Alignments for a candidate for metH in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Azospirillum lipoferum B510

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_012973546.1 AZL_RS04900 methionine synthase

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



>NCBI__GCF_000010725.1:WP_012973546.1
          Length = 1163

 Score = 1058 bits (2736), Expect = 0.0
 Identities = 596/1212 (49%), Positives = 790/1212 (65%), Gaps = 62/1212 (5%)

Query: 19   LDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAGA 78
            LD L + VL+ DG  G+++Q  DLDVEKD+   E C +IL  +RPD++R IHR YFEAGA
Sbjct: 5    LDTLRDRVLLCDGGFGSRIQALDLDVEKDYWGHENCTDILPLSRPDIVRDIHRGYFEAGA 64

Query: 79   DLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPG 138
            D+VET+TFG +   L ++ I+++  E+  +   +ARE A+      +G  RFV+GS+GPG
Sbjct: 65   DMVETDTFGASPVTLGEFGISEKAFEINRRAVELAREAAESF---TDGQPRFVIGSIGPG 121

Query: 139  TKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDT 198
            TKLPSLGH  Y      +   A G+I GG DA L+ET QD LQ+KAAV+G++ A  E  +
Sbjct: 122  TKLPSLGHIAYQPAEDSFHVQAAGLIAGGADAILVETCQDPLQIKAAVNGIKRARLEAKS 181

Query: 199  FLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHAD 258
              P+   VTVETTGT+L+G++I AA T +Q L + ++GLNCATGP EMSEH+R+L+++  
Sbjct: 182  DTPVFVQVTVETTGTLLVGTDIAAAATIIQALDVPLMGLNCATGPLEMSEHVRWLAQNWP 241

Query: 259  IPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRD 318
              +SV PNAGLP L      YPL A D A  L  FV E G+++VGGCCGT   HI A   
Sbjct: 242  GLISVQPNAGLPELVDGKTHYPLLAGDFAHWLERFVVEDGVNLVGGCCGTNVPHIAAA-- 299

Query: 319  AVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSNG 378
                   Q    L    +       R V    +VASLY+ V L QE     IGER N+NG
Sbjct: 300  ------NQMLRKLAPAGSHRPNPKGRTVHWVPAVASLYSQVTLRQENAFFAIGERCNANG 353

Query: 379  SKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTLP 438
            SK +RE     DW+ CV++A++Q ++G+H LD+C  +VGRD  A+M  + +  A S T P
Sbjct: 354  SKKWRELQERNDWDGCVEMAREQVKEGSHSLDVCTAFVGRDEVAEMNAVISRFAGSVTAP 413

Query: 439  IMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTIDE 498
            ++IDSTE +V+   L   GG++I+NS+NFEDG+ P    +  ++L K+ GAAV+ALTIDE
Sbjct: 414  LVIDSTEYKVLEQALALYGGKAILNSINFEDGEEPA---RLRLELAKKFGAAVIALTIDE 470

Query: 499  EGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAIR 558
            EG A+T + K+ IAKRL D     YGL   D++ D LTF I+TG E+ R+  I T+E I 
Sbjct: 471  EGMAKTPDRKLAIAKRLYDLAVTEYGLAPSDLLFDPLTFTIATGNEDDRKLAIWTLEGIE 530

Query: 559  ELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRID 618
             + +  P     LGLSN+SFGLN AAR VLNSVFL+  ++ G+  AI H SKILP+++I 
Sbjct: 531  AISREMPGCQIILGLSNVSFGLNAAARHVLNSVFLDHAVKKGMTGAIVHVSKILPLHQIP 590

Query: 619  DRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADA-KDARAEQLAAMPLFERLAQRII 677
            +++ + A D+++DRR+E YDPLQ F+ LFEG  AADA K ARAE +      ERL +RI+
Sbjct: 591  EKEVKTAEDLIFDRRSEGYDPLQAFIALFEGRKAADAKKKARAETVE-----ERLKERIV 645

Query: 678  DGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAV 737
            DGD+ GLEDDL   MK   P+ IIN  LL+GMK VGELFG+G+MQLPFVLQSAETMK AV
Sbjct: 646  DGDRTGLEDDLAEAMKTHPPLEIINTYLLDGMKVVGELFGAGKMQLPFVLQSAETMKAAV 705

Query: 738  AYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQ 797
            A+LEP ME+        + + KG +V+ATVKGDVHDIGKNLVDIIL+NNGY VVNLGIKQ
Sbjct: 706  AWLEPHMEK-------VEGQQKGTLVLATVKGDVHDIGKNLVDIILTNNGYKVVNLGIKQ 758

Query: 798  PLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYVE 857
            P+SA+++AA+EHKA  +GMSGLLVKSTVVM+ENLEEM   G    PV+LGGAALTR YVE
Sbjct: 759  PVSAIIQAAKEHKATAVGMSGLLVKSTVVMRENLEEMTREGL-EVPVLLGGAALTRAYVE 817

Query: 858  NDLNEVY-TGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNER 916
             D    Y +G V YA DAF+GL LMD+V+     + L      AI+QAK+    KA N R
Sbjct: 818  GDCVASYGSGRVAYAGDAFDGLTLMDKVVEGSFDQQL------AIQQAKRAG--KATNRR 869

Query: 917  SRKIAAERKANAAPV----IVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERA 972
             R +     A   PV    +   R  ++   P   PPFWG +++  +PL   +  L+ER 
Sbjct: 870  -RVLGQATSAATGPVDKDAVRARRHRLAEGVPVPTPPFWGPKLIDHVPLKTLVTYLNERM 928

Query: 973  LFMGQWGLKSTRGNEGPSYEDLVE---TEGRPRLRYWLDRLKSEGILDHVALVYGYFPAV 1029
            L+  QWG +     +G S+E+  E    E RP L   L     E IL   A VYGY+ A 
Sbjct: 929  LYQLQWGYR----KDGKSFEEFKEWAKKELRPVLDRILQIAAKEEILRPTA-VYGYWKAA 983

Query: 1030 AEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVT 1089
            A+G+DV++ E  +    E  RFS PRQ +    CIADF+R     V D + DV+  Q+VT
Sbjct: 984  ADGNDVILFE--EDGTTEAARFSLPRQAKEDGECIADFLRD----VTDPERDVIGLQVVT 1037

Query: 1090 MGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDP 1149
            MG   AD A + FA N Y++YL +HG+ V++TEA+AEY H+R+R+EL     G  A+ D 
Sbjct: 1038 MGQHCADVARDWFAENRYQDYLYLHGLSVEMTEAMAEYVHARIRAEL-----GYGAE-DS 1091

Query: 1150 EDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAF 1209
             DK K     YRG+R+SFGY +CP+L+D+ +L++LL+ GRIG+E+S+E QLHPEQST A 
Sbjct: 1092 RDKEKLLQQAYRGSRYSFGYPACPNLKDQEQLLKLLDAGRIGIEMSDEDQLHPEQSTSAI 1151

Query: 1210 VLYHPEAKYFNV 1221
            VL+HP AKYF+V
Sbjct: 1152 VLHHPRAKYFSV 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: 3260
Number of extensions: 154
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: 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_012973546.1 AZL_RS04900 (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.19534.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 1247.7   0.0          0 1247.5   0.0    1.0  1  lcl|NCBI__GCF_000010725.1:WP_012973546.1  AZL_RS04900 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012973546.1  AZL_RS04900 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1247.5   0.0         0         0       2    1182 .]       9    1163 .]       8    1163 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1247.5 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLt.eadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                + r+l+ DG++G  +q+ +L+ e+d+ g         + + d+L l++P+++++ihr yfeaGaD+v
  lcl|NCBI__GCF_000010725.1:WP_012973546.1    9 RDRVLLCDGGFGSRIQALDLDvEKDYWG--------HENCTDILPLSRPDIVRDIHRGYFEAGADMV 67  
                                                789*****************93456666........699**************************** PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                et+tF++++++l+++++ +ka e+n++a +lare+a+ ft    ++Rfv+Gs+GP++kl++l+    
  lcl|NCBI__GCF_000010725.1:WP_012973546.1   68 ETDTFGASPVTLGEFGISEKAFEINRRAVELAREAAESFT--DGQPRFVIGSIGPGTKLPSLG---- 128 
                                                ***************************************9..8899*****************.... PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                     ++ y+   d++++q+ gl+ GG+D++L+et++D l++kaa+++++++  e++++ P++++ v
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  129 -----HIAYQPAEDSFHVQAAGLIAGGADAILVETCQDPLQIKAAVNGIKRARLEAKSDTPVFVQ-V 189 
                                                .....************************************************************.* PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                +v+++G++L+G++++a++++++  ++ ++GLnCa+G+ e++e+v+ l+++ + l+sv PnaGLP+ +
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  190 TVETTGTLLVGTDIAAAATIIQALDVPLMGLNCATGPLEMSEHVRWLAQNWPGLISVQPNAGLPELV 256 
                                                ******************************************************************9 PP

                                 TIGR02082  269 g...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqe........le 324 
                                                    +Y+l++   a+ l+ f+ e ++n+vGGCCGt   hi+a  ++ ++++p   ++        + 
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  257 DgktHYPLLAGDFAHWLERFVVEDGVNLVGGCCGTNVPHIAAANQMLRKLAPAGSHRpnpkgrtvHW 323 
                                                87889*****************************************999987432221123333388 PP

                                 TIGR02082  325 eksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDe 391 
                                                 + v+s+++++++ qe+ f  iGeR+n++Gskk r+l + +d++ ++++a++qv+eG++ lD++   
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  324 VPAVASLYSQVTLRQENAFFAIGERCNANGSKKWRELQERNDWDGCVEMAREQVKEGSHSLDVCTAF 390 
                                                899**************************************************************** PP

                                 TIGR02082  392 vllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekak 458 
                                                v++D +a+m++++s+ a++  + + Pl++Ds+e++vle+ L   +Gkai+nsi+++dGee    +++
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  391 VGRDEVAEMNAVISRFAGS--V-TAPLVIDSTEYKVLEQALALYGGKAILNSINFEDGEEPARLRLE 454 
                                                *******************..6.99****************************************** PP

                                 TIGR02082  459 likeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdry 525 
                                                l+k++Gaav+++++DeeG+a+t d+k+ iakR+y+l++ ++g+ p+d++fDp+++tiatG e++++ 
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  455 LAKKFGAAVIALTIDEEGMAKTPDRKLAIAKRLYDLAVTEYGLAPSDLLFDPLTFTIATGNEDDRKL 521 
                                                ******************************************************************* PP

                                 TIGR02082  526 aidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavy 592 
                                                ai ++e i+ i +e+P ++i +G+snvsF+l+   a+R++l+svFL +a+k G+  +iv+ +k++++
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  522 AIWTLEGIEAISREMPGCQIILGLSNVSFGLN--AAARHVLNSVFLDHAVKKGMTGAIVHVSKILPL 586 
                                                ********************************..9******************************** PP

                                 TIGR02082  593 ddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGer 659 
                                                ++i++   +++edli+drr+e +++L+ ++ l++g k++++k    ++ r   veeRL++++v+G r
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  587 HQIPEKEVKTAEDLIFDRRSEGYDPLQAFIALFEGRKAADAK----KKARAETVEERLKERIVDGDR 649 
                                                *************************************99665....5667789************** PP

                                 TIGR02082  660 egieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePyleke 726 
                                                 g+e+dl ea+ k+++pleii+++LldGmkvvG+LFG+Gkm+LP+v++sa++mk+ava+LeP++ek 
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  650 TGLEDDLAEAM-KTHPPLEIINTYLLDGMKVVGELFGAGKMQLPFVLQSAETMKAAVAWLEPHMEKV 715 
                                                ***********.899*************************************************987 PP

                                 TIGR02082  727 keedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGL 793 
                                                +   ++kG++vlatvkGDvhDiGkn+vd++L++ngy+vv+lG+k+Pv  i++aak++ka  +g+sGL
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  716 E--GQQKGTLVLATVKGDVHDIGKNLVDIILTNNGYKVVNLGIKQPVSAIIQAAKEHKATAVGMSGL 780 
                                                6..899************************************************************* PP

                                 TIGR02082  794 ivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdklls 859 
                                                +vks+++m e++eem+r+g+++P+llGGaal++a+v+ ++  +Y +g+v y+ da+++++++dk+++
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  781 LVKSTVVMRENLEEMTREGLEVPVLLGGAALTRAYVEGDCVASYgSGRVAYAGDAFDGLTLMDKVVE 847 
                                                ****************************************9999679*******************9 PP

                                 TIGR02082  860 ekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrse...dlevpapkflGtkvle 923 
                                                    ++ + +  ++  ++ ++ +   + + a+ +    k+ +   r+     + vp+p+f+G k ++
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  848 GSFDQQLAIQQAKRAGKATNRRRVLGQATSAA-TGPVDKDAVRARRHRlaeGVPVPTPPFWGPKLID 913 
                                                98766655444444444444433333333333.33333333333332233378899*********** PP

                                 TIGR02082  924 as.ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvG 988 
                                                ++ +++l+ y+++++l+  qW+ r+  +  + +e ++  +++l++ ++ +l+   +e+ lr+++v+G
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  914 HVpLKTLVTYLNERMLYQlQWGYRKDGK--SFEEFKEWAKKELRPVLDRILQIAAKEEILRPTAVYG 978 
                                                *****************99****99876..778899999**************************** PP

                                 TIGR02082  989 lfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvt 1055
                                                ++ a   g+d+ +++++++        t  +++  +rq ++   c+aDf+++ +  ++D++g+++vt
  lcl|NCBI__GCF_000010725.1:WP_012973546.1  979 YWKAAADGNDVILFEEDGT--------TEAARFSLPRQAKEDGECIADFLRDVTDPERDVIGLQVVT 1037
                                                ***************8887........344568999****99************************* PP

                                 TIGR02082 1056 aglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYr 1122
                                                +g++ ++ a++++a++ ++d++++++l++ ++ea+ae++h r+R el  y++e++ dke+ll++ Yr
  lcl|NCBI__GCF_000010725.1:WP_012973546.1 1038 MGQHCADVARDWFAENRYQDYLYLHGLSVEMTEAMAEYVHARIRAELG-YGAEDSRDKEKLLQQAYR 1103
                                                **********************************************96.66999************* PP

                                 TIGR02082 1123 GirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                G+r++fGYpacP+++++ +ll+Ll+a riG++++++ +l+Pe+s+s+++++hp+akYf+v
  lcl|NCBI__GCF_000010725.1:WP_012973546.1 1104 GSRYSFGYPACPNLKDQEQLLKLLDAGRIGIEMSDEDQLHPEQSTSAIVLHHPRAKYFSV 1163
                                                **********************************************************97 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 0.03s 00:00:00.15 Elapsed: 00:00:00.14
# Mc/sec: 9.22
//
[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