Alignments for a candidate for ald-dh-CoA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Burkholderia phytofirmans PsJN

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate BPHYT_RS07245 BPHYT_RS07245 acetaldehyde dehydrogenase

Query= SwissProt::Q9KWS1
         (316 letters)



>FitnessBrowser__BFirm:BPHYT_RS07245
          Length = 314

 Score =  426 bits (1094), Expect = e-124
 Identities = 218/307 (71%), Positives = 251/307 (81%)

Query: 4   DRLSVAIIGSGNIGTDLMIKIMRNSKLLKVGAMVGIDPKSDGLARAQRLGVPTTAEGVDG 63
           D+ +VAIIGSGNIGTDLMIK++R++K L++GAMVGIDP SDGLARA+RLGV TTA G++G
Sbjct: 6   DKQAVAIIGSGNIGTDLMIKVLRDAKHLEMGAMVGIDPASDGLARAKRLGVATTAHGIEG 65

Query: 64  LLDMPAFRDIKIAFDATSAGAQAIHNQKLQAHGVRVIDLTPAAIGPYVIPVVNFDQHVDA 123
           L+ MP F  I+IAFDATSAGA   H   L+ HGV VIDLTPAAIGP+V+PVVN   H+DA
Sbjct: 66  LVTMPNFGAIRIAFDATSAGAHHRHAAVLREHGVTVIDLTPAAIGPFVVPVVNLFAHLDA 125

Query: 124 PNINMVTCGGQATIPIVHAVSKVSPVHYAEIVASISSKSAGPGTRANIDEFTETTSKAIL 183
           PN+NMVTCGGQATIPIVHAVS+V+PV YAEIVASI+S+SAGPGTRANIDEFTETTSKAI 
Sbjct: 126 PNLNMVTCGGQATIPIVHAVSRVAPVRYAEIVASIASRSAGPGTRANIDEFTETTSKAIE 185

Query: 184 EVGGAAQGRAIIILNPAEPPLIMRDTVYCFVSAEANIDAITDSVEQMVKSVQEYVPGYRL 243
            VGGAA+G+AII+LNPAEPPL+MRDTVYC    EA+ D I  S+  MV +V  YVPGYRL
Sbjct: 186 TVGGAARGKAIIVLNPAEPPLMMRDTVYCLTEEEADTDEIESSIRAMVSAVASYVPGYRL 245

Query: 244 KQKVQFEKIVAGNEQNIPGLGWSTGLKVSVFLEVEGAGHYLPSYAGNLDIMTSAGLTVAE 303
           KQ VQF++  A N   +       GLKVSVFLEVEGA HYLPSYAGNLDIMTSA L  AE
Sbjct: 246 KQAVQFDRYTAANPLALHANERRAGLKVSVFLEVEGAAHYLPSYAGNLDIMTSAALAAAE 305

Query: 304 RIAGSGV 310
           +IA S V
Sbjct: 306 QIAASRV 312


Lambda     K      H
   0.317    0.134    0.380 

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: 351
Number of extensions: 8
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: 316
Length of database: 314
Length adjustment: 27
Effective length of query: 289
Effective length of database: 287
Effective search space:    82943
Effective search space used:    82943
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS07245 BPHYT_RS07245 (acetaldehyde dehydrogenase)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

# 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/TIGR03215.hmm
# target sequence database:        /tmp/gapView.15679.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03215  [M=285]
Accession:   TIGR03215
Description: ac_ald_DH_ac: acetaldehyde dehydrogenase (acetylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.2e-146  473.5   6.2   1.4e-146  473.2   6.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07245  BPHYT_RS07245 acetaldehyde dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07245  BPHYT_RS07245 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.2   6.2  1.4e-146  1.4e-146       2     284 ..       8     312 ..       7     313 .. 0.98

  Alignments for each domain:
  == domain 1  score: 473.2 bits;  conditional E-value: 1.4e-146
                                TIGR03215   2 vkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didi 67 
                                                vaiiGsGnigtdl+ik+lr +++le+ ++vGidp+sdGlara++lgv+t+a+G+++l++++    i+i
  lcl|FitnessBrowser__BFirm:BPHYT_RS07245   8 QAVAIIGSGNIGTDLMIKVLRdAKHLEMGAMVGIDPASDGLARAKRLGVATTAHGIEGLVTMPnfgAIRI 77 
                                              679******************99***************************************988889** PP

                                TIGR03215  68 vfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsr 137
                                              +fdatsa ah+++a++l+e+g++vidltPaa+Gp+vvP+vnl ++lda+n+n+vtCgGqatiPiv+avsr
  lcl|FitnessBrowser__BFirm:BPHYT_RS07245  78 AFDATSAGAHHRHAAVLREHGVTVIDLTPAAIGPFVVPVVNLFAHLDAPNLNMVTCGGQATIPIVHAVSR 147
                                              ********************************************************************** PP

                                TIGR03215 138 vakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv. 206
                                              va+v+yaeivasias+saGpgtranideftettska+e+vgGa++gkaii+lnPaePpl+mrdtvy+l+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07245 148 VAPVRYAEIVASIASRSAGPGTRANIDEFTETTSKAIETVGGAARGKAIIVLNPAEPPLMMRDTVYCLTe 217
                                              *********************************************************************8 PP

                                TIGR03215 207 eeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylP 259
                                              eead+++ie+s+++mv++v++yvpGyrlkq v++d                 g kvsv+leveGa++ylP
  lcl|FitnessBrowser__BFirm:BPHYT_RS07245 218 EEADTDEIESSIRAMVSAVASYVPGYRLKQAVQFDrytaanplalhanerraGLKVSVFLEVEGAAHYLP 287
                                              899******************************************************************* PP

                                TIGR03215 260 kyaGnldiltaaalavaeklaeell 284
                                              +yaGnldi+t+aala+ae++a++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07245 288 SYAGNLDIMTSAALAAAEQIAASRV 312
                                              *********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (314 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.62
//
[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