Alignments for a candidate for metH in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Acidimicrobium ferrooxidans DSM 10331

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_015798162.1 AFER_RS03720 methionine synthase

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000023265.1:WP_015798162.1
          Length = 1151

 Score = 1080 bits (2792), Expect = 0.0
 Identities = 599/1205 (49%), Positives = 775/1205 (64%), Gaps = 66/1205 (5%)

Query: 20   DALANHVLIGDGAMGTQLQGFDLDVEKDFLD--LEGCNEILNDTRPDVLRQIHRAYFEAG 77
            + L   V++ DGAMGT LQ   L  + DF    LEGCNEIL  TRP+ +  +H ++   G
Sbjct: 6    ELLRERVVVFDGAMGTNLQLAGLGAD-DFGGPALEGCNEILVVTRPEAVAAVHDSFLAVG 64

Query: 78   ADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGP 137
             D+VET+TFG   P LA+Y IA+R  EL  +   +AR+VA   G       RFV GS+GP
Sbjct: 65   VDVVETDTFGALAPVLAEYGIAERAYELNLRAAQLARDVAS--GYATPDHPRFVAGSMGP 122

Query: 138  GTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELD 197
            GTKLPSLG  P+ DLR  Y+  A G+I GG D  L+ET  DLL  KAAV G + AM  L 
Sbjct: 123  GTKLPSLGQIPFEDLRDAYEVQAEGLIAGGVDLLLVETVYDLLSAKAAVIGARRAMRRLG 182

Query: 198  TFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHA 257
              +P+   VT+ETTG ML G+E+GAAL AL+ L    IG+NCATGP+EM EHLRYLS+H 
Sbjct: 183  RSVPVQVQVTIETTGRMLPGTEVGAALAALERLDPVAIGINCATGPEEMGEHLRYLSEHQ 242

Query: 258  DIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVR 317
             +P+S +PNAG+P +      Y L  + LA A   FV E G+ +VGGCCGT PEH+RAV 
Sbjct: 243  RVPISCLPNAGMPHVVDGHMHYDLTPDALAAAHRRFVDELGVGIVGGCCGTRPEHLRAVV 302

Query: 318  DAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSN 377
            +AV                G      R       VASLY +V L Q+  I+ +GERTN+N
Sbjct: 303  EAV----------------GEAVPRERHPTPRAQVASLYQAVELRQDLAITAVGERTNAN 346

Query: 378  GSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTL 437
            GS+ FR+AML+ DW+ CV +A+ Q RDGAHM+DLCVDY G DGT  M  L++ LAT+STL
Sbjct: 347  GSRRFRDAMLARDWDTCVRMAQDQVRDGAHMIDLCVDYTGEDGTVAMEELSSRLATASTL 406

Query: 438  PIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTID 497
            PIMIDSTE  V+ T L HLGGR I+NSVN E+G+G  +R+   ++L K +GAAVVA  ID
Sbjct: 407  PIMIDSTEAAVVETALRHLGGRPIINSVNLEEGEGSNTRFDSFLRLAKDYGAAVVATCID 466

Query: 498  EEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAI 557
            EEGQARTA  KV IAKR++      YGL   DI++D L  P++TG EE+RRD +ETIEA+
Sbjct: 467  EEGQARTAARKVEIAKRIVALAVERYGLATDDIIIDPLVLPVTTGMEESRRDALETIEAL 526

Query: 558  RELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRI 617
            R +    P + T +GLSN+SFG+N AAR+ LNSVFL EC  AGL  AI H S+I P+ RI
Sbjct: 527  RRITAEMPGVSTLVGLSNVSFGINAAAREALNSVFLAECQAAGLSMAILHPSRIQPLARI 586

Query: 618  DDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRII 677
             +  R + LD++YDRR +  DPL   ++ F  V A        E+L A+ + ERL +RI+
Sbjct: 587  PEDVRAICLDLIYDRRGQG-DPLARLIERFADVQAV---AVTGEELEALSVPERLHRRIV 642

Query: 678  DGDKNGLEDDLEAGMKE-KSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTA 736
            D ++ GLEDDL A + E  S + +IN+ LL  M  VG+LFGSGQMQLPFVL SAETMK A
Sbjct: 643  DANRQGLEDDLAAALGEGMSALGVINDVLLPAMAEVGDLFGSGQMQLPFVLASAETMKQA 702

Query: 737  VAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIK 796
            VA+LEP+++        A    +G +V+ATV+GDVHDIGKNLVDIIL+NNGY VVNLGIK
Sbjct: 703  VAWLEPYLDR-------ASVNDRGTVVLATVQGDVHDIGKNLVDIILTNNGYRVVNLGIK 755

Query: 797  QPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYV 856
              LS ML AAEEH AD IGMSGLLVKST+VM++NL EMN  G ++ PVILGGAALTRT+V
Sbjct: 756  VALSEMLAAAEEHHADAIGMSGLLVKSTLVMRDNLVEMNERGMAHLPVILGGAALTRTFV 815

Query: 857  ENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNER 916
            E DL +VY G V+Y +DAFEGL +++ +   +RGE  DP    +I Q+  +  R  R   
Sbjct: 816  ERDLRQVYDGRVFYGKDAFEGLDVLERLGRIRRGELDDPEFGRSIRQSSTRTPRLLRRST 875

Query: 917  SRKIAAERKANAAPVIVPERS-DVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALFM 975
            S +               ERS  V+ D P   PPF GTR+VKG+ L +    ++E ALF 
Sbjct: 876  SER--------------TERSPTVAMDNPIFRPPFLGTRVVKGIALDDIAAYVNETALFR 921

Query: 976  GQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDR-LKSEGILDHVALVYGYFPAVAEGDD 1034
             QWG +     EG   +   +   R  LR  LDR L  + ++  V  VYGYF A +EG+D
Sbjct: 922  HQWGYRP----EGDEDDAAFKQRLRAELRRQLDRALVDQSLVPQV--VYGYFVAASEGND 975

Query: 1035 VVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGNPI 1094
            +V+  + +    E  RF FPRQ++  +LCIADF RP    +   ++D + F +VTMG  I
Sbjct: 976  LVVF-ADEAREHELARFRFPRQEQEPYLCIADFFRP----LAGPEIDYVAFHVVTMGPRI 1030

Query: 1095 ADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTK 1154
             + A   F  N Y+EYL +HG+GV+LTEALAEYWH+R+R+E          D D      
Sbjct: 1031 TEVAKRAFDENRYQEYLLLHGLGVELTEALAEYWHARIRAE------WGFGDEDGPTLAG 1084

Query: 1155 FFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHP 1214
             F   YRG+R+S+GY +CPDLED   +V+LL+ GRIGV +S+  QL PEQ+T A +++HP
Sbjct: 1085 LFRQQYRGSRYSWGYPACPDLEDNRTVVDLLDAGRIGVSVSDTFQLEPEQTTTAIIVHHP 1144

Query: 1215 EAKYF 1219
            +AKYF
Sbjct: 1145 QAKYF 1149


Lambda     K      H
   0.316    0.135    0.386 

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: 3345
Number of extensions: 168
Number of successful extensions: 12
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: 1221
Length of database: 1151
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1104
Effective search space:  1296096
Effective search space used:  1296096
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_015798162.1 AFER_RS03720 (methionine synthase)
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.1409.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 1287.2   0.0          0 1287.0   0.0    1.0  1  lcl|NCBI__GCF_000023265.1:WP_015798162.1  AFER_RS03720 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015798162.1  AFER_RS03720 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1287.0   0.0         0         0       2    1181 ..       9    1150 ..       8    1151 .] 0.95

  Alignments for each domain:
  == domain 1  score: 1287.0 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68  
                                                ++r++v+DGamGt+lq a L ++dF g        l+G+n++L+ t+Pe++aa+h +++  G D+ve
  lcl|NCBI__GCF_000023265.1:WP_015798162.1    9 RERVVVFDGAMGTNLQLAGLGADDFGGP------ALEGCNEILVVTRPEAVAAVHDSFLAVGVDVVE 69  
                                                79*************************5......9******************************** PP

                                 TIGR02082   69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135 
                                                t+tF++   +la+Y+++++ayeln +aa+lar va  +  tp+++RfvaGs+GP++kl++l+     
  lcl|NCBI__GCF_000023265.1:WP_015798162.1   70 TDTFGALAPVLAEYGIAERAYELNLRAAQLARDVASGYA-TPDHPRFVAGSMGPGTKLPSLG----- 130 
                                                ***************************************.**********************..... PP

                                 TIGR02082  136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202 
                                                    ++ +++l+daY++q++gl+ GGvDllL+etv+D+l akaa++++++++ + gr++P+ ++ v+
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  131 ----QIPFEDLRDAYEVQAEGLIAGGVDLLLVETVYDLLSAKAAVIGARRAMRRLGRSVPVQVQ-VT 192 
                                                ....9***********************************************************.** PP

                                 TIGR02082  203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269 
                                                ++++Gr+L G++++a+la+le+ + +++G+nCa+G++e+ e++++lse++++++s+ PnaG+P+ + 
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  193 IETTGRMLPGTEVGAALAALERLDPVAIGINCATGPEEMGEHLRYLSEHQRVPISCLPNAGMPHVVD 259 
                                                ****************************************************************998 PP

                                 TIGR02082  270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333 
                                                   +Ydltp+ la+a + f+ e+++ ivGGCCGt+Peh+ra+ eav +  pr+r+ ++ + v+s+++
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  260 ghmHYDLTPDALAAAHRRFVDELGVGIVGGCCGTRPEHLRAVVEAVGEAVPRERHPTPRAQVASLYQ 326 
                                                899**************************************************************** PP

                                 TIGR02082  334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400 
                                                a+++ q+  +  +GeRtn++Gs++fr+++ a d++ ++ +a++qv++Ga+++D++vD+++ Dg+ +m
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  327 AVELRQDLAITAVGERTNANGSRRFRDAMLARDWDTCVRMAQDQVRDGAHMIDLCVDYTGEDGTVAM 393 
                                                ******************************************************************* PP

                                 TIGR02082  401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdG...eerFlekaklikeyG 464 
                                                ++l s+la+    +++P+m+Ds+e +v+e+ L++++G+ i+ns++l++G   + rF   ++l+k+yG
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  394 EELSSRLATA---STLPIMIDSTEAAVVETALRHLGGRPIINSVNLEEGegsNTRFDSFLRLAKDYG 457 
                                                *********9...8***********************************666689************ PP

                                 TIGR02082  465 aavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfie 531 
                                                aavv+  +DeeGqarta++k+eiakR++ l++e++g+  +dii+Dp++l+++tG+ee++r+a+++ie
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  458 AAVVATCIDEEGQARTAARKVEIAKRIVALAVERYGLATDDIIIDPLVLPVTTGMEESRRDALETIE 524 
                                                ******************************************************************* PP

                                 TIGR02082  532 aireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidke 598 
                                                a+r+i  e+P + ++ G+snvsF+++   a+Real+svFL e++ aGl m+i ++++++++++i+++
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  525 ALRRITAEMPGVSTLVGLSNVSFGIN--AAAREALNSVFLAECQAAGLSMAILHPSRIQPLARIPED 589 
                                                **************************..9************************************** PP

                                 TIGR02082  599 lrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieed 665 
                                                 r +++dli+drr +  ++L +l+e++ ++++        +e+  l+v eRL+r++v+ +r+g+e+d
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  590 VRAICLDLIYDRRGQ-GDPLARLIERFADVQAV---AVTGEELEALSVPERLHRRIVDANRQGLEDD 652 
                                                ***********9876.69************999...567899************************* PP

                                 TIGR02082  666 leearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedks 732 
                                                l +a+ +  ++l +i+  Ll  m  vGdLFGsG+m+LP+v+ sa++mk+ava+LePyl++     + 
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  653 LAAALGEGMSALGVINDVLLPAMAEVGDLFGSGQMQLPFVLASAETMKQAVAWLEPYLDRAS--VND 717 
                                                **********************************************************9987..678 PP

                                 TIGR02082  733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799 
                                                +G++vlatv+GDvhDiGkn+vd++L++ngy+vv+lG+kv   ++l aa++++aD ig+sGL+vks+ 
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  718 RGTVVLATVQGDVHDIGKNLVDIILTNNGYRVVNLGIKVALSEMLAAAEEHHADAIGMSGLLVKSTL 784 
                                                9****************************************************************** PP

                                 TIGR02082  800 emvevaeemerrgvk.iPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkae 865 
                                                +m  ++ em++rg++ +P++lGGaal++++v+ ++ + Y+g+v y+kda+e++ v+++l   ++   
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  785 VMRDNLVEMNERGMAhLPVILGGAALTRTFVERDLRQVYDGRVFYGKDAFEGLDVLERLGRIRRG-- 849 
                                                **************98******************************************9877753.. PP

                                 TIGR02082  866 elekikeeyeeirekfgekkekl..ialsekaarkevfaldrsedlevpapkflGtkvleas.ieel 929 
                                                el+   e   +ir++ ++   +l  ++ se++ r++++a+    d  +  p+flGt+v++ + ++++
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  850 ELD-DPEFGRSIRQSSTR-TPRLlrRSTSERTERSPTVAM----DNPIFRPPFLGTRVVKGIaLDDI 910 
                                                222.22333445544433.333300233333333333333....566999***************** PP

                                 TIGR02082  930 lkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsv 995 
                                                  y++++alF  qW+ r   p  + de   + +++l+++++  ld+   +++l +++v+G+f a s+
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  911 AAYVNETALFRhQWGYR---P--EGDEDDAAFKQRLRAELRRQLDRALVDQSLVPQVVYGYFVAASE 972 
                                                **********99**876...4..5567788899********************************** PP

                                 TIGR02082  996 gddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaee 1062
                                                g+d+++++de++    +++a     ++++rq+++ ylc+aDf+++ +  + Dy+++ +vt+g  ++e
  lcl|NCBI__GCF_000023265.1:WP_015798162.1  973 GNDLVVFADEAR---EHELAR----FRFPRQEQEPYLCIADFFRPLAGPEIDYVAFHVVTMGPRITE 1032
                                                *********999...555555....57******************9999****************** PP

                                 TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129
                                                 ak+ ++++ +++++l+++l++ l+ealae++h r+R e+ ++ +e+    + l++++YrG+r++ G
  lcl|NCBI__GCF_000023265.1:WP_015798162.1 1033 VAKRAFDENRYQEYLLLHGLGVELTEALAEYWHARIRAEWGFG-DEDGPTLAGLFRQQYRGSRYSWG 1098
                                                **************************************97776.999999***************** PP

                                 TIGR02082 1130 YpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfa 1181
                                                YpacPd+++++t+++Ll+a riG+ +++ ++l+Pe+++++++++hp+akYf 
  lcl|NCBI__GCF_000023265.1:WP_015798162.1 1099 YPACPDLEDNRTVVDLLDAGRIGVSVSDTFQLEPEQTTTAIIVHHPQAKYFV 1150
                                                ***************************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1151 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: 00:00:00.14
# Mc/sec: 9.16
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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