Alignments for a candidate for metH in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Pseudomonas simiae WCS417

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate GFF2414 PS417_12310 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__WCS417:GFF2414
          Length = 1236

 Score = 1617 bits (4187), Expect = 0.0
 Identities = 823/1235 (66%), Positives = 976/1235 (79%), Gaps = 15/1235 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S +++ L   L ERIL+LDGGMGTMIQSY+L E D+RG+RFADWP D+KGNNDLLV+++P
Sbjct: 5    SVRLQALHQALKERILILDGGMGTMIQSYKLEENDYRGKRFADWPSDVKGNNDLLVITRP 64

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
            +VI  I  AY +AGADI+ETNTFN+T I+MADY ME+L+ E+N   A+LAR  AD  TA 
Sbjct: 65   DVIGGIEKAYLDAGADILETNTFNATRISMADYGMEALAFELNVEGARLARKIADAKTAE 124

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            TP+KPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV  Y E+TK L+EGGADLILIE
Sbjct: 125  TPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIE 184

Query: 182  TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
            T+FDTLNAKAA+FAV+  FE L +ELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185  TIFDTLNAKAAIFAVQGVFEELNIELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244

Query: 242  TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
            + GLNCALG  ELR Y++ELS  A  +V+AHPNAGLPN FGEYD      AK I E+AQ+
Sbjct: 245  SVGLNCALGASELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPSQTAKVIEEFAQS 304

Query: 302  GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
            GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP  I   SLFVNVGE
Sbjct: 305  GFLNIVGGCCGTTPGHIEAIAKAVAGYAPRQIPDIPKACRLSGLEPFTIDRSSLFVNVGE 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+RVPIMIDSSKWDVIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425  GEPDISRVPIMIDSSKWDVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 484

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

Query: 542  FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
            FI AC  I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIRNG+ MGIVNAGQ
Sbjct: 545  FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQ 604

Query: 602  LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
            L IYD +PAELRDAVEDV+LNR  DGT+ LL +A+KY+G        A+  EWR W+VNK
Sbjct: 605  LEIYDQIPAELRDAVEDVVLNRTPDGTDALLAIADKYKGD--GSVKEAETEEWRGWDVNK 662

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE++LVKGIT  I +DTEE+R    RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663  RLEHALVKGITTHIVEDTEESRLSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKS 722

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

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVPAEKIL+ AKE   D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSKA
Sbjct: 783  GVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKA 842

Query: 841  HTAVKIEQNYSG-PTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
            HTAVKIE  YS    VYV +ASR VGV   LLS   +  FV RTR+EY  VR +   +  
Sbjct: 843  HTAVKIEPKYSNDAVVYVTDASRAVGVATQLLSKELKAGFVERTREEYVEVRERTSNRSA 902

Query: 900  RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
            RT  ++  AA      FDW  Y+P V    G + ++   ++ L  YIDWTPFF++W LAG
Sbjct: 903  RTERLSYPAAIAKKPQFDWSTYSPVVPTFTGAKVLDNIDLKVLAEYIDWTPFFISWDLAG 962

Query: 959  KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
            K+PRIL DEVVG  A  L+ DA +ML KL  EK ++ R V G +P N+V  DD+E+Y D+
Sbjct: 963  KFPRILTDEVVGEAATALYADAQEMLKKLIDEKLISARAVFGFWPTNQVQDDDLEVYGDD 1022

Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
             +   I   HHLRQQ  KT G  N+ LADFVAPK SG  DYIG F  T G+  + +A A+
Sbjct: 1023 GQP--IAKLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYIGGFITTAGIGAEEVAKAY 1080

Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
            +   DDYN IMVKALADRLAEA AE+LH++VRK +WGYA +E L NE LI+E Y GIRPA
Sbjct: 1081 QDAGDDYNSIMVKALADRLAEACAEWLHQQVRKEHWGYAKDEQLDNEALIKEQYSGIRPA 1140

Query: 1137 PGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
            PGYPACP+HTEKA +++LL+ E        +G+ LTE +AM+P A+VSGWYF+HP ++Y+
Sbjct: 1141 PGYPACPDHTEKAQLFQLLDPEAREMHAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYF 1200

Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            AV ++ +DQV  Y  RKG  ++  ERWLAPNLGYD
Sbjct: 1201 AVGKVDKDQVASYTARKGQDLSVTERWLAPNLGYD 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: 3790
Number of extensions: 163
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 GFF2414 PS417_12310 (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.17553.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 1756.7   0.0          0 1756.5   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2414  PS417_12310 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2414  PS417_12310 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1756.5   0.0         0         0       1    1182 []      15    1202 ..      15    1202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1756.5 bits;  conditional E-value: 0
                           TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72  
                                          l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL++t+P+vi  i +ay++aGaDi+etntF
  lcl|FitnessBrowser__WCS417:GFF2414   15 LKERILILDGGMGTMIQSYKLEENDYRGKrFADWPSDVKGNNDLLVITRPDVIGGIEKAYLDAGADILETNTF 87  
                                          579********************************************************************** PP

                           TIGR02082   73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144 
                                          n+t i++adY++e++a eln ++a+lar++ad  t  tp+k+RfvaG+lGPt+++ +lspdv++p++rnvt+d
  lcl|FitnessBrowser__WCS417:GFF2414   88 NATRISMADYGMEALAFELNVEGARLARKIADAKTaETPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFD 160 
                                          ********************************99999************************************ PP

                           TIGR02082  145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217 
                                          elv+ Y+e++kgl++GG+Dl+Liet+fDtlnakaa+fav+ vfee ++elPi+isg+i+d+sGrtLsGqt+ea
  lcl|FitnessBrowser__WCS417:GFF2414  161 ELVENYTEATKGLIEGGADLILIETIFDTLNAKAAIFAVQGVFEELNIELPIMISGTITDASGRTLSGQTTEA 233 
                                          ************************************************************************* PP

                           TIGR02082  218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290 
                                          f +s+ ha+ +++GLnCalGa elr++++els++a++ vs++PnaGLPn++geYd++p+++ak+++efa+ g+
  lcl|FitnessBrowser__WCS417:GFF2414  234 FWNSVAHAKPISVGLNCALGASELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPSQTAKVIEEFAQSGF 306 
                                          ************************************************************************* PP

                           TIGR02082  291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363 
                                          lnivGGCCGttP hi aia+av++ +pr+ ++++++++lsgle+++i++ s fvn+GeRtn++Gs+kf++li+
  lcl|FitnessBrowser__WCS417:GFF2414  307 LNIVGGCCGTTPGHIEAIAKAVAGYAPRQIPDIPKACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIR 379 
                                          ************************************************************************* PP

                           TIGR02082  364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436 
                                          +++y eal++a qqve Gaq++Din+De++lD++++m+++l+l+a+epdi++vP+m+Dss+++v+eaGLk+iq
  lcl|FitnessBrowser__WCS417:GFF2414  380 EDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIAGEPDISRVPIMIDSSKWDVIEAGLKCIQ 452 
                                          ************************************************************************* PP

                           TIGR02082  437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509 
                                          Gk+ivnsis+k+G+e+F+++akl k+yGaavvvmafDe Gqa+t ++k ei+kR y++l+++vgfppediifD
  lcl|FitnessBrowser__WCS417:GFF2414  453 GKGIVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEAGQADTEARKKEICKRSYDILVNEVGFPPEDIIFD 525 
                                          ************************************************************************* PP

                           TIGR02082  510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582 
                                          pni+++atGieeh++ya+dfi+a+  i+ elP+a +sgGvsnvsFs+rgn++vRea+hsvFL +ai++Gl mg
  lcl|FitnessBrowser__WCS417:GFF2414  526 PNIFAVATGIEEHNNYAVDFINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRNGLTMG 598 
                                          ************************************************************************* PP

                           TIGR02082  583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655 
                                          ivnag+l++yd+i++elr++ved++l+r ++ t+ Ll +a++ykg  +   kea+++ewr+++v++RLe+alv
  lcl|FitnessBrowser__WCS417:GFF2414  599 IVNAGQLEIYDQIPAELRDAVEDVVLNRTPDGTDALLAIADKYKGDGSV--KEAETEEWRGWDVNKRLEHALV 669 
                                          *********************************************9998..999******************* PP

                           TIGR02082  656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 
                                          kG++ +i ed+ee+r    +p+e+iegpL+ Gm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e ek 
  lcl|FitnessBrowser__WCS417:GFF2414  670 KGITTHIVEDTEESRLSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIELEKG 742 
                                          ***********************************************************************98 PP

                           TIGR02082  729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 
                                          ++ ++kGki++atvkGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++ak++k D+iglsGLi++slde
  lcl|FitnessBrowser__WCS417:GFF2414  743 DKpEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDE 815 
                                          77689******************************************************************** PP

                           TIGR02082  801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekike 872 
                                          mv+va+em+r+ +++Pl++GGa++skah+avki++kY+   vvyv+das+av v+ +lls++ ka ++e+++e
  lcl|FitnessBrowser__WCS417:GFF2414  816 MVHVAREMQRQDFHLPLMIGGATTSKAHTAVKIEPKYSNdAVVYVTDASRAVGVATQLLSKELKAGFVERTRE 888 
                                          *************************************872699****************************** PP

                           TIGR02082  873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944 
                                          ey e+re+ +++  +++ ls  aa  ++ ++d+s  +++++p+f G kvl+++ ++ l +yiDw+++F++W+l
  lcl|FitnessBrowser__WCS417:GFF2414  889 EYVEVRERTSNRSARTERLSYPAAIAKKPQFDWS-TYSPVVPTFTGAKVLDNIdLKVLAEYIDWTPFFISWDL 960 
                                          **********************************.9************************************* PP

                           TIGR02082  945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiat 1016
                                          +gk+p+il+de++g+ a+ l++da+e+l+kl+ ekl+ ar+v+G++P+++v+ dd+e+y d++      pia 
  lcl|FitnessBrowser__WCS417:GFF2414  961 AGKFPRILTDEVVGEAATALYADAQEMLKKLIDEKLISARAVFGFWPTNQVQdDDLEVYGDDGQ-----PIAK 1028
                                          ************************************************9765268*****8877.....8999 PP

                           TIGR02082 1017 vrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlae 1088
                                          +++ ++q+ +  ++ + +laDf+a+k+sG +Dy+g +++tag+gaee ak++++  ddy+si+vkaladrlae
  lcl|FitnessBrowser__WCS417:GFF2414 1029 LHHLRQQIIKTDGKpNFSLADFVAPKDSGVTDYIGGFITTAGIGAEEVAKAYQDAGDDYNSIMVKALADRLAE 1101
                                          988888888888888********************************************************** PP

                           TIGR02082 1089 alaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleae.......riGlk 1154
                                          a ae+lh++vRke+wgya++e+ld+e l+ke+Y Girpa+GYpacPdhteka+l++Ll++e       r G+ 
  lcl|FitnessBrowser__WCS417:GFF2414 1102 ACAEWLHQQVRKEHWGYAKDEQLDNEALIKEQYSGIRPAPGYPACPDHTEKAQLFQLLDPEaremhagRSGVF 1174
                                          **********************************************************9875555444579** PP

                           TIGR02082 1155 lteslalaPeasvsglyfahpeakYfav 1182
                                          lte +a+ P+a+vsg+yfahp+a+Yfav
  lcl|FitnessBrowser__WCS417:GFF2414 1175 LTEHYAMFPAAAVSGWYFAHPQAQYFAV 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 11.79
//
[ok]

This GapMind analysis is from Apr 09 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