Alignments for a candidate for aceA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Escherichia coli BW25113

Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate 18043 b4015 isocitrate lyase (NCBI)

Query= SwissProt::P0A9G6
         (434 letters)



>FitnessBrowser__Keio:18043
          Length = 434

 Score =  874 bits (2259), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MKTRTQQIEELQKEWTQPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE 60
           MKTRTQQIEELQKEWTQPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE
Sbjct: 1   MKTRTQQIEELQKEWTQPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE 60

Query: 61  SKKGYINSLGALTGGQALQQAKAGIEAVYLSGWQVAADANLAASMYPDQSLYPANSVPAV 120
           SKKGYINSLGALTGGQALQQAKAGIEAVYLSGWQVAADANLAASMYPDQSLYPANSVPAV
Sbjct: 61  SKKGYINSLGALTGGQALQQAKAGIEAVYLSGWQVAADANLAASMYPDQSLYPANSVPAV 120

Query: 121 VERINNTFRRADQIQWSAGIEPGDPRYVDYFLPIVADAEAGFGGVLNAFELMKAMIEAGA 180
           VERINNTFRRADQIQWSAGIEPGDPRYVDYFLPIVADAEAGFGGVLNAFELMKAMIEAGA
Sbjct: 121 VERINNTFRRADQIQWSAGIEPGDPRYVDYFLPIVADAEAGFGGVLNAFELMKAMIEAGA 180

Query: 181 AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVTGVPTLLVARTDADAADL 240
           AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVTGVPTLLVARTDADAADL
Sbjct: 181 AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVTGVPTLLVARTDADAADL 240

Query: 241 ITSDCDPYDSEFITGERTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELARR 300
           ITSDCDPYDSEFITGERTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELARR
Sbjct: 241 ITSDCDPYDSEFITGERTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELARR 300

Query: 301 FAQAIHAKYPGKLLAYNCSPSFNWQKNLDDKTIASFQQQLSDMGYKFQFITLAGIHSMWF 360
           FAQAIHAKYPGKLLAYNCSPSFNWQKNLDDKTIASFQQQLSDMGYKFQFITLAGIHSMWF
Sbjct: 301 FAQAIHAKYPGKLLAYNCSPSFNWQKNLDDKTIASFQQQLSDMGYKFQFITLAGIHSMWF 360

Query: 361 NMFDLANAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS 420
           NMFDLANAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS
Sbjct: 361 NMFDLANAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS 420

Query: 421 SVTALTGSTEESQF 434
           SVTALTGSTEESQF
Sbjct: 421 SVTALTGSTEESQF 434


Lambda     K      H
   0.317    0.132    0.392 

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: 820
Number of extensions: 7
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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: 51 (24.3 bits)

Align candidate 18043 b4015 (isocitrate lyase (NCBI))
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

# 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/TIGR01346.hmm
# target sequence database:        /tmp/gapView.23194.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01346  [M=527]
Accession:   TIGR01346
Description: isocit_lyase: isocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.9e-222  725.3   3.7   8.2e-128  413.0   0.0    2.0  2  lcl|FitnessBrowser__Keio:18043  b4015 isocitrate lyase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18043  b4015 isocitrate lyase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.0   0.0  8.2e-128  8.2e-128       1     254 [.       8     255 ..       8     256 .. 0.99
   2 !  313.2   1.7   1.4e-97   1.4e-97     353     527 .]     256     434 .]     255     434 .] 1.00

  Alignments for each domain:
  == domain 1  score: 413.0 bits;  conditional E-value: 8.2e-128
                       TIGR01346   1 veeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka. 78 
                                     +ee+qkeW t++rwe+i+r+ysa+dvvklrGsv++e++l++ +a+k+wr+l+ esk k+++++lGal+++q++qqaka 
  lcl|FitnessBrowser__Keio:18043   8 IEELQKEW-TQPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGESK-KGYINSLGALTGGQALQQAKAg 84 
                                     68******.8*********************************************9.5********************* PP

                       TIGR01346  79 ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivada 157
                                     ++avylsGWqv++danl+++++Pd+++yPa++vP++ver++++++++d++q++a++++ d+      y+dy++Pivada
  lcl|FitnessBrowser__Keio:18043  85 IEAVYLSGWQVAADANLAASMYPDQSLYPANSVPAVVERINNTFRRADQIQWSAGIEPGDP-----RYVDYFLPIVADA 158
                                     ************************************************************9.....5************ PP

                       TIGR01346 158 daGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaea 236
                                     +aGfGGvl++f+l+k++ie+Gaa+vh+edql+s+kkCGh++Gkvlvp+qe++++lvaarlaadv+gv+tllvartda+a
  lcl|FitnessBrowser__Keio:18043 159 EAGFGGVLNAFELMKAMIEAGAAAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVTGVPTLLVARTDADA 237
                                     ******************************************************************************* PP

                       TIGR01346 237 atlitsdvdardhefivG 254
                                     a+litsd+d++d+efi+G
  lcl|FitnessBrowser__Keio:18043 238 ADLITSDCDPYDSEFITG 255
                                     *****************9 PP

  == domain 2  score: 313.2 bits;  conditional E-value: 1.4e-97
                       TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaleddeik 431
                                     ert+eGf+r+++g+e+ai+r+ a+aPyadlvW+etstPdle+a++fa+++++k+P+kllayn+sPsfnW+k+l+d++i+
  lcl|FitnessBrowser__Keio:18043 256 ERTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELARRFAQAIHAKYPGKLLAYNCSPSFNWQKNLDDKTIA 334
                                     8****************************************************************************** PP

                       TIGR01346 432 kfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfdqllk 506
                                     +f+++l+d+GykfqfitlaG+hs+++++fdla+++a+ eGmk+yvekvqq+e+   +dG+++++hq+e+G++yfd++++
  lcl|FitnessBrowser__Keio:18043 335 SFQQQLSDMGYKFQFITLAGIHSMWFNMFDLANAYAQgEGMKHYVEKVQQPEFaaaKDGYTFVSHQQEVGTGYFDKVTT 413
                                     *******************************************************9*********************** PP

                       TIGR01346 507 lvqgGvsataalaksveedqf 527
                                     ++qgG+s+++al++s+ee+qf
  lcl|FitnessBrowser__Keio:18043 414 IIQGGTSSVTALTGSTEESQF 434
                                     ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (434 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.58
//
[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