Alignments for a candidate for deoA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Escherichia coli BW25113

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 18403 b4382 thymidine phosphorylase (NCBI)

Query= BRENDA::P07650
         (440 letters)



>FitnessBrowser__Keio:18403
          Length = 440

 Score =  855 bits (2210), Expect = 0.0
 Identities = 440/440 (100%), Positives = 440/440 (100%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT
Sbjct: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60

Query: 61  MAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHT 120
           MAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHT
Sbjct: 61  MAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHT 120

Query: 121 GGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI
Sbjct: 121 GGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180

Query: 181 PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
           PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT
Sbjct: 181 PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKL 300
           DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKL
Sbjct: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALG 360
           QAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALG
Sbjct: 301 QAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALG 360

Query: 361 MAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAA 420
           MAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAA
Sbjct: 361 MAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAA 420

Query: 421 IKLADKAPESTPTVYRRISE 440
           IKLADKAPESTPTVYRRISE
Sbjct: 421 IKLADKAPESTPTVYRRISE 440


Lambda     K      H
   0.318    0.134    0.377 

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: 763
Number of extensions: 13
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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: 51 (24.3 bits)

Align candidate 18403 b4382 (thymidine phosphorylase (NCBI))
to HMM TIGR02643 (deoA: thymidine phosphorylase (EC 2.4.2.4))

# 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/TIGR02643.hmm
# target sequence database:        /tmp/gapView.19297.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02643  [M=437]
Accession:   TIGR02643
Description: T_phosphoryl: thymidine phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.4e-242  789.2   7.6   6.1e-242  789.0   7.6    1.0  1  lcl|FitnessBrowser__Keio:18403  b4382 thymidine phosphorylase (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18403  b4382 thymidine phosphorylase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.0   7.6  6.1e-242  6.1e-242       1     437 []       2     438 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 789.0 bits;  conditional E-value: 6.1e-242
                       TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdldlngP 79 
                                     +l+qeiirkkrdg++lsdeei+ f++g++d+++segqiaalam+++f+++++ e+v+lt+amrdsG+vldwk+l+lngP
  lcl|FitnessBrowser__Keio:18403   2 FLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGP 80 
                                     79***************************************************************************** PP

                       TIGR02643  80 vvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGvaiiGqtad 158
                                     +vdkhstGGvGdv+slml+P+vaacGgy+PmisGrGlGhtGGtldkle+iPG+d++Pd+++fr+++kdvGvaiiGqt++
  lcl|FitnessBrowser__Keio:18403  81 IVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSS 159
                                     ******************************************************************************* PP

                       TIGR02643 159 laPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslvevangaGvrttal 237
                                     laPadkr+ya+rd+tatv+siplitasil+kkla+Gldalv+dvkvG+Gafm+++e se+la+++v vangaGvrttal
  lcl|FitnessBrowser__Keio:18403 160 LAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTAL 238
                                     ******************************************************************************* PP

                       TIGR02643 238 itdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakleavlesGraaerfarmv 316
                                     +tdmnq+las+aGnavevreav+fltGe+r++rl +vt+al++e+l+sgkla+d+aea+akl+avl++G+aae+f+rmv
  lcl|FitnessBrowser__Keio:18403 239 LTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAVLDNGKAAEVFGRMV 317
                                     ******************************************************************************* PP

                       TIGR02643 317 aalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddkldlsvGltdllelGekveke 395
                                     aa++GP+dfve+++kyl++a+++kav+a++eg++se+dtr+lG+avva+GGGrr+a+d++d+svG+td+++lG++v+ +
  lcl|FitnessBrowser__Keio:18403 318 AAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQ 396
                                     ******************************************************************************* PP

                       TIGR02643 396 eplavvhaadeedaeeaakavkkalkiadeaPeeakvvleri 437
                                     +plav+ha+de++++eaakavk+a+k+ad+aPe++++v++ri
  lcl|FitnessBrowser__Keio:18403 397 RPLAVIHAKDENNWQEAAKAVKAAIKLADKAPESTPTVYRRI 438
                                     ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (440 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: 11.27
//
[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