GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas fluorescens GW456-L13

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate PfGW456L13_4960 Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)

Query= reanno::pseudo3_N2E3:AO353_15560
         (211 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960
          Length = 211

 Score =  391 bits (1004), Expect = e-114
 Identities = 188/211 (89%), Positives = 199/211 (94%)

Query: 1   MELFTYYRSTSSFRVRIALALKGLEYQALPINLIAPQGGEHQQPAYLHINPQGRVPALRT 60
           MEL+TYYRSTSS+RVRIALALKGL+YQ+LP+NLIAPQGGEH+QP YL INPQGRVPALRT
Sbjct: 1   MELYTYYRSTSSYRVRIALALKGLDYQSLPVNLIAPQGGEHRQPPYLGINPQGRVPALRT 60

Query: 61  DEGELLIQSPAIIEYLEERYPQVPLLSKDLARRAHERGVAALIGCDIHPLHNVSVLNQLR 120
           DEGELLIQSPAIIEYLEERYPQVPLLSKDLA RAHERGVAA+IGCD+HPLHNVSVLN+LR
Sbjct: 61  DEGELLIQSPAIIEYLEERYPQVPLLSKDLAARAHERGVAAVIGCDVHPLHNVSVLNRLR 120

Query: 121 QLGHDEPQVVHWIGHWITQGLAAVEHLIGDEGYCFGNAPGLADVYLIPQLYAAERFNISL 180
           Q GHDEPQVV WIGHWI QGLA VE LIGD+GYCFG  PGLADVYLIPQLYAAERFN+SL
Sbjct: 121 QSGHDEPQVVEWIGHWIGQGLATVEQLIGDDGYCFGPEPGLADVYLIPQLYAAERFNVSL 180

Query: 181 EAYPRIRRVAALAVQHPAFIKAHPANQPDTP 211
           EAYPRIRRVAALA  HPAFIKAHPANQPDTP
Sbjct: 181 EAYPRIRRVAALAATHPAFIKAHPANQPDTP 211


Lambda     K      H
   0.322    0.139    0.427 

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: 313
Number of extensions: 9
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: 211
Length of database: 211
Length adjustment: 21
Effective length of query: 190
Effective length of database: 190
Effective search space:    36100
Effective search space used:    36100
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate PfGW456L13_4960 (Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18))
to HMM TIGR01262 (maiA: maleylacetoacetate isomerase (EC 5.2.1.2))

# 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/TIGR01262.hmm
# target sequence database:        /tmp/gapView.20085.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01262  [M=211]
Accession:   TIGR01262
Description: maiA: maleylacetoacetate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    7.7e-86  273.1   0.0    8.6e-86  272.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960  Maleylacetoacetate isomerase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960  Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-tra
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.9   0.0   8.6e-86   8.6e-86       2     210 ..       3     210 ..       2     211 .] 0.97

  Alignments for each domain:
  == domain 1  score: 272.9 bits;  conditional E-value: 8.6e-86
                                               TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd..GeqkkeefkalNPqelvPt 54 
                                                             lY+y+rS++syRvRiaLaLkg+dy+s pvnL++   Ge++++ +  +NPq++vP+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960   3 LYTYYRSTSSYRVRIALALKGLDYQSLPVNLIAPqgGEHRQPPYLGINPQGRVPA 57 
                                                             9******************************986679****************** PP

                                               TIGR01262  55 LkidegevltqSlAiieyLeetypepaLlpkdpakrarvralalliacdihPlqN 109
                                                             L++dege l qS AiieyLee+yp+++Ll+kd a+ra++r +a++i+cd+hPl+N
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960  58 LRTDEGELLIQSPAIIEYLEERYPQVPLLSKDLAARAHERGVAAVIGCDVHPLHN 112
                                                             ******************************************************* PP

                                               TIGR01262 110 lrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekagafcvGdevtladv 164
                                                             ++vl++l+++ g+de +  ew+ hwi +Gla++E+l+ +  g +c+G e++ladv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960 113 VSVLNRLRQS-GHDEPQVVEWIGHWIGQGLATVEQLIGD-DG-YCFGPEPGLADV 164
                                                             ********66.89************************98.45.************ PP

                                               TIGR01262 165 cLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210
                                                             +L+pq+y+Aerf+v+l++yP+++r+++ +a++paf +ahp+nqpdt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4960 165 YLIPQLYAAERFNVSLEAYPRIRRVAALAATHPAFIKAHPANQPDT 210
                                                             *********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (211 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.25
//
[ok]

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

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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