Alignments for a candidate for metH in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Sulfurimonas denitrificans DSM 1251

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_011373645.1 SUDEN_RS10540 methionine synthase

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



>NCBI__GCF_000012965.1:WP_011373645.1
          Length = 1163

 Score =  847 bits (2187), Expect = 0.0
 Identities = 498/1227 (40%), Positives = 719/1227 (58%), Gaps = 95/1227 (7%)

Query: 19   LDALANHVLIGDGAMGTQLQGFDLDVEKDFLD-LEGCNEILNDTRPDVLRQIHRAYFEAG 77
            L  + N  LI DGAMGTQLQ  D  + K+  +  EGCNE+LN T P++L +I  AY  +G
Sbjct: 8    LKTIKNRPLIIDGAMGTQLQQRDDKISKEAWEGNEGCNELLNVTAPEILSEIFHAYLTSG 67

Query: 78   ADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGP 137
            AD V TNTFG     L +Y I  R  EL Y G  +A++   +     +   RF +GS+GP
Sbjct: 68   ADFVTTNTFGSFSWVLDEYQIGHRAYELTYAGAKLAKDECKKFSTPTHP--RFCLGSIGP 125

Query: 138  GTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELD 197
            GTKLPSLGH  Y ++   Y E  L +IDGG D FL+ETAQD LQ+KAA+H   +A  +  
Sbjct: 126  GTKLPSLGHITYDEMYKGYTEFCLALIDGGVDVFLLETAQDPLQIKAALHACNEASKQRG 185

Query: 198  TFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHA 257
              +PI+  VT+E +GTML+G++     T L+P  I  +G NC TGP+++ +H++ LS+  
Sbjct: 186  VEIPIMVSVTIELSGTMLIGTDAQTIATILEPFDILSLGFNCGTGPEQVLKHVKTLSEIW 245

Query: 258  DIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVR 317
              P+SV  NAGLP        YP+  ++ A     F+   G+S +GGCCGTTP+HIRA+ 
Sbjct: 246  HKPISVHANAGLPQNRGGYTYYPMGPDEFAAKQQSFLEFDGVSFLGGCCGTTPQHIRALV 305

Query: 318  DAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSN 377
            + V       +    K P+G         + E+S+ASL+++VPL QE+   +IGER+N+ 
Sbjct: 306  NLV-------SDIAPKAPSG---------KHENSLASLFSTVPLMQESSALLIGERSNAT 349

Query: 378  GSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTL 437
            GSKAFRE +L+ D+E  + +A+QQ R GAH+LD+ V + GRD T DM  + +L A    L
Sbjct: 350  GSKAFRELLLAEDYEGTLSVAQQQVRAGAHVLDVSVGFAGRDETKDMNRVMSLYAQKIAL 409

Query: 438  PIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTID 497
            P+M DST+   +   L+ +G + I+NSVN EDG     ++  +  L K+ GAA+V LTID
Sbjct: 410  PLMPDSTQTAALEEALKLIGAKPIINSVNLEDG---IEKFDAVCSLAKKFGAALVCLTID 466

Query: 498  EEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAI 557
            E G A++ E K+ +A+R+ D     +G+  +++V D LTF + +G EE    GI TIEAI
Sbjct: 467  EIGMAKSVERKLEVAERIYDLAVNKHGIRAENLVFDLLTFTLGSGDEEYLDAGINTIEAI 526

Query: 558  RELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRI 617
            REL++ +PE+  TLGLSNISFGL+  AR  LNS+FL+ C EAGL S I + + I+P+N+I
Sbjct: 527  RELRRRHPEVGATLGLSNISFGLDKDARPYLNSMFLHHCNEAGLTSVIINVAHIIPINKI 586

Query: 618  DDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRII 677
                +E+  +++++R+  +   L EF+  F    A D  +A  E   AM   E++A+ ++
Sbjct: 587  SKEDQEICDNLIFNRK-PNAAALFEFIDHFSTKEAVD-NNAVDEAYLAMSDEEKIAKLLM 644

Query: 678  DGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAV 737
            DGDK+ +   +E    + +P  I+NE L++ MK VGELFGSGQMQLPFVLQSAETMK  V
Sbjct: 645  DGDKDRMIPLVEEARHKVAPEKIVNEILIDAMKVVGELFGSGQMQLPFVLQSAETMKKTV 704

Query: 738  AYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQ 797
             YL P++ +  ++  +  A G       TVKGDVHD+GKNLVDIILSNNG+ V NLGIK 
Sbjct: 705  DYLNPYLPKIDKSVDTTLALG-------TVKGDVHDVGKNLVDIILSNNGFKVKNLGIKV 757

Query: 798  PLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYVE 857
             +   +++ +E  A  +GMSGLLVKST VMKENLE +   G    PV+LGGAALTR++++
Sbjct: 758  DIGEFIQSIKESNATALGMSGLLVKSTQVMKENLETLQKEGI-KIPVLLGGAALTRSFID 816

Query: 858  NDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNERS 917
            +    +Y G ++Y +DAF+G+  M  + A      L P               K   E+ 
Sbjct: 817  DFCRPLYDGPIFYCKDAFDGVTAMSRIEAGNFDTNLHP---------------KDSQEKI 861

Query: 918  RKIAAERKANAAPVIVPERSDV---STDTPTAAPPFWGTRIVKGLP--LAEFLGNLDERA 972
             KI  E       VI+P  S++   S D     PPFWG R +K  P  +      ++ + 
Sbjct: 862  VKIKEE-------VIIPPFSELKMPSRDVTVPTPPFWGRRELKLTPQQIEMAFDWINHKL 914

Query: 973  LFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEG 1032
            LF  +WG  S++G    +YE  +     P       R   E + +   ++YGY+P  ++ 
Sbjct: 915  LFKSRWGY-SSKGLSEEAYEKQLNDIVWPAYEKLKKRFIEEKLFE-PTIIYGYWPCRSDD 972

Query: 1033 DDVVIL-ESPDPHAAERM--------------RFSFPRQQRGRFLCIADFIRPREQAVKD 1077
            D ++I  ES   ++ E +              +F+FPRQ R     ++DF          
Sbjct: 973  DSLLIFDESRGYNSQEEINREDLDKVRNQAIEKFTFPRQSRQPHRALSDFFH-------S 1025

Query: 1078 GQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELK 1137
             + DV+ F  V+ G+ ++D    ++   EY EY + HG+GV+L EALAE  H ++R +L 
Sbjct: 1026 DRDDVVAFTCVSAGSKLSDVERGIYDRGEYTEYYQFHGLGVELAEALAEIVHKQIRLDLN 1085

Query: 1138 LNDGGSVADFDPEDKTKFFDLD---YRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVEL 1194
            ++DG         + +K  D+    Y+G+R+SFGY +CPDLE    L  LL+P   G+EL
Sbjct: 1086 ISDG---------EGSKLSDVQMNRYQGSRYSFGYAACPDLELNRPLFNLLKPEEFGIEL 1136

Query: 1195 SEELQLHPEQSTDAFVLYHPEAKYFNV 1221
            SE  Q+HPEQST A V+YHP A Y+NV
Sbjct: 1137 SETFQIHPEQSTSALVVYHPNATYYNV 1163


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: 3068
Number of extensions: 140
Number of successful extensions: 14
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: 1163
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1116
Effective search space:  1310184
Effective search space used:  1310184
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_011373645.1 SUDEN_RS10540 (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.23505.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 1111.2   0.0          0 1110.9   0.0    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011373645.1  SUDEN_RS10540 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011373645.1  SUDEN_RS10540 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1110.9   0.0         0         0       2    1182 .]      12    1163 .]      11    1163 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1110.9 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68  
                                                ++r l++DGamGtqlq+ + +  +  +e        +G+n+lLn t Pe++++i +ay+ +GaD v 
  lcl|NCBI__GCF_000012965.1:WP_011373645.1   12 KNRPLIIDGAMGTQLQQRDDKISKEAWE------GNEGCNELLNVTAPEILSEIFHAYLTSGADFVT 72  
                                                57889***********986554444443......57******************************* PP

                                 TIGR02082   69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135 
                                                tntF+s + +l +Y++ ++ayel  ++akla+  +++f+ tp ++Rf +Gs+GP++kl++l+     
  lcl|NCBI__GCF_000012965.1:WP_011373645.1   73 TNTFGSFSWVLDEYQIGHRAYELTYAGAKLAKDECKKFS-TPTHPRFCLGSIGPGTKLPSLG----- 133 
                                                ***************************************.**********************..... PP

                                 TIGR02082  136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202 
                                                    ++tyde+ + Y+e   +l+dGGvD++L+et +D l++kaal a +e+ +++g+e+Pi++s v+
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  134 ----HITYDEMYKGYTEFCLALIDGGVDVFLLETAQDPLQIKAALHACNEASKQRGVEIPIMVS-VT 195 
                                                ....************************************************************.** PP

                                 TIGR02082  203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269 
                                                ++ sG++L+G++ ++++++le+ +il+lG nC +G++++ ++vk+lse+ + ++sv+ naGLP++ g
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  196 IELSGTMLIGTDAQTIATILEPFDILSLGFNCGTGPEQVLKHVKTLSEIWHKPISVHANAGLPQNRG 262 
                                                *****************************************************************99 PP

                                 TIGR02082  270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333 
                                                    Y+  p+e a++ ++f e  +++ +GGCCGttP+hira+ + v di+p+     +e+s++s+++
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  263 gytYYPMGPDEFAAKQQSFLEFDGVSFLGGCCGTTPQHIRALVNLVSDIAPKAPSGKHENSLASLFS 329 
                                                787889999********************************************************** PP

                                 TIGR02082  334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400 
                                                ++++ qess + iGeR n++Gsk fr+l+ aedye +l++a+qqv+ Ga++lD++v  +++D ++dm
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  330 TVPLMQESSALLIGERSNATGSKAFRELLLAEDYEGTLSVAQQQVRAGAHVLDVSVGFAGRDETKDM 396 
                                                ******************************************************************* PP

                                 TIGR02082  401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467 
                                                ++++sl a++  i  +Plm Ds++++ le  Lk i+ k i+ns++l+dG e+F     l+k++Gaa+
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  397 NRVMSLYAQK--I-ALPLMPDSTQTAALEEALKLIGAKPIINSVNLEDGIEKFDAVCSLAKKFGAAL 460 
                                                *********9..8.8**************************************************** PP

                                 TIGR02082  468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534 
                                                v +++De G+a+  ++k+e+a+R+y+l+++k g+ +e+++fD +++t++ G ee    +i++ieair
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  461 VCLTIDEIGMAKSVERKLEVAERIYDLAVNKHGIRAENLVFDLLTFTLGSGDEEYLDAGINTIEAIR 527 
                                                ******************************************************************* PP

                                 TIGR02082  535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601 
                                                e+++++P++  ++G+sn+sF+l   + +R  l+s+FL+++ +aGl + i+n +++ ++++i ke +e
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  528 ELRRRHPEVGATLGLSNISFGLD--KDARPYLNSMFLHHCNEAGLTSVIINVAHIIPINKISKEDQE 592 
                                                ***********************..99**************************************** PP

                                 TIGR02082  602 vvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedlee 668 
                                                ++ +li++r+++a   L e+++++  +++  +++a  +++  ++ ee++++ l++G ++ +   +ee
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  593 ICDNLIFNRKPNAA-ALFEFIDHFSTKEAV-DNNAVDEAYLAMSDEEKIAKLLMDGDKDRMIPLVEE 657 
                                                **********9986.79******9987777.7778888899999*********************** PP

                                 TIGR02082  669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGk 735 
                                                ar ++ ap +i+++ L+d mkvvG+LFGsG+m+LP+v++sa++mkk v+yL+Pyl k +  ++ + +
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  658 AR-HKVAPEKIVNEILIDAMKVVGELFGSGQMQLPFVLQSAETMKKTVDYLNPYLPKID--KSVDTT 721 
                                                **.78899***********************************************9987..78899* PP

                                 TIGR02082  736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802 
                                                + l tvkGDvhD+Gkn+vd++Ls+ng++v +lG+kv + + ++  k+ +a  +g+sGL+vks+++m+
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  722 LALGTVKGDVHDVGKNLVDIILSNNGFKVKNLGIKVDIGEFIQSIKESNATALGMSGLLVKSTQVMK 788 
                                                ******************************************************************* PP

                                 TIGR02082  803 evaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelek 869 
                                                e++e ++++g+kiP+llGGaal++++++  + + Y+g++ y kda+++v+ ++++   +   + + +
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  789 ENLETLQKEGIKIPVLLGGAALTRSFIDDFCRPLYDGPIFYCKDAFDGVTAMSRIEAGNF--DTNLH 853 
                                                *****************************************************9977663..22222 PP

                                 TIGR02082  870 ikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas...ieellkyi 933 
                                                 k+ +    ek  + ke++i  + ++ +     +  + d++vp+p+f+G+++l+ +   ie  +++i
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  854 PKDSQ----EKIVKIKEEVIIPPFSELK-----MPSR-DVTVPTPPFWGRRELKLTpqqIEMAFDWI 910 
                                                22222....2222223333333333333.....3333.899************977678******** PP

                                 TIGR02082  934 DwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddi 999 
                                                + k lF   W+   k    +++ +e++++  +++  ++l+++ ++ekl +++ ++G++P++s +d +
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  911 NHKLLFKsRWGYSSKG--LSEEAYEKQLNDIVWPAYEKLKKRFIEEKLFEPTIIYGYWPCRSDDDSL 975 
                                                *******99*998765..59999******************************************** PP

                                 TIGR02082 1000 eiytdetvsq.........etkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtag 1057
                                                 i+++                k+ + ++ek+ ++rq ++ + +l+Df+ s      D++++  v+ag
  lcl|NCBI__GCF_000012965.1:WP_011373645.1  976 LIFDESRGYNsqeeinredLDKVRNQAIEKFTFPRQSRQPHRALSDFFHS---DRDDVVAFTCVSAG 1039
                                                **9976533322434333223455677788******************88...789*********** PP

                                 TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGi 1124
                                                 + ++  + + ++ +++++ ++++l++ laealae +h+++R +l  + + e  + +d+  +rY+G+
  lcl|NCBI__GCF_000012965.1:WP_011373645.1 1040 SKLSDVERGIYDRGEYTEYYQFHGLGVELAEALAEIVHKQIRLDLNIS-DGEGSKLSDVQMNRYQGS 1105
                                                *********************************************998.9999************** PP

                                 TIGR02082 1125 rpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                r++fGY acPd++ ++ l++Ll++e+ G++l+e ++++Pe+s+s+l+++hp+a Y++v
  lcl|NCBI__GCF_000012965.1:WP_011373645.1 1106 RYSFGYAACPDLELNRPLFNLLKPEEFGIELSETFQIHPEQSTSALVVYHPNATYYNV 1163
                                                ********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1163 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 8.95
//
[ok]

This GapMind analysis is from Apr 10 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