Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

Align acetaldehyde dehydrogenase; EC 1.2.1.10 (characterized)
to candidate WP_012967941.1 KVAR_RS10760 acetaldehyde dehydrogenase

Query= CharProtDB::CH_002283
         (316 letters)



>NCBI__GCF_000025465.1:WP_012967941.1
          Length = 316

 Score =  531 bits (1369), Expect = e-156
 Identities = 275/316 (87%), Positives = 292/316 (92%)

Query: 1   MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60
           M KRKVAIIGSGNIGTDLMIKILRH QHLEMAVMVGIDPQSDGLARARRMGVATTHEGV 
Sbjct: 1   MRKRKVAIIGSGNIGTDLMIKILRHSQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVG 60

Query: 61  GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120
           GLM M EFADID VFDATSAGAH+KNDAALREAKP IR+IDLTPAAIGPYCVPVVNL AN
Sbjct: 61  GLMQMAEFADIDFVFDATSAGAHIKNDAALREAKPGIRVIDLTPAAIGPYCVPVVNLAAN 120

Query: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180
           + Q NVNMVTCGGQATIPMVAAVSRVA+VHYAEI+ASIAS+SAGPGTRANIDEFTETTS+
Sbjct: 121 LHQGNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASIASQSAGPGTRANIDEFTETTSQ 180

Query: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240
           AIE VGGA KGKAIIVLNPAEPPLMMRDTVYVLS+ ASQ+ I ASI EMA AVQAYVPGY
Sbjct: 181 AIEKVGGAGKGKAIIVLNPAEPPLMMRDTVYVLSELASQEAIAASIAEMAAAVQAYVPGY 240

Query: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300
           RLKQ+VQFEVIP+DKPVNLPGVG FSGLKTA++LEVEGAAHYLPAYAGNLDIMTS+ALAT
Sbjct: 241 RLKQQVQFEVIPEDKPVNLPGVGCFSGLKTAIYLEVEGAAHYLPAYAGNLDIMTSAALAT 300

Query: 301 AEKMAQSLARKAGEAA 316
           AE+MA ++   AG  A
Sbjct: 301 AEQMAGAMHSAAGATA 316


Lambda     K      H
   0.317    0.132    0.368 

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: 394
Number of extensions: 6
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: 316
Length adjustment: 27
Effective length of query: 289
Effective length of database: 289
Effective search space:    83521
Effective search space used:    83521
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 WP_012967941.1 KVAR_RS10760 (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.798570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-143  463.2   8.0   1.9e-143  462.9   8.0    1.0  1  NCBI__GCF_000025465.1:WP_012967941.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012967941.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.9   8.0  1.9e-143  1.9e-143       1     283 [.       3     308 ..       3     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: 462.9 bits;  conditional E-value: 1.9e-143
                             TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivf 69 
                                           k kvaiiGsGnigtdl+ik+lr s++le+a++vGidp+sdGlarar++gv+t++eGv +l+++    did vf
  NCBI__GCF_000025465.1:WP_012967941.1   3 KRKVAIIGSGNIGTDLMIKILRhSQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVGGLMQMAefaDIDFVF 75 
                                           679*******************9**************************************9988899***** PP

                             TIGR03215  70 datsakahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvak 140
                                           datsa ah +n+++l+e+  g++vidltPaa+Gpy+vP+vnl ++l++ nvn+vtCgGqatiP+vaavsrvak
  NCBI__GCF_000025465.1:WP_012967941.1  76 DATSAGAHIKNDAALREAkpGIRVIDLTPAAIGPYCVPVVNLAANLHQGNVNMVTCGGQATIPMVAAVSRVAK 148
                                           ***************998779**************************************************** PP

                             TIGR03215 141 vkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeea 213
                                           v+yaeivasias+saGpgtranideftetts+a+e+vgGa kgkaii+lnPaePpl+mrdtvy+l+e a++ea
  NCBI__GCF_000025465.1:WP_012967941.1 149 VHYAEIVASIASQSAGPGTRANIDEFTETTSQAIEKVGGAGKGKAIIVLNPAEPPLMMRDTVYVLSELASQEA 221
                                           ************************************************************************* PP

                             TIGR03215 214 ieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylPkyaGnldilt 269
                                           i+as++em ++vq+yvpGyrlkq+v+++                 g k++++leveGa++ylP+yaGnldi+t
  NCBI__GCF_000025465.1:WP_012967941.1 222 IAASIAEMAAAVQAYVPGYRLKQQVQFEvipedkpvnlpgvgcfsGLKTAIYLEVEGAAHYLPAYAGNLDIMT 294
                                           ************************************************************************* PP

                             TIGR03215 270 aaalavaeklaeel 283
                                           +aala+ae++a ++
  NCBI__GCF_000025465.1:WP_012967941.1 295 SAALATAEQMAGAM 308
                                           **********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (316 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: 16.10
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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