Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 18047 b4019 B12-dependent methionine synthase (NCBI)
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Keio:18047 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.3858.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: 0.09u 0.03s 00:00:00.12 Elapsed: 00:00:00.11 # Mc/sec: 12.91 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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