Alignments for a candidate for metE in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for metE in Klebsiella michiganensis M5al

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate BWI76_RS01280 BWI76_RS01280 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__Koxy:BWI76_RS01280
          Length = 753

 Score = 1440 bits (3728), Expect = 0.0
 Identities = 701/752 (93%), Positives = 734/752 (97%)

Query: 1   MTILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLP 60
           MTI+NHTLGFPRVGLRRELKKAQESYWAGN+ REELLAVGRELRARHWDQQKQAG+DLLP
Sbjct: 1   MTIINHTLGFPRVGLRRELKKAQESYWAGNTGREELLAVGRELRARHWDQQKQAGVDLLP 60

Query: 61  VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN 120
           VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN
Sbjct: 61  VGDFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFN 120

Query: 121 TNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDR 180
           TNYHYMVPEFVKGQ+FKL+WTQLLDEVDEALALGHK KPVLLGPVT+LWLGKVKGE FDR
Sbjct: 121 TNYHYMVPEFVKGQRFKLSWTQLLDEVDEALALGHKAKPVLLGPVTYLWLGKVKGEPFDR 180

Query: 181 LSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQVKLLL 240
           LSLLNDILPVY+QVLAELAKRGIEWVQIDEPALVLELPQAWLDA+KPAY+AL G+VKLLL
Sbjct: 181 LSLLNDILPVYRQVLAELAKRGIEWVQIDEPALVLELPQAWLDAFKPAYEALNGEVKLLL 240

Query: 241 TTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD 300
           TTYFEG+  NLDTITALPVQGLHVDLVHG+D+VAELHKRLP+DWLLSAGLINGRNVWRAD
Sbjct: 241 TTYFEGIADNLDTITALPVQGLHVDLVHGQDNVAELHKRLPADWLLSAGLINGRNVWRAD 300

Query: 301 LTEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR 360
           L+EKYAQ+K IVGKR+LWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKC ELALLR
Sbjct: 301 LSEKYAQVKAIVGKRELWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCEELALLR 360

Query: 361 DALNSGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
           DALNSGDTAA+AEWSAPIQARRHSTRVHN AVEKRLAAITAQDSQR + Y+VRA AQRAR
Sbjct: 361 DALNSGDTAAIAEWSAPIQARRHSTRVHNAAVEKRLAAITAQDSQRQSAYQVRAAAQRAR 420

Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
           FKLPAWPTTTIGSFPQTTEIR LRLDFKKGNLDANNYRTGIAEHI+QAI+EQERLGLDVL
Sbjct: 421 FKLPAWPTTTIGSFPQTTEIRGLRLDFKKGNLDANNYRTGIAEHIRQAIMEQERLGLDVL 480

Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
           VHGEAERNDMVEYFGEHLDGF+FTQNGWVQSYGSRCVKPP+VIGD+SRP  ITVEWAKYA
Sbjct: 481 VHGEAERNDMVEYFGEHLDGFIFTQNGWVQSYGSRCVKPPVVIGDVSRPEAITVEWAKYA 540

Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
           QSLT+KPVKGMLTGPVTILCWSFPREDV+RETIAKQIALALRDEVADLEAAGIGIIQIDE
Sbjct: 541 QSLTEKPVKGMLTGPVTILCWSFPREDVTRETIAKQIALALRDEVADLEAAGIGIIQIDE 600

Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
           PALREGLPL+RSDWDAYL WGVEAFRINAAVA+DDTQIHTHMCYCEFNDIMDSIAALDAD
Sbjct: 601 PALREGLPLKRSDWDAYLAWGVEAFRINAAVAQDDTQIHTHMCYCEFNDIMDSIAALDAD 660

Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
           VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAA+RIPAERL
Sbjct: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAQRIPAERL 720

Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
           WVNPDCGLKTRGWPET +AL NMV+AAQNLR+
Sbjct: 721 WVNPDCGLKTRGWPETLSALTNMVKAAQNLRQ 752


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: 2037
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 BWI76_RS01280 BWI76_RS01280 (5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase)
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.24034.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 1121.6   0.0          0 1121.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS01280  BWI76_RS01280 5-methyltetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS01280  BWI76_RS01280 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1121.4   0.0         0         0       1     753 [.       8     752 ..       8     753 .] 0.98

  Alignments for each domain:
  == domain 1  score: 1121.4 bits;  conditional E-value: 0
                               TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllg 71 
                                             lgfPr+g +Relkka+e+yw+g++ +eell+v ++lr++++++qk+agvd++pv+df++YDhvL+t++llg
  lcl|FitnessBrowser__Koxy:BWI76_RS01280   8 LGFPRVGLRRELKKAQESYWAGNTGREELLAVGRELRARHWDQQKQAGVDLLPVGDFAWYDHVLTTSLLLG 78 
                                             79********************************************************************* PP

                               TIGR01371  72 aiperfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeyk 140
                                             ++p+r++++ d+++d+dt+F+i+RG +   + +aa emtkwfntnYhY+vPe+ k ++fkls+++ll+e++
  lcl|FitnessBrowser__Koxy:BWI76_RS01280  79 NVPARHQNK-DGSVDIDTLFRIGRGRAPtgEPAAAAEMTKWFNTNYHYMVPEFVKGQRFKLSWTQLLDEVD 148
                                             ********8.8889***********98755668899*********************************** PP

                               TIGR01371 141 eakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldls 211
                                             ea +lg+++kPvllGp+t+l+L+k k +e +++l+ll+++lpvY++vl +la++g+ewvqideP+lvl+l+
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 149 EALALGHKAKPVLLGPVTYLWLGKVK-GEPFDRLSLLNDILPVYRQVLAELAKRGIEWVQIDEPALVLELP 218
                                             ***********************999.699***************************************** PP

                               TIGR01371 212 keelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvL 282
                                             +++l+a+k aye+l+    e+klll+tYf+ + ++l++++ lpv++l++Dlv+++++ +  ++++++d++L
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 219 QAWLDAFKPAYEALNG---EVKLLLTTYFEGIADNLDTITALPVQGLHVDLVHGQDNVAELHKRLPADWLL 286
                                             ***************8...79************************************9999********** PP

                               TIGR01371 283 vaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakeklee 353
                                             +aG+i+Grn+w+adl+++ +++k++  k+  +l+v++scsllh+p+dl+ e++ld+e+k+++afa +k+ee
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 287 SAGLINGRNVWRADLSEKYAQVKAIVGKR--ELWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCEE 355
                                             **************************887..8*************************************** PP

                               TIGR01371 354 lkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlP 424
                                             l++l++al++   +++a+++++a+i+ar++s+rv++++v++rl+a+++++++r+s ++ Ra+aq+++++lP
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 356 LALLRDALNS--GDTAAIAEWSAPIQARRHSTRVHNAAVEKRLAAITAQDSQRQSAYQVRAAAQRARFKLP 424
                                             *********7..66778889999************************************************ PP

                               TIGR01371 425 llPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFg 495
                                             + PtttiGsfPqt+e+R  R +f+kg++++++Y + i e+i+++i  qe+lglDvLvhGe+eRnDmveyFg
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 425 AWPTTTIGSFPQTTEIRGLRLDFKKGNLDANNYRTGIAEHIRQAIMEQERLGLDVLVHGEAERNDMVEYFG 495
                                             *********************************************************************** PP

                               TIGR01371 496 eklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvRe 566
                                             e+l+Gf+ftqngWvqsYGsRcvkPp+++gdvsrp+++tv++ kyaqslt+kpvkGmLtGPvtil+Wsf+Re
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 496 EHLDGFIFTQNGWVQSYGSRCVKPPVVIGDVSRPEAITVEWAKYAQSLTEKPVKGMLTGPVTILCWSFPRE 566
                                             *********************************************************************** PP

                               TIGR01371 567 DlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetq 637
                                             D+ r++ia+qialalrdev+dLe+agi iiqiDepalReglPl++sd+++Yl w veaFr+ a+ ++d+tq
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 567 DVTRETIAKQIALALRDEVADLEAAGIGIIQIDEPALREGLPLKRSDWDAYLAWGVEAFRINAAVAQDDTQ 637
                                             *********************************************************************** PP

                               TIGR01371 638 ihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelael 708
                                             ihthmCY+efn+i+++iaaldaDvi+ie+srsdmell++++e ++y++eiG+GvyDihsp+vPs+e++++l
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 638 IHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEE-FDYPNEIGPGVYDIHSPNVPSVEWIEAL 707
                                             ******************************************.77************************** PP

                               TIGR01371 709 lekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
                                             l+ka +++p+erlWvnPDCGLktR w+e+ +al+n+v+aa++lR+
  lcl|FitnessBrowser__Koxy:BWI76_RS01280 708 LKKAAQRIPAERLWVNPDCGLKTRGWPETLSALTNMVKAAQNLRQ 752
                                             *******************************************97 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.06
# Mc/sec: 8.28
//
[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