GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Escherichia coli BW25113

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 16403 b2296 acetate kinase (NCBI)

Query= BRENDA::P0A6A3
         (400 letters)



>FitnessBrowser__Keio:16403
          Length = 400

 Score =  794 bits (2050), Expect = 0.0
 Identities = 400/400 (100%), Positives = 400/400 (100%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGEEYLSGLAECFHLPEARIKWKMDGNKQEAALGAG 60
           MSSKLVLVLNCGSSSLKFAIIDAVNGEEYLSGLAECFHLPEARIKWKMDGNKQEAALGAG
Sbjct: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGEEYLSGLAECFHLPEARIKWKMDGNKQEAALGAG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDAASFA 120
           AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDAASFA
Sbjct: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDAASFA 120

Query: 121 PLHNPAHLIGIEEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYNLYKEHGIRRYG 180
           PLHNPAHLIGIEEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYNLYKEHGIRRYG
Sbjct: 121 PLHNPAHLIGIEEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYNLYKEHGIRRYG 180

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
           AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM
Sbjct: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDAINKLLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTRSGDIDPAIIFHLHDTLGMSVDAINKLLTKESGLLGLTEVTSDCRYVEDNYATKEDAK
Sbjct: 241 GTRSGDIDPAIIFHLHDTLGMSVDAINKLLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300

Query: 301 RAMDVYCHRLAKYIGAYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RAMDVYCHRLAKYIGAYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER
Sbjct: 301 RAMDVYCHRLAKYIGAYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360

Query: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA
Sbjct: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400


Lambda     K      H
   0.318    0.135    0.386 

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: 664
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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: 50 (23.9 bits)

Align candidate 16403 b2296 (acetate kinase (NCBI))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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.carbon/TIGR00016.hmm
# target sequence database:        /tmp/gapView.30850.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate kinase
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-191  622.0   0.1   2.2e-191  621.9   0.1    1.0  1  lcl|FitnessBrowser__Keio:16403  b2296 acetate kinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16403  b2296 acetate kinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.9   0.1  2.2e-191  2.2e-191       1     404 [.       1     399 [.       1     400 [] 0.99

  Alignments for each domain:
  == domain 1  score: 621.9 bits;  conditional E-value: 2.2e-191
                       TIGR00016   1 mkskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdk 79 
                                     m+sk++lvln+Gssslkfa++da n+e++ lsgl+e+++l+earik+++dg+k+e++  a ++h+ea+++++nt+ ++k
  lcl|FitnessBrowser__Keio:16403   1 MSSKLVLVLNCGSSSLKFAIIDAVNGEEY-LSGLAECFHLPEARIKWKMDGNKQEAALGAGAAHSEALNFIVNTILAQK 78 
                                     57899************************.9*********************************************866 PP

                       TIGR00016  80 kilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHq 158
                                        ++++++++iGHR+vhGgek+t+sv+++++v+++ikd++++APlHnpa+l+gie++lk++++lk+knvavFDtafHq
  lcl|FitnessBrowser__Keio:16403  79 --PELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDAASFAPLHNPAHLIGIEEALKSFPQLKDKNVAVFDTAFHQ 155
                                     ..99*************************************************************************** PP

                       TIGR00016 159 tipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltP 237
                                     t+pee+ylYalPy+lyke+g+RrYG+HGtsh yvtq+aak+lnkp+++ln+i+cHlGnG+svsa++nGk++dtsmGltP
  lcl|FitnessBrowser__Keio:16403 156 TMPEESYLYALPYNLYKEHGIRRYGAHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTP 234
                                     ******************************************************************************* PP

                       TIGR00016 238 LeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiak 316
                                     LeGlvmGtRsGdiDpaii++l++tlg+s+d+i+++l+k+sGllg+++++sD+R+++d++ +++e+ak+A++vy+hR+ak
  lcl|FitnessBrowser__Keio:16403 235 LEGLVMGTRSGDIDPAIIFHLHDTLGMSVDAINKLLTKESGLLGLTEVTSDCRYVEDNY-ATKEDAKRAMDVYCHRLAK 312
                                     ***********************************************************.8999*************** PP

                       TIGR00016 317 yigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelv 395
                                     yig+y+a ++g+lDa+vFtgGiGenaa+vrel+l kl vlG+++d+e+n aar+gk+++i+ +e++  ++viptneelv
  lcl|FitnessBrowser__Keio:16403 313 YIGAYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFIN-KEGTRPAVVIPTNEELV 390
                                     ************************************************************9.89999************ PP

                       TIGR00016 396 iaeDalrla 404
                                     ia+Da rl+
  lcl|FitnessBrowser__Keio:16403 391 IAQDASRLT 399
                                     *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.23
//
[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