Alignments for a candidate for metH in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Magnetospirillum magneticum AMB-1

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_043743213.1 AMB_RS02225 methionine synthase

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



>NCBI__GCF_000009985.1:WP_043743213.1
          Length = 1157

 Score =  989 bits (2556), Expect = 0.0
 Identities = 573/1213 (47%), Positives = 757/1213 (62%), Gaps = 64/1213 (5%)

Query: 16   SEFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFE 75
            +  LD L+ HVL+ DG  G  +Q  +L VEKDF  LE C EIL  +RPDV+R IH  YFE
Sbjct: 2    TNILDHLSRHVLLCDGGTGALVQAMNLSVEKDFQGLENCTEILVKSRPDVIRGIHARYFE 61

Query: 76   AGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEM-GPGRNGMRRFVVGS 134
            AGAD+VE +TFG +   LA++ IA+R  EL      +A E A++  G GR    RFV+G+
Sbjct: 62   AGADMVEADTFGASPITLAEFGIAERAHELNQAAIELAWEAAEQFKGDGRT---RFVLGA 118

Query: 135  LGPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMA 194
            +GPGTKLPSLGH  Y +L   Y   A G I GG  AFL+ET QD LQ+KAAV+G + A A
Sbjct: 119  IGPGTKLPSLGHIGYDELEAAYVIQAAGQIAGGVSAFLVETCQDPLQIKAAVNGCKIANA 178

Query: 195  ELDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLS 254
               T +P+   VTVETTGT+L+G++I AA T +Q LG+ ++GLNCA GP EM EH ++L 
Sbjct: 179  AAGTDVPVFVQVTVETTGTLLVGADIAAAATVVQSLGVPLMGLNCAAGPQEMGEHFKWLI 238

Query: 255  KHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIR 314
             +    VS+ PNAGLP L      YPL   +LA     FVS  G +++GGCCGTTP HI 
Sbjct: 239  DNWTGFVSIQPNAGLPELVDGQTRYPLLPAELAVWHERFVSA-GANLLGGCCGTTPPHIS 297

Query: 315  AVRDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERT 374
            A  + +  +         K          R V    SVASLYT VPL QE     IGER 
Sbjct: 298  ATNEMLKRIGNGYRPNPVK----------RSVHWVPSVASLYTQVPLRQENAFLSIGERC 347

Query: 375  NSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATS 434
            N+NGSK FR+   + DW+    IA++Q ++G+H LD+C  +VGR+  ADM  + + L  +
Sbjct: 348  NANGSKKFRDLQDAEDWDGITAIAREQVKEGSHTLDVCTAFVGRNEVADMTEVVSRLRGA 407

Query: 435  STLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVAL 494
             T P++IDSTE  V+  GL+  GG++I+NS+NFE+G+  +    R++ L ++ GAAVVAL
Sbjct: 408  VTTPLVIDSTELPVLEAGLKLYGGKAILNSINFENGE--KDAADRLV-LARKFGAAVVAL 464

Query: 495  TIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETI 554
            TIDE+G A+ A  K+RIAKRL D     +GL   D++ D LTF I TG E+ R+  +ET+
Sbjct: 465  TIDEDGMAKDAAAKLRIAKRLYDFAVTKHGLPASDLLFDPLTFTICTGNEDDRKLAVETL 524

Query: 555  EAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPM 614
            +AI  + +  PE    LGLSN+SFGL PAARQVLNSVF++  I+ G+  AI H SKI+P+
Sbjct: 525  DAIEMITREMPECGIVLGLSNVSFGLKPAARQVLNSVFIDHAIKRGMTGAIVHVSKIVPL 584

Query: 615  NRIDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQ 674
            + + + + + A D++YDR   D   L  ++ LF    AA+ K  R  +       +RL Q
Sbjct: 585  HTLPEEEVKAAEDLIYDR---DPQALSRYIALFGDRKAAEIKKERPAKAE-----DRLKQ 636

Query: 675  RIIDGDKNGLEDDLEAGMKEK-SPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETM 733
            RIIDGD+ GLEDDL   M+E   P+ IIN  LL+GMK VGELFGSG+MQLPFVLQSAETM
Sbjct: 637  RIIDGDRTGLEDDLAQVMEEGWKPLDIINTLLLDGMKVVGELFGSGKMQLPFVLQSAETM 696

Query: 734  KTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNL 793
            K +VA+LEP ME+       A  + K  +V+ATVKGDVHDIGKNLVDIIL+NNGY V+N+
Sbjct: 697  KASVAFLEPHMEK-------ADGQQKATMVLATVKGDVHDIGKNLVDIILTNNGYKVINI 749

Query: 794  GIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTR 853
            GIKQP++ +++AA+EHKAD +GMSGLLVKSTV+M+ENLEEM NAG  + PV+LGGAALTR
Sbjct: 750  GIKQPVAEIIKAAKEHKADAVGMSGLLVKSTVIMRENLEEMTNAGL-DVPVLLGGAALTR 808

Query: 854  TYVENDLNEVY-TGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKA 912
             YVE D ++ Y +G V YARDAF+GL LM +V           +       A K A    
Sbjct: 809  KYVEEDCSKAYGSGRVAYARDAFDGLDLMAKV----------ADGSFDAHVAAKAASPHR 858

Query: 913  RNERSRKIAAERKANAAPV----IVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNL 968
                SR +    +    PV    I   R+++  D P   PPFWG R+++  PL   +  L
Sbjct: 859  PGSPSRTLGEAAQPATRPVDWDEINLRRAELHKDVPAPVPPFWGARVIESAPLQNLIPFL 918

Query: 969  DERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPA 1028
            +E  L+   WG +  +G     ++     E RP     L R   E IL   A VYGY+ A
Sbjct: 919  NETMLYQFHWGYRK-QGKSIEEFKAWAHKEIRPVAMDMLKRCAKEEILRPQA-VYGYWKA 976

Query: 1029 VAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLV 1088
             ++ D VV+    +    E  RF FPRQ +   LCIADF RP    V D   DV+  Q+V
Sbjct: 977  ASDNDSVVLF--AEDGTTEVARFPFPRQAKDGGLCIADFFRP----VSDPVRDVIGLQVV 1030

Query: 1089 TMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFD 1148
            TMG    + A + F A++Y++YL +HG+ V++ EA+AEY H R+RSEL     G  A+ D
Sbjct: 1031 TMGKRATEVAQDWFKADKYQDYLYLHGLSVEMAEAMAEYVHKRIRSEL-----GFAAE-D 1084

Query: 1149 PEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDA 1208
              D  +    +YRG+RFSFGY +CP +ED+ +L+ LL   RIGV LSEE QL PEQST A
Sbjct: 1085 AADMDRLLKQNYRGSRFSFGYPACPRIEDQTQLLSLLGAERIGVTLSEEFQLEPEQSTSA 1144

Query: 1209 FVLYHPEAKYFNV 1221
             V  HP+AKYF+V
Sbjct: 1145 IVTVHPQAKYFSV 1157


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: 3167
Number of extensions: 142
Number of successful extensions: 13
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: 1157
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1110
Effective search space:  1303140
Effective search space used:  1303140
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: 59 (27.3 bits)

Align candidate WP_043743213.1 AMB_RS02225 (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.28883.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 1227.4   0.0          0 1227.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1227.3   0.0         0         0       2    1182 .]       9    1157 .]       8    1157 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1227.3 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLt.eadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                ++++l+ DG+ G  +q++nL  e+dF+g        l+ + ++L++++P+vi+ ih +yfeaGaD+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1    9 SRHVLLCDGGTGALVQAMNLSvEKDFQG--------LENCTEILVKSRPDVIRGIHARYFEAGADMV 67  
                                                789*****************8478****........8****************************** PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                e +tF++++i+la+++++++a+eln++a +la e+a++f+    + Rfv+G++GP++kl++l+    
  lcl|NCBI__GCF_000009985.1:WP_043743213.1   68 EADTFGASPITLAEFGIAERAHELNQAAIELAWEAAEQFK-GDGRTRFVLGAIGPGTKLPSLG---- 129 
                                                ****************************************.77889*****************.... PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                     ++ ydel +aY+ q+ g + GGv ++L+et++D l++kaa+++ + + +++g+++P++++ v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  130 -----HIGYDELEAAYVIQAAGQIAGGVSAFLVETCQDPLQIKAAVNGCKIANAAAGTDVPVFVQ-V 190 
                                                .....************************************************************.* PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                +v+++G++L+G +++a+++ ++  ++ ++GLnCa G++e+ e+ k l  + + +vs+ PnaGLP+ +
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  191 TVETTGTLLVGADIAAAATVVQSLGVPLMGLNCAAGPQEMGEHFKWLIDNWTGFVSIQPNAGLPELV 257 
                                                ******************************************************************9 PP

                                 TIGR02082  269 g...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdi......kprkrqeleek 326 
                                                     Y+l+p ela   + f+++g  n++GGCCGttP hi a  e+ k i      +p kr  +  +
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  258 DgqtRYPLLPAELAVWHERFVSAG-ANLLGGCCGTTPPHISATNEMLKRIgngyrpNPVKRSVHWVP 323 
                                                77889***************9876.6********************999844443335566669999 PP

                                 TIGR02082  327 svlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevl 393 
                                                sv+s+++++++ qe+ f+ iGeR+n++Gskkfr+l  aed++    ia++qv+eG++ lD++   v+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  324 SVASLYTQVPLRQENAFLSIGERCNANGSKKFRDLQDAEDWDGITAIAREQVKEGSHTLDVCTAFVG 390 
                                                ******************************************************************* PP

                                 TIGR02082  394 lDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekakli 460 
                                                ++ +adm++++s+l +   + + Pl++Ds+e  vleaGLk  +Gkai+nsi++++Ge++ ++++ l+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  391 RNEVADMTEVVSRLRGA--V-TTPLVIDSTELPVLEAGLKLYGGKAILNSINFENGEKDAADRLVLA 454 
                                                ****************9..6.99******************************************** PP

                                 TIGR02082  461 keyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryai 527 
                                                +++Gaavv++++De+G+a++a+ k++iakR+y+ ++ k g+p++d++fDp+++ti tG e++++ a+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  455 RKFGAAVVALTIDEDGMAKDAAAKLRIAKRLYDFAVTKHGLPASDLLFDPLTFTICTGNEDDRKLAV 521 
                                                ******************************************************************* PP

                                 TIGR02082  528 dfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavydd 594 
                                                ++++ai+ i +e+P++ i +G+snvsF+l+  +a+R++l+svF+ +aik G+  +iv+ +k+ +++ 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  522 ETLDAIEMITREMPECGIVLGLSNVSFGLK--PAARQVLNSVFIDHAIKRGMTGAIVHVSKIVPLHT 586 
                                                ******************************..*********************************** PP

                                 TIGR02082  595 idkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGereg 661 
                                                +++e  +++edli+dr+++a   L +++ l+ + k+++      ++ r  + e+RL++++++G r g
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  587 LPEEEVKAAEDLIYDRDPQA---LSRYIALFGDRKAAEI-----KKERPAKAEDRLKQRIIDGDRTG 645 
                                                ****************9986...7889999999888843.....466788899************** PP

                                 TIGR02082  662 ieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 
                                                +e+dl + +++  +pl+ii++ LldGmkvvG+LFGsGkm+LP+v++sa++mk++va+LeP++ek + 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  646 LEDDLAQVMEEGWKPLDIINTLLLDGMKVVGELFGSGKMQLPFVLQSAETMKASVAFLEPHMEKAD- 711 
                                                **************************************************************9988. PP

                                 TIGR02082  729 edkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLiv 795 
                                                  ++k ++vlatvkGDvhDiGkn+vd++L++ngy+v+++G+k+Pv++i++aak++kaD +g+sGL+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  712 -GQQKATMVLATVKGDVHDIGKNLVDIILTNNGYKVINIGIKQPVAEIIKAAKEHKADAVGMSGLLV 777 
                                                .78899************************************************************* PP

                                 TIGR02082  796 ksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsek 861 
                                                ks++ m e++eem++ g+++P+llGGaal++++v+ ++ ++Y +g+v y++da++++ +++k+ +  
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  778 KSTVIMRENLEEMTNAGLDVPVLLGGAALTRKYVEEDCSKAYgSGRVAYARDAFDGLDLMAKVADGS 844 
                                                ******************************************7799****************99888 PP

                                 TIGR02082  862 kkaeelekikeeye...eirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas 925 
                                                  a+ ++k  + +      r+  +  +  ++ +     + +    ++++d+  p+p+f+G +v+e+ 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  845 FDAHVAAKAASPHRpgsPSRTLGEAAQPATRPVD--WDEINLRRAELHKDVPAPVPPFWGARVIESA 909 
                                                6544444333322200022222222222233332..2333344455555999**************9 PP

                                 TIGR02082  926 .ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlf 990 
                                                 +++l++++++++l+  +W+ r++ +  + +e +    +++++ a ++l++  +e+ lr+++v+G++
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  910 pLQNLIPFLNETMLYQfHWGYRKQGK--SIEEFKAWAHKEIRPVAMDMLKRCAKEEILRPQAVYGYW 974 
                                                9**************99*****9987..66788899999**************************** PP

                                 TIGR02082  991 PaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtag 1057
                                                 a s +d +++++++++        t  +++ ++rq +d  lc+aDf+++ +   +D++g+++vt+g
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  975 KAASDNDSVVLFAEDGT--------TEVARFPFPRQAKDGGLCIADFFRPVSDPVRDVIGLQVVTMG 1033
                                                *************8887........4455789*********************************** PP

                                 TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGi 1124
                                                + a+e a+++++ ++++d++++++l++ +aea+ae++h+r+R el +  +e++ d++ llk++YrG+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1034 KRATEVAQDWFKADKYQDYLYLHGLSVEMAEAMAEYVHKRIRSELGFA-AEDAADMDRLLKQNYRGS 1099
                                                *********************************************998.88999************* PP

                                 TIGR02082 1125 rpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                r++fGYpacP  +++++ll+Ll aeriG++l+e+++l+Pe+s+s+++  hp+akYf+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1100 RFSFGYPACPRIEDQTQLLSLLGAERIGVTLSEEFQLEPEQSTSAIVTVHPQAKYFSV 1157
                                                ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1157 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: 0.11u 0.03s 00:00:00.14 Elapsed: 00:00:00.15
# Mc/sec: 9.07
//
[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