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.2060.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: 9.66
//
[ok]

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

Links

Downloads

Related tools

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