Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate PfGW456L13_2847 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
Query= BRENDA::P13009
(1227 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847
Length = 1236
Score = 1606 bits (4158), Expect = 0.0
Identities = 819/1235 (66%), Positives = 977/1235 (79%), Gaps = 15/1235 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S +++ L+ L ERIL+LDGGMGTMIQSY+L E D+RG+RFADWP D+KGNNDLLVL++P
Sbjct: 5 SVRLQALKHALKERILILDGGMGTMIQSYKLEEQDYRGKRFADWPSDVKGNNDLLVLTRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+VI I AY +AGADI+ETNTFN+T I+MADY ME L+ E+N A+LAR AD T
Sbjct: 65 DVIGGIEKAYLDAGADILETNTFNATRISMADYGMEKLAYELNVEGARLARKVADAKTLE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
P+KPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV Y E+TK L+EGGADLILIE
Sbjct: 125 NPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ FE LGVELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQGVFEELGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG ELR Y++ELS A +V+AHPNAGLPN FGEYD AK I E+AQ+
Sbjct: 245 SVGLNCALGARELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPSETAKVIEEFAQS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP I +SLFVNVGE
Sbjct: 305 GFLNIVGGCCGTTPGHIEAIAKAVAGYAPREIPDIPKACRLSGLEPFTIDRNSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTN+TGSAKF RLI+E+ Y+EAL+VA QQVE GAQ+IDINMDEGMLD++ AMV FLNLIA
Sbjct: 365 RTNITGSAKFARLIREDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+R+Y IL EV FPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485 VMAFDEAGQADTEARKKEICKRSYDILVNEVDFPPEDIIFDPNIFAVATGIEEHNNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI AC I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIR+G+ MGIVNAGQ
Sbjct: 545 FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRSGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
L IYD +P ELRDAVEDVILNR +GT+ LL +A+KY+G A+ EWR+W+VNK
Sbjct: 605 LEIYDQIPVELRDAVEDVILNRTPEGTDALLAIADKYKGD--GSVKEAETEEWRNWDVNK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT I +DTEE+RQ RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITTHIIEDTEESRQSFARPIEVIEGPLMAGMNIVGDLFGAGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVA+L PFIE K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723 ARVMKQAVAHLIPFIELEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+ A+E D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSKA
Sbjct: 783 GVMVPAEKILQVAREQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKA 842
Query: 841 HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKIE YS V YV +ASR VGV LLS + FV +TR++Y VR + +
Sbjct: 843 HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKAGFVEKTRQDYIEVRERTSNRSA 902
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
RT ++ AA FDW +YTP G + ++ ++ L YIDWTPFF++W LAG
Sbjct: 903 RTERLSYGAAIAKKPQFDWASYTPVKPTFTGARVLDNIDLDVLAEYIDWTPFFISWDLAG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
K+PRIL+DEVVG A L+ DA +ML KL EK ++ R V G +PAN+V DDIE+Y D+
Sbjct: 963 KFPRILQDEVVGEAATSLYNDAREMLRKLIDEKLISARAVFGFWPANQVHDDDIELYGDD 1022
Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+ + HHLRQQ KT G N+ LADFVAPK S DY+G F T G+ + +A A+
Sbjct: 1023 GKP--MTKLHHLRQQIIKTDGKPNFSLADFVAPKDSEVTDYVGGFITTAGIGAEEVAKAY 1080
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
+ DDYN IMVKALADRLAEA AE+LH++VRK YWGYA +E L NE LI+E Y GIRPA
Sbjct: 1081 QDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYAKDEALDNEALIKEQYSGIRPA 1140
Query: 1137 PGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
PGYPACP+HTEKA ++ LL+ E +G+ LTE +AM+P A+VSGWYF+HP ++Y+
Sbjct: 1141 PGYPACPDHTEKAQLFALLDPEAQEMRAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYF 1200
Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
AV +I +DQV+ Y RKG ++ ERWLAPNLGYD
Sbjct: 1201 AVGKIDKDQVQSYTSRKGQELSVTERWLAPNLGYD 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: 3825
Number of extensions: 169
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: 1236
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1189
Effective search space: 1403020
Effective search space used: 1403020
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 PfGW456L13_2847 (5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13))
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.31303.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 1756.8 0.0 0 1756.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 5-methyltetrahydrofolate--homocy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 5-methyltetrahydrofolate--homocysteine methyltransferase (EC
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1756.7 0.0 0 0 1 1182 [] 15 1202 .. 15 1202 .. 0.98
Alignments for each domain:
== domain 1 score: 1756.7 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPevi 52
l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL+lt+P+vi
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 15 LKERILILDGGMGTMIQSYKLEEQDYRGKrFADWPSDVKGNNDLLVLTRPDVI 67
579************************************************** PP
TIGR02082 53 aaihrayfeaGaDivetntFnsteialadYdledkayelnkkaaklarevade 105
i +ay++aGaDi+etntFn+t i++adY++e++ayeln ++a+lar+vad
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 68 GGIEKAYLDAGADILETNTFNATRISMADYGMEKLAYELNVEGARLARKVADA 120
***************************************************** PP
TIGR02082 106 ft.ltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYkeqvkgl 157
t +p+k+RfvaG+lGPt+++ +lspdv++p++rnvt+delv+ Y+e++kgl
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 121 KTlENPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGL 173
9989************************************************* PP
TIGR02082 158 ldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtL 210
++GG+Dl+Liet+fDtlnakaa+fav+ vfee g+elPi+isg+i+d+sGrtL
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 174 IEGGADLILIETIFDTLNAKAAIFAVQGVFEELGVELPIMISGTITDASGRTL 226
***************************************************** PP
TIGR02082 211 sGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaG 263
sGqt+eaf +s+ ha+ +++GLnCalGa elr++++els++a++ vs++PnaG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 227 SGQTTEAFWNSVAHAKPISVGLNCALGARELRPYLEELSNKANTHVSAHPNAG 279
***************************************************** PP
TIGR02082 264 LPnalgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdik 316
LPn++geYd++p+e+ak+++efa+ g+lnivGGCCGttP hi aia+av++ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 280 LPNEFGEYDELPSETAKVIEEFAQSGFLNIVGGCCGTTPGHIEAIAKAVAGYA 332
***************************************************** PP
TIGR02082 317 prkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyee 369
pr+ ++++++++lsgle+++i+++s fvn+GeRtn++Gs+kf++li++++y e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 333 PREIPDIPKACRLSGLEPFTIDRNSLFVNVGERTNITGSAKFARLIREDNYTE 385
***************************************************** PP
TIGR02082 370 alkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDs 422
al++a qqve Gaq++Din+De++lD++++m+++l+l+a+epdi++vP+m+Ds
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 386 ALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIAGEPDISRVPIMIDS 438
***************************************************** PP
TIGR02082 423 sefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDee 475
s++ev+eaGLk+iqGk+ivnsis+k+G+e+F+++akl k+yGaavvvmafDe
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 439 SKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEA 491
***************************************************** PP
TIGR02082 476 GqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaid 528
Gqa+t ++k ei+kR y++l+++v+fppediifDpni+++atGieeh++ya+d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 492 GQADTEARKKEICKRSYDILVNEVDFPPEDIIFDPNIFAVATGIEEHNNYAVD 544
***************************************************** PP
TIGR02082 529 fieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDm 581
fi+a+ i+ elP+a +sgGvsnvsFs+rgn++vRea+hsvFL +ai++Gl m
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 545 FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRSGLTM 597
***************************************************** PP
TIGR02082 582 givnagklavyddidkelrevvedlildrrreatekLlelaelykgtkekssk 634
givnag+l++yd+i+ elr++ved+il+r +e t+ Ll +a++ykg + k
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 598 GIVNAGQLEIYDQIPVELRDAVEDVILNRTPEGTDALLAIADKYKGDGSV--K 648
**********************************************9998..9 PP
TIGR02082 635 eaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldG 687
ea+++ewrn++v++RLe+alvkG++ +i ed+ee+r+ +p+e+iegpL++G
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 649 EAETEEWRNWDVNKRLEHALVKGITTHIIEDTEESRQSFARPIEVIEGPLMAG 701
99*************************************************** PP
TIGR02082 688 mkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivla 739
m++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e ek ++ ++kGki++a
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 702 MNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIELEKGDKpEAKGKILMA 754
***************************************9877689******* PP
TIGR02082 740 tvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsG 792
tvkGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++a+++k D+iglsG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 755 TVKGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQVAREQKCDIIGLSG 807
***************************************************** PP
TIGR02082 793 LivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyv 844
Li++sldemv+va+em+r+ +++Pl++GGa++skah+avki++kY+ v+yv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 808 LITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKAHTAVKIEPKYSNdAVIYV 860
*********************************************872599** PP
TIGR02082 845 kdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaar 897
+das+av v+ +lls++ ka ++ek++++y e+re+ +++ +++ ls aa
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 861 TDASRAVGVATQLLSKELKAGFVEKTRQDYIEVRERTSNRSARTERLSYGAAI 913
***************************************************** PP
TIGR02082 898 kevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkyp 949
++ ++d+ +++++p+f G +vl+++ ++ l +yiDw+++F++W+l+gk+p
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 914 AKKPQFDWA-SYTPVKPTFTGARVLDNIdLDVLAEYIDWTPFFISWDLAGKFP 965
*********.9****************************************** PP
TIGR02082 950 kilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsv.gddiei 1001
+il+de++g+ a+ l++da+e+l kl+ ekl+ ar+v+G++Pa++v +ddie+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 966 RILQDEVVGEAATSLYNDAREMLRKLIDEKLISARAVFGFWPANQVhDDDIEL 1018
*******************************************9761578*** PP
TIGR02082 1002 ytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgall 1053
y d++ p++ +++ ++q+ + ++ + +laDf+a+k+s +Dy+g ++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 1019 YGDDGK-----PMTKLHHLRQQIIKTDGKpNFSLADFVAPKDSEVTDYVGGFI 1066
**9887.....5555555556666666656*********************** PP
TIGR02082 1054 vtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgya 1106
+tag+gaee ak++++ ddy+si+vkaladrlaea ae+lh++vRk++wgya
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 1067 TTAGIGAEEVAKAYQDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYA 1119
***************************************************** PP
TIGR02082 1107 eeenldkedllkerYrGirpafGYpacPdhtekatlleLleae.......riG 1152
++e+ld+e l+ke+Y Girpa+GYpacPdhteka+l++Ll++e r G
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 1120 KDEALDNEALIKEQYSGIRPAPGYPACPDHTEKAQLFALLDPEaqemragRSG 1172
****************************************9875555444569 PP
TIGR02082 1153 lklteslalaPeasvsglyfahpeakYfav 1182
+ lte +a+ P+a+vsg+yfahp+a+Yfav
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2847 1173 VFLTEHYAMFPAAAVSGWYFAHPQAQYFAV 1202
****************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1236 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: 00:00:00.16
# Mc/sec: 8.90
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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, or view the source code, or see 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