Alignments for a candidate for ald-dh-CoA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Cupriavidus basilensis 4G11

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate RR42_RS32630 RR42_RS32630 acetaldehyde dehydrogenase

Query= SwissProt::Q52060
         (312 letters)



>FitnessBrowser__Cup4G11:RR42_RS32630
          Length = 314

 Score =  456 bits (1172), Expect = e-133
 Identities = 237/309 (76%), Positives = 267/309 (86%), Gaps = 2/309 (0%)

Query: 4   KLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGVEGL 63
           K KVAIIGSGNIGTDLMIKV+RN + LEMGAMVGIDAASDGLARA R+GV TT  G+EGL
Sbjct: 8   KHKVAIIGSGNIGTDLMIKVMRNGRQLEMGAMVGIDAASDGLARAARLGVPTTAEGIEGL 67

Query: 64  IKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEEHLG 123
           +++  F DI   FDATSA AH  +  +L+Q   GI++IDLTPAAIGPY VPVVNL++ LG
Sbjct: 68  VRMAGFGDIRIAFDATSAGAHAHHNQILQQH--GIQVIDLTPAAIGPYVVPVVNLDQQLG 125

Query: 124 KLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSKAI 183
             N+NMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS+AI
Sbjct: 126 ASNINMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSQAI 185

Query: 184 EVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPGYRL 243
             +GGAA+GKAII++NPAEPPL+MRDTV+ LS  AD+AA+ ASV  M +AVQAYVPGYRL
Sbjct: 186 CSVGGAARGKAIIVLNPAEPPLMMRDTVFTLSEDADEAAIEASVQAMAKAVQAYVPGYRL 245

Query: 244 KQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALATAE 303
           KQ+VQF+ I  SAPLNIPGLG  SGLKTS+FLEVEGAAHYLPAYAGNLDIMTSAALA AE
Sbjct: 246 KQRVQFERIDPSAPLNIPGLGLMSGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALACAE 305

Query: 304 RMAQSMLNA 312
           R+AQ+ L A
Sbjct: 306 RLAQTRLAA 314


Lambda     K      H
   0.317    0.132    0.362 

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: 320
Number of extensions: 3
Number of successful extensions: 2
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: 312
Length of database: 314
Length adjustment: 27
Effective length of query: 285
Effective length of database: 287
Effective search space:    81795
Effective search space used:    81795
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS32630 RR42_RS32630 (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.18300.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-145  469.9   5.9   1.6e-145  469.7   5.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS32630  RR42_RS32630 acetaldehyde dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS32630  RR42_RS32630 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.7   5.9  1.6e-145  1.6e-145       1     284 [.       8     312 ..       8     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 469.7 bits;  conditional E-value: 1.6e-145
                                 TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...di 65 
                                               k kvaiiGsGnigtdl+ik++r +++le+ ++vGid++sdGlara++lgv t+aeG+++l+++    di
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630   8 KHKVAIIGSGNIGTDLMIKVMRnGRQLEMGAMVGIDAASDGLARAARLGVPTTAEGIEGLVRMAgfgDI 76 
                                               689*******************999**************************************9999** PP

                                 TIGR03215  66 divfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaa 134
                                               +i+fdatsa aha+++++l+++g++vidltPaa+GpyvvP+vnl+++l a+n+n+vtCgGqatiP+vaa
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630  77 RIAFDATSAGAHAHHNQILQQHGIQVIDLTPAAIGPYVVPVVNLDQQLGASNINMVTCGGQATIPMVAA 145
                                               ********************************************************************* PP

                                 TIGR03215 135 vsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvy 203
                                               vsrvakv+yaeivasi+sksaGpgtranideftetts+a+ +vgGa++gkaii+lnPaePpl+mrdtv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 146 VSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSQAICSVGGAARGKAIIVLNPAEPPLMMRDTVF 214
                                               ********************************************************************* PP

                                 TIGR03215 204 alveeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGag 255
                                               +l+e+ade+aieasv++m ++vq+yvpGyrlkq+v+++                 g k+s++leveGa+
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 215 TLSEDADEAAIEASVQAMAKAVQAYVPGYRLKQRVQFEridpsaplnipglglmsGLKTSIFLEVEGAA 283
                                               ********************************************************************* PP

                                 TIGR03215 256 dylPkyaGnldiltaaalavaeklaeell 284
                                               +ylP+yaGnldi+t+aala+ae+la+++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS32630 284 HYLPAYAGNLDIMTSAALACAERLAQTRL 312
                                               *************************9876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.37
//
[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