GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metH in Shewanella loihica PV-4

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate 5208198 Shew_0710 B12-dependent methionine synthase (RefSeq)

Query= BRENDA::P13009
         (1227 letters)



>lcl|FitnessBrowser__PV4:5208198 Shew_0710 B12-dependent methionine
            synthase (RefSeq)
          Length = 1240

 Score = 1612 bits (4175), Expect = 0.0
 Identities = 812/1227 (66%), Positives = 966/1227 (78%), Gaps = 9/1227 (0%)

Query: 6    EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
            + +RA+LN+ IL+LDG MGTMIQ+++L EADFRGERF  WPCDLKGNNDLLVL++PE+I 
Sbjct: 15   DAIRARLNKEILILDGAMGTMIQNHKLEEADFRGERFKQWPCDLKGNNDLLVLTQPELIK 74

Query: 66   AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
             IH  Y  AGADIIETNTFN+T +AMADY+M+ LS EIN   A+LAR   DE  A +  +
Sbjct: 75   QIHRDYLLAGADIIETNTFNATQVAMADYEMQELSREINLEGARLARTACDEVAAESGRQ 134

Query: 126  PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
              YVAGVLGPTNRT SISPDVNDP +RNI FD LV AY EST+AL+EGGAD+I++ET+FD
Sbjct: 135  C-YVAGVLGPTNRTCSISPDVNDPGYRNIHFDDLVEAYIESTQALIEGGADIIMVETIFD 193

Query: 186  TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
            TLNAKAA+FA++T F+ LG  LP+MISGTITDASGRTL+GQTTEAFYNSLRH + L+ GL
Sbjct: 194  TLNAKAALFAIETLFDQLGQRLPVMISGTITDASGRTLTGQTTEAFYNSLRHVKPLSIGL 253

Query: 246  NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
            NCALGP ELR YV+ELS+IAECYV+AHPNAGLPN FG YD   + MA+ I  WA+ G LN
Sbjct: 254  NCALGPQELRPYVEELSKIAECYVSAHPNAGLPNEFGGYDETPEQMAEVIGPWAEEGLLN 313

Query: 306  IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNV 365
            I+GGCCGTTP HI A+  AV     R+LP++PVACRLSGLEPL I  DSLFVNVGERTNV
Sbjct: 314  IIGGCCGTTPDHIKAIRAAVIKHGARELPDLPVACRLSGLEPLTIDADSLFVNVGERTNV 373

Query: 366  TGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPD 425
            TGSAKF RLIK  +Y EAL VAR QVENGAQIIDINMDEGMLD    M +FLNLIA EPD
Sbjct: 374  TGSAKFLRLIKTGEYEEALSVARDQVENGAQIIDINMDEGMLDGVEVMQKFLNLIASEPD 433

Query: 426  IARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAF 485
            I+RVPIMIDSSKW+VIE GLKCIQGKG+VNSIS+KEG   FI  A L++RYGAA ++MAF
Sbjct: 434  ISRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEAKFIEQATLVKRYGAAAIIMAF 493

Query: 486  DEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGA 545
            DE GQADT ARKIEIC RAY++L ++VGFPPEDIIFDPNIFA+ATGI+EH+NYA DFI A
Sbjct: 494  DEVGQADTMARKIEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHDNYAVDFIEA 553

Query: 546  CEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIY 605
              +IKR LPHA+ISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAGQLAIY
Sbjct: 554  TREIKRTLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAIY 613

Query: 606  DDLPAELRDAVEDVILN-----RRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
            DD+  +L+  VE V+ N     +  + TE+LLE+AE+YRG      A  +  EWRSW VN
Sbjct: 614  DDIDPDLKARVEAVVQNLPCPVQGSNNTEQLLEIAEQYRGDGAAG-AKKEDLEWRSWPVN 672

Query: 661  KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
            KRLE++LVKGITEFI+QDTEEARQ A+RP++VIEGPLMDGMNVVGDLFG GKMFLPQVVK
Sbjct: 673  KRLEHALVKGITEFIDQDTEEARQLASRPLDVIEGPLMDGMNVVGDLFGSGKMFLPQVVK 732

Query: 721  SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            SARVMK+AVAYL P+IEA K +G++NGK+++ TVKGDVHDIGKNIVGVVL CN YE+VDL
Sbjct: 733  SARVMKKAVAYLNPYIEAEKVEGESNGKILMVTVKGDVHDIGKNIVGVVLACNGYEVVDL 792

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVP EKI+  AK    D+IG+SGLITPSLDEMV+  K   + G  IP +IGGAT SK 
Sbjct: 793  GVMVPVEKIIEVAKAEKVDIIGMSGLITPSLDEMVHNVKAFHKAGLNIPSIIGGATCSKI 852

Query: 841  HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
            HTAVKI  +     +Y+ +ASR V +VA L++   R   +    +EY  +R +   +  R
Sbjct: 853  HTAVKIAPHAPEGAIYIADASRAVPMVAKLINKETRQATIDAAYEEYRVMRDKRNSQAKR 912

Query: 901  TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGK 959
               V+LEAAR+N    DW A+TP V ++LG Q   +  +E L + IDWTPFF +W L G 
Sbjct: 913  KQIVSLEAARENRCQQDWNAHTPFVPNQLGRQVFDDYPLEDLVDRIDWTPFFRSWELHGH 972

Query: 960  YPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDET 1018
            +P+IL+DEVVG EA++L++DA  ML  +  EK L  + V+GLFPAN V  DDIEIY DE+
Sbjct: 973  FPKILDDEVVGEEARKLYQDAKAMLKTIIDEKWLTAKAVIGLFPANTVNYDDIEIYTDES 1032

Query: 1019 RTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEA 1078
            R+ V   +HHLR Q E+ G  N+CLADFVAPK SG ADY+G FAVT G   D     FEA
Sbjct: 1033 RSKVEMTTHHLRMQIERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGIDEHVARFEA 1092

Query: 1079 QHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPG 1138
             HDDY+ IM+K LADRL EAFAE +HERVRK +WGYA +ENL NE LIRE Y+GIRPAPG
Sbjct: 1093 NHDDYSAIMLKCLADRLVEAFAERMHERVRKEFWGYAADENLDNEALIREKYKGIRPAPG 1152

Query: 1139 YPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRD 1198
            YPACP+HTEK  +WELL+ ++   +K+TES+AM+P A+VSGWYF+HP S+Y+ V  I RD
Sbjct: 1153 YPACPDHTEKGLLWELLKPDETIDLKITESYAMFPTAAVSGWYFAHPQSRYFGVTNIGRD 1212

Query: 1199 QVEDYARRKGMSVTEVERWLAPNLGYD 1225
            QVEDYA+RKGMSV E ERWLAP L YD
Sbjct: 1213 QVEDYAKRKGMSVEETERWLAPVLDYD 1239


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: 3712
Number of extensions: 143
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: 1240
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1192
Effective search space:  1405368
Effective search space used:  1405368
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 5208198 Shew_0710 (B12-dependent methionine synthase (RefSeq))
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.10309.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 1758.5   0.1          0 1758.3   0.1    1.0  1  lcl|FitnessBrowser__PV4:5208198  Shew_0710 B12-dependent methioni


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208198  Shew_0710 B12-dependent methionine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1758.3   0.1         0         0       1    1182 []      21    1206 ..      21    1206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1758.3 bits;  conditional E-value: 0
                        TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnst 75  
                                       lnk+il+lDGamGt++q+++L+eadFrge +++++++lkGnndlL+lt+Pe+i++ihr+y+ aGaDi+etntFn+t
  lcl|FitnessBrowser__PV4:5208198   21 LNKEILILDGAMGTMIQNHKLEEADFRGErFKQWPCDLKGNNDLLVLTQPELIKQIHRDYLLAGADIIETNTFNAT 96  
                                       6899************************************************************************ PP

                        TIGR02082   76 eialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYk 151 
                                       ++a+adY+++++++e+n ++a+lar ++de+  ++ ++ +vaG+lGPtn++ ++spdv++p++rn+++d+lv+aY 
  lcl|FitnessBrowser__PV4:5208198   97 QVAMADYEMQELSREINLEGARLARTACDEVAAESGRQCYVAGVLGPTNRTCSISPDVNDPGYRNIHFDDLVEAYI 172 
                                       **************************************************************************** PP

                        TIGR02082  152 eqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflaslehaei 227 
                                       e++++l++GG+D++++et+fDtlnakaalfa+e++f++ g++lP++isg+i+d+sGrtL+Gqt+eaf++sl+h + 
  lcl|FitnessBrowser__PV4:5208198  173 ESTQALIEGGADIIMVETIFDTLNAKAALFAIETLFDQLGQRLPVMISGTITDASGRTLTGQTTEAFYNSLRHVKP 248 
                                       **************************************************************************** PP

                        TIGR02082  228 lilGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPe 303 
                                       l++GLnCalG++elr++v+els++ae++vs++PnaGLPn++g Yd+tpe++a+++  +aeegllni+GGCCGttP+
  lcl|FitnessBrowser__PV4:5208198  249 LSIGLNCALGPQELRPYVEELSKIAECYVSAHPNAGLPNEFGGYDETPEQMAEVIGPWAEEGLLNIIGGCCGTTPD 324 
                                       **************************************************************************** PP

                        TIGR02082  304 hiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqve 379 
                                       hi+ai +av +   r+ ++l+ +++lsgle+l+i+ +s fvn+GeRtnv+Gs+kf +lik ++yeeal++a++qve
  lcl|FitnessBrowser__PV4:5208198  325 HIKAIRAAVIKHGARELPDLPVACRLSGLEPLTIDADSLFVNVGERTNVTGSAKFLRLIKTGEYEEALSVARDQVE 400 
                                       **************************************************************************** PP

                        TIGR02082  380 eGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455 
                                       +Gaqi+Din+De++lDg++ m+k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk++vnsislk+Ge++F+e
  lcl|FitnessBrowser__PV4:5208198  401 NGAQIIDINMDEGMLDGVEVMQKFLNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEAKFIE 476 
                                       **************************************************************************** PP

                        TIGR02082  456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfie 531 
                                       +a l+k+yGaa+++mafDe Gqa+t+++kiei++Ray++l++kvgfppediifDpni++iatGi+ehd+ya+dfie
  lcl|FitnessBrowser__PV4:5208198  477 QATLVKRYGAAAIIMAFDEVGQADTMARKIEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHDNYAVDFIE 552 
                                       **************************************************************************** PP

                        TIGR02082  532 aireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedli 607 
                                       a+reik++lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+la+yddid++l+  ve ++
  lcl|FitnessBrowser__PV4:5208198  553 ATREIKRTLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAIYDDIDPDLKARVEAVV 628 
                                       **************************************************************************** PP

                        TIGR02082  608 ldrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkaple 678 
                                        +       +++te+Lle+ae+y+g  ++ + +++  ewr++pv++RLe+alvkG++e+i++d+eear+ +++pl+
  lcl|FitnessBrowser__PV4:5208198  629 QNLPcpvqgSNNTEQLLEIAEQYRGDGAAGA-KKEDLEWRSWPVNKRLEHALVKGITEFIDQDTEEARQLASRPLD 703 
                                       *977777779*****************9955.58899*************************************** PP

                        TIGR02082  679 iiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivd 754 
                                       +iegpL+dGm+vvGdLFGsGkmfLPqvvksarvmkkavayL+Py+e+ek e +s+Gki++ tvkGDvhDiGkniv+
  lcl|FitnessBrowser__PV4:5208198  704 VIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMKKAVAYLNPYIEAEKVEGESNGKILMVTVKGDVHDIGKNIVG 779 
                                       **************************************************************************** PP

                        TIGR02082  755 vvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahva 830 
                                       vvL+cngyevvdlGv+vPveki+e+ak +k D+ig+sGLi++sldemv++++ +++ g++iP ++GGa+ sk h+a
  lcl|FitnessBrowser__PV4:5208198  780 VVLACNGYEVVDLGVMVPVEKIIEVAKAEKVDIIGMSGLITPSLDEMVHNVKAFHKAGLNIPSIIGGATCSKIHTA 855 
                                       **************************************************************************** PP

                        TIGR02082  831 vkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrs 906 
                                       vkia++     +y  das+av +v+kl++++++++ +++  eey  +r k +++ ++++ +s++aar+++ + d++
  lcl|FitnessBrowser__PV4:5208198  856 VKIAPHAPEGAIYIADASRAVPMVAKLINKETRQATIDAAYEEYRVMRDKRNSQAKRKQIVSLEAARENRCQQDWN 931 
                                       **************************************************************************** PP

                        TIGR02082  907 edlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekll 981 
                                        + ++ +p++lG++v++++ +e+l++ iDw+++F +Wel+g++pkil+de++g+earkl++dak++l++++ ek l
  lcl|FitnessBrowser__PV4:5208198  932 -AHTPFVPNQLGRQVFDDYpLEDLVDRIDWTPFFRSWELHGHFPKILDDEVVGEEARKLYQDAKAMLKTIIDEKWL 1006
                                       .999************************************************************************ PP

                        TIGR02082  982 rargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvta 1056
                                       +a++v+GlfPa++v+ ddieiytde++s    +++t  + + q+++  + + claDf+a+k+sG +Dy+g ++vta
  lcl|FitnessBrowser__PV4:5208198 1007 TAKAVIGLFPANTVNyDDIEIYTDESRS--KVEMTTH-HLRMQIERVGNDNFCLADFVAPKDSGVADYMGGFAVTA 1079
                                       ************77549********993..3344444.4455555556669************************* PP

                        TIGR02082 1057 glgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
                                       g g++e   ++ea++ddy++i++k ladrl ea+ae +hervRke+wgya++enld+e l++e+Y+Girpa+GYpa
  lcl|FitnessBrowser__PV4:5208198 1080 GHGIDEHVARFEANHDDYSAIMLKCLADRLVEAFAERMHERVRKEFWGYAADENLDNEALIREKYKGIRPAPGYPA 1155
                                       **************************************************************************** PP

                        TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                       cPdhtek  l+eLl++++ i lk+tes+a+ P+a+vsg+yfahp+++Yf v
  lcl|FitnessBrowser__PV4:5208198 1156 CPDHTEKGLLWELLKPDEtIDLKITESYAMFPTAAVSGWYFAHPQSRYFGV 1206
                                       ***************9888******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1240 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 0.04s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 9.07
//
[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