GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB 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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.14373.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.75
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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