Alignments for a candidate for pcaD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Burkholderia phytofirmans PsJN

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate BPHYT_RS21430 BPHYT_RS21430 3-oxoadipate enol-lactonase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__BFirm:BPHYT_RS21430
          Length = 263

 Score =  501 bits (1291), Expect = e-147
 Identities = 246/263 (93%), Positives = 256/263 (97%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           MPYAAVNGTELHYRIDG+RHGNAPWIVLSNSLGTDLSMWA QVAALSKHFRVLRYDTRGH
Sbjct: 1   MPYAAVNGTELHYRIDGDRHGNAPWIVLSNSLGTDLSMWASQVAALSKHFRVLRYDTRGH 60

Query: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120
           GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCG+SMGGLTGVALAARH +R ERV LC
Sbjct: 61  GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGISMGGLTGVALAARHGNRFERVVLC 120

Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180
           NTAARIGSPEVWVPRA KAR+EGM ALADAVLPRWFTADY+EREPVVLA+IRDVFVHTDK
Sbjct: 121 NTAARIGSPEVWVPRAAKARSEGMLALADAVLPRWFTADYIEREPVVLALIRDVFVHTDK 180

Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELDAS 240
           EGYASNC+AIDAADLRPEAPGIK+PALVISGTHDLAATPAQGRELAQ+I GARYVELDAS
Sbjct: 181 EGYASNCDAIDAADLRPEAPGIKLPALVISGTHDLAATPAQGRELAQSIPGARYVELDAS 240

Query: 241 HISNIERADAFTKTVVDFLTEQK 263
           HISNIE+ADAFTKTVVDFLTEQK
Sbjct: 241 HISNIEKADAFTKTVVDFLTEQK 263


Lambda     K      H
   0.320    0.134    0.402 

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: 364
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: 263
Length of database: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate BPHYT_RS21430 BPHYT_RS21430 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# 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/TIGR02427.hmm
# target sequence database:        /tmp/gapView.4172886.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   4.9e-104  333.1   0.1   5.6e-104  333.0   0.1    1.0  1  FitnessBrowser__BFirm:BPHYT_RS21430  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__BFirm:BPHYT_RS21430  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.0   0.1  5.6e-104  5.6e-104       2     251 .]      11     260 ..      10     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 333.0 bits;  conditional E-value: 5.6e-104
                            TIGR02427   2 lhyrlegae.adkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallD 74 
                                          lhyr++g++  ++p++vl+nSLGtdl++w+++++al+k+frvlryD+rGHG+S++p+gpy+ie+l++dvl+l+D
  FitnessBrowser__BFirm:BPHYT_RS21430  11 LHYRIDGDRhGNAPWIVLSNSLGTDLSMWASQVAALSKHFRVLRYDTRGHGHSEAPKGPYTIEQLTGDVLGLMD 84 
                                          9*****8762589************************************************************* PP

                            TIGR02427  75 algiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFtp 148
                                          +l+i++a++cG+S+GGl++ aLaar+++r+e++vl+ntaa+ig++e+W +R+a+ r+eG+ aladavl rwFt+
  FitnessBrowser__BFirm:BPHYT_RS21430  85 TLKIARANFCGISMGGLTGVALAARHGNRFERVVLCNTAARIGSPEVWVPRAAKARSEGMLALADAVLPRWFTA 158
                                          ************************************************************************** PP

                            TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpga 222
                                          ++ e+ep  l+l+r+++v++++egYa++c+Ai +adlr ++  i++P+lvi+G++D ++ p++ re+a+++pga
  FitnessBrowser__BFirm:BPHYT_RS21430 159 DYIEREPVVLALIRDVFVHTDKEGYASNCDAIDAADLRPEAPGIKLPALVISGTHDLAATPAQGRELAQSIPGA 232
                                          ************************************************************************** PP

                            TIGR02427 223 rfaeieeaaHlpnleqpeafaallrdflk 251
                                          r++e++ a+H++n+e+++af+++++dfl+
  FitnessBrowser__BFirm:BPHYT_RS21430 233 RYVELD-ASHISNIEKADAFTKTVVDFLT 260
                                          ******.********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (263 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: 21.93
//
[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