Alignments for a candidate for metH in Methyloferula stellata AR4T

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Methyloferula stellata AR4T

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_020177190.1 A3OQ_RS0119825 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000385335.1:WP_020177190.1
          Length = 1242

 Score = 1514 bits (3921), Expect = 0.0
 Identities = 777/1226 (63%), Positives = 932/1226 (76%), Gaps = 11/1226 (0%)

Query: 8    LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
            LRA   E+ILVLDG MGTMIQ ++  EADFR ERFADWP DL+GNNDLLVL++P  I AI
Sbjct: 10   LRAAAREKILVLDGAMGTMIQQHKFTEADFRAERFADWPRDLRGNNDLLVLTQPHAIRAI 69

Query: 68   HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
            H AY +AGADII TNTF+ST IA ADY ME L  E+NF AA+LA   A E   R   +  
Sbjct: 70   HLAYCDAGADIIATNTFSSTRIAQADYGMERLVPELNFEAARLACEAAHESEERHGRR-H 128

Query: 128  YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
            +VAG LGPTNRTASISPDVN+P FR ++FD L  AY E+ +AL+EGG D++++ET+FDTL
Sbjct: 129  FVAGALGPTNRTASISPDVNNPGFRAVSFDELRDAYAEAARALIEGGVDILIVETIFDTL 188

Query: 188  NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
            NAKAA+  +   F+ +G +LP+MISGTITD SGRTLSGQT  AF+NSLRHA+  T GLNC
Sbjct: 189  NAKAALVGIDQVFDDMGKKLPVMISGTITDLSGRTLSGQTPTAFWNSLRHAKPFTIGLNC 248

Query: 248  ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
            ALG  E+R ++ E+SRIA+ YV A+PNAGLPN FG YD   + MA  I E+A++G +NIV
Sbjct: 249  ALGAREMRAHLAEISRIADTYVCAYPNAGLPNEFGLYDESPEYMASLIGEFAESGLVNIV 308

Query: 308  GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
            GGCCGTTP HI A+++ V G+APRK+PEI    RLSGLEP  + ++  FVNVGERTNVTG
Sbjct: 309  GGCCGTTPPHIHAIAKRVVGIAPRKIPEIVPLLRLSGLEPFALTKEIRFVNVGERTNVTG 368

Query: 368  SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
            SAKF++LIKE  +S ALDVAR QV  GAQ+IDINMDEG+LD+E AMV FLNL+A EPDIA
Sbjct: 369  SAKFRKLIKEGDFSAALDVARDQVVAGAQVIDINMDEGLLDSEKAMVDFLNLVAAEPDIA 428

Query: 428  RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
            RVP+M+DSSK+ VIE GLKCIQGK IVNSISMKEG + F+  AKL+RRYGAAVVVMAFDE
Sbjct: 429  RVPVMVDSSKFQVIESGLKCIQGKPIVNSISMKEGEEKFVEVAKLVRRYGAAVVVMAFDE 488

Query: 488  QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
            QGQADT ARKIEIC RAYKILTE VGFPPEDIIFDPNIFAVATGIEEHNNY  DFI A  
Sbjct: 489  QGQADTCARKIEICSRAYKILTETVGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATR 548

Query: 548  DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
            ++++  P   ISGGVSN+SFSFRGN+ VR+A+H+VFLY+AI  GMDMGIVNAGQL++Y+D
Sbjct: 549  EVRKRFPLVHISGGVSNLSFSFRGNEMVRQAMHSVFLYHAISAGMDMGIVNAGQLSVYED 608

Query: 608  LPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSL 667
            +  ELRDA EDV+LNRR DGTERLL LAE+++G  T+     +   WRS  V KRLE++L
Sbjct: 609  IDPELRDACEDVVLNRRPDGTERLLALAERFKGQGTERA--EKDLVWRSEPVEKRLEHAL 666

Query: 668  VKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQ 727
            V GITEFI+ DTEEAR ++TRP++VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQ
Sbjct: 667  VNGITEFIDADTEEARAKSTRPLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKQ 726

Query: 728  AVAYLEPFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGV 782
            AVAYL P++E  K +      K  GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGV
Sbjct: 727  AVAYLMPYMEEEKRKNGGAERKNAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGV 786

Query: 783  MVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHT 842
            MVP  KIL  A+    D IGLSGLITPSLDEM  VA EMER+GF++PLLIGGATTS+ HT
Sbjct: 787  MVPCAKILDVARTEKVDAIGLSGLITPSLDEMCFVASEMEREGFSMPLLIGGATTSRVHT 846

Query: 843  AVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
            AVKI  NY+ G TVYV +ASR VGVV  L S   R  ++   + EYE V   H R +   
Sbjct: 847  AVKINPNYTKGQTVYVTDASRAVGVVQNLFSPAARGPYIEAIKTEYENVAEAHMRNEAEK 906

Query: 902  PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKY 960
                L  AR N    DW AY PP    LG +      +  L  YIDWTPFF TW + G+Y
Sbjct: 907  NRQPLPRARANALKLDWAAYEPPHPTFLGTRIFRTYDVAELVPYIDWTPFFQTWEMRGRY 966

Query: 961  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
            P IL D   G  AQ+LF DA  ML ++  E   +P+ V+G +PAN +GDDI++Y  E+R+
Sbjct: 967  PDILSDPEKGAAAQQLFDDAQAMLARIVEEHWFDPKAVIGFWPANAIGDDIKLYTGESRS 1026

Query: 1021 HVINVSHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
             V+   H LRQQ +++ G  N  ++D++AP  S K DY+G F VT G  E+ +AD F   
Sbjct: 1027 EVLATFHTLRQQLSKRDGRPNIAMSDYIAPVESLKPDYLGGFVVTAGAREEKIADRFAKA 1086

Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
            +DDY  IMVKALADR+AEAFAE +HERVRK +W YAP+E L+ +ELI E Y+GIRPAPGY
Sbjct: 1087 NDDYGSIMVKALADRIAEAFAERMHERVRKEFWAYAPDEALAPDELITEPYRGIRPAPGY 1146

Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
            PA P+HTEKAT++ LLE E+  G+ LTESFAMWPG+SVSG Y SHPD++Y+ VA+I+RDQ
Sbjct: 1147 PAQPDHTEKATLFRLLEPERRIGVTLTESFAMWPGSSVSGLYLSHPDARYFGVAKIERDQ 1206

Query: 1200 VEDYARRKGMSVTEVERWLAPNLGYD 1225
            VEDYA RKGM   E+ERWLAP L YD
Sbjct: 1207 VEDYALRKGMDFAEMERWLAPILNYD 1232


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: 3675
Number of extensions: 155
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: 1242
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1194
Effective search space:  1407726
Effective search space used:  1407726
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 WP_020177190.1 A3OQ_RS0119825 (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.2142.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 1753.4   0.0          0 1753.2   0.0    1.0  1  lcl|NCBI__GCF_000385335.1:WP_020177190.1  A3OQ_RS0119825 methionine syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000385335.1:WP_020177190.1  A3OQ_RS0119825 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1753.2   0.0         0         0       2    1182 .]      15    1199 ..      14    1199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1753.2 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                +++ilvlDGamGt++q+++ teadFr e +ad++r+l+GnndlL+lt+P +i+aih ay +aGaDi+
  lcl|NCBI__GCF_000385335.1:WP_020177190.1   15 REKILVLDGAMGTMIQQHKFTEADFRAErFADWPRDLRGNNDLLVLTQPHAIRAIHLAYCDAGADII 81  
                                                689**************************************************************** PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                 tntF+st ia+adY++e ++ eln++aa+la e+a+e +    ++ fvaG+lGPtn++a++spdv+
  lcl|NCBI__GCF_000385335.1:WP_020177190.1   82 ATNTFSSTRIAQADYGMERLVPELNFEAARLACEAAHESEERHGRRHFVAGALGPTNRTASISPDVN 148 
                                                ****************************************888999********************* PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                +p+fr v +del+daY e++++l++GGvD+l++et+fDtlnakaal+++ +vf++ g++lP++isg+
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  149 NPGFRAVSFDELRDAYAEAARALIEGGVDILIVETIFDTLNAKAALVGIDQVFDDMGKKLPVMISGT 215 
                                                ******************************************************************* PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                i+d sGrtLsGqt  af +sl+ha+ +++GLnCalGa e+r ++ e+s++a+++v ++PnaGLPn++
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  216 ITDLSGRTLSGQTPTAFWNSLRHAKPFTIGLNCALGAREMRAHLAEISRIADTYVCAYPNAGLPNEF 282 
                                                ******************************************************************* PP

                                 TIGR02082  269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335 
                                                g Yd+ pe +a+ + efae gl+nivGGCCGttP hi+aia+ v +i+prk +e+ + ++lsgle++
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  283 GLYDESPEYMASLIGEFAESGLVNIVGGCCGTTPPHIHAIAKRVVGIAPRKIPEIVPLLRLSGLEPF 349 
                                                ******************************************************************* PP

                                 TIGR02082  336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402 
                                                 +++e  fvn+GeRtnv+Gs+kfrklik++d+++al++a++qv  Gaq++Din+De+llD+e++m+ 
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  350 ALTKEIRFVNVGERTNVTGSAKFRKLIKEGDFSAALDVARDQVVAGAQVIDINMDEGLLDSEKAMVD 416 
                                                ******************************************************************* PP

                                 TIGR02082  403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469 
                                                +l+l+a+epdia+vP+m+Dss+f+v+e GLk+iqGk ivnsis+k+Gee+F+e akl+++yGaavvv
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  417 FLNLVAAEPDIARVPVMVDSSKFQVIESGLKCIQGKPIVNSISMKEGEEKFVEVAKLVRRYGAAVVV 483 
                                                ******************************************************************* PP

                                 TIGR02082  470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536 
                                                mafDe+Gqa+t ++kiei++Rayk+lte vgfppediifDpni+++atGieeh++y++dfiea+re+
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  484 MAFDEQGQADTCARKIEICSRAYKILTETVGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATREV 550 
                                                ******************************************************************* PP

                                 TIGR02082  537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 
                                                ++++P ++isgGvsn+sFs+rgn+ vR+a+hsvFLy+ai aG+Dmgivnag+l vy+did+elr+++
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  551 RKRFPLVHISGGVSNLSFSFRGNEMVRQAMHSVFLYHAISAGMDMGIVNAGQLSVYEDIDPELRDAC 617 
                                                ******************************************************************* PP

                                 TIGR02082  604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670 
                                                ed++l+rr++ te+Ll lae++kg+ ++  + ++   wr+ pve+RLe+alv+G++e+i++d+eear
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  618 EDVVLNRRPDGTERLLALAERFKGQGTE--RAEKDLVWRSEPVEKRLEHALVNGITEFIDADTEEAR 682 
                                                ***************************9..5568889****************************** PP

                                 TIGR02082  671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.....ks 732 
                                                 k ++pl++iegpL++Gm+vvGdLFGsGkmfLPqvvksarvmk+avayL+Py+e+ek ++     k+
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  683 AKSTRPLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKQAVAYLMPYMEEEKRKNggaerKN 749 
                                                *********************************************************9999999999 PP

                                 TIGR02082  733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799 
                                                +Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++kil++a+ +k D iglsGLi++sld
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  750 AGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPCAKILDVARTEKVDAIGLSGLITPSLD 816 
                                                ******************************************************************* PP

                                 TIGR02082  800 emvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsekkkae 865 
                                                em +va emer+g+++Pll+GGa++s+ h+avki+++Y kg++vyv+das+av vv++l+s  ++ +
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  817 EMCFVASEMEREGFSMPLLIGGATTSRVHTAVKINPNYtKGQTVYVTDASRAVGVVQNLFSPAARGP 883 
                                                **************************************669************************** PP

                                 TIGR02082  866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931 
                                                ++e+ik+eye++ e + +++ +++  ++ +ar + ++ld+  ++e+p+p+flGt++++++ ++el++
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  884 YIEAIKTEYENVAEAHMRNEAEKNRQPLPRARANALKLDWA-AYEPPHPTFLGTRIFRTYdVAELVP 949 
                                                *****************************************.************************* PP

                                 TIGR02082  932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998 
                                                yiDw+++F +We+rg+yp il+d+ +g+ a++lf+da+++l ++++e+   +++v+G++Pa+ +gdd
  lcl|NCBI__GCF_000385335.1:WP_020177190.1  950 YIDWTPFFQTWEMRGRYPDILSDPEKGAAAQQLFDDAQAMLARIVEEHWFDPKAVIGFWPANAIGDD 1016
                                                ******************************************************************* PP

                                 TIGR02082  999 ieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeela 1064
                                                i++yt+e++    +++at+++ ++ql +  +r +++++D+ia+ es + Dylg ++vtag  +e++a
  lcl|NCBI__GCF_000385335.1:WP_020177190.1 1017 IKLYTGESR---SEVLATFHTLRQQLSKRDGRpNIAMSDYIAPVESLKPDYLGGFVVTAGAREEKIA 1080
                                                *****9999...889999999999999999999********************************** PP

                                 TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
                                                +++ + +ddy+si+vkaladr+aea+ae +hervRke+w+ya +e+l+ ++l+ e YrGirpa+GYp
  lcl|NCBI__GCF_000385335.1:WP_020177190.1 1081 DRFAKANDDYGSIMVKALADRIAEAFAERMHERVRKEFWAYAPDEALAPDELITEPYRGIRPAPGYP 1147
                                                ******************************************************************* PP

                                 TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                a+Pdhtekatl++Lle+er iG++ltes+a++P +svsgly++hp+a+Yf v
  lcl|NCBI__GCF_000385335.1:WP_020177190.1 1148 AQPDHTEKATLFRLLEPERrIGVTLTESFAMWPGSSVSGLYLSHPDARYFGV 1199
                                                **************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1242 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: 0.12u 0.05s 00:00:00.17 Elapsed: 00:00:00.17
# Mc/sec: 8.43
//
[ok]

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

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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