GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas fluorescens FW300-N2C3

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate AO356_16835 AO356_16835 maleylacetoacetate isomerase

Query= reanno::pseudo5_N2C3_1:AO356_16835
         (211 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16835
          Length = 211

 Score =  429 bits (1102), Expect = e-125
 Identities = 211/211 (100%), Positives = 211/211 (100%)

Query: 1   MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60
           MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT
Sbjct: 1   MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60

Query: 61  DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120
           DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR
Sbjct: 61  DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120

Query: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180
           QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL
Sbjct: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180

Query: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211
           QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP
Sbjct: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211


Lambda     K      H
   0.321    0.138    0.422 

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: 317
Number of extensions: 5
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 AO356_16835 AO356_16835 (maleylacetoacetate isomerase)
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.30391.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-88  279.6   0.0    8.6e-88  279.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835  AO356_16835 maleylacetoacetate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835  AO356_16835 maleylacetoacetate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.5   0.0   8.6e-88   8.6e-88       2     210 ..       3     210 ..       2     211 .] 0.98

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 8.6e-88
                                       TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd..GeqkkeefkalNPqelvPtLkidegev 62 
                                                     lY+y+rS++syRvRiaLaLkg+dy++ pvnL++   Ge++++++ a+NPq++vP+L++deg+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835   3 LYTYYRSTSSYRVRIALALKGLDYQALPVNLIAApgGEHRQPAYLAINPQGRVPALRTDEGAL 65 
                                                     9*******************************98889************************** PP

                                       TIGR01262  63 ltqSlAiieyLeetypepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdee 125
                                                     l qS AiieyLee+yp+++Ll++d a ra++r +a+li+cdihPl+N++vl++l+ ++g+de+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835  66 LVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR-QWGHDEA 127
                                                     ******************************************************9.89***** PP

                                       TIGR01262 126 ekkewlkhwiekGlaalEellkekagafcvGdevtladvcLvpqvynAerfevdlaqyPtlkr 188
                                                     + +ew+ hwi++Glaa+E+l+ +  g +c+G+ ++ladv+L+pq+y+Aerf+v+l+ yP+++r
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 128 QVTEWIGHWISQGLAAVEQLIGD-DG-YCFGALPGLADVFLIPQLYAAERFNVSLQGYPRIRR 188
                                                     *********************98.45.************************************ PP

                                       TIGR01262 189 ieealaelpafqeahpenqpdt 210
                                                     +++ +a +pafq+ahp++qpdt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16835 189 VAALAAVHPAFQQAHPAKQPDT 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: 7.25
//
[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:

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