Alignments for a candidate for metH in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Pseudomonas putida KT2440

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate PP_2375 PP_2375 cobalamin-dependent methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Putida:PP_2375
          Length = 1235

 Score = 1607 bits (4160), Expect = 0.0
 Identities = 821/1235 (66%), Positives = 978/1235 (79%), Gaps = 14/1235 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S++++ L+  L ERIL+LDGGMGTMIQSYRL E D+RG RFADWP D+KGNNDLL+LS+P
Sbjct: 5    SARLQALQNALKERILILDGGMGTMIQSYRLEEHDYRGTRFADWPSDVKGNNDLLLLSRP 64

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
            +VIAAI  AY +AGADI+ETNTFN+T I+ ADY MESL  E+N   A++AR  AD  T  
Sbjct: 65   DVIAAIEKAYLDAGADILETNTFNATQISQADYGMESLVYELNVEGARIARQVADAKTLE 124

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            TP+KPR+VAGVLGPT+RT SISPDVNDP FRN+TFD LV  Y E+T+ L+EGGADLILIE
Sbjct: 125  TPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFDELVENYIEATRGLIEGGADLILIE 184

Query: 182  TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
            T+FDTLNAKAA+FAV+  FE   VELPIMISGTITDASGRTLSGQTTEAF+NS+RHA+ +
Sbjct: 185  TIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEAFWNSVRHAKPI 244

Query: 242  TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
            + GLNCALG  +LR Y++EL+  A+ +V+AHPNAGLPNAFGEYD     MA  + E+A +
Sbjct: 245  SVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAAS 304

Query: 302  GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
            GFLNI+GGCCGTTP HI A++ AV    PR++PEI  ACRLSGLEP  I   SLFVNVGE
Sbjct: 305  GFLNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGE 364

Query: 362  RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
            RTN+TGSAKF RLI+EE Y+EAL+VA QQVE GAQ+IDINMDEGMLD++AAMVRFLNLIA
Sbjct: 365  RTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIA 424

Query: 422  GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
            GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ F HHA+L +RYGAAVV
Sbjct: 425  GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKHHARLCKRYGAAVV 484

Query: 482  VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
            VMAFDE GQADT ARK EIC+R+Y IL  EVGFPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485  VMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVD 544

Query: 542  FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
            FI AC  I+  LPHAL SGGVSNVSFSFRGN+PVREAIH+VFLY+AI+NG+ MGIVNAGQ
Sbjct: 545  FIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMGIVNAGQ 604

Query: 602  LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
            L IYD++PA+LR+ VEDV+LNR   GT+ LL +A+ Y+G     T   +  EWRS  V K
Sbjct: 605  LEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGA--TKEVENEEWRSLPVEK 662

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE++LVKGIT FI +DTE  RQQ  RPIEVIEGPLM+GMNVVGDLFG GKMFLPQVVKS
Sbjct: 663  RLEHALVKGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKS 722

Query: 722  ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            ARVMKQAVA+L PFIEA K ++ +  GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723  ARVMKQAVAHLIPFIEAEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVPAEKIL+TA+E   D+IGLSGLITPSLDEMV+VA+EM+RQGF +PL+IGGATTSKA
Sbjct: 783  GVMVPAEKILQTAREQKCDIIGLSGLITPSLDEMVHVAREMQRQGFELPLMIGGATTSKA 842

Query: 841  HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
            HTAVKIE  YS   V YV +ASR VGV   LLS   +  FV +TR EY  VR +   +  
Sbjct: 843  HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKPGFVEKTRLEYVDVRERTANRSA 902

Query: 900  RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
            RT  ++   A      +DW  Y P      GV+ +E   + TL  YIDWTPFF++W LAG
Sbjct: 903  RTERLSYAQAIAAKPQYDWAGYQPTAPSFTGVKVLEDIDLRTLAEYIDWTPFFISWDLAG 962

Query: 959  KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
            K+PRIL DEVVG  A  L+KDA +MLDKL  EK ++ R V G +PAN+V  DDIE+Y ++
Sbjct: 963  KFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDDDDIEVYGED 1022

Query: 1018 TRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
             +   +   HHLRQQT K  G  N+ LADFVAPK SG  DY+G F  T G+  + +A A+
Sbjct: 1023 GQ--ALATLHHLRQQTIKPDGKPNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAY 1080

Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
            + + DDY+ IMVKALADRLAEA AE+LHE+VRK +WGYA +E+L NE LI+E Y GIRPA
Sbjct: 1081 QDKGDDYSSIMVKALADRLAEACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPA 1140

Query: 1137 PGYPACPEHTEKATIWELLE-----VEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYA 1191
            PGYPACP+HTEK T++ LL+         +G+ LTE FAM+P A+VSGWYF+HP +KY+A
Sbjct: 1141 PGYPACPDHTEKETLFRLLDGTAIGETGPSGVYLTEHFAMFPAAAVSGWYFAHPQAKYFA 1200

Query: 1192 VAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDA 1226
            V ++ +DQ+E Y+ RKG  ++  ERWLAPNLGYD+
Sbjct: 1201 VGKVDKDQIERYSARKGQDISVSERWLAPNLGYDS 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: 3851
Number of extensions: 160
Number of successful extensions: 8
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: 1235
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1188
Effective search space:  1401840
Effective search space used:  1401840
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 PP_2375 PP_2375 (cobalamin-dependent 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.6897.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 1766.9   0.0          0 1766.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2375  PP_2375 cobalamin-dependent meth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2375  PP_2375 cobalamin-dependent methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1766.7   0.0         0         0       1    1182 []      15    1201 ..      15    1201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1766.7 bits;  conditional E-value: 0
                           TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72  
                                          l++ril+lDG+mGt++qs++L+e+d+rg  +ad+++++kGnndlL l++P+viaai +ay++aGaDi+etntF
  lcl|FitnessBrowser__Putida:PP_2375   15 LKERILILDGGMGTMIQSYRLEEHDYRGTrFADWPSDVKGNNDLLLLSRPDVIAAIEKAYLDAGADILETNTF 87  
                                          579********************************************************************** PP

                           TIGR02082   73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144 
                                          n+t+i++adY++e+++yeln ++a++ar+vad  t  tp+k+RfvaG+lGPt+++ ++spdv++p+frnvt+d
  lcl|FitnessBrowser__Putida:PP_2375   88 NATQISQADYGMESLVYELNVEGARIARQVADAKTlETPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFD 160 
                                          *********************************99899*********************************** PP

                           TIGR02082  145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217 
                                          elv+ Y e+++gl++GG+Dl+Liet+fDtlnakaa+fav++vfe+ ++elPi+isg+i+d+sGrtLsGqt+ea
  lcl|FitnessBrowser__Putida:PP_2375  161 ELVENYIEATRGLIEGGADLILIETIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEA 233 
                                          ************************************************************************* PP

                           TIGR02082  218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290 
                                          f +s++ha+ +++GLnCalGa++lr++++el+ +a++ vs++PnaGLPna+geYd+tp e+a++++efa+ g+
  lcl|FitnessBrowser__Putida:PP_2375  234 FWNSVRHAKPISVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAASGF 306 
                                          ************************************************************************* PP

                           TIGR02082  291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363 
                                          lni+GGCCGttP hi+aiaeav++ kpr+ +e+ ++++lsgle+++i+++s fvn+GeRtn++Gs+kf++li+
  lcl|FitnessBrowser__Putida:PP_2375  307 LNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGERTNITGSAKFARLIR 379 
                                          ************************************************************************* PP

                           TIGR02082  364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436 
                                          +e+y eal++a qqve Gaq++Din+De++lD++a+m+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iq
  lcl|FitnessBrowser__Putida:PP_2375  380 EENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQ 452 
                                          ************************************************************************* PP

                           TIGR02082  437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509 
                                          Gk+ivnsis+k+G+e+F ++a+l k+yGaavvvmafDe Gqa+ta++k ei++R y++l+++vgfppediifD
  lcl|FitnessBrowser__Putida:PP_2375  453 GKGIVNSISMKEGVEQFKHHARLCKRYGAAVVVMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFD 525 
                                          ************************************************************************* PP

                           TIGR02082  510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582 
                                          pni+++atGieeh++ya+dfiea+  i+ +lP+a  sgGvsnvsFs+rgn++vRea+hsvFLy+ai++Gl mg
  lcl|FitnessBrowser__Putida:PP_2375  526 PNIFAVATGIEEHNNYAVDFIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMG 598 
                                          ************************************************************************* PP

                           TIGR02082  583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655 
                                          ivnag+l++yd+i+++lre+ved++l+r ++ t+ Ll +a+ ykg  ++  ke +++ewr+lpve+RLe+alv
  lcl|FitnessBrowser__Putida:PP_2375  599 IVNAGQLEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGAT--KEVENEEWRSLPVEKRLEHALV 669 
                                          *********************************************9999..8999****************** PP

                           TIGR02082  656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 
                                          kG++ +i ed+e+ r++  +p+e+iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek 
  lcl|FitnessBrowser__Putida:PP_2375  670 KGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKG 742 
                                          ************************************************************************8 PP

                           TIGR02082  729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 
                                          ++ ++kGki++atvkGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++a+++k D+iglsGLi++slde
  lcl|FitnessBrowser__Putida:PP_2375  743 DKpEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQTAREQKCDIIGLSGLITPSLDE 815 
                                          87689******************************************************************** PP

                           TIGR02082  801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekike 872 
                                          mv+va+em+r+g+++Pl++GGa++skah+avki++kY+   v+yv+das+av v+ +lls++ k  ++ek++ 
  lcl|FitnessBrowser__Putida:PP_2375  816 MVHVAREMQRQGFELPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKPGFVEKTRL 888 
                                          *************************************872599****************************** PP

                           TIGR02082  873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944 
                                          ey ++re+  ++  +++ ls ++a   + + d+   ++++ap f G+kvle++ + +l +yiDw+++F++W+l
  lcl|FitnessBrowser__Putida:PP_2375  889 EYVDVRERTANRSARTERLSYAQAIAAKPQYDWA-GYQPTAPSFTGVKVLEDIdLRTLAEYIDWTPFFISWDL 960 
                                          **********************************.9************************************* PP

                           TIGR02082  945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiat 1016
                                          +gk+p+il+de++g+ a+ l+kda+e+ldkl+ ekl+ ar+v+G++Pa++v+ ddie+y +++       +at
  lcl|FitnessBrowser__Putida:PP_2375  961 AGKFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDdDDIEVYGEDGQ-----ALAT 1028
                                          ************************************************9875268*****8776.....6677 PP

                           TIGR02082 1017 vrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlae 1088
                                          +++ ++q+ +  ++ + +laDf+a+k+sG +Dy+g +++tag+gaee ak++++k ddy+si+vkaladrlae
  lcl|FitnessBrowser__Putida:PP_2375 1029 LHHLRQQTIKPDGKpNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAYQDKGDDYSSIMVKALADRLAE 1101
                                          666555555555556********************************************************** PP

                           TIGR02082 1089 alaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeri......Glkl 1155
                                          a ae+lhe+vRke+wgya++e+ld+e l+ke+Y Girpa+GYpacPdhtek tl++Ll+   i      G++l
  lcl|FitnessBrowser__Putida:PP_2375 1102 ACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPAPGYPACPDHTEKETLFRLLDGTAIgetgpsGVYL 1174
                                          **********************************************************987663333337*** PP

                           TIGR02082 1156 teslalaPeasvsglyfahpeakYfav 1182
                                          te +a+ P+a+vsg+yfahp+akYfav
  lcl|FitnessBrowser__Putida:PP_2375 1175 TEHFAMFPAAAVSGWYFAHPQAKYFAV 1201
                                          *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1235 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 0.05s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.60
//
[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