Alignments for a candidate for metH in Thiomicrospira pelophila DSM 1534

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Thiomicrospira pelophila DSM 1534

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_029933551.1 N746_RS0101265 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000711195.1:WP_029933551.1
          Length = 1239

 Score = 1575 bits (4077), Expect = 0.0
 Identities = 781/1234 (63%), Positives = 970/1234 (78%), Gaps = 15/1234 (1%)

Query: 4    KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEV 63
            ++ QL++ L ER++VLDG MGTMIQ+ +L+E DFRG RFAD+  D+KGNND+LVL++P++
Sbjct: 7    RIAQLKSLLTERVVVLDGAMGTMIQNLQLSEDDFRGARFADYHMDIKGNNDILVLTQPQL 66

Query: 64   IAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTP 123
            I  IH ++   G D++ETN+FN+TTIA ADY MES   +IN  AA++AR  A E      
Sbjct: 67   IRDIHLSFLRQGVDLLETNSFNATTIAQADYDMESQVRDINLHAAQVARE-ACEIAQNED 125

Query: 124  EKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETV 183
             KPR+VAGVLGPTNRTASISPDVNDP FRN  FD LV AY ++T+AL++GGAD+ILIET+
Sbjct: 126  GKPRFVAGVLGPTNRTASISPDVNDPGFRNTHFDELVEAYVQATQALLDGGADVILIETI 185

Query: 184  FDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTF 243
            FDTLNAKAA+FAVK   + LG E+PIMISGTITDASGRTLSGQTTEAFYN++RHA+ L+ 
Sbjct: 186  FDTLNAKAAIFAVKQVEDTLGEEVPIMISGTITDASGRTLSGQTTEAFYNAIRHAKPLSI 245

Query: 244  GLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGF 303
            GLNCALGP+ELR YV+ELSRI E +V+ HPNAGLPN FGEYD   + MA +++ WA+ G+
Sbjct: 246  GLNCALGPEELRPYVEELSRICETHVSVHPNAGLPNEFGEYDETPEQMAAEVKTWAERGW 305

Query: 304  LNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERT 363
            LNI+GGCCGTTP H+AAM++A    APR +P   + CRLSGLEP+NIGE SLFVNVGER 
Sbjct: 306  LNIIGGCCGTTPDHVAAMAKAALAFAPRNIPTPKIECRLSGLEPMNIGETSLFVNVGERN 365

Query: 364  NVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGE 423
            NVTGSA FKRLI E+ Y +A+++A +QV +GAQIID+NMDEGML+A+A M RFLN++AGE
Sbjct: 366  NVTGSALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLNAKACMTRFLNMMAGE 425

Query: 424  PDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVM 483
            PD ARVPIMIDSSKW+ IE GLKCIQGKGIVNSIS+KEG + F+  AK+++RYGAA +VM
Sbjct: 426  PDAARVPIMIDSSKWEAIEAGLKCIQGKGIVNSISLKEGEENFLAQAKMIQRYGAATIVM 485

Query: 484  AFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFI 543
            AFDE GQADT  RK EIC+R+Y +L    GFPPEDIIFDPNIFA+ATGIEEHNNYA DFI
Sbjct: 486  AFDEDGQADTFERKKEICKRSYDLLVAN-GFPPEDIIFDPNIFAIATGIEEHNNYAMDFI 544

Query: 544  GACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLA 603
             A + IK+ LPHALISGGVSNVSFSFRGN+PVREAIH+VFLYYAI+ GMDMGIVNA Q+A
Sbjct: 545  NAVDWIKKNLPHALISGGVSNVSFSFRGNNPVREAIHSVFLYYAIQKGMDMGIVNAAQMA 604

Query: 604  IYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAE--WRSWEVNK 661
            +YDDL  EL+ AVEDV+LN+     +RLLE+AEK+RG   D +  +++++  WR   V K
Sbjct: 605  VYDDLDPELKQAVEDVVLNKDSGAADRLLEVAEKFRG---DGSVQSKESDIRWREASVEK 661

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE+SLVKGIT++IE DTEEAR     P++VIEGPLMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 662  RLEHSLVKGITDYIEDDTEEARTTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 721

Query: 722  ARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
            ARVMK+AVAYL+P++EA K  G+  GK+V+ATVKGDVHDIGKNIVGVVLQCNN++++DLG
Sbjct: 722  ARVMKRAVAYLQPYLEAEKASGQAKGKIVMATVKGDVHDIGKNIVGVVLQCNNFDVIDLG 781

Query: 782  VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
            VMVP EKIL TA + NA++IGLSGLITPSL+EMVNVAKEM+R+G  +PLLIGGATTSKAH
Sbjct: 782  VMVPTEKILDTAIKENANVIGLSGLITPSLEEMVNVAKEMQRRGMNLPLLIGGATTSKAH 841

Query: 842  TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
            TAVKIE  Y  P VYV++ASR VGV  +L+S+  + D+ A+ R EYE +R +   +  + 
Sbjct: 842  TAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKVDYAAKIRAEYEQLREERKARSKQV 901

Query: 902  PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKY 960
                L  AR+N    DW  Y PP    LG +   +  +  L + +DW+PFF +W L G Y
Sbjct: 902  KRTPLNKARENPIPVDWTNYVPPKPSFLGTKVFDDIPLTELLDRLDWSPFFQSWDLHGLY 961

Query: 961  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
            PRIL+D++VG EA+++F DA  ML  +  EK L  R V+G +PAN V DDIE+Y+D++R 
Sbjct: 962  PRILDDKLVGEEARKVFADAKTMLQTIIKEKWLTARAVIGFYPANSVVDDIELYKDDSRE 1021

Query: 1021 HVINVSHHLRQQTE-KTGFANYCLADFVAPKLSGK------ADYIGAFAVTGGLEEDALA 1073
             V+   H+LRQQ + K G  N CL+D++APK + +       DYIGAFAVT G+  D   
Sbjct: 1022 EVLTRLHNLRQQADKKAGQYNQCLSDYIAPKANKQQPGLVLEDYIGAFAVTAGIGIDEHI 1081

Query: 1074 DAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGI 1133
              FEA HDDY  IM+KALADRLAEA AEY+HE+VRK +WGYA +E L+NEE+I+E Y+GI
Sbjct: 1082 ARFEAAHDDYQAIMLKALADRLAEALAEYMHEKVRKEFWGYAADEQLTNEEMIKEKYRGI 1141

Query: 1134 RPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVA 1193
            RPAPGYPA PEHTEK T+W LL+ +   G++LT S+AM P A+VSGWYF+HP+SKY+ V 
Sbjct: 1142 RPAPGYPANPEHTEKGTLWSLLKPDSEIGLELTSSYAMTPTAAVSGWYFAHPESKYFGVG 1201

Query: 1194 QIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
             I RDQ EDYA+RK  ++ E E+WLAPNLGYD +
Sbjct: 1202 SIGRDQAEDYAKRKNWTIQEAEKWLAPNLGYDPE 1235


Lambda     K      H
   0.318    0.134    0.391 

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: 3748
Number of extensions: 151
Number of successful extensions: 7
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: 1227
Length of database: 1239
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1192
Effective search space:  1406560
Effective search space used:  1406560
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 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate WP_029933551.1 N746_RS0101265 (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.3695386.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 1747.4   0.7          0 1747.2   0.7    1.0  1  NCBI__GCF_000711195.1:WP_029933551.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711195.1:WP_029933551.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1747.2   0.7         0         0       2    1182 .]      16    1200 ..      15    1200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1747.2 bits;  conditional E-value: 0
                             TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71  
                                             +r++vlDGamGt++q+ +L e+dFrg+ +ad++++ kGnnd+L+lt+P++i++ih +++  G D++etn 
  NCBI__GCF_000711195.1:WP_029933551.1   16 TERVVVLDGAMGTMIQNLQLSEDDFRGArFADYHMDIKGNNDILVLTQPQLIRDIHLSFLRQGVDLLETNS 86  
                                            68********************************************************************* PP

                             TIGR02082   72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 
                                            Fn+t+ia+adYd+e++++++n +aa++are+++  + +  k+RfvaG+lGPtn++a++spdv++p+frn++
  NCBI__GCF_000711195.1:WP_029933551.1   87 FNATTIAQADYDMESQVRDINLHAAQVAREACEIAQNEDGKPRFVAGVLGPTNRTASISPDVNDPGFRNTH 157 
                                            ************************************9********************************** PP

                             TIGR02082  143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 
                                            +delv+aY++++++lldGG+D++Liet+fDtlnakaa+fav++v +  g+e+Pi+isg+i+d+sGrtLsGq
  NCBI__GCF_000711195.1:WP_029933551.1  158 FDELVEAYVQATQALLDGGADVILIETIFDTLNAKAAIFAVKQVEDTLGEEVPIMISGTITDASGRTLSGQ 228 
                                            *********************************************************************** PP

                             TIGR02082  214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalke 284 
                                            t+eaf+++++ha+ l++GLnCalG++elr++v+els++ e+ vsv+PnaGLPn++geYd+tpe++a+++k 
  NCBI__GCF_000711195.1:WP_029933551.1  229 TTEAFYNAIRHAKPLSIGLNCALGPEELRPYVEELSRICETHVSVHPNAGLPNEFGEYDETPEQMAAEVKT 299 
                                            *********************************************************************** PP

                             TIGR02082  285 faeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGs 355 
                                            +ae g lni+GGCCGttP+h++a+a+a+   +pr+ ++ + +++lsgle+++i++ s fvn+GeR nv+Gs
  NCBI__GCF_000711195.1:WP_029933551.1  300 WAERGWLNIIGGCCGTTPDHVAAMAKAALAFAPRNIPTPKIECRLSGLEPMNIGETSLFVNVGERNNVTGS 370 
                                            *********************************************************************** PP

                             TIGR02082  356 kkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefe 426 
                                            + f++li++++ye+a++ia +qv++Gaqi+D+n+De++l+++a m+++l+++a+epd a+vP+m+Dss++e
  NCBI__GCF_000711195.1:WP_029933551.1  371 ALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLNAKACMTRFLNMMAGEPDAARVPIMIDSSKWE 441 
                                            *********************************************************************** PP

                             TIGR02082  427 vleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykllte 497 
                                             +eaGLk+iqGk+ivnsislk+Gee+Fl +ak+i++yGaa +vmafDe+Gqa+t ++k ei+kR y+ll++
  NCBI__GCF_000711195.1:WP_029933551.1  442 AIEAGLKCIQGKGIVNSISLKEGEENFLAQAKMIQRYGAATIVMAFDEDGQADTFERKKEICKRSYDLLVA 512 
                                            **********************************************************************9 PP

                             TIGR02082  498 kvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhs 568 
                                              gfppediifDpni++iatGieeh++ya+dfi+a+ +ik++lP+a isgGvsnvsFs+rgn++vRea+hs
  NCBI__GCF_000711195.1:WP_029933551.1  513 -NGFPPEDIIFDPNIFAIATGIEEHNNYAMDFINAVDWIKKNLPHALISGGVSNVSFSFRGNNPVREAIHS 582 
                                            .8********************************************************************* PP

                             TIGR02082  569 vFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqea 639 
                                            vFLy+ai+ G+Dmgivna+++avydd+d+el+++ved++l++++ a ++Lle+ae+++g  + +sk +   
  NCBI__GCF_000711195.1:WP_029933551.1  583 VFLYYAIQKGMDMGIVNAAQMAVYDDLDPELKQAVEDVVLNKDSGAADRLLEVAEKFRGDGSVQSK-ESDI 652 
                                            *************************************************************99777.6678 PP

                             TIGR02082  640 ewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksar 710 
                                             wr+ +ve+RLe++lvkG++++ie+d+eear +l +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksar
  NCBI__GCF_000711195.1:WP_029933551.1  653 RWREASVEKRLEHSLVKGITDYIEDDTEEARTTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSAR 723 
                                            9********************************************************************** PP

                             TIGR02082  711 vmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaak 781 
                                            vmk+avayL+Pyle+ek++ ++kGkiv+atvkGDvhDiGkniv+vvL+cn+++v+dlGv+vP+ekil++a 
  NCBI__GCF_000711195.1:WP_029933551.1  724 VMKRAVAYLQPYLEAEKASGQAKGKIVMATVKGDVHDIGKNIVGVVLQCNNFDVIDLGVMVPTEKILDTAI 794 
                                            *********************************************************************** PP

                             TIGR02082  782 kkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavk 852 
                                            k++a+viglsGLi++sl+emv+va+em+rrg+++Pll+GGa++skah+avki+++Y+ +vvyvkdas+av 
  NCBI__GCF_000711195.1:WP_029933551.1  795 KENANVIGLSGLITPSLEEMVNVAKEMQRRGMNLPLLIGGATTSKAHTAVKIEPQYDHPVVYVKDASRAVG 865 
                                            *********************************************************************** PP

                             TIGR02082  853 vvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvle 923 
                                            v+++l+s++ k ++++ki++eye++re+ + + ++++  ++++ar++ + +d++ ++ +p+p flGtkv++
  NCBI__GCF_000711195.1:WP_029933551.1  866 VAQSLISNDLKVDYAAKIRAEYEQLREERKARSKQVKRTPLNKARENPIPVDWT-NYVPPKPSFLGTKVFD 935 
                                            ******************************************************.9*************** PP

                             TIGR02082  924 as.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaq 993 
                                            ++ + ell+ +Dw ++F +W+l+g yp+il+d+l+g+eark+f+dak +l+++++ek l+ar+v+G++Pa+
  NCBI__GCF_000711195.1:WP_029933551.1  936 DIpLTELLDRLDWSPFFQSWDLHGLYPRILDDKLVGEEARKVFADAKTMLQTIIKEKWLTARAVIGFYPAN 1006
                                            *********************************************************************** PP

                             TIGR02082  994 svgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskes....G..ikDylgallvtag 1057
                                            sv ddie+y+d+++    ++++ +++ ++q+ ++ ++ ++cl+D+ia+k+     G   +Dy+ga++vtag
  NCBI__GCF_000711195.1:WP_029933551.1 1007 SVVDDIELYKDDSR---EEVLTRLHNLRQQADKKAGQyNQCLSDYIAPKANkqqpGlvLEDYIGAFAVTAG 1074
                                            **********9999...44555555556777777777799********955445652258*********** PP

                             TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpaf 1128
                                            +g++e   ++ea +ddy++i++kaladrlaealae++he+vRke+wgya++e+l +e+++ke+YrGirpa+
  NCBI__GCF_000711195.1:WP_029933551.1 1075 IGIDEHIARFEAAHDDYQAIMLKALADRLAEALAEYMHEKVRKEFWGYAADEQLTNEEMIKEKYRGIRPAP 1145
                                            *********************************************************************** PP

                             TIGR02082 1129 GYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                            GYpa P+htek tl++Ll++++ iGl+lt s+a++P+a+vsg+yfahpe+kYf v
  NCBI__GCF_000711195.1:WP_029933551.1 1146 GYPANPEHTEKGTLWSLLKPDSeIGLELTSSYAMTPTAAVSGWYFAHPESKYFGV 1200
                                            *********************99******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1239 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: 0.02u 0.06s 00:00:00.08 Elapsed: 00:00:00.09
# Mc/sec: 15.90
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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