Alignments for a candidate for deoA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Klebsiella michiganensis M5al

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate BWI76_RS04135 BWI76_RS04135 thymidine phosphorylase

Query= BRENDA::P07650
         (440 letters)



>FitnessBrowser__Koxy:BWI76_RS04135
          Length = 440

 Score =  793 bits (2049), Expect = 0.0
 Identities = 404/440 (91%), Positives = 426/440 (96%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNT+SEGQIAALAMTIFFHDM+MPERVSLT
Sbjct: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTVSEGQIAALAMTIFFHDMSMPERVSLT 60

Query: 61  MAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHT 120
           MAMRDSGTVLDWK L+LNGPIVDKHSTGGVGDVTSLMLGPMVAACGGY+PMISGRGLGHT
Sbjct: 61  MAMRDSGTVLDWKHLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHT 120

Query: 121 GGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDKLE+IPGFDIFPDD+RFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI
Sbjct: 121 GGTLDKLEAIPGFDIFPDDSRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180

Query: 181 PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
           PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELS ALAEAIVGV+NGAGVRTTALLT
Sbjct: 181 PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSAALAEAIVGVSNGAGVRTTALLT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKL 300
           DMNQVLASSAGNAVEVREAVQFLTGEYRNPRL +VTMALCVEMLISGKLA+++A+ARAKL
Sbjct: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLLEVTMALCVEMLISGKLAENEADARAKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALG 360
           QAVLDNGKAA+VFGRMVAAQKGP DFVENY KYLP AML+KAVYA+ EGFV+EMDTRALG
Sbjct: 301 QAVLDNGKAADVFGRMVAAQKGPNDFVENYDKYLPAAMLSKAVYAEGEGFVAEMDTRALG 360

Query: 361 MAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAA 420
           MAVV+MGGGRRQASD IDYSVGFTDM RLG +VD Q+PLAVIHAKDEN+WQEAA+AVKAA
Sbjct: 361 MAVVSMGGGRRQASDLIDYSVGFTDMVRLGARVDAQQPLAVIHAKDENSWQEAARAVKAA 420

Query: 421 IKLADKAPESTPTVYRRISE 440
           IKL  KAPE TPTVYRRI+E
Sbjct: 421 IKLGAKAPEMTPTVYRRITE 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: 705
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 BWI76_RS04135 BWI76_RS04135 (thymidine phosphorylase)
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.11777.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     4e-238  776.4   8.4   4.5e-238  776.3   8.4    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04135  BWI76_RS04135 thymidine phosphor


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04135  BWI76_RS04135 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  776.3   8.4  4.5e-238  4.5e-238       1     437 []       2     438 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 776.3 bits;  conditional E-value: 4.5e-238
                               TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldw 71 
                                             +l+qeiirkkrdg++lsdeei+ f++g++d++vsegqiaalam+++f+++++ e+v+lt+amrdsG+vldw
  lcl|FitnessBrowser__Koxy:BWI76_RS04135   2 FLAQEIIRKKRDGHALSDEEIRFFINGIRDNTVSEGQIAALAMTIFFHDMSMPERVSLTMAMRDSGTVLDW 72 
                                             79********************************************************************* PP

                               TIGR02643  72 kdldlngPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfr 142
                                             k+l+lngP+vdkhstGGvGdv+slml+P+vaacGgyvPmisGrGlGhtGGtldkleaiPG+d++Pd+++fr
  lcl|FitnessBrowser__Koxy:BWI76_RS04135  73 KHLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHTGGTLDKLEAIPGFDIFPDDSRFR 143
                                             *********************************************************************** PP

                               TIGR02643 143 kvvkdvGvaiiGqtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesl 213
                                             +++kdvGvaiiGqt++laPadkr+ya+rd+tatv+siplitasil+kkla+Gldalv+dvkvG+Gafm+++
  lcl|FitnessBrowser__Koxy:BWI76_RS04135 144 EIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTY 214
                                             *********************************************************************** PP

                               TIGR02643 214 eeseelarslvevangaGvrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellv 284
                                             e s++la+++v v+ngaGvrttal+tdmnq+las+aGnavevreav+fltGe+r++rl evt+al++e+l+
  lcl|FitnessBrowser__Koxy:BWI76_RS04135 215 ELSAALAEAIVGVSNGAGVRTTALLTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLLEVTMALCVEMLI 285
                                             *********************************************************************** PP

                               TIGR02643 285 sgklaadeaeaeakleavlesGraaerfarmvaalgGPadfvekpekylakaaiakavkaaregylseidt 355
                                             sgkla++ea+a+akl+avl++G+aa++f+rmvaa++GP+dfve+++kyl+ a++ kav+a+ eg+++e+dt
  lcl|FitnessBrowser__Koxy:BWI76_RS04135 286 SGKLAENEADARAKLQAVLDNGKAADVFGRMVAAQKGPNDFVENYDKYLPAAMLSKAVYAEGEGFVAEMDT 356
                                             *********************************************************************** PP

                               TIGR02643 356 relGlavvalGGGrrkaddkldlsvGltdllelGekvekeeplavvhaadeedaeeaakavkkalkiadea 426
                                             r+lG+avv++GGGrr+a+d +d+svG+td+++lG++v++++plav+ha+de++++eaa+avk+a+k++++a
  lcl|FitnessBrowser__Koxy:BWI76_RS04135 357 RALGMAVVSMGGGRRQASDLIDYSVGFTDMVRLGARVDAQQPLAVIHAKDENSWQEAARAVKAAIKLGAKA 427
                                             *********************************************************************** PP

                               TIGR02643 427 Peeakvvleri 437
                                             Pe +++v++ri
  lcl|FitnessBrowser__Koxy:BWI76_RS04135 428 PEMTPTVYRRI 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: 10.65
//
[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