GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metH in Pseudomonas fluorescens FW300-N1B4

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate Pf1N1B4_5661 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)

Query= BRENDA::P13009
         (1227 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661
            5-methyltetrahydrofolate--homocysteine methyltransferase
            (EC 2.1.1.13)
          Length = 1236

 Score = 1615 bits (4183), Expect = 0.0
 Identities = 824/1235 (66%), Positives = 978/1235 (79%), Gaps = 15/1235 (1%)

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

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

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

Query: 182  TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
            T+FDTLNAKAA+FAV+  FE LGVELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185  TIFDTLNAKAAIFAVQGVFEELGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244

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

Query: 302  GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
            GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP  I   SLFVNVGE
Sbjct: 305  GFLNIVGGCCGTTPGHIEAIAKAVAGYAPREIPDIPKACRLSGLEPFTIDRSSLFVNVGE 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+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425  GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 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 +PAELRDAVEDVILNR  +GT+ LL +A+KY+G        A+  EWR+W+VNK
Sbjct: 605  LEIYDQIPAELRDAVEDVILNRTPEGTDALLAIADKYKGD--GSVKEAETEEWRNWDVNK 662

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE++LVKGIT  I +DTEE+RQ   RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663  RLEHALVKGITTHIVEDTEESRQSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKS 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  HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
            HTAVKIE  YS   V YV +ASR VGV   LLS   +  FV +TR EY  VR +   +  
Sbjct: 843  HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKAGFVEKTRLEYIDVRERTANRSA 902

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

Query: 959  KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
            K+PRIL+DEVVG  A  L+ DA +ML KL  EK ++ R V G +PAN+V  DDIE+Y D+
Sbjct: 963  KFPRILKDEVVGEAATALYADAQEMLAKLIDEKLISARAVFGFWPANQVRDDDIEVYDDD 1022

Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
             +   +   HHLRQQ  KT G  N+ LADFVAPK SG  DY+G F  T G+  + +A A+
Sbjct: 1023 GKP--LAKLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAY 1080

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

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

Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            AV +I +DQV+ Y  RKG  ++  ERWLAPNLGYD
Sbjct: 1201 AVGKIDKDQVQSYTSRKGQELSVTERWLAPNLGYD 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: 3806
Number of extensions: 174
Number of successful extensions: 7
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 Pf1N1B4_5661 (5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13))
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.29412.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 1760.6   0.0          0 1760.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  5-methyltetrahydrofolate--homocy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1760.4   0.0         0         0       1    1182 []      15    1202 ..      15    1202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1760.4 bits;  conditional E-value: 0
                                      TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfe 61  
                                                     l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL+lt+P+vi  i +ay++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661   15 LKERILILDGGMGTMIQSYKLEEQDYRGKrFADWPSDVKGNNDLLVLTRPDVIGGIEKAYLD 76  
                                                     579*********************************************************** PP

                                      TIGR02082   62 aGaDivetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGP 122 
                                                     aGaDi+etntFn+t i++adY++e++ayeln ++a+lar++ad  t  +p+k+RfvaG+lGP
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661   77 AGADILETNTFNATRISMADYGMEELAYELNVEGARLARKIADAKTlENPDKPRFVAGVLGP 138 
                                                     ********************************************9989************** PP

                                      TIGR02082  123 tnklatlspdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfave 184 
                                                     t+++ +lspdv++p++rnvt+delv+ Y+e++kgl++GG+Dl+Liet+fDtlnakaa+fav+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  139 TSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIETIFDTLNAKAAIFAVQ 200 
                                                     ************************************************************** PP

                                      TIGR02082  185 evfeekgrelPilisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvk 246 
                                                      vfee g+elPi+isg+i+d+sGrtLsGqt+eaf +s+ ha+ +++GLnCalGa elr++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  201 GVFEELGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPISVGLNCALGASELRPYLE 262 
                                                     ************************************************************** PP

                                      TIGR02082  247 elsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehirai 308 
                                                     els++a++ vs++PnaGLPn++geYd++p ++ak+++efa+ g+lnivGGCCGttP hi ai
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  263 ELSNKANTHVSAHPNAGLPNEFGEYDELPAQTAKVIEEFAQSGFLNIVGGCCGTTPGHIEAI 324 
                                                     ************************************************************** PP

                                      TIGR02082  309 aeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeea 370 
                                                     a+av++ +pr+ ++++++++lsgle+++i++ s fvn+GeRtn++Gs+kf++li++++y ea
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  325 AKAVAGYAPREIPDIPKACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIREDNYTEA 386 
                                                     ************************************************************** PP

                                      TIGR02082  371 lkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGL 432 
                                                     l++a qqve Gaq++Din+De++lD++++m+++l+l+a+epdi++vP+m+Dss++ev+eaGL
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  387 LEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIAGEPDISRVPIMIDSSKWEVIEAGL 448 
                                                     ************************************************************** PP

                                      TIGR02082  433 kviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykl 494 
                                                     k+iqGk+ivnsis+k+G+e+F+++akl k+yGaavvvmafDe Gqa+t ++k ei+kR y++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  449 KCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEAGQADTEARKKEICKRSYDI 510 
                                                     ************************************************************** PP

                                      TIGR02082  495 ltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFsl 556 
                                                     l+++vgfppediifDpni+++atGieeh++ya+dfi+a+  i+ elP+a +sgGvsnvsFs+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  511 LVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVDFINACAYIRDELPYALTSGGVSNVSFSF 572 
                                                     ************************************************************** PP

                                      TIGR02082  557 rgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekL 618 
                                                     rgn++vRea+hsvFL +ai++Gl mgivnag+l++yd+i++elr++ved+il+r +e t+ L
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  573 RGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQLEIYDQIPAELRDAVEDVILNRTPEGTDAL 634 
                                                     ************************************************************** PP

                                      TIGR02082  619 lelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleii 680 
                                                     l +a++ykg  +   kea+++ewrn++v++RLe+alvkG++ +i ed+ee+r+   +p+e+i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  635 LAIADKYKGDGSV--KEAETEEWRNWDVNKRLEHALVKGITTHIVEDTEESRQSFARPIEVI 694 
                                                     *********9998..999******************************************** PP

                                      TIGR02082  681 egpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatv 741 
                                                     egpL+ Gm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e ek ++ ++kGki++atv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  695 EGPLMSGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIELEKGDKpEAKGKILMATV 756 
                                                     **********************************************9877689********* PP

                                      TIGR02082  742 kGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemve 803 
                                                     kGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++ak++k D+iglsGLi++sldemv+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  757 KGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVH 818 
                                                     ************************************************************** PP

                                      TIGR02082  804 vaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkka 864 
                                                     va+em+r+ +++Pl++GGa++skah+avki++kY+   v+yv+das+av v+ +lls++ ka
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  819 VAREMQRQDFHLPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKA 880 
                                                     **********************************872599********************** PP

                                      TIGR02082  865 eelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas. 925 
                                                      ++ek++ ey ++re+  ++  +++ ls   a  ++ ++d+   +e+++p+f G kvl+++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  881 GFVEKTRLEYIDVRERTANRSARTERLSYPVAIAKKPQFDWG-SYEPVKPTFTGAKVLDNId 941 
                                                     ******************************************.9****************** PP

                                      TIGR02082  926 ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvv 987 
                                                     ++ l +yiDw+++F++W+l+gk+p+ilkde++g+ a+ l++da+e+l kl+ ekl+ ar+v+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  942 LKVLAEYIDWTPFFISWDLAGKFPRILKDEVVGEAATALYADAQEMLAKLIDEKLISARAVF 1003
                                                     ************************************************************** PP

                                      TIGR02082  988 GlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikD 1047
                                                     G++Pa++v +ddie+y+d++      p+a +++ ++q+ +  ++ + +laDf+a+k+sG +D
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1004 GFWPANQVrDDDIEVYDDDGK-----PLAKLHHLRQQIIKTDGKpNFSLADFVAPKDSGVTD 1060
                                                     *****9762578*****8877.....8888888888888888877***************** PP

                                      TIGR02082 1048 ylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeee 1109
                                                     y+g +++tag+gaee ak++++  ddy+si+vkaladrlaea ae+lh++vRk++wgya++e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1061 YVGGFITTAGIGAEEVAKAYQDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYAKDE 1122
                                                     ************************************************************** PP

                                      TIGR02082 1110 nldkedllkerYrGirpafGYpacPdhtekatlleLleae.......riGlklteslalaPe 1164
                                                      ld+e l+ke+Y Girpa+GYpacPdhtekatl++Ll++e       r G+ lte +a+ P+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1123 TLDNEALIKEQYTGIRPAPGYPACPDHTEKATLFKLLDPEaeelkagRSGVFLTEHYAMFPA 1184
                                                     *************************************9875455444579************ PP

                                      TIGR02082 1165 asvsglyfahpeakYfav 1182
                                                     a+vsg+yfahp+a+Yfav
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1185 AAVSGWYFAHPQAQYFAV 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.39
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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:

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:

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:

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, or view the source code, or see 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