GapMind for Amino acid biosynthesis

 

Alignments 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= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661
          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.12018.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: 0.11u 0.05s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.23
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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