Alignments for a candidate for metH in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Haloglycomyces albus DSM 45210

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_025274553.1 HALAL_RS0113755 methionine synthase

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



>NCBI__GCF_000527155.1:WP_025274553.1
          Length = 1154

 Score = 1395 bits (3612), Expect = 0.0
 Identities = 715/1191 (60%), Positives = 893/1191 (74%), Gaps = 42/1191 (3%)

Query: 33   MGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAGADLVETNTFGCNLPN 92
            MGT L  FD   E D+   EGC+++L  TRPD++  +H A+ EAG+D +ETN+F  N   
Sbjct: 1    MGTMLHTFD-PTEADYDGYEGCSDMLCLTRPDIVTSVHDAFLEAGSDAIETNSFNANFGG 59

Query: 93   LADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPGTKLPSLGHAPYADL 152
            L +YDI +R  ELAY    +AR+  D          R+V+GS+GPGTKLPSLGHAP+A L
Sbjct: 60   LVEYDIVERAEELAYSAARLARDSCDAFSTEEKP--RYVLGSMGPGTKLPSLGHAPFARL 117

Query: 153  RGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDTFLPIICHVTVETTG 212
            R  Y + A G++ GG DA L+ET+QDLLQ KAAV G   A+A  D  +PII HVTVETTG
Sbjct: 118  RDSYADCARGLLRGGSDALLVETSQDLLQTKAAVIGAHRAIASTDIHVPIIAHVTVETTG 177

Query: 213  TMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHADIPVSVMPNAGLPVL 272
            TML+GSEIGAALT+L  LG+DM+GLNCATGP EM+EHLRYLS+H+ +P+SVMPNAGLP L
Sbjct: 178  TMLVGSEIGAALTSLTALGVDMVGLNCATGPAEMTEHLRYLSRHSRLPLSVMPNAGLPQL 237

Query: 273  GKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRDAVVGVPEQETSTLT 332
              +GA +PL+ ++LA+AL  F ++YG ++VGGCCGTTPEHI+AV + + G          
Sbjct: 238  SSDGAYFPLQPDELAEALDEFTADYGFTLVGGCCGTTPEHIKAVTERLNG---------- 287

Query: 333  KIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSNGSKAFREAMLSGDWE 392
                 PV   SR  + E  V+S Y  VP  Q+  I  +GERTN+NGSKAFREAML  DW+
Sbjct: 288  ---RTPV---SRSPQPEPGVSSSYHHVPFRQDATILNVGERTNANGSKAFREAMLDADWD 341

Query: 393  KCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTLPIMIDSTEPEVIRTG 452
             CVDIA++Q + G+H+LDLCVDYVGRDGT DMA LA   +T+STLPIM+DSTEP VI  G
Sbjct: 342  ACVDIAREQNQGGSHLLDLCVDYVGRDGTVDMAELAGRFSTASTLPIMLDSTEPAVIEAG 401

Query: 453  LEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTIDEEGQARTAEHKVRIA 512
            LE LGGR ++NSVNFEDGDGPESR+QRIM +V +HGAAVVAL IDE+GQAR  + KVR+A
Sbjct: 402  LEQLGGRCVINSVNFEDGDGPESRFQRIMPIVAEHGAAVVALCIDEDGQARDRDWKVRVA 461

Query: 513  KRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAIRELKKLYPEIHTTLG 572
            +RLI ++TG++G++++DI +D LTFP++TGQEETRRDG+ETI AI E+ + YP I+ TLG
Sbjct: 462  ERLISELTGTWGMNVEDIFIDALTFPVTTGQEETRRDGLETIAAITEIARRYPGINFTLG 521

Query: 573  LSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRIDDRQREVALDMVYDR 632
            +SNISFG+NPAARQVLNSVFL+EC+ AGL+SAI HS+KILPM +I D Q+EVALD+VYDR
Sbjct: 522  ISNISFGVNPAARQVLNSVFLHECVSAGLNSAIVHSTKILPMGQIPDEQKEVALDLVYDR 581

Query: 633  RTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRIIDGDKNGLEDDLEAGM 692
            R EDYDPLQ+ ++LF+GV+   +K ARAE L A+PL ERLAQRIIDG+K+GLE DL+A +
Sbjct: 582  RGEDYDPLQQLIELFDGVTTKGSKAARAEALNALPLEERLAQRIIDGNKDGLEQDLDAAL 641

Query: 693  KEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAVAYLEPFMEEEAEATG 752
               S + IIN  LL GMK VG+ FGSGQMQLPFVLQSAETMKTAVA LEP ME++     
Sbjct: 642  SRHSALDIINRHLLEGMKIVGDRFGSGQMQLPFVLQSAETMKTAVAQLEPHMEQD----- 696

Query: 753  SAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQPLSAMLEAAEEHKAD 812
               A+GKG IV+ATV+GDVHDIGKNLVDIILSNNGY VVNLGIKQP+  +++AAE+H AD
Sbjct: 697  --DADGKGTIVLATVRGDVHDIGKNLVDIILSNNGYSVVNLGIKQPIGDIIDAAEQHGAD 754

Query: 813  VIGMSGLLVKSTVVMKENLEEMNNAG-ASNYPVILGGAALTRTYVENDLNEVY-TGEVYY 870
             IGMSGLLVKSTV+M++NL E+   G A  +PV+LGGAALTR+YVE+DL E +  GEV+Y
Sbjct: 755  AIGMSGLLVKSTVIMRDNLAELTARGLAGRWPVLLGGAALTRSYVEDDLRENFDDGEVHY 814

Query: 871  ARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNERSRKIAAERKANAAP 930
            ARDAFEGL LMD +MA +RG   D       EQ  K A R+ R ER++ +  E+  +   
Sbjct: 815  ARDAFEGLELMDRLMAHQRG---DIGEILTEEQKAKIAARRRRRERTKNLKREQLPSLDD 871

Query: 931  VIVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPS 990
              V  RSD S D P   PPFWG RIVKGLP A++   LDERA F+GQWGLK TRG EGP 
Sbjct: 872  TTV--RSDTSLDNPVPRPPFWGNRIVKGLPQADYAAFLDERATFLGQWGLKGTRGTEGPG 929

Query: 991  YEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMR 1050
            YE+LVETEGRPRLRYWL+RL ++ +LD   +VYGY+PA AEG+ VV+L+  +    +  R
Sbjct: 930  YEELVETEGRPRLRYWLERLAADNVLD-PQIVYGYYPAYAEGNSVVVLD--EDRDKQIAR 986

Query: 1051 FSFPRQQRGRFLCIADFIRPREQAVKDG-QVDVMPFQLVTMGNPIADFANELFAANEYRE 1109
            F FPRQ+  + LC++DF  P     KDG  +DV+  QLVT+G+ ++D+ N+LF  +EYR+
Sbjct: 987  FDFPRQRHDKRLCLSDFFHP-----KDGDDLDVIAMQLVTLGSQVSDYTNKLFENDEYRD 1041

Query: 1110 YLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGY 1169
            YLEVHG+ VQLTEALAEYWH+RVR E +   GG+VAD DPE     F  +Y G R+SFGY
Sbjct: 1042 YLEVHGLTVQLTEALAEYWHARVRGEWQYPQGGAVADSDPESIGGMFRTEYAGCRYSFGY 1101

Query: 1170 GSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHPEAKYFN 1220
             +CP+L DRA LV++L   RIGV+LSE  QLHPEQSTDA +L+HPEA YFN
Sbjct: 1102 PACPNLADRAVLVDILGADRIGVQLSEGDQLHPEQSTDAVILHHPEASYFN 1152


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: 3639
Number of extensions: 175
Number of successful extensions: 10
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: 1154
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1107
Effective search space:  1299618
Effective search space used:  1299618
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_025274553.1 HALAL_RS0113755 (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.11192.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 1333.0   0.0          0 1332.8   0.0    1.0  1  lcl|NCBI__GCF_000527155.1:WP_025274553.1  HALAL_RS0113755 methionine synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_025274553.1  HALAL_RS0113755 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1332.8   0.0         0         0      12    1181 ..       1    1152 [.       1    1153 [. 0.97

  Alignments for each domain:
  == domain 1  score: 1332.8 bits;  conditional E-value: 0
                                 TIGR02082   12 mGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnsteia 78  
                                                mGt+l +++ tead+ g        ++G+ d+L lt+P++++++h a++eaG+D++etn Fn++   
  lcl|NCBI__GCF_000527155.1:WP_025274553.1    1 MGTMLHTFDPTEADYDG--------YEGCSDMLCLTRPDIVTSVHDAFLEAGSDAIETNSFNANFGG 59  
                                                9****************........9***************************************** PP

                                 TIGR02082   79 ladYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtyde 145 
                                                l +Yd+ ++a el  +aa+lar  +d f+ t ek+R+v+Gs+GP++kl++l+         +  ++ 
  lcl|NCBI__GCF_000527155.1:WP_025274553.1   60 LVEYDIVERAEELAYSAARLARDSCDAFS-TEEKPRYVLGSMGPGTKLPSLG---------HAPFAR 116 
                                                *****************************.9*********************.........9***** PP

                                 TIGR02082  146 lvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsG 212 
                                                l+d+Y + ++gll GG D+lL+et +D+l+ kaa++++++++++  +++Pi+++ v+v+++G++L+G
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  117 LRDSYADCARGLLRGGSDALLVETSQDLLQTKAAVIGAHRAIASTDIHVPIIAH-VTVETTGTMLVG 182 
                                                ******************************************************.************ PP

                                 TIGR02082  213 qtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdltpe 276 
                                                ++++a+l+sl   +++++GLnCa+G++e+ e++++ls+++++++sv+PnaGLP+  +    ++l+p+
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  183 SEIGAALTSLTALGVDMVGLNCATGPAEMTEHLRYLSRHSRLPLSVMPNAGLPQLSSdgaYFPLQPD 249 
                                                *****************************************************9887665789**** PP

                                 TIGR02082  277 elakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessf 343 
                                                ela+al ef ++++  +vGGCCGttPehi+a++e  ++ +p  r   +e+ v+s ++ +++ q++++
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  250 ELAEALDEFTADYGFTLVGGCCGTTPEHIKAVTERLNGRTPVSRSPQPEPGVSSSYHHVPFRQDATI 316 
                                                ******************************************************************* PP

                                 TIGR02082  344 vniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllase 410 
                                                +n+GeRtn++Gsk fr+++ + d++++++ia++q + G+++lD++vD+v++Dg+ dm +l+ +  + 
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  317 LNVGERTNANGSKAFREAMLDADWDACVDIAREQNQGGSHLLDLCVDYVGRDGTVDMAELAGRFSTA 383 
                                                *****************************************************************99 PP

                                 TIGR02082  411 pdiakvPlmlDssefevleaGLkviqGkaivnsislkdG...eerFlekaklikeyGaavvvmafDe 474 
                                                   +++P+mlDs+e +v+eaGL++++G++++ns++++dG   e+rF + + +++e+Gaavv++ +De
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  384 ---STLPIMLDSTEPAVIEAGLEQLGGRCVINSVNFEDGdgpESRFQRIMPIVAEHGAAVVALCIDE 447 
                                                ...8***********************************999************************* PP

                                 TIGR02082  475 eGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelP 541 
                                                +Gqar++d k+++a+R+++ lt  +g++ edi++D+++++++tG+ee +r+++++i ai ei +++P
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  448 DGQARDRDWKVRVAERLISELTGTWGMNVEDIFIDALTFPVTTGQEETRRDGLETIAAITEIARRYP 514 
                                                ******************************************************************* PP

                                 TIGR02082  542 dakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlil 608 
                                                 ++ ++G+sn+sF+++  +a+R++l+svFL+e++ aGl+++iv+++k++++ +i++e++ev++dl++
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  515 GINFTLGISNISFGVN--PAARQVLNSVFLHECVSAGLNSAIVHSTKILPMGQIPDEQKEVALDLVY 579 
                                                ****************..************************************************* PP

                                 TIGR02082  609 drrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklka 675 
                                                drr e++++L++l+el+ g+++k sk a+ +++  lp+eeRL++++++G+++g+e+dl++a+   ++
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  580 DRRGEDYDPLQQLIELFDGVTTKGSKAARAEALNALPLEERLAQRIIDGNKDGLEQDLDAAL-SRHS 645 
                                                **************************************************************.999* PP

                                 TIGR02082  676 pleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvk 742 
                                                +l+ii+ +Ll+Gmk+vGd FGsG+m+LP+v++sa++mk ava LeP++e+++   + kG+ivlatv+
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  646 ALDIINRHLLEGMKIVGDRFGSGQMQLPFVLQSAETMKTAVAQLEPHMEQDD--ADGKGTIVLATVR 710 
                                                **************************************************99..5689********* PP

                                 TIGR02082  743 GDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeeme 809 
                                                GDvhDiGkn+vd++Ls+ngy vv+lG+k+P+  i++aa+++ aD ig+sGL+vks++ m  ++ e++
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  711 GDVHDIGKNLVDIILSNNGYSVVNLGIKQPIGDIIDAAEQHGADAIGMSGLLVKSTVIMRDNLAELT 777 
                                                ******************************************************************* PP

                                 TIGR02082  810 rrgvk..iPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkaeelekikee 873 
                                                 rg++   P+llGGaal++++v+ ++ e+++ gev+y++da+e+++++d+l+ +++    +++i +e
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  778 ARGLAgrWPVLLGGAALTRSYVEDDLRENFDdGEVHYARDAFEGLELMDRLMAHQR--GDIGEILTE 842 
                                                ****8889********************99548********************997..445789999 PP

                                 TIGR02082  874 yeeirekfge.kkeklialsekaarkevfaldrse...dlevpapkflGtkvleas.ieellkyiDw 935 
                                                +++++  +++ ++e++++l++++  + + ++ rs+   d  vp p+f+G ++++ +  +++  ++D+
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  843 EQKAKIAARRrRRERTKNLKREQLPSLDDTTVRSDtslDNPVPRPPFWGNRIVKGLpQADYAAFLDE 909 
                                                999988776514567778888887777777777777779999**************9********** PP

                                 TIGR02082  936 kalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddiei 1001
                                                +a F+ qW+l+g+++ ++ + +e+l++++ +++++++l++l a++ l ++ v+G++Pa  +g+ +++
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  910 RATFLgQWGLKGTRG-TEGPGYEELVETEGRPRLRYWLERLAADNVLDPQIVYGYYPAYAEGNSVVV 975 
                                                ***************.99************************************************* PP

                                 TIGR02082 1002 ytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkle 1068
                                                ++++      k+    +++++++rq  d++lcl+Df+ +k+    D+++++lvt g +++++++kl+
  lcl|NCBI__GCF_000527155.1:WP_025274553.1  976 LDEDRD----KQ----IARFDFPRQRHDKRLCLSDFFHPKDGDDLDVIAMQLVTLGSQVSDYTNKLF 1034
                                                *95544....33....45679********************************************** PP

                                 TIGR02082 1069 akeddydsilvkaladrlaealaellhervRkelwgya.....eeenldkedllkerYrGirpafGY 1130
                                                ++++++d+++v++l+++l+ealae++h rvR e++        +++++++  +++++Y G r++fGY
  lcl|NCBI__GCF_000527155.1:WP_025274553.1 1035 ENDEYRDYLEVHGLTVQLTEALAEYWHARVRGEWQYPQggavaDSDPESIGGMFRTEYAGCRYSFGY 1101
                                                *******************************99764323445599********************** PP

                                 TIGR02082 1131 pacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfa 1181
                                                pacP++ ++a l+++l a+riG++l+e  +l+Pe+s+++++++hpea Yf+
  lcl|NCBI__GCF_000527155.1:WP_025274553.1 1102 PACPNLADRAVLVDILGADRIGVQLSEGDQLHPEQSTDAVILHHPEASYFN 1152
                                                **************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1154 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 11.26
//
[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)
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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