Alignments for a candidate for metE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for metE in Escherichia coli BW25113

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 17877 b3829 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (NCBI)

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__Keio:17877
          Length = 753

 Score = 1527 bits (3953), Expect = 0.0
 Identities = 753/753 (100%), Positives = 753/753 (100%)

Query: 1   MTILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLP 60
           MTILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLP
Sbjct: 1   MTILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLP 60

Query: 61  VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN 120
           VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN
Sbjct: 61  VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN 120

Query: 121 TNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDR 180
           TNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDR
Sbjct: 121 TNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDR 180

Query: 181 LSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQVKLLL 240
           LSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQVKLLL
Sbjct: 181 LSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQVKLLL 240

Query: 241 TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD 300
           TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD
Sbjct: 241 TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD 300

Query: 301 LTEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR 360
           LTEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR
Sbjct: 301 LTEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR 360

Query: 361 DALNSGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
           DALNSGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR
Sbjct: 361 DALNSGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420

Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
           FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL
Sbjct: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480

Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
           VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA
Sbjct: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540

Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
           QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE
Sbjct: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600

Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
           PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD
Sbjct: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660

Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
           VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL
Sbjct: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720

Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLRRG 753
           WVNPDCGLKTRGWPETRAALANMVQAAQNLRRG
Sbjct: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLRRG 753


Lambda     K      H
   0.319    0.135    0.416 

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: 2107
Number of extensions: 89
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: 753
Length of database: 753
Length adjustment: 40
Effective length of query: 713
Effective length of database: 713
Effective search space:   508369
Effective search space used:   508369
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

Align candidate 17877 b3829 (5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (NCBI))
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))

# 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/TIGR01371.hmm
# target sequence database:        /tmp/gapView.21495.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01371  [M=754]
Accession:   TIGR01371
Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
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 1124.8   0.0          0 1124.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:17877  b3829 5-methyltetrahydropteroylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17877  b3829 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1124.6   0.0         0         0       1     753 [.       8     752 ..       8     753 .] 0.98

  Alignments for each domain:
  == domain 1  score: 1124.6 bits;  conditional E-value: 0
                       TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperfke 79 
                                     lgfPr+g +Relkka+e+yw+g++++eell+v ++lr++++++qk+ag+d++pv+df++YDhvL+t++llg++p+r+++
  lcl|FitnessBrowser__Keio:17877   8 LGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFAWYDHVLTTSLLLGNVPARHQN 86 
                                     79***************************************************************************** PP

                       TIGR01371  80 laddesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvllGp 156
                                     + d+++d+dt+F+i+RG +   + +aa emtkwfntnYhY+vPe+ k ++fkl++++ll+e++ea +lg+++kPvllGp
  lcl|FitnessBrowser__Keio:17877  87 K-DGSVDIDTLFRIGRGRAPtgEPAAAAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGP 164
                                     8.8889***********98755668899*************************************************** PP

                       TIGR01371 157 itflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelkll 235
                                     +t+l+L+k k +e++++l+ll+++lpvY++vl +la++g+ewvqideP+lvl+l++++l+a+k ay++l+    ++kll
  lcl|FitnessBrowser__Keio:17877 165 VTWLWLGKVK-GEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQG---QVKLL 239
                                     *******999.699********************************************************8...79*** PP

                       TIGR01371 236 lqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdk 314
                                     l+tYf+ v+ +l++++ lpv++l++Dlv++k++ +  ++++++d++L+aG+i+Grn+w+adl+++ +++k++  k+   
  lcl|FitnessBrowser__Keio:17877 240 LTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEKYAQIKDIVGKR--D 316
                                     *********************************9999************************************888..6 PP

                       TIGR01371 315 lvvstscsllhvpvdleleekldkelkellafakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvk 393
                                     l+v++scsllh+p+dl+ e++ld+e+k+++afa +k++el++l++al++   +++al++++a+i+ar++s+rv++ +v+
  lcl|FitnessBrowser__Keio:17877 317 LWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRDALNS--GDTAALAEWSAPIQARRHSTRVHNPAVE 393
                                     ************************************************7..66677888999***************** PP

                       TIGR01371 394 erlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklq 472
                                     +rl+a+++++++r++ +e Raeaq+++++lP+ PtttiGsfPqt+e+R+ R +f+kg++++++Y + i e+ik++i  q
  lcl|FitnessBrowser__Keio:17877 394 KRLAAITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQ 472
                                     ******************************************************************************* PP

                       TIGR01371 473 eelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGm 551
                                     e+lglDvLvhGe+eRnDmveyFge+l+Gf+ftqngWvqsYGsRcvkPpi++gd+srp+p+tv++ kyaqslt+kpvkGm
  lcl|FitnessBrowser__Keio:17877 473 ERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYAQSLTDKPVKGM 551
                                     ******************************************************************************* PP

                       TIGR01371 552 LtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaas 630
                                     LtGPvtil+Wsf+ReD++r++ia+qialalrdev+dLe+agi iiqiDepalReglPlr+sd+++Yl+w veaFr+ a+
  lcl|FitnessBrowser__Keio:17877 552 LTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAA 630
                                     ******************************************************************************* PP

                       TIGR01371 631 gvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaell 709
                                      +kd+tqihthmCY+efn+i+++iaaldaDvi+ie+srsdmell++++e ++y++eiG+GvyDihsp+vPs+e++++ll
  lcl|FitnessBrowser__Keio:17877 631 VAKDDTQIHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEE-FDYPNEIGPGVYDIHSPNVPSVEWIEALL 708
                                     *************************************************.77*************************** PP

                       TIGR01371 710 ekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
                                     +ka k++p+erlWvnPDCGLktR w+e++aal n+v+aa++lR 
  lcl|FitnessBrowser__Keio:17877 709 KKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
                                     *****************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (753 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 7.99
//
[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