Alignments for a candidate for metH in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Kyrpidia tusciae DSM 2912

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_013074393.1 BTUS_RS01655 methionine synthase

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



>NCBI__GCF_000092905.1:WP_013074393.1
          Length = 1159

 Score =  756 bits (1953), Expect = 0.0
 Identities = 489/1214 (40%), Positives = 668/1214 (55%), Gaps = 99/1214 (8%)

Query: 22   LANHVLIGDGAMGTQLQGFDLDVEKDFLD--LEGCNEILNDTRPDVLRQIHRAYFEAGAD 79
            L   +L+ DGAMGT +Q   L    DF     EGCNE+LN TRPDV+  IH AY EAGAD
Sbjct: 24   LKEAILVLDGAMGTMIQQQGLTAA-DFGGEAQEGCNEVLNLTRPDVITSIHEAYLEAGAD 82

Query: 80   LVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPGT 139
            ++ETNTFG     LA+Y +  +   +      +AR  AD  G       RFV G++GP T
Sbjct: 83   IIETNTFGATRVVLAEYGLEGKAYAINRTAAELARRAAD--GYSTPDRPRFVAGAMGPTT 140

Query: 140  KLPSL-GHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDT 198
            K  S+ G   +  L   Y E A G++DGG D  L+ETAQD L VKAA  G+  A AEL  
Sbjct: 141  KTLSVTGGIDFDTLAAAYAEQAKGLLDGGVDLLLVETAQDTLNVKAAGVGIHRAFAELGF 200

Query: 199  FLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHAD 258
             +P++   T+E  GT L G  I A   +++ L    +GLNCATGP+ M++HLR LS  A 
Sbjct: 201  EVPVMISGTIEPMGTTLAGQGIDAFYVSVEHLHPVAVGLNCATGPEFMTDHLRTLSGLAK 260

Query: 259  IPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRD 318
              VS  PNAGLP        Y    + LA+ +AGF  +  +++VGGCCGTTPEHIRA+  
Sbjct: 261  TAVSCYPNAGLP---DEEGHYHESPQSLAEKMAGFARQGWVNVVGGCCGTTPEHIRALAQ 317

Query: 319  AVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSNG 378
            AV G+P        + PA     A   VE          +V L  +    ++GERTN  G
Sbjct: 318  AVRGLPP-------RTPAADHPPAVSGVE----------AVFLEGDNRPLLVGERTNVIG 360

Query: 379  SKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTLP 438
            S+ FRE + SG +E+  +IA+ Q R GA ++D+C+    RD  ADM      +     +P
Sbjct: 361  SRKFRELIQSGRFEEAAEIARAQVRGGAQIIDVCLADPDRDEYADMDQFLKYVTRMVKVP 420

Query: 439  IMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTIDE 498
            +MIDST+P V+   L+   G++I+NS+N EDG   E R+ ++  L +++GAAVV  TIDE
Sbjct: 421  LMIDSTDPRVVELALQRSQGKAIINSINLEDG---EKRFAQVAPLARRYGAAVVVGTIDE 477

Query: 499  EGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAIR 558
            EG A T E K+ +A+R    +T  YG+  +D++ D L FP+ TG E       ET+ A+R
Sbjct: 478  EGMAVTRERKLAVAQRSYQLLTEEYGIPPEDLIFDPLVFPVGTGDENYVGAAAETVAALR 537

Query: 559  ELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRID 618
             LK+ +P   T LG+SN+SFGL PA R+VLN+VFL  C +AGLD AI +  K+     I 
Sbjct: 538  MLKERFPRSATILGISNVSFGLPPAGREVLNAVFLYHCTKAGLDYAIVNPEKLQRYASIP 597

Query: 619  DRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRIID 678
            + +R +A  ++++   E    L  F   F+   A      R E L+   L ERLA+ +++
Sbjct: 598  EEERRLAEALLFETGQE---TLARFHDRFKDRPA--GPPVRRETLS---LNERLARCVVE 649

Query: 679  GDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAVA 738
            G K GL DDL   ++  SPI IIN  L+ GM  VG LF   Q+ +  VLQSAE MK AVA
Sbjct: 650  GSKEGLLDDLSEALQSASPIEIINGPLMAGMDEVGRLFNDNQLIVAEVLQSAEVMKAAVA 709

Query: 739  YLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQP 798
            YLEP ME+       A+   K KI++ATVKGDVHDIGKNLV+IILSNNG++VVNLGIK  
Sbjct: 710  YLEPHMEK-------AETAKKAKILLATVKGDVHDIGKNLVEIILSNNGFEVVNLGIKVA 762

Query: 799  LSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYVEN 858
               ++EA    + D IG+SGLLVKS   M    +++  AG S  P+++GGAALT  +   
Sbjct: 763  PEVLIEAVRREEPDAIGLSGLLVKSAQQMVVTAQDLRAAGVS-LPLLVGGAALTAKFAYT 821

Query: 859  DLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNERSR 918
             +   Y G V YA+DA EGL + + +        +DP       + + + ERK    R  
Sbjct: 822  RIAPEYEGLVLYAKDAMEGLEIANRL--------VDP-------EGRPELERKTAELR-- 864

Query: 919  KIAAERKANAAPVIV----PERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALF 974
              A+     AAP +     P RS VS   P A PP     + +  P       ++ + L 
Sbjct: 865  --ASLTDRPAAPAVSTGSRPRRSSVSRTVPVAVPPDCRRHLWRDYPFDHVQPYINLQMLL 922

Query: 975  MGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRL-------KSEGILDHVALVYGYFP 1027
                GL   RGN      D +  E  P+   W++RL       K EG+L  +  VY +FP
Sbjct: 923  GRHMGL---RGN-----VDKLLAERDPKAVEWVERLNALIAEAKGEGLL-RLHAVYQFFP 973

Query: 1028 AVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQL 1087
            + +EGDD++I +   P      RF+FPRQ R  +LC++D++RP    V+ G++D + F  
Sbjct: 974  SQSEGDDILIYDPEQPGRVIE-RFTFPRQGREPYLCLSDYVRP----VESGEMDYVAFFA 1028

Query: 1088 VTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADF 1147
            VT G  I D A E  A  EY +   +  + ++  EA AE  H  +R              
Sbjct: 1029 VTAGAGIRDKAEEWKARGEYVKSHFLQALALETAEAFAERLHGMIRDLWGFP-------- 1080

Query: 1148 DPEDKT--KFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQS 1205
            DP D T  + F   YRG R SFGY +CP+LED+AKL  LL P  IG+ L++   + PE S
Sbjct: 1081 DPPDMTMRERFQAKYRGIRVSFGYPACPNLEDQAKLFRLLRPEEIGIRLTDGFMMDPEAS 1140

Query: 1206 TDAFVLYHPEAKYF 1219
              A V  HPEA YF
Sbjct: 1141 VSALVFSHPEAVYF 1154


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: 3147
Number of extensions: 153
Number of successful extensions: 14
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: 1159
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1112
Effective search space:  1305488
Effective search space used:  1305488
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_013074393.1 BTUS_RS01655 (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.28638.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 1262.9   0.0          0 1262.7   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074393.1  BTUS_RS01655 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074393.1  BTUS_RS01655 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1262.7   0.0         0         0       2    1181 ..      25    1155 ..      24    1156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1262.7 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68  
                                                ++ ilvlDGamGt++q++ Lt+adF ge       ++G+n++Lnlt+P+vi++ih+ay+eaGaDi+e
  lcl|NCBI__GCF_000092905.1:WP_013074393.1   25 KEAILVLDGAMGTMIQQQGLTAADFGGE------AQEGCNEVLNLTRPDVITSIHEAYLEAGADIIE 85  
                                                688************************7......89******************************* PP

                                 TIGR02082   69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135 
                                                tntF++t ++la+Y+le kay++n++aa+lar++ad ++ tp+++RfvaG++GPt+k+ +++     
  lcl|NCBI__GCF_000092905.1:WP_013074393.1   86 TNTFGATRVVLAEYGLEGKAYAINRTAAELARRAADGYS-TPDRPRFVAGAMGPTTKTLSVT----- 146 
                                                ***************************************.*********************9..... PP

                                 TIGR02082  136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202 
                                                     +++d+l +aY eq+kglldGGvDllL+et +Dtln+kaa ++++++f+e g e+P++isg+i
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  147 ---GGIDFDTLAAAYAEQAKGLLDGGVDLLLVETAQDTLNVKAAGVGIHRAFAELGFEVPVMISGTI 210 
                                                ...78***********************************************************875 PP

                                 TIGR02082  203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269 
                                                 + +G+tL Gq ++af++s+eh + +++GLnCa+G++ + +++++ls  a++ vs++PnaGLP++ g
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  211 -EPMGTTLAGQGIDAFYVSVEHLHPVAVGLNCATGPEFMTDHLRTLSGLAKTAVSCYPNAGLPDEEG 276 
                                                .99**************************************************************** PP

                                 TIGR02082  270 eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealk 336 
                                                +Y++ p++la++++ fa++g +n+vGGCCGttPehira+a+av+++ pr     +++ ++sg+ea+ 
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  277 HYHESPQSLAEKMAGFARQGWVNVVGGCCGTTPEHIRALAQAVRGLPPRTPA-ADHPPAVSGVEAVF 342 
                                                **********************************************999765.5666788******* PP

                                 TIGR02082  337 iaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkl 403 
                                                ++ ++  + +GeRtnv Gs+kfr+li+ + +eea +ia+ qv+ Gaqi+D+++ +  +D  adm ++
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  343 LEGDNRPLLVGERTNVIGSRKFRELIQSGRFEEAAEIARAQVRGGAQIIDVCLADPDRDEYADMDQF 409 
                                                ******************************************************************* PP

                                 TIGR02082  404 lsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvm 470 
                                                l+ ++    + kvPlm+Ds++  v+e  L++ qGkai+nsi+l+dGe+rF++ a l+++yGaavvv 
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  410 LKYVTRM--V-KVPLMIDSTDPRVVELALQRSQGKAIINSINLEDGEKRFAQVAPLARRYGAAVVVG 473 
                                                **99988..5.******************************************************** PP

                                 TIGR02082  471 afDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireik 537 
                                                ++DeeG+a t+++k+ +a+R y+llte++g+pped+ifDp++++++tG e+    a +++ a+r +k
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  474 TIDEEGMAVTRERKLAVAQRSYQLLTEEYGIPPEDLIFDPLVFPVGTGDENYVGAAAETVAALRMLK 540 
                                                ******************************************************************* PP

                                 TIGR02082  538 eelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevve 604 
                                                e++P   + +G+snvsF+l   +a Re+l++vFLy++ kaGlD +ivn+ kl+ y+ i++e r ++e
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  541 ERFPRSATILGISNVSFGLP--PAGREVLNAVFLYHCTKAGLDYAIVNPEKLQRYASIPEEERRLAE 605 
                                                ********************..********************************************* PP

                                 TIGR02082  605 dlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleeark 671 
                                                 l+++     +e L ++ +++k+  +             l+++eRL+r +v+G +eg+ +dl ea+ 
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  606 ALLFET---GQETLARFHDRFKDRPAGPP-----VRRETLSLNERLARCVVEGSKEGLLDDLSEAL- 663 
                                                ****85...67889*********999833.....3456799*************************. PP

                                 TIGR02082  672 klkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivl 738 
                                                +  +p+eii+gpL++Gm+ vG LF + ++ +  v++sa+vmk+avayLeP++ek +  + +k ki+l
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  664 QSASPIEIINGPLMAGMDEVGRLFNDNQLIVAEVLQSAEVMKAAVAYLEPHMEKAE--TAKKAKILL 728 
                                                899*************************************************9876..788999*** PP

                                 TIGR02082  739 atvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemveva 805 
                                                atvkGDvhDiGkn+v+++Ls+ng+evv+lG+kv  e ++ea +++++D iglsGL+vks ++mv  a
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  729 ATVKGDVHDIGKNLVEIILSNNGFEVVNLGIKVAPEVLIEAVRREEPDAIGLSGLLVKSAQQMVVTA 795 
                                                ******************************************************************* PP

                                 TIGR02082  806 eemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekike 872 
                                                ++++  gv++Pll+GGaal+ ++  + ia++Y+g v+y+kda+e+++++++l++ +   +e   +++
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  796 QDLRAAGVSLPLLVGGAALTAKFAYTRIAPEYEGLVLYAKDAMEGLEIANRLVDPEG-RPE---LER 858 
                                                *****************************************************9995.444...344 PP

                                 TIGR02082  873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkal 938 
                                                +  e+r + +  +    a+s+   r+ + ++ r+  + v++p++  ++  +++  +++ +yi++++l
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  859 KTAELRASLTD-RPAAPAVST-GSRPRRSSVSRT--VPVAVPPDCRRHLWRDYpFDHVQPYINLQML 921 
                                                44556655554.444555554.445566666666..88999************************** PP

                                 TIGR02082  939 Fv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytd 1004
                                                   + +lrg+ +k l +  ++ +a +  +++++l+ + + e+llr ++v+ +fP+qs+gddi iy++
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  922 LGrHMGLRGNVDKLLAE--RDPKAVEWVERLNALIAEAKGEGLLRLHAVYQFFPSQSEGDDILIYDP 986 
                                                99899*******98887..567788999**************************************6 PP

                                 TIGR02082 1005 etvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleake 1071
                                                e+          v+e++ ++rq ++ ylcl+D++++ esG+ Dy+++++vtag g+++ a++++a+ 
  lcl|NCBI__GCF_000092905.1:WP_013074393.1  987 EQP-------GRVIERFTFPRQGREPYLCLSDYVRPVESGEMDYVAFFAVTAGAGIRDKAEEWKARG 1046
                                                654.......6677899************************************************** PP

                                 TIGR02082 1072 ddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhte 1138
                                                ++ +s  ++ala   aea+ae lh  +R  lwg  +  +  +++ ++ +YrGir +fGYpacP++++
  lcl|NCBI__GCF_000092905.1:WP_013074393.1 1047 EYVKSHFLQALALETAEAFAERLHGMIRD-LWGFPDPPDMTMRERFQAKYRGIRVSFGYPACPNLED 1112
                                                ***************************96.6777688888999************************ PP

                                 TIGR02082 1139 katlleLleaeriGlklteslalaPeasvsglyfahpeakYfa 1181
                                                +a+l++Ll +e+iG++lt+ +++ Peasvs+l+f+hpea Yf 
  lcl|NCBI__GCF_000092905.1:WP_013074393.1 1113 QAKLFRLLRPEEIGIRLTDGFMMDPEASVSALVFSHPEAVYFR 1155
                                                ******************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1159 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 0.04s 00:00:00.12 Elapsed: 00:00:00.12
# Mc/sec: 11.04
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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