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_RS05100 RR42_RS05100 acetaldehyde dehydrogenase

Query= SwissProt::Q9KWS1
         (316 letters)



>FitnessBrowser__Cup4G11:RR42_RS05100
          Length = 321

 Score =  445 bits (1144), Expect = e-130
 Identities = 225/305 (73%), Positives = 256/305 (83%)

Query: 2   SDDRLSVAIIGSGNIGTDLMIKIMRNSKLLKVGAMVGIDPKSDGLARAQRLGVPTTAEGV 61
           S  RL  AIIGSGNIGTDLMIKI+R+ + L+VGAMVGID  SDGLARAQRLGVPTT EG+
Sbjct: 5   SRTRLRAAIIGSGNIGTDLMIKILRHGQHLEVGAMVGIDAASDGLARAQRLGVPTTHEGI 64

Query: 62  DGLLDMPAFRDIKIAFDATSAGAQAIHNQKLQAHGVRVIDLTPAAIGPYVIPVVNFDQHV 121
           +GLL MP F DI++AFDATSAGA   HN  LQ HG++VIDLTPAAIGPYV+PVVN D H+
Sbjct: 65  EGLLGMPGFADIRVAFDATSAGAHMHHNAVLQKHGIQVIDLTPAAIGPYVVPVVNLDAHL 124

Query: 122 DAPNINMVTCGGQATIPIVHAVSKVSPVHYAEIVASISSKSAGPGTRANIDEFTETTSKA 181
           DAPN+NMVTCGGQATIPIV AVS+V+PV YAEIVASI+S+SAGPGTRANIDEFTETTS A
Sbjct: 125 DAPNLNMVTCGGQATIPIVRAVSQVAPVSYAEIVASIASRSAGPGTRANIDEFTETTSNA 184

Query: 182 ILEVGGAAQGRAIIILNPAEPPLIMRDTVYCFVSAEANIDAITDSVEQMVKSVQEYVPGY 241
           I++VGGAA G+AII+LNPAEPPL+MRDTV+C  +A+A  DAI  SVE+MV  V  YVPGY
Sbjct: 185 IVQVGGAAHGKAIIVLNPAEPPLLMRDTVFCLTAADAGQDAIRASVERMVAQVAAYVPGY 244

Query: 242 RLKQKVQFEKIVAGNEQNIPGLGWSTGLKVSVFLEVEGAGHYLPSYAGNLDIMTSAGLTV 301
           RLKQ VQFE+I       +PG+G   GLKVSVFLEVEGA HYLP+YAGNLDIMTSA L  
Sbjct: 245 RLKQHVQFERIDPACPLTLPGIGRLAGLKVSVFLEVEGAAHYLPAYAGNLDIMTSAALAA 304

Query: 302 AERIA 306
           AER+A
Sbjct: 305 AERVA 309


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: 392
Number of extensions: 13
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: 321
Length adjustment: 27
Effective length of query: 289
Effective length of database: 294
Effective search space:    84966
Effective search space used:    84966
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 RR42_RS05100 RR42_RS05100 (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.14492.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-144  465.9   3.4   2.7e-144  465.7   3.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05100  RR42_RS05100 acetaldehyde dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05100  RR42_RS05100 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.7   3.4  2.7e-144  2.7e-144       1     284 [.       8     313 ..       8     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.7 bits;  conditional E-value: 2.7e-144
                                 TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...di 65 
                                               ++++aiiGsGnigtdl+ik+lr +++le+ ++vGid++sdGlara++lgv t++eG+++ll ++   di
  lcl|FitnessBrowser__Cup4G11:RR42_RS05100   8 RLRAAIIGSGNIGTDLMIKILRhGQHLEVGAMVGIDAASDGLARAQRLGVPTTHEGIEGLLGMPgfaDI 76 
                                               5799******************99***************************************9999** PP

                                 TIGR03215  66 divfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaa 134
                                               +++fdatsa ah++++++l+++g++vidltPaa+GpyvvP+vnl+++lda+n+n+vtCgGqatiPiv a
  lcl|FitnessBrowser__Cup4G11:RR42_RS05100  77 RVAFDATSAGAHMHHNAVLQKHGIQVIDLTPAAIGPYVVPVVNLDAHLDAPNLNMVTCGGQATIPIVRA 145
                                               ********************************************************************* PP

                                 TIGR03215 135 vsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvy 203
                                               vs+va+v+yaeivasias+saGpgtranideftetts+a+ qvgGa++gkaii+lnPaePpllmrdtv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05100 146 VSQVAPVSYAEIVASIASRSAGPGTRANIDEFTETTSNAIVQVGGAAHGKAIIVLNPAEPPLLMRDTVF 214
                                               ********************************************************************* PP

                                 TIGR03215 204 alv.eeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGa 254
                                               +l+ ++a ++ai+asve+mv++v++yvpGyrlkq+v+++                 g kvsv+leveGa
  lcl|FitnessBrowser__Cup4G11:RR42_RS05100 215 CLTaADAGQDAIRASVERMVAQVAAYVPGYRLKQHVQFEridpacpltlpgigrlaGLKVSVFLEVEGA 283
                                               **988999************************************************************* PP

                                 TIGR03215 255 gdylPkyaGnldiltaaalavaeklaeell 284
                                               ++ylP+yaGnldi+t+aala+ae++a++ l
  lcl|FitnessBrowser__Cup4G11:RR42_RS05100 284 AHYLPAYAGNLDIMTSAALAAAERVARHKL 313
                                               **************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (321 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: 9.16
//
[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