Alignments for a candidate for galK in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Escherichia coli BW25113

Align galactose kinase (characterized)
to candidate 14882 b0757 galactokinase (NCBI)

Query= CharProtDB::CH_024146
         (382 letters)



>FitnessBrowser__Keio:14882
          Length = 382

 Score =  761 bits (1964), Expect = 0.0
 Identities = 382/382 (100%), Positives = 382/382 (100%)

Query: 1   MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD 60
           MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD
Sbjct: 1   MSLKEKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRD 60

Query: 61  DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN 120
           DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN
Sbjct: 61  DRKVRVMAADYENQLDEFSLDAPIVAHENYQWANYVRGVVKHLQLRNNSFGGVDMVISGN 120

Query: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180
           VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL
Sbjct: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180

Query: 181 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240
           GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP
Sbjct: 181 GKKDHALLIDCRSLGTKAVSMPKGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQP 240

Query: 241 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS 300
           ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS
Sbjct: 241 ALRDVTIEEFNAVAHELDPIVAKRVRHILTENARTVEAASALEQGDLKRMGELMAESHAS 300

Query: 301 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY 360
           MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY
Sbjct: 301 MRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQY 360

Query: 361 EAKTGIKETFYVCKPSQGAGQC 382
           EAKTGIKETFYVCKPSQGAGQC
Sbjct: 361 EAKTGIKETFYVCKPSQGAGQC 382


Lambda     K      H
   0.318    0.134    0.389 

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: 576
Number of extensions: 8
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 14882 b0757 (galactokinase (NCBI))
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

# 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/TIGR00131.hmm
# target sequence database:        /tmp/gapView.18489.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00131  [M=388]
Accession:   TIGR00131
Description: gal_kin: galactokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.4e-180  584.6   0.1     5e-180  584.4   0.1    1.0  1  lcl|FitnessBrowser__Keio:14882  b0757 galactokinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14882  b0757 galactokinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.4   0.1    5e-180    5e-180       2     388 .]       5     382 .]       4     382 .] 0.99

  Alignments for each domain:
  == domain 1  score: 584.4 bits;  conditional E-value: 5e-180
                       TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkldlp 80 
                                     e+++++Fa+a++++++++++aPGRvnliGeh+DYndg+vlP+aid++t+++++ rdd++v++++a+++n+l+e++ld+p
  lcl|FitnessBrowser__Keio:14882   5 EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKVRVMAADYENQLDEFSLDAP 83 
                                     789**************************************************************************** PP

                       TIGR00131  81 ldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldskeillriqkv 159
                                     ++++e+++WanYv+gv+k+lq R+ns++ G+d+visg+vP+gaGLsssa+levav++vl++l++l+ld+++i+l++q++
  lcl|FitnessBrowser__Keio:14882  84 IVAHENYQWANYVRGVVKHLQLRNNSFG-GVDMVISGNVPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEA 161
                                     ****************************.************************************************** PP

                       TIGR00131 160 eehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvlak 238
                                     e++fvG+ncG+mDql+s+lG++dhall+++r+L +++v++p+ ++a+vi+n+n+k++l++seYn+Rr+++e++a+++++
  lcl|FitnessBrowser__Keio:14882 162 ENQFVGCNCGIMDQLISALGKKDHALLIDCRSLGTKAVSMPK-GVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQ 239
                                     ******************************************.************************************ PP

                       TIGR00131 239 ksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvp 317
                                          aLrDv+ eef+   a +++l+++v+k R++h+++en+R+++a+++l+++dlk++G+Lm+es+as++dd+eitvp
  lcl|FitnessBrowser__Keio:14882 240 P----ALRDVTIEEFN---AVAHELDPIVAK-RVRHILTENARTVEAASALEQGDLKRMGELMAESHASMRDDFEITVP 310
                                     *....***********...************.*********************************************** PP

                       TIGR00131 318 eidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskealgel 388
                                     +id+lve++++v+G ++G+R+tG+GfGGC+val+p+e v++v++a+ae+Ye+kt++k++f+v+++++++g++
  lcl|FitnessBrowser__Keio:14882 311 QIDTLVEIVKAVIGdKGGVRMTGGGFGGCIVALIPEELVPAVQQAVAEQYEAKTGIKETFYVCKPSQGAGQC 382
                                     **************9*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (382 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: 7.85
//
[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:

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

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 catabolism of small carbon sources