Alignments for a candidate for ilvA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Escherichia coli BW25113

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 17824 b3772 threonine dehydratase (NCBI)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Keio:17824
          Length = 514

 Score = 1021 bits (2639), Expect = 0.0
 Identities = 514/514 (100%), Positives = 514/514 (100%)

Query: 1   MADSQPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHS 60
           MADSQPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHS
Sbjct: 1   MADSQPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHS 60

Query: 61  FKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDA 120
           FKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDA
Sbjct: 61  FKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDA 120

Query: 121 VRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHL 180
           VRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHL
Sbjct: 121 VRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHL 180

Query: 181 DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE 240
           DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE
Sbjct: 181 DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE 240

Query: 241 GVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI 300
           GVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI
Sbjct: 241 GVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI 300

Query: 301 ALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG 360
           ALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG
Sbjct: 301 ALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG 360

Query: 361 GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVR 420
           GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVR
Sbjct: 361 GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVR 420

Query: 421 YMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE 480
           YMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE
Sbjct: 421 YMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE 480

Query: 481 LGDHEPDFETRLNELGYDCHDETNNPAFRFFLAG 514
           LGDHEPDFETRLNELGYDCHDETNNPAFRFFLAG
Sbjct: 481 LGDHEPDFETRLNELGYDCHDETNNPAFRFFLAG 514


Lambda     K      H
   0.321    0.138    0.403 

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: 950
Number of extensions: 25
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: 514
Length of database: 514
Length adjustment: 35
Effective length of query: 479
Effective length of database: 479
Effective search space:   229441
Effective search space used:   229441
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: 52 (24.6 bits)

Align candidate 17824 b3772 (threonine dehydratase (NCBI))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

# 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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.1897.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.6e-273  893.7   0.0   1.8e-273  893.5   0.0    1.0  1  lcl|FitnessBrowser__Keio:17824  b3772 threonine dehydratase (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17824  b3772 threonine dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  893.5   0.0  1.8e-273  1.8e-273       1     499 []      15     512 ..      15     512 .. 1.00

  Alignments for each domain:
  == domain 1  score: 893.5 bits;  conditional E-value: 1.8e-273
                       TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaqG 79 
                                     +ylra+l+a vyeaa++tpl+k++kls+rl+n +l+kred+qpv+sfklrGay++ma l++eqka+Gvi+asaGnhaqG
  lcl|FitnessBrowser__Keio:17824  15 EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQG 93 
                                     69***************************************************************************** PP

                       TIGR01124  80 valsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtvale 158
                                     va+s+++lGvka+ivmp++t++ikvdav++fGgev+lhG+n+deakaka+el+q++g+t+++pfd+p+viaGqGt+ale
  lcl|FitnessBrowser__Keio:17824  94 VAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALE 172
                                     ******************************************************************************* PP

                       TIGR01124 159 llrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGde 237
                                     ll+q++ +ld+vfvpvGGGGl+aGva+l+kql+p+ikvi+veaedsa+lk+al+aG++v+l +vGlfa+Gvavk++Gde
  lcl|FitnessBrowser__Keio:17824 173 LLQQDA-HLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
                                     *****9.************************************************************************ PP

                       TIGR01124 238 tfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvse 316
                                     tfrlc+eylddi++vd+d++caa+kd+fed+rav+ep+GalalaG+kky+a ++i++++l++ilsGan+nf+ lryvse
  lcl|FitnessBrowser__Keio:17824 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVNFHGLRYVSE 329
                                     ******************************************************************************* PP

                       TIGR01124 317 raelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvd 394
                                     r+elGeqreallavtipeekGs+lkf+++lG r++tefnyr+ad+++a+ifvGv+l++  eerke+l++l++ gy+vvd
  lcl|FitnessBrowser__Keio:17824 330 RCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGlEERKEILQMLNDGGYSVVD 408
                                     ********************************************************998899***************** PP

                       TIGR01124 395 ltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeae 473
                                     l+dde+aklhvry+vGGr+++  +erlysfefpe+pGall+fl+tl ++wnislfhyr+hG+dyGrvl+++e+ d+e +
  lcl|FitnessBrowser__Keio:17824 409 LSDDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPD 487
                                     *****************************************************************************99 PP

                       TIGR01124 474 efeqflaelgyryedetenpayrlfl 499
                                      fe++l+elgy+++det+npa+r+fl
  lcl|FitnessBrowser__Keio:17824 488 -FETRLNELGYDCHDETNNPAFRFFL 512
                                     .************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (514 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.82
//
[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