GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metH in Escherichia coli BW25113

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate 18047 b4019 B12-dependent methionine synthase (NCBI)

Query= BRENDA::P13009
         (1227 letters)



>lcl|FitnessBrowser__Keio:18047 b4019 B12-dependent methionine
            synthase (NCBI)
          Length = 1227

 Score = 2441 bits (6327), Expect = 0.0
 Identities = 1227/1227 (100%), Positives = 1227/1227 (100%)

Query: 1    MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
            MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK
Sbjct: 1    MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60

Query: 61   PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
            PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA
Sbjct: 61   PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120

Query: 121  RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
            RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI
Sbjct: 121  RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180

Query: 181  ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
            ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA
Sbjct: 181  ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240

Query: 241  LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
            LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ
Sbjct: 241  LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300

Query: 301  AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
            AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG
Sbjct: 301  AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360

Query: 361  ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
            ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI
Sbjct: 361  ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420

Query: 421  AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
            AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV
Sbjct: 421  AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480

Query: 481  VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
            VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ
Sbjct: 481  VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540

Query: 541  DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
            DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG
Sbjct: 541  DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600

Query: 601  QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
            QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN
Sbjct: 601  QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660

Query: 661  KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
            KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK
Sbjct: 661  KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720

Query: 721  SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL
Sbjct: 721  SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA
Sbjct: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840

Query: 841  HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
            HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR
Sbjct: 841  HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900

Query: 901  TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY 960
            TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY
Sbjct: 901  TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY 960

Query: 961  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
            PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT
Sbjct: 961  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020

Query: 1021 HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH 1080
            HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH
Sbjct: 1021 HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH 1080

Query: 1081 DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP 1140
            DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP
Sbjct: 1081 DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP 1140

Query: 1141 ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV 1200
            ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV
Sbjct: 1141 ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV 1200

Query: 1201 EDYARRKGMSVTEVERWLAPNLGYDAD 1227
            EDYARRKGMSVTEVERWLAPNLGYDAD
Sbjct: 1201 EDYARRKGMSVTEVERWLAPNLGYDAD 1227


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: 4078
Number of extensions: 122
Number of successful extensions: 1
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: 1227
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1180
Effective search space:  1392400
Effective search space used:  1392400
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 18047 b4019 (B12-dependent methionine synthase (NCBI))
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.18214.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 1994.1   0.0          0 1993.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:18047  b4019 B12-dependent methionine s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18047  b4019 B12-dependent methionine synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1993.9   0.0         0         0       1    1182 []      12    1192 ..      12    1192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1993.9 bits;  conditional E-value: 0
                       TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnste 76  
                                      ln+rilvlDG+mGt++qs++L+eadFrge +ad++++lkGnndlL+l+kPeviaaih+ayfeaGaDi+etntFnst+
  lcl|FitnessBrowser__Keio:18047   12 LNERILVLDGGMGTMIQSYRLNEADFRGErFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTT 88  
                                      689************************************************************************** PP

                       TIGR02082   77 ialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYke 152 
                                      ia+adY++e++++e+n++aaklar++ade+t +tpek+R+vaG+lGPtn++a++spdv++p+frn+t+d lv+aY+e
  lcl|FitnessBrowser__Keio:18047   89 IAMADYQMESLSAEINFAAAKLARACADEWTaRTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRE 165 
                                      ***************************************************************************** PP

                       TIGR02082  153 qvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflaslehaeili 229 
                                      ++k+l++GG+Dl+LietvfDtlnakaa+fav+++fe+ g+elPi+isg+i+d+sGrtLsGqt+eaf++sl+hae+l+
  lcl|FitnessBrowser__Keio:18047  166 STKALVEGGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242 
                                      ***************************************************************************** PP

                       TIGR02082  230 lGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehir 306 
                                      +GLnCalG+delr++v+els++ae++v+++PnaGLPna+geYdl+++++ak+++e+a++g+lnivGGCCGttP+hi+
  lcl|FitnessBrowser__Keio:18047  243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGTTPQHIA 319 
                                      ***************************************************************************** PP

                       TIGR02082  307 aiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaq 383 
                                      a+++av++++prk +e++ +++lsgle+l+i+++s fvn+GeRtnv+Gs+kf++lik+e+y+eal++a+qqve+Gaq
  lcl|FitnessBrowser__Keio:18047  320 AMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQ 396 
                                      ***************************************************************************** PP

                       TIGR02082  384 ilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekakli 460 
                                      i+Din+De++lD+ea+m+++l+l+a+epdia+vP+m+Dss+++v+e+GLk+iqGk+ivnsis+k+G+++F+++akl+
  lcl|FitnessBrowser__Keio:18047  397 IIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLL 473 
                                      ***************************************************************************** PP

                       TIGR02082  461 keyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireik 537 
                                      ++yGaavvvmafDe+Gqa+t+++kiei++Rayk+lte+vgfppediifDpni+++atGieeh++ya+dfi a+++ik
  lcl|FitnessBrowser__Keio:18047  474 RRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIK 550 
                                      ***************************************************************************** PP

                       TIGR02082  538 eelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrrea 614 
                                      +elP+a isgGvsnvsFs+rgnd+vRea+h+vFLy+ai++G+Dmgivnag+la+ydd+++elr++ved+il+rr++ 
  lcl|FitnessBrowser__Keio:18047  551 RELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDG 627 
                                      ***************************************************************************** PP

                       TIGR02082  615 tekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvv 691 
                                      te+Llelae+y+g k++++++aq+aewr+++v++RLe++lvkG++e+ie+d+eear+++++p+e+iegpL+dGm+vv
  lcl|FitnessBrowser__Keio:18047  628 TERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVV 704 
                                      ***************************************************************************** PP

                       TIGR02082  692 GdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlG 768 
                                      GdLFG+GkmfLPqvvksarvmk+avayLeP++e++ke+ k++Gk+v+atvkGDvhDiGkniv+vvL+cn+ye+vdlG
  lcl|FitnessBrowser__Keio:18047  705 GDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781 
                                      ***************************************************************************** PP

                       TIGR02082  769 vkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvk 845 
                                      v+vP+ekil++ak+ +aD+iglsGLi++sldemv+va+emer+g++iPll+GGa++skah+avki+++Y+g++vyv+
  lcl|FitnessBrowser__Keio:18047  782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQ 858 
                                      ***************************************************************************** PP

                       TIGR02082  846 daseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvl 922 
                                      +as++v vv++lls+++++++++++++eye++r ++g+kk ++  ++++aar+++fa+d++ ++++p++++lG++++
  lcl|FitnessBrowser__Keio:18047  859 NASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQ-AYTPPVAHRLGVQEV 934 
                                      *************************************************************.*************** PP

                       TIGR02082  923 easieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddi 999 
                                      easie+l++yiDw+++F++W+l+gkyp+il+de++g+ea++lfkda+++ldklsaek+l++rgvvGlfPa++vgddi
  lcl|FitnessBrowser__Keio:18047  935 EASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDI 1011
                                      ***************************************************************************** PP

                       TIGR02082 1000 eiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleakeddyds 1076
                                      eiy+det+   t++i+++++ ++q+++    ++claDf+a+k sG++Dy+ga++vt gl++++la+++ea++ddy++
  lcl|FitnessBrowser__Keio:18047 1012 EIYRDETR---THVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNK 1085
                                      ******99...99999996555555555555********************************************** PP

                       TIGR02082 1077 ilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iG 1152
                                      i+vkaladrlaea+ae+lhervRk +wgya +enl++e+l++e+Y+Girpa+GYpacP+htekat++eLle+e+ +G
  lcl|FitnessBrowser__Keio:18047 1086 IMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKhTG 1162
                                      ***************************************************************************** PP

                       TIGR02082 1153 lklteslalaPeasvsglyfahpeakYfav 1182
                                      +kltes+a++P asvsg+yf+hp++kY+av
  lcl|FitnessBrowser__Keio:18047 1163 MKLTESFAMWPGASVSGWYFSHPDSKYYAV 1192
                                      ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1227 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: 13.56
//
[ok]

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

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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 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