIDPELKVRVENVVLNLPCPVEGSNNTEQLLEIAEKFRGDGS-SSAKKED 666

Query: 652  AEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEG 711
             EWRSW VN+RL ++LVKGITEFI++DTE ARQ A+RP++VIEGPLMDGMN+VGDLFG G
Sbjct: 667  LEWRSWPVNQRLAHALVKGITEFIDEDTEAARQAASRPLDVIEGPLMDGMNIVGDLFGSG 726

Query: 712  KMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQ 771
            KMFLPQVVKSARVMK+AVAYL PFIE  K  G++NGK+++ TVK DVHDIGKNIVGVVL 
Sbjct: 727  KMFLPQVVKSARVMKKAVAYLNPFIEKEKVAGQSNGKILMVTVKSDVHDIGKNIVGVVLA 786

Query: 772  CNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLL 831
            CN +E+ DLGVMV  E+IL   KE N D+IG+SGLITPSLDEMV+  K   R+G TIP +
Sbjct: 787  CNGFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLTIPAI 846

Query: 832  IGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVR 891
            IGGAT SK HTAVKI  +Y    +Y+ +ASR V +V+ L+++  R   +  T  EY+ +R
Sbjct: 847  IGGATCSKIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVNNETRQATIDETYAEYDDMR 906

Query: 892  IQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPF 950
             +   +  R   V+LEAAR+N    DW  Y+P   + LG Q   +  +  L + IDWTPF
Sbjct: 907  TKRLSQAKRKEIVSLEAARENRCQHDWANYSPFKPNVLGRQVFDDYPLTDLVDRIDWTPF 966

Query: 951  FMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-D 1009
            F  W L G YP IL D+VVGVEAQ+LF D   ML K+  EK L  +GV+GLFPAN VG D
Sbjct: 967  FRAWELHGHYPEILSDKVVGVEAQKLFSDGKAMLKKIIEEKWLTAKGVIGLFPANTVGFD 1026

Query: 1010 DIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEE 1069
            DIE+Y DETRT V   +HHLR Q E+ G  N+CLADFVAPK SG ADY+G FAVT G   
Sbjct: 1027 DIELYTDETRTEVELTTHHLRMQLERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGI 1086

Query: 1070 DALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIREN 1129
            D     FEA HDDYN IM+K LADRLAEAFAE +HERVRK +WGYA +E L NE LIRE 
Sbjct: 1087 DEHVARFEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLDNEALIREK 1146

Query: 1130 YQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
            Y+GIRPAPGYPACP+HTEK  +WELL+  +   + +TES+AM+P A+VSGWYF+HP S+Y
Sbjct: 1147 YKGIRPAPGYPACPDHTEKGLLWELLKPNETIDLNITESYAMFPTAAVSGWYFAHPKSRY 1206

Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
            + V+ I RDQVEDYA+RKGM+V E E+WLAP L YD +
Sbjct: 1207 FGVSNIGRDQVEDYAKRKGMTVAETEKWLAPVLDYDPE 1244


Lambda     K      H
   0.318    0.134    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3818
Number of extensions: 145
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 1244
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1196
Effective search space:  1410084
Effective search space used:  1410084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate 200213 SO1030 (5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file))
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR02082.hmm
# target sequence database:        /tmp/gapView.27226.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02082  [M=1182]
Accession:   TIGR02082
Description: metH: methionine synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1757.9   0.0          0 1757.7   0.0    1.0  1  lcl|FitnessBrowser__MR1:200213  SO1030 5-methyltetrahydrofolate-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200213  SO1030 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1757.7   0.0         0         0       2    1182 .]      20    1209 ..      19    1209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1757.7 bits;  conditional E-value: 0
                       TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnstei 77  
                                      + ril+lDGamGt++q ++L+ead+rge ++d+++++kGnndlL+lt+P +i++ih +y+ aGaDi+etntFn+t+i
  lcl|FitnessBrowser__MR1:200213   20 STRILILDGAMGTMIQGYKLEEADYRGErFKDWHTDVKGNNDLLVLTQPHIIKQIHTDYLLAGADIIETNTFNATTI 96  
                                      78*************************************************************************** PP

                       TIGR02082   78 aladYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYkeqv 154 
                                      a+adYd++++++e+n+++a+lare++d +++ + k+R+vaG+lGPtn++ ++spdv++p+frn+++delv aY e++
  lcl|FitnessBrowser__MR1:200213   97 AMADYDMQSLSAEINREGARLAREACDAIEQATGKPRYVAGVLGPTNRTCSISPDVNDPGFRNIHFDELVTAYCEST 173 
                                      ***************************************************************************** PP

                       TIGR02082  155 kglldGGvDllLietvfDtlnakaalfaveevfee.....kgrelPilisgvivdksGrtLsGqtleaflaslehae 226 
                                      ++l++GG+D++++et+fDtlnakaalfa+e+vf+e       ++lP++isg+i+d+sGrtL+Gqt+eaf++sl+h +
  lcl|FitnessBrowser__MR1:200213  174 RALIEGGADIIMVETIFDTLNAKAALFAIETVFDElfganSPARLPVMISGTITDASGRTLTGQTTEAFYNSLRHIK 250 
                                      *********************************86222215689********************************* PP

                       TIGR02082  227 ililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPe 303 
                                       l++GLnCalG++elr++v+els++ae++vs++PnaGLPn++g Yd+tpe +ak+++e+a+eg+lni+GGCCG+tPe
  lcl|FitnessBrowser__MR1:200213  251 PLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMAKVIQEWAREGMLNIIGGCCGSTPE 327 
                                      ***************************************************************************** PP

                       TIGR02082  304 hiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqvee 380 
                                      hi+ i eav++ +pr  +e++ +++l+gle+l+i+ ++ fvn+GeRtnv+Gs+kf klik++++e+al++a++qve+
  lcl|FitnessBrowser__MR1:200213  328 HIKVIREAVEQFAPRVLPEIPVACRLAGLEPLTIDAQTLFVNVGERTNVTGSAKFLKLIKEGKFEQALDVAREQVES 404 
                                      ***************************************************************************** PP

                       TIGR02082  381 GaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFleka 457 
                                      Gaqi+Din+De++lDg++ m+k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsislk+Gee+F+e+a
  lcl|FitnessBrowser__MR1:200213  405 GAQIIDINMDEGMLDGVEIMHKFLNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEKFIEQA 481 
                                      ***************************************************************************** PP

                       TIGR02082  458 klikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534 
                                       l+k+yGaa+++mafDe+Gqa+t+++k+ei++Ray++l++kvgfppediifDpni++iatGi+ehd+ya+dfi+ai+
  lcl|FitnessBrowser__MR1:200213  482 TLVKRYGAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHDNYAVDFIDAIK 558 
                                      ***************************************************************************** PP

                       TIGR02082  535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrr 611 
                                      eik +lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+aik+G+Dmgivnag+la++ddid+el+  ve+++l+  
  lcl|FitnessBrowser__MR1:200213  559 EIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGIVNAGQLAIFDDIDPELKVRVENVVLNLP 635 
                                      ***************************************************************************88 PP

                       TIGR02082  612 .....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegp 683 
                                           +++te+Lle+ae+++g  ++s ++++  ewr++pv++RL++alvkG++e+i+ed+e+ar+ +++pl++iegp
  lcl|FitnessBrowser__MR1:200213  636 cpvegSNNTEQLLEIAEKFRGDGSSS-AKKEDLEWRSWPVNQRLAHALVKGITEFIDEDTEAARQAASRPLDVIEGP 711 
                                      888889****************9995.558899******************************************** PP

                       TIGR02082  684 LldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscn 760 
                                      L+dGm++vGdLFGsGkmfLPqvvksarvmkkavayL+P++ekek + +s+Gki++ tvk DvhDiGkniv+vvL+cn
  lcl|FitnessBrowser__MR1:200213  712 LMDGMNIVGDLFGSGKMFLPQVVKSARVMKKAVAYLNPFIEKEKVAGQSNGKILMVTVKSDVHDIGKNIVGVVLACN 788 
                                      ***************************************************************************** PP

                       TIGR02082  761 gyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY 837 
                                      g+ev dlGv+v ve+ilea k+++ D+ig+sGLi++sldemv++++ ++r+g++iP ++GGa+ sk h+avkia++Y
  lcl|FitnessBrowser__MR1:200213  789 GFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLTIPAIIGGATCSKIHTAVKIAPHY 865 
                                      ***************************************************************************** PP

                       TIGR02082  838 kgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpap 914 
                                          +y  das+av +v+kl++++++++ ++++ +ey+++r+k  ++ ++++ +s++aar+++ + d+  ++++ +p
  lcl|FitnessBrowser__MR1:200213  866 PHGAIYIADASRAVPMVSKLVNNETRQATIDETYAEYDDMRTKRLSQAKRKEIVSLEAARENRCQHDWA-NYSPFKP 941 
                                      *********************************************************************.9****** PP

                       TIGR02082  915 kflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlf 990 
                                      + lG++v++++ + +l++ iDw+++F +Wel+g+yp+il+d+++g+ea+klf+d k++l+k+++ek l+a+gv+Glf
  lcl|FitnessBrowser__MR1:200213  942 NVLGRQVFDDYpLTDLVDRIDWTPFFRAWELHGHYPEILSDKVVGVEAQKLFSDGKAMLKKIIEEKWLTAKGVIGLF 1018
                                      ***************************************************************************** PP

                       TIGR02082  991 Paqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakk 1066
                                      Pa++vg ddie+ytdet+   t++  t+++ + ql++  + + claDf+a+k+sG +Dy+g ++vtag g++e   +
  lcl|FitnessBrowser__MR1:200213 1019 PANTVGfDDIELYTDETR---TEVELTTHHLRMQLERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGIDEHVAR 1092
                                      ***98769*********9...44444444455566666666************************************ PP

                       TIGR02082 1067 leakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatll 1143
                                      +ea++ddy++i++k ladrlaea+ae +hervRke+wgya++e+ld+e l++e+Y+Girpa+GYpacPdhtek  l+
  lcl|FitnessBrowser__MR1:200213 1093 FEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLDNEALIREKYKGIRPAPGYPACPDHTEKGLLW 1169
                                      ***************************************************************************** PP

                       TIGR02082 1144 eLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                      eLl++++ i l++tes+a+ P+a+vsg+yfahp+++Yf v
  lcl|FitnessBrowser__MR1:200213 1170 ELLKPNEtIDLNITESYAMFPTAAVSGWYFAHPKSRYFGV 1209
                                      ****9887******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1244 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.10u 0.05s 00:00:00.15 Elapsed: 00:00:00.15
# Mc/sec: 9.78
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis