GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Pseudomonas simiae WCS417

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF991 PS417_05025 maleylacetoacetate isomerase

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



>FitnessBrowser__WCS417:GFF991
          Length = 213

 Score =  354 bits (909), Expect = e-103
 Identities = 171/211 (81%), Positives = 182/211 (86%)

Query: 1   MELYTYYRSTSSYRVRIALALKGLDYQALPVNLIAAPGGEHRQPAYLAINPQGRVPALRT 60
           MELYTYYRSTSSYRVRIALALKGLD+ A+PVNL+   GG HRQP YLAINPQGRVPALRT
Sbjct: 1   MELYTYYRSTSSYRVRIALALKGLDFTAVPVNLLVPAGGAHRQPEYLAINPQGRVPALRT 60

Query: 61  DEGALLVQSPAIIEYLEERYPQVPLLSADLAVRAHERGVAALIGCDIHPLHNVSVLNQLR 120
           +EG LL+QSPAIIEYL+ERYPQ PLLS DLA RAHER VA++IGCDIHPLHN S  N LR
Sbjct: 61  EEGELLIQSPAIIEYLDERYPQAPLLSRDLATRAHERAVASIIGCDIHPLHNSSTQNLLR 120

Query: 121 QWGHDEAQVTEWIGHWISQGLAAVEQLIGDDGYCFGALPGLADVFLIPQLYAAERFNVSL 180
           QWGHDEAQ+ EWIGHWISQGL AVEQLIGD G+CFG  PGLAD FLIPQLYAAERF V L
Sbjct: 121 QWGHDEAQLLEWIGHWISQGLGAVEQLIGDQGFCFGEQPGLADTFLIPQLYAAERFKVPL 180

Query: 181 QGYPRIRRVAALAAVHPAFQQAHPAKQPDTP 211
             YPRI RVAALAA HPAF +AHPA QPDTP
Sbjct: 181 ASYPRIGRVAALAAQHPAFVRAHPANQPDTP 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: 260
Number of extensions: 10
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: 213
Length adjustment: 21
Effective length of query: 190
Effective length of database: 192
Effective search space:    36480
Effective search space used:    36480
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 GFF991 PS417_05025 (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.904446.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.5e-84  268.2   0.0    2.8e-84  268.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF991  PS417_05025 maleylacetoacetate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF991  PS417_05025 maleylacetoacetate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.0   0.0   2.8e-84   2.8e-84       2     210 ..       3     210 ..       2     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 268.0 bits;  conditional E-value: 2.8e-84
                          TIGR01262   2 lYsyfrSsasyRvRiaLaLkgidyesvpvnLlkd..GeqkkeefkalNPqelvPtLkidegevltqSlAiieyLee 75 
                                        lY+y+rS++syRvRiaLaLkg+d+++vpvnLl    G+++++e+ a+NPq++vP+L+++ege l qS AiieyL+e
  lcl|FitnessBrowser__WCS417:GFF991   3 LYTYYRSTSSYRVRIALALKGLDFTAVPVNLLVPagGAHRQPEYLAINPQGRVPALRTEEGELLIQSPAIIEYLDE 78 
                                        9******************************976679*************************************** PP

                          TIGR01262  76 typepaLlpkdpakrarvralalliacdihPlqNlrvlqlleeklgvdeeekkewlkhwiekGlaalEellkekag 151
                                        +yp+ +Ll++d a+ra++ra+a++i+cdihPl+N + ++ll+ ++g+de++  ew+ hwi++Gl a+E+l+ + +g
  lcl|FitnessBrowser__WCS417:GFF991  79 RYPQAPLLSRDLATRAHERAVASIIGCDIHPLHNSSTQNLLR-QWGHDEAQLLEWIGHWISQGLGAVEQLIGD-QG 152
                                        ************************************999999.89**************************98.45 PP

                          TIGR01262 152 afcvGdevtladvcLvpqvynAerfevdlaqyPtlkrieealaelpafqeahpenqpdt 210
                                         fc+G++++lad +L+pq+y+Aerf+v la+yP++ r+++ +a++paf +ahp+nqpdt
  lcl|FitnessBrowser__WCS417:GFF991 153 -FCFGEQPGLADTFLIPQLYAAERFKVPLASYPRIGRVAALAAQHPAFVRAHPANQPDT 210
                                        .*********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (213 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: 14.45
//
[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