Alignments for a candidate for metH in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Bacteroides thetaiotaomicron VPI-5482

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 349708 BT0180 5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Btheta:349708
          Length = 915

 Score = 1049 bits (2713), Expect = 0.0
 Identities = 522/904 (57%), Positives = 680/904 (75%), Gaps = 5/904 (0%)

Query: 12  LNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAY 71
           ++ERIL+LDG MGTMIQ Y L E DFRGERFA  P  LKGNNDLL L++P+VI  IH  Y
Sbjct: 9   VSERILILDGAMGTMIQQYNLKEEDFRGERFAHIPGQLKGNNDLLCLTRPDVIQDIHRKY 68

Query: 72  FEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAG 131
            EAGADIIETNTF+STT++MADY +E    EIN AA +LAR  ADE+TA++P+KPR+VAG
Sbjct: 69  LEAGADIIETNTFSSTTVSMADYHVEEYVREINLAATRLARELADEYTAKSPDKPRFVAG 128

Query: 132 VLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKA 191
            +GPTN+T S+SPDVN+PAFR +++D L A+Y++  +A++EGG D ILIET+FDTLNAKA
Sbjct: 129 SVGPTNKTCSMSPDVNNPAFRALSYDELAASYQQQMEAMLEGGVDAILIETIFDTLNAKA 188

Query: 192 AVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGP 251
           A+FA     +  G+E+P+M+S T++D  GRTLSGQT EAF  S++HA   + GLNC+ G 
Sbjct: 189 AIFAAGQAMKVTGIEVPVMLSVTVSDIGGRTLSGQTLEAFLASVQHANIFSVGLNCSFGA 248

Query: 252 DELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCC 311
            +L+ ++++L+  A  Y++A+PNAGLPN+ G+YD     MA +++E+ Q G +NI+GGCC
Sbjct: 249 RQLKPFLEQLASRAPYYISAYPNAGLPNSLGKYDQTPADMAHEVKEYIQEGLVNIIGGCC 308

Query: 312 GTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKF 371
           GTT  +IA     + G  P      P    LSGLE L +  +  FVN+GER NV GS KF
Sbjct: 309 GTTDAYIAEYQTLIAGAKPHVPAPKPDCMWLSGLELLEVKPEINFVNIGERCNVAGSRKF 368

Query: 372 KRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPI 431
            RL+ E+KY EAL +ARQQVE+GA +ID+NMD+G+LDA   M  FLNLI  EP+IARVP+
Sbjct: 369 LRLVNEKKYDEALSIARQQVEDGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPV 428

Query: 432 MIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQA 491
           MIDSSKW+VIE GLKC+QGK IVNSIS+KEG + F+ HA+++++YGAA VVMAFDE+GQA
Sbjct: 429 MIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVMAFDEKGQA 488

Query: 492 DTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKR 551
           DT ARKIE+C RAY++L ++VGF P DIIFDPN+ AVATGIEEHNNYA DFI A   I++
Sbjct: 489 DTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRK 548

Query: 552 ELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAE 611
            LP A +SGGVSN+SFSFRGN+ +REA+HAVFLY+AI+ GMDMGIVN G   +Y D+PA+
Sbjct: 549 NLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPAD 608

Query: 612 LRDAVEDVILNRRDDGTERLLELAEKYRGSK--TDDTANAQQAEWRSWEVNKRLEYSLVK 669
             + +EDV+LNRR D  ERL+ELAE  + +   T   A  +Q  WR   V +RL+Y+L+K
Sbjct: 609 TLEKIEDVVLNRRPDAAERLIELAEALKETMGGTSGQAAVKQDAWREESVQERLKYALMK 668

Query: 670 GITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAV 729
           GI +++EQD  EA     + ++VIEGPLMDGMN VG+LFG GKMFLPQVVK+AR MK+AV
Sbjct: 669 GIGDYLEQDLAEALPLYDKAVDVIEGPLMDGMNYVGELFGAGKMFLPQVVKTARTMKKAV 728

Query: 730 AYLEPFIEASKEQGKTN-GKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788
           A L+P IE+ K +G ++ GK+++ATVKGDVHDIGKNIV VV+ CN Y+IVDLGVMVPAE 
Sbjct: 729 AILQPIIESEKVEGSSSAGKVLLATVKGDVHDIGKNIVAVVMACNGYDIVDLGVMVPAET 788

Query: 789 ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848
           I++ A E   D+IGLSGLITPSL+EM +VA E+E+ G  IPLLIGGATTSK HTA+KI  
Sbjct: 789 IVQRAIEEKVDMIGLSGLITPSLEEMTHVAAELEKAGLDIPLLIGGATTSKMHTALKIAP 848

Query: 849 NYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEA 908
            Y  P V++++AS+   V + LL+   + + +     EY+ +R + G  +  T  V+LE 
Sbjct: 849 VYHAPVVHLKDASQNASVASRLLNSQMKAELINELDAEYQALREKSGLLRRET--VSLEE 906

Query: 909 ARDN 912
           A+ N
Sbjct: 907 AQKN 910


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: 2561
Number of extensions: 104
Number of successful extensions: 3
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: 915
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 870
Effective search space:  1028340
Effective search space used:  1028340
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: 58 (26.9 bits)

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 349777 BT0249 5-methyltetrahydrofolate--homocysteine methyltransferase or methionine synthase (NCBI ptt file)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Btheta:349777
          Length = 300

 Score =  195 bits (495), Expect = 5e-54
 Identities = 125/304 (41%), Positives = 169/304 (55%), Gaps = 30/304 (9%)

Query: 938  IETLRNYIDWTPFFMTWSLAGKYPRIL------------------EDEVVGVEAQRLFKD 979
            I  +  YI+W  FF  W    ++  I                   ED     EA +LFK+
Sbjct: 7    IHNVAPYINWIYFFHAWGFQPRFAAIANIHGCDVCRASWLTTFPEEDRNKASEAMQLFKE 66

Query: 980  ANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKT-GF 1038
            AN MLD L  +K    R +  L  AN  GD++ I   E  T    V   LRQQT K  G 
Sbjct: 67   ANRMLDLL--DKDYEVRTIFKLCKANSDGDNLVI---EKETDQFLVFPLLRQQTPKRDGS 121

Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
              +CL+DF+ P  SG  D IGAFA     + + L +      D Y  ++V+ L+DRLAEA
Sbjct: 122  PFFCLSDFIRPLSSGIPDTIGAFASCIDADMEGLYE-----QDPYKHLLVQTLSDRLAEA 176

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
              E +HE VRK  WGYA +E LS  +L+ E YQGIRPA GYP+ P+ +    + ELL++ 
Sbjct: 177  ATEKMHEYVRKEAWGYAKDEILSMPDLLVEKYQGIRPAVGYPSLPDQSINFLLDELLDM- 235

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
            K  G+ LTE+ AM+P ASV G  F+HP ++Y++V +I  DQ+EDYARR+G S  E+ ++L
Sbjct: 236  KQIGITLTENGAMYPHASVCGLMFAHPAAEYFSVGKIGEDQLEDYARRRGKSTEEMRKFL 295

Query: 1219 APNL 1222
            A NL
Sbjct: 296  AANL 299


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: 760
Number of extensions: 30
Number of successful extensions: 5
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: 300
Length adjustment: 37
Effective length of query: 1190
Effective length of database: 263
Effective search space:   312970
Effective search space used:   312970
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: 53 (25.0 bits)

Align candidate 349708 BT0180 (5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file))
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.15593.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 1339.5   5.2          0 1339.2   5.2    1.0  1  lcl|FitnessBrowser__Btheta:349708  BT0180 5-methyltetrahydrofolate-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:349708  BT0180 5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1339.2   5.2         0         0       2     900 ..      10     911 ..       9     914 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1339.2 bits;  conditional E-value: 0
                          TIGR02082   2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnste 76 
                                        ++ril+lDGamGt++q++nL+e+dFrge +a+++ +lkGnndlL lt+P+vi++ihr+y+eaGaDi+etntF+st+
  lcl|FitnessBrowser__Btheta:349708  10 SERILILDGAMGTMIQQYNLKEEDFRGErFAHIPGQLKGNNDLLCLTRPDVIQDIHRKYLEAGADIIETNTFSSTT 85 
                                        68************************************************************************** PP

                          TIGR02082  77 ialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYk 151
                                        +++adY++e+ ++e+n +a++lare ade+t ++p+k+RfvaGs+GPtnk+ ++spdv++p+fr + ydel ++Y+
  lcl|FitnessBrowser__Btheta:349708  86 VSMADYHVEEYVREINLAATRLARELADEYTaKSPDKPRFVAGSVGPTNKTCSMSPDVNNPAFRALSYDELAASYQ 161
                                        **************************************************************************** PP

                          TIGR02082 152 eqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflaslehaei 227
                                        +q++++l+GGvD++Liet+fDtlnakaa+fa+ ++++  g+e+P+++s ++ d  GrtLsGqtleaflas++ha+i
  lcl|FitnessBrowser__Btheta:349708 162 QQMEAMLEGGVDAILIETIFDTLNAKAAIFAAGQAMKVTGIEVPVMLSVTVSDIGGRTLSGQTLEAFLASVQHANI 237
                                        **************************************************************************** PP

                          TIGR02082 228 lilGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPe 303
                                        +++GLnC++Ga +l++f+++l+  a+ ++s++PnaGLPn+lg+Yd+tp  +a+++ke+++egl+ni+GGCCGtt +
  lcl|FitnessBrowser__Btheta:349708 238 FSVGLNCSFGARQLKPFLEQLASRAPYYISAYPNAGLPNSLGKYDQTPADMAHEVKEYIQEGLVNIIGGCCGTTDA 313
                                        **************************************************************************** PP

                          TIGR02082 304 hiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqve 379
                                        +i++  + +++ kp+     ++ + lsgle l++++e +fvniGeR+nvaGs+kf +l+++++y+eal+ia+qqve
  lcl|FitnessBrowser__Btheta:349708 314 YIAEYQTLIAGAKPHVPAPKPDCMWLSGLELLEVKPEINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVE 389
                                        **************************************************************************** PP

                          TIGR02082 380 eGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455
                                        +Ga ++D+n+D++llD++++m+++l+l+ sep+ia+vP+m+Dss++ev+eaGLk++qGk+ivnsislk+Gee Fle
  lcl|FitnessBrowser__Btheta:349708 390 DGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPVMIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLE 465
                                        **************************************************************************** PP

                          TIGR02082 456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfie 531
                                        +a++ik+yGaa vvmafDe+Gqa+ta++kie+++Ray+ll++kvgf+p+diifDpn+l++atGieeh++ya+dfie
  lcl|FitnessBrowser__Btheta:349708 466 HARIIKQYGAATVVMAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIE 541
                                        **************************************************************************** PP

                          TIGR02082 532 aireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedli 607
                                        a+ +i+++lP a++sgGvsn+sFs+rgn+ +Rea+h+vFLy+ai++G+Dmgivn+g   +y di+++ +e++ed++
  lcl|FitnessBrowser__Btheta:349708 542 ATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPADTLEKIEDVV 617
                                        **************************************************************************** PP

                          TIGR02082 608 ldrrreatekLlelaelykgtkeks..skeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiie 681
                                        l+rr++a e+L elae  k+t   +  ++  ++++wr+ +v+eRL++al+kG+ +++e+dl ea+  + +++++ie
  lcl|FitnessBrowser__Btheta:349708 618 LNRRPDAAERLIELAEALKETMGGTsgQAAVKQDAWREESVQERLKYALMKGIGDYLEQDLAEALPLYDKAVDVIE 693
                                        ******************998654411567799******************************************* PP

                          TIGR02082 682 gpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatvkGDvhDiGknivdvv 756
                                        gpL+dGm+ vG+LFG+GkmfLPqvvk ar+mkkava L+P +e ek e  +s+Gk++latvkGDvhDiGkniv vv
  lcl|FitnessBrowser__Btheta:349708 694 GPLMDGMNYVGELFGAGKMFLPQVVKTARTMKKAVAILQPIIESEKVEGsSSAGKVLLATVKGDVHDIGKNIVAVV 769
                                        **********************************************8864889*********************** PP

                          TIGR02082 757 LscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavk 832
                                        ++cngy++vdlGv+vP+e+i++ a ++k D+iglsGLi++sl+em++va e+e+ g++iPll+GGa++sk h+a k
  lcl|FitnessBrowser__Btheta:349708 770 MACNGYDIVDLGVMVPAETIVQRAIEEKVDMIGLSGLITPSLEEMTHVAAELEKAGLDIPLLIGGATTSKMHTALK 845
                                        **************************************************************************** PP

                          TIGR02082 833 iaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkev 900
                                        ia+ Y+++vv+ kdas++ +v+++ll+ + kae ++++ +ey+ +rek g    +++++s+++a+k++
  lcl|FitnessBrowser__Btheta:349708 846 IAPVYHAPVVHLKDASQNASVASRLLNSQMKAELINELDAEYQALREKSGL--LRRETVSLEEAQKNK 911
                                        ************************************************999..566667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (915 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 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 8.75
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis