Alignments for a candidate for metH in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Bacillus alkalinitrilicus DSM 22532

Align Methionine synthase; EC 2.1.1.13; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12 dependent; MS (uncharacterized)
to candidate WP_078430828.1 BK574_RS10060 methionine synthase

Query= curated2:Q5E814
         (1226 letters)



>NCBI__GCF_002019605.1:WP_078430828.1
          Length = 1148

 Score =  810 bits (2093), Expect = 0.0
 Identities = 471/1194 (39%), Positives = 724/1194 (60%), Gaps = 57/1194 (4%)

Query: 7    KVQIEKQLSERILLIDGGMGTMIQGYKFEEEDYRGERFNKWHCDLKGNNDLLVLSQPQII 66
            K + E+QL ++IL++DG MGTM+Q      ED+ GE +       +G N+ L ++ P +I
Sbjct: 3    KNKFEQQLEKKILVLDGAMGTMLQDANLTAEDFGGEEY-------EGCNEYLNITAPHVI 55

Query: 67   RDIHEAYLEAGADILETNTFNATTIAMADYDMESLSEEINFEAAKLAREVADKWTEKTPN 126
              IH AY EAGADI+ETNTF AT I + DYD++ L+EE+N +AA++A++VA++++  T  
Sbjct: 56   EYIHRAYFEAGADIVETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS--TSE 113

Query: 127  KPRYVAGVLGPTNRTCSISPDVNDPGFRNVSFDELVEAYSESTRALIRGGSDLILIETIF 186
             PR+VAG +GPT ++ S++          V+FD+L++AY +    LI+GG D++L+ET  
Sbjct: 114  HPRFVAGAMGPTTKSLSVTG--------GVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQ 165

Query: 187  DTLNAKACSFAVESVFEELDITLPVMISGTITDASGRTLSGQTTEAFYNALRHVKPISFG 246
            DT N KA    +E  F++L++ +P+++SGTI +  G TL+GQ  EAFY ++ H+ P   G
Sbjct: 166  DTRNVKAAYLGIERAFKQLNVKMPILVSGTI-EPMGTTLAGQNIEAFYLSIEHMTPTVVG 224

Query: 247  LNCALGPDELREYVSDLSRISECYVSAHPNAGLPNAFGEYDLSPEDMAEHVAEWASSGFL 306
            LNCA GP+ +++++  LS ++  YVS +PNAGLP+  G+Y  +PE + + +  +A  G+L
Sbjct: 225  LNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDEDGKYHETPESLTKKLTAFAEKGWL 284

Query: 307  NLIGGCCGTTPEHIRQMALVVEGVKPRQLPE-LPVACRLSGLEPLTIEKDSLFINVGERT 365
            NL+GGCCGTTP HI+ M+  ++  +PR+L E  P A  +SG+EPL  ++    + VGERT
Sbjct: 285  NLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPHA--VSGIEPLVYDESMRPLFVGERT 342

Query: 366  NVTGSARFKRLIKEELYDEALSVAQEQVENGAQIIDINMDEGMLDAEACMVRFLNLCASE 425
            NV GS +FK LI + LY+EA  +A+ QV+ GA IIDI + +   + +  M  FL    ++
Sbjct: 343  NVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEHFLKYVVNK 402

Query: 426  PEISKVPVMVDSSKWEVIEAGLKCIQGKGIVNSISLKEGKEKFVHQAKLIRRYGAAVIVM 485
                KVP+M+DS+  EV+E  L   QGK I+NSI+L++G+E+F     L+ RYGAAV+V 
Sbjct: 403  V---KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVVG 459

Query: 486  AFDEVGQADTRERKIEICTNAYNILVDEVGFPPEDIIFDPNIFAVATGIDEHNNYAVDFI 545
              DE G A T +RK+E+   +Y++LV++ G  P DIIFDP +F V TG +++   A + +
Sbjct: 460  TIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETV 519

Query: 546  EAVGDIKRTLPHAMISGGVSNVSFSFRGNNYVREAIHAVFLYHCFKNGMDMGIVNAGQLE 605
            E +  IK  LP  +   GVSNVSF        RE ++AV+LYHC + G+D  IVN  +LE
Sbjct: 520  EGIRLIKEALPECLTILGVSNVSFGL--PQVGREVLNAVYLYHCTQAGLDYAIVNTEKLE 577

Query: 606  IYDNVPEDLREAVEDVVLNRRDDSTERLLDIATEYLERAVGKVEDKSALEWRDWPVEKRL 665
             Y ++PE+ ++  + ++ +  D   E L +    Y    V KVE K  ++  +  +E+RL
Sbjct: 578  RYASIPENEKQLSDKLLFDTND---ETLAEFTAFY---RVKKVEKK--VQTSNLSLEERL 629

Query: 666  EHSLVKGITEFIVEDTEEARINAEKPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSAR 725
               +V+G  E ++ED ++A     +P+++I GPLM+GM+ VG LF   ++ + +V++SA 
Sbjct: 630  ASYIVEGTKEGLIEDLKQALEKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAE 689

Query: 726  VMKQAVAHLEPFINASKEVGATNGKILLATVKGDVHDIGKNIVGVVLQCNNYEIIDLGVM 785
            VMK +VA LE ++   K      GKILLATVKGDVHDIGKN+V ++L  N ++I++LG+ 
Sbjct: 690  VMKASVAFLEQYME-KKSGDNGKGKILLATVKGDVHDIGKNLVEIILGNNGFKIVNLGIK 748

Query: 786  VSCETILKVAKEENVDIIGLSGLITPSLDEMVHVAKEMERQGFDLPLLIGGATTSKAHTA 845
            V+   +++  K EN D IGLSGL+  S  +MV  A++++ Q   +P+L+GGA  ++  T 
Sbjct: 749  VTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLTAQDLKEQNISIPILVGGAALTRKFTD 808

Query: 846  VKIEQNYSQPVVYVNNASRAVGVCTSLL-SDELKPSFVEKLDIDYERVREQHSRKQPRTK 904
             +I + Y   V+Y  +A   + +   L+  DELK     KL+ D +   +Q   ++   K
Sbjct: 809  NRISREYDGVVLYAKDAMNGLDLANKLVKEDELK-----KLEEDKQTKLQQVGNEETEKK 863

Query: 905  -PVTLEVARANKVAIDWASYTPPVPLKPGVHIFDNFDVSTLRNYIDWTPFF-MTWSLVGK 962
              VT E+ R+    +       P  L+P  HI   + +S L  YI+          L GK
Sbjct: 864  NKVTTELPRSKVSQV--VPIHKPNDLQP--HILKEYKISHLEPYINLQMLLGKHLGLHGK 919

Query: 963  YPKILDHEEVGEEAKRLFKDANDLLDRVEKEGLLKARGMCALFPASSVGDDIEVY-TDES 1021
              ++L   E  E+A  L    + LL   +  GLL+ARGM   FPA S G+DI +Y   + 
Sbjct: 920  VSRLL--AEGDEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYDPQDE 977

Query: 1022 RTKVAKVLHNLRQQTEKPKGFNYCLSDYIAPKESGKNDWIGGFAVTGGIGERELADEYKA 1081
            +T++ +   +  +Q  +P     CL+DY+   +SG+ D++G  AVT GIG RE A + K 
Sbjct: 978  KTEIER--FSFPRQNHEP---FLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKD 1032

Query: 1082 NGDDYNAIMIQAVADRLAEAFAEYLHEKVRKEIWGYSPNETLSNDDLIREKYQGIRPAPG 1141
             GD   + +IQA A  LAE FAE  H+ +R + WG+     L+  D    KYQG+R + G
Sbjct: 1033 EGDYLFSHLIQATALELAEGFAERTHQLIRDQ-WGFPDPVELTMVDRFSAKYQGVRVSFG 1091

Query: 1142 YPACPEHTEKGALWELMNVEESIGMSLTSSYAMWPGASVSGMYFSHPDSRYFAI 1195
            YPACP   ++  L++L+   E IG+ LT  + M P ASV+ M FSHP+ RYF +
Sbjct: 1092 YPACPNLEDQAKLFKLLQ-PEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144


Lambda     K      H
   0.317    0.135    0.394 

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: 3211
Number of extensions: 169
Number of successful extensions: 16
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: 1226
Length of database: 1148
Length adjustment: 47
Effective length of query: 1179
Effective length of database: 1101
Effective search space:  1298079
Effective search space used:  1298079
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_078430828.1 BK574_RS10060 (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.27554.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 1295.1   3.9          0 1294.9   3.9    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078430828.1  BK574_RS10060 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078430828.1  BK574_RS10060 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1294.9   3.9         0         0       1    1182 []      10    1144 ..      10    1144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1294.9 bits;  conditional E-value: 0
                                 TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                l+k+ilvlDGamGt+lq anLt++dF ge      e++G+n++Ln+t P vi+ ihrayfeaGaDiv
  lcl|NCBI__GCF_002019605.1:WP_078430828.1   10 LEKKILVLDGAMGTMLQDANLTAEDFGGE------EYEGCNEYLNITAPHVIEYIHRAYFEAGADIV 70  
                                                579*************************7......9******************************* PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                etntF++t i+l+dYdl+++a eln kaa++a++va+ef+ t+e++RfvaG++GPt+k  +++    
  lcl|NCBI__GCF_002019605.1:WP_078430828.1   71 ETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS-TSEHPRFVAGAMGPTTKSLSVT---- 132 
                                                ****************************************.*******************999.... PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                      vt+d+l +aY++qv gl+ GGvD+lL+et +Dt n+kaa +++e++f++ ++++Pil+sg+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  133 ----GGVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQDTRNVKAAYLGIERAFKQLNVKMPILVSGT 195 
                                                ....789**********************************************************87 PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                i + +G+tL Gq++eaf+ s+eh+   ++GLnCa+G++ ++++++ ls  a+ +vs++PnaGLP++ 
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  196 I-EPMGTTLAGQNIEAFYLSIEHMTPTVVGLNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDED 261 
                                                5.99*************************************************************** PP

                                 TIGR02082  269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335 
                                                g+Y++tpe+l k+l+ fae+g ln+vGGCCGttP+hi+a++ea+k  +prk +e +++ ++sg+e+l
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  262 GKYHETPESLTKKLTAFAEKGWLNLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPH-AVSGIEPL 327 
                                                ***************************************************9987665.679***** PP

                                 TIGR02082  336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402 
                                                 +++    + +GeRtnv Gs+kf++li ++ yeea +ia++qv++Ga+i+Di++ +  ++ ++dm++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  328 VYDESMRPLFVGERTNVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEH 394 
                                                ******************************************************************* PP

                                 TIGR02082  403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469 
                                                +l+ ++++  + kvPlm+Ds++ evle  L   qGkai+nsi+l+dGeerF + + l+++yGaavvv
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  395 FLKYVVNK--V-KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVV 458 
                                                ********..6.******************************************************* PP

                                 TIGR02082  470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536 
                                                 ++DeeG+a ta++k+e+akR y+ll++k+g++p+diifDp++++++tG e     a++++e ir i
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  459 GTIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETVEGIRLI 525 
                                                ******************************************************************* PP

                                 TIGR02082  537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 
                                                ke lP++ + +GvsnvsF+l   +  Re+l++v+Ly++ +aGlD +ivn+ kl+ y+ i+++ +++ 
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  526 KEALPECLTILGVSNVSFGLP--QVGREVLNAVYLYHCTQAGLDYAIVNTEKLERYASIPENEKQLS 590 
                                                ********************9..999***************************************** PP

                                 TIGR02082  604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670 
                                                  l++d ++   e L e++  y+ +k +     ++ +  nl++eeRL+  +v+G++eg+ edl++a+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  591 DKLLFDTND---ETLAEFTAFYRVKKVE-----KKVQTSNLSLEERLASYIVEGTKEGLIEDLKQAL 649 
                                                *****9876...5688899888877777.....34567899************************** PP

                                 TIGR02082  671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737 
                                                +k+++pl+ii+gpL++Gm+ vG LF + ++ +  v++sa+vmk++va+Le y+ek+   d+ kGki+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  650 EKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAEVMKASVAFLEQYMEKKS-GDNGKGKIL 715 
                                                ******************************************************976.999****** PP

                                 TIGR02082  738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804 
                                                latvkGDvhDiGkn+v+++L++ng+++v+lG+kv  ++++ea k++++D iglsGL+vks ++mv  
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  716 LATVKGDVHDIGKNLVEIILGNNGFKIVNLGIKVTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLT 782 
                                                ******************************************************************* PP

                                 TIGR02082  805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871 
                                                a+++++++++iP+l+GGaal+++++++ i ++Y+g v+y+kda++++ +++kl++e++ ++  e  +
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  783 AQDLKEQNISIPILVGGAALTRKFTDNRISREYDGVVLYAKDAMNGLDLANKLVKEDELKKLEEDKQ 849 
                                                ******************************************************9997555434333 PP

                                 TIGR02082  872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937 
                                                +   ++++  +e+ ek+++++++  r++v ++     + + +p++l  ++l+++ i +l +yi++++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  850 T---KLQQVGNEETEKKNKVTTELPRSKVSQV-----VPIHKPNDLQPHILKEYkISHLEPYINLQM 908 
                                                3...4444445555666777777777544443.....456789999999****************** PP

                                 TIGR02082  938 lFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiyt 1003
                                                l   + +l+gk  + l +   +++a+ l +++++ll + ++++ll+arg++ +fPaqs+g+di iy+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  909 LLGkHLGLHGKVSRLLAEG--DEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYD 973 
                                                *99799*******888775..667899999************************************* PP

                                 TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleak 1070
                                                ++          t +e++ ++rq+ + +lclaD+++s +sG+ Dy+g+l+vtag+g++e a k +++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  974 PQ-------DEKTEIERFSFPRQNHEPFLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKDE 1033
                                                44.......446778899************************************************* PP

                                 TIGR02082 1071 eddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdht 1137
                                                 d+  s l++a a  lae +ae +h+ +R ++ +  +  +l + d +  +Y+G+r +fGYpacP+++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1 1034 GDYLFSHLIQATALELAEGFAERTHQLIRDQWGFP-DPVELTMVDRFSAKYQGVRVSFGYPACPNLE 1099
                                                *****************************987777.77778999*********************** PP

                                 TIGR02082 1138 ekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                ++a+l++Ll++e+iG+klte+++++Peasv++++f+hpe +Yf+v
  lcl|NCBI__GCF_002019605.1:WP_078430828.1 1100 DQAKLFKLLQPEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144
                                                *******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1148 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: 0.08u 0.02s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 12.73
//
[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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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