Alignments for a candidate for metH in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Rhodospirillum rubrum ATCC 11170

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate YP_426618.1 Rru_A1531 methionine synthase (B12-dependent)

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



>NCBI__GCF_000013085.1:YP_426618.1
          Length = 1182

 Score = 1009 bits (2609), Expect = 0.0
 Identities = 582/1231 (47%), Positives = 779/1231 (63%), Gaps = 75/1231 (6%)

Query: 16   SEFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFE 75
            S FLD L N VL+ DG MG+ +Q  DL V+ DF+  E C E+LN +RPDV+R IH  YF 
Sbjct: 2    SRFLDHLRNRVLLCDGGMGSLVQAMDLSVDGDFMGRENCTEVLNLSRPDVVRDIHTRYFA 61

Query: 76   AGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSL 135
            AGAD VETNTFG +   LA++D+ADR RE+  +   +ARE A+    GR+   RFV+GS+
Sbjct: 62   AGADCVETNTFGGSTLTLAEFDLADRTREINRRAAEIAREAAESFADGRD---RFVLGSI 118

Query: 136  GPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAE 195
            GPGTKLPSLGH  Y  L+        G+I+GG DA L+ET QD LQ KAA++  + A   
Sbjct: 119  GPGTKLPSLGHIDYDTLKDAITVQCEGLIEGGADAILVETCQDPLQFKAAINAAKAARLA 178

Query: 196  LDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSK 255
            L +   I+  VTVETTGT+L+G++I AA T    LG+D +GLNCATGP EMSEH+R+L +
Sbjct: 179  LGSDTAILLQVTVETTGTLLVGADIAAAATVAHALGVDSLGLNCATGPQEMSEHVRWLKE 238

Query: 256  HADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRA 315
            +    +S+ PNAGLP L      YPL   +LA     F+ E G++++GGCCGTTP+HI A
Sbjct: 239  NWPGLISLQPNAGLPELLDGKTHYPLTPAELADWHGRFIREDGVNLIGGCCGTTPDHIAA 298

Query: 316  VRDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTN 375
            V   +      ET    + PA PV+   R V    SVASLY +VP+ QE     IGER N
Sbjct: 299  VNAML------ETLGQGRRPA-PVK---RSVHWVPSVASLYGAVPMRQENAFLSIGERCN 348

Query: 376  SNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSS 435
            +NGSK FR    + DW+  V +A++Q ++G+H LD+C  +VGR   ADM  + + L    
Sbjct: 349  ANGSKKFRTFQDNEDWDAIVGMAREQVKEGSHTLDVCTAFVGRKEGADMTEVVSRLRGGV 408

Query: 436  TLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALT 495
              P++IDSTE  V+   L+  GG++I+NS+NFEDG+  ES  QR + L ++ GAAV+ALT
Sbjct: 409  NAPLVIDSTETPVLTQALKLYGGKAIINSINFEDGE--ESAAQR-LALAREFGAAVIALT 465

Query: 496  IDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIE 555
            IDEEG A+ AE K+RIA RL D     +GL   D++ D LTF I TG  + RR G+ET++
Sbjct: 466  IDEEGMAKDAEAKLRIAHRLYDFAVTQHGLPASDLMFDPLTFTICTGNTDDRRLGLETLD 525

Query: 556  AIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMN 615
            AIR ++   PE    LGLSNISFGL P AR VLNSVFL++ +EAG+  AI H SKILP++
Sbjct: 526  AIRRIRTELPECQIILGLSNISFGLKPVARHVLNSVFLDKAVEAGMTGAIVHISKILPLH 585

Query: 616  RIDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQR 675
            +I   + + A D+++DRR   YDPL  F+ LFE  S       RAE +      ERL QR
Sbjct: 586  KIPADEVKAAEDLIFDRRAPGYDPLHAFIALFEDRSETKVAVKRAETVE-----ERLKQR 640

Query: 676  IIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKT 735
            I+DGD+ GL+ DL   M +  P+ IIN  LL+GMK VGELFG+G+MQLPFVLQSAETMK 
Sbjct: 641  IVDGDRLGLDADLTEAMGKYPPLEIINSLLLDGMKVVGELFGAGKMQLPFVLQSAETMKA 700

Query: 736  AVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGI 795
            AVA+LEP ME+        + + KG IV+ATVKGDVHDIGKNLVDIILSNNGY V+N+GI
Sbjct: 701  AVAFLEPHMEK-------IEGQEKGIIVLATVKGDVHDIGKNLVDIILSNNGYKVINIGI 753

Query: 796  KQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTY 855
            KQP++A+L +A E++AD IGMSGLLVKSTV+MK+NLEEM   G  N PV+LGGAALTR +
Sbjct: 754  KQPIAAILASARENRADAIGMSGLLVKSTVIMKDNLEEMAREG-WNTPVLLGGAALTRAF 812

Query: 856  VENDLNEVY--TGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKAR 913
            VE D    Y  +G V YARDAF+GL LM +V      EG       A++Q  K+A R +R
Sbjct: 813  VEEDCVSAYAGSGRVAYARDAFDGLDLMAKV-----AEGRFDTHLSAVQQ--KRAGRPSR 865

Query: 914  ----------NERSRKIA---------AERKANAAPV----IVPERSDVSTDTPTAAPPF 950
                      N+ S KIA         A  K +  PV    I+  R++++ D     PPF
Sbjct: 866  RPKAPPLWPANDPSSKIAPRTLDDQDTAIHKISERPVDAEEILLRRAELARDHVVPTPPF 925

Query: 951  WGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRL 1010
            WG ++++ + L   +  ++E  LF  QWG +   G     ++D   +E RP +   L   
Sbjct: 926  WGAKVLESISLKSLVPYINEATLFQFQWGFRK-GGRTREEWKDWAASEIRPIMFDMLKTC 984

Query: 1011 KSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRP 1070
              E IL   A VYG++ A ++GD +V+    +    E  RF  PRQ     +C+ADF+R 
Sbjct: 985  AQEEILKPRA-VYGFWKAASQGDAIVLF--AEDGTTEVGRFDLPRQTIEGGICLADFVRD 1041

Query: 1071 REQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHS 1130
                +  G+ DV+  Q VT+G   +D   + FAAN Y++YL +HGI V++ EA+AEY H 
Sbjct: 1042 ----IDSGERDVIALQAVTVGARASDVCRDWFAANRYKDYLYLHGISVEVAEAMAEYVHK 1097

Query: 1131 RVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRI 1190
            R+R+EL     G  A+ +  D  +    +YRG+R+SFGY +CP+L D+ +L++LL   RI
Sbjct: 1098 RIRAEL-----GFAAE-EARDIERMIKQEYRGSRYSFGYPACPNLGDQRQLLDLLGAERI 1151

Query: 1191 GVELSEELQLHPEQSTDAFVLYHPEAKYFNV 1221
             ++LS+E +L PEQST A VL HP+AKYF +
Sbjct: 1152 ELDLSDEDELVPEQSTSALVLLHPQAKYFRI 1182


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: 3187
Number of extensions: 129
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: 1182
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1135
Effective search space:  1332490
Effective search space used:  1332490
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 YP_426618.1 Rru_A1531 (methionine synthase (B12-dependent))
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.21243.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 1252.2   0.0          0 1252.0   0.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_426618.1  Rru_A1531 methionine synthase (B


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_426618.1  Rru_A1531 methionine synthase (B12-dependent)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1252.0   0.0         0         0       1    1182 []       8    1182 .]       8    1182 .] 0.95

  Alignments for each domain:
  == domain 1  score: 1252.0 bits;  conditional E-value: 0
                              TIGR02082    1 lnkrilvlDGamGtqlqsanLtea.dFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivet 69  
                                             l++r+l+ DG+mG  +q+++L  + dF g         + + ++Lnl++P+v+++ih +yf aGaD vet
  lcl|NCBI__GCF_000013085.1:YP_426618.1    8 LRNRVLLCDGGMGSLVQAMDLSVDgDFMGR--------ENCTEVLNLSRPDVVRDIHTRYFAAGADCVET 69  
                                             579******************96449***5........89****************************** PP

                              TIGR02082   70 ntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefr 139 
                                             ntF++++++la++dl+d+++e+n++aa++are+a+ f     + Rfv+Gs+GP++kl++l+         
  lcl|NCBI__GCF_000013085.1:YP_426618.1   70 NTFGGSTLTLAEFDLADRTREINRRAAEIAREAAESFA--DGRDRFVLGSIGPGTKLPSLG--------- 128 
                                             *************************************9..7889*****************......... PP

                              TIGR02082  140 nvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrt 209 
                                             +++yd+l+da ++q +gl++GG+D++L+et++D l+ kaa++a++ +  + g++  il++ v+v+++G++
  lcl|NCBI__GCF_000013085.1:YP_426618.1  129 HIDYDTLKDAITVQCEGLIEGGADAILVETCQDPLQFKAAINAAKAARLALGSDTAILLQ-VTVETTGTL 197 
                                             ************************************************************.********* PP

                              TIGR02082  210 LsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdltpe 276 
                                             L+G +++a+++  +  ++++lGLnCa+G++e++e+v+ l e+ + l+s+ PnaGLP+ l    +Y+ltp 
  lcl|NCBI__GCF_000013085.1:YP_426618.1  198 LVGADIAAAATVAHALGVDSLGLNCATGPQEMSEHVRWLKENWPGLISLQPNAGLPELLDgktHYPLTPA 267 
                                             *********************************************************997788******* PP

                              TIGR02082  277 elakalkefaeegllnivGGCCGttPehiraiaeavkdi......kprkrqeleeksvlsglealkiaqe 340 
                                             ela     f++e ++n++GGCCGttP+hi+a+ ++ + +      +p kr  +  +sv+s++ a+++ qe
  lcl|NCBI__GCF_000013085.1:YP_426618.1  268 ELADWHGRFIREDGVNLIGGCCGTTPDHIAAVNAMLETLgqgrrpAPVKRSVHWVPSVASLYGAVPMRQE 337 
                                             ***********************************999833222234455558899************** PP

                              TIGR02082  341 ssfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllase 410 
                                             + f+ iGeR+n++Gskkfr    +ed+++ + +a++qv+eG++ lD++   v++   adm++++s+l + 
  lcl|NCBI__GCF_000013085.1:YP_426618.1  338 NAFLSIGERCNANGSKKFRTFQDNEDWDAIVGMAREQVKEGSHTLDVCTAFVGRKEGADMTEVVSRLRGG 407 
                                             *********************************************************************9 PP

                              TIGR02082  411 pdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqart 480 
                                               + + Pl++Ds+e+ vl + Lk  +Gkai+nsi+++dGee  +++++l++e+Gaav+++++DeeG+a++
  lcl|NCBI__GCF_000013085.1:YP_426618.1  408 --V-NAPLVIDSTETPVLTQALKLYGGKAIINSINFEDGEESAAQRLALAREFGAAVIALTIDEEGMAKD 474 
                                             ..5.78**************************************************************** PP

                              TIGR02082  481 adkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvs 550 
                                             a+ k++ia+R+y+ ++ + g+p++d++fDp+++ti tG  +++r ++++++air+i+ elP+++i +G+s
  lcl|NCBI__GCF_000013085.1:YP_426618.1  475 AEAKLRIAHRLYDFAVTQHGLPASDLMFDPLTFTICTGNTDDRRLGLETLDAIRRIRTELPECQIILGLS 544 
                                             ********************************************************************** PP

                              TIGR02082  551 nvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLle 620 
                                             n+sF+l+  + +R++l+svFL +a++aG+  +iv+ +k++++++i+++  +++edli+drr   +++L  
  lcl|NCBI__GCF_000013085.1:YP_426618.1  545 NISFGLK--PVARHVLNSVFLDKAVEAGMTGAIVHISKILPLHKIPADEVKAAEDLIFDRRAPGYDPLHA 612 
                                             *******..************************************************************* PP

                              TIGR02082  621 laelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkv 690 
                                             ++ l+++ +e+     + a  r   veeRL++++v+G r g+++dl ea+  +++pleii+  LldGmkv
  lcl|NCBI__GCF_000013085.1:YP_426618.1  613 FIALFEDRSET-----KVAVKRAETVEERLKQRIVDGDRLGLDADLTEAM-GKYPPLEIINSLLLDGMKV 676 
                                             *******9998.....467788999*************************.8889*************** PP

                              TIGR02082  691 vGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscn 760 
                                             vG+LFG+Gkm+LP+v++sa++mk+ava+LeP++ek +   + kG ivlatvkGDvhDiGkn+vd++Ls+n
  lcl|NCBI__GCF_000013085.1:YP_426618.1  677 VGELFGAGKMQLPFVLQSAETMKAAVAFLEPHMEKIE--GQEKGIIVLATVKGDVHDIGKNLVDIILSNN 744 
                                             *********************************9876..889**************************** PP

                              TIGR02082  761 gyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahva 830 
                                             gy+v+++G+k+P++ il  a++++aD ig+sGL+vks++ m+ ++eem r+g ++P+llGGaal++a+v+
  lcl|NCBI__GCF_000013085.1:YP_426618.1  745 GYKVINIGIKQPIAAILASARENRADAIGMSGLLVKSTVIMKDNLEEMAREGWNTPVLLGGAALTRAFVE 814 
                                             ********************************************************************** PP

                              TIGR02082  831 vkiaekY..kgevvyvkdaseavkvvdkllsekkk....................aeelekikeeyeeir 878 
                                              ++ ++Y  +g+v y++da++++ +++k+ + +                       +   ++    + + 
  lcl|NCBI__GCF_000013085.1:YP_426618.1  815 EDCVSAYagSGRVAYARDAFDGLDLMAKVAEGRFDthlsavqqkragrpsrrpkaPPLWPANDPSSKIAP 884 
                                             *******44468****************998877688999999********9996334444444455555 PP

                              TIGR02082  879 ekfgekkeklialsekaarkevfaldrse...dlevpapkflGtkvleas.ieellkyiDwkalFv.qWe 943 
                                             ++   + + ++++se+    e++ l r e   d  vp+p+f+G kvle++ ++ l++yi++ +lF  qW+
  lcl|NCBI__GCF_000013085.1:YP_426618.1  885 RTLDDQDTAIHKISERPVDAEEILLRRAElarDHVVPTPPFWGAKVLESIsLKSLVPYINEATLFQfQWG 954 
                                             66666777777888888777787777777777999**************99**************99*** PP

                              TIGR02082  944 lrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkp 1013
                                             +r+     +++e ++  a ++++++ ++l++  +e+ l++r+v+G++ a s+gd i++++++++      
  lcl|NCBI__GCF_000013085.1:YP_426618.1  955 FRKGGR--TREEWKDWAASEIRPIMFDMLKTCAQEEILKPRAVYGFWKAASQGDAIVLFAEDGT------ 1016
                                             *98655..99**************************************************8887...... PP

                              TIGR02082 1014 iatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkala 1083
                                               t   +++ +rq  +  +claDf+++ +sG++D++++++vt+g  a++  ++++a + ++d++++++++
  lcl|NCBI__GCF_000013085.1:YP_426618.1 1017 --TEVGRFDLPRQTIEGGICLADFVRDIDSGERDVIALQAVTVGARASDVCRDWFAANRYKDYLYLHGIS 1084
                                             ..556789************************************************************** PP

                              TIGR02082 1084 drlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGl 1153
                                             + +aea+ae++h+r+R el +  +ee+ d+e ++k++YrG+r++fGYpacP++ ++++ll+Ll aeri l
  lcl|NCBI__GCF_000013085.1:YP_426618.1 1085 VEVAEAMAEYVHKRIRAELGFA-AEEARDIERMIKQEYRGSRYSFGYPACPNLGDQRQLLDLLGAERIEL 1153
                                             *******************998.8999******************************************* PP

                              TIGR02082 1154 klteslalaPeasvsglyfahpeakYfav 1182
                                              l+++ +l Pe+s+s+l++ hp+akYf +
  lcl|NCBI__GCF_000013085.1:YP_426618.1 1154 DLSDEDELVPEQSTSALVLLHPQAKYFRI 1182
                                             ***************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1182 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: 0.10u 0.04s 00:00:00.14 Elapsed: 00:00:00.13
# Mc/sec: 10.56
//
[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)
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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