Alignments for a candidate for ald-dh-CoA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Escherichia coli BW25113

Align acetaldehyde dehydrogenase; EC 1.2.1.10 (characterized)
to candidate 14489 b0351 acetaldehyde dehydrogenase (NCBI)

Query= CharProtDB::CH_002283
         (316 letters)



>FitnessBrowser__Keio:14489
          Length = 316

 Score =  612 bits (1579), Expect = e-180
 Identities = 316/316 (100%), Positives = 316/316 (100%)

Query: 1   MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60
           MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI
Sbjct: 1   MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60

Query: 61  GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120
           GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN
Sbjct: 61  GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120

Query: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180
           VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR
Sbjct: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180

Query: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240
           AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY
Sbjct: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240

Query: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300
           RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT
Sbjct: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300

Query: 301 AEKMAQSLARKAGEAA 316
           AEKMAQSLARKAGEAA
Sbjct: 301 AEKMAQSLARKAGEAA 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: 451
Number of extensions: 3
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 14489 b0351 (acetaldehyde dehydrogenase (NCBI))
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.18824.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.5e-146  471.5   5.4   5.2e-146  471.3   5.4    1.0  1  lcl|FitnessBrowser__Keio:14489  b0351 acetaldehyde dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14489  b0351 acetaldehyde dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  471.3   5.4  5.2e-146  5.2e-146       1     283 [.       3     308 ..       3     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: 471.3 bits;  conditional E-value: 5.2e-146
                       TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfdatsak 75 
                                     k kvaiiGsGnigtdl+ik+lr +++le+a++vGidp+sdGlarar++gv+t++eGv +l++++   didivfdatsa 
  lcl|FitnessBrowser__Keio:14489   3 KRKVAIIGSGNIGTDLMIKILRhGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVIGLMNMPefaDIDIVFDATSAG 81 
                                     679*******************99***************************************99999*********** PP

                       TIGR03215  76 ahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyaeivasias 152
                                     ah++n+++l+e+  ++++idltPaa+Gpy+vP+vnle+++d+ nvn+vtCgGqatiP+vaavsrva+v+yaei+asias
  lcl|FitnessBrowser__Keio:14489  82 AHVKNDAALREAkpDIRLIDLTPAAIGPYCVPVVNLEANVDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIAS 160
                                     *********9987789*************************************************************** PP

                       TIGR03215 153 ksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeeaieasveemveevqkyvpG 231
                                     ksaGpgtranideftetts+a+e vgGa+kgkaii+lnPaePpl+mrdtvy+l++ea++++ieas++em e+vq+yvpG
  lcl|FitnessBrowser__Keio:14489 161 KSAGPGTRANIDEFTETTSRAIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPG 239
                                     ******************************************************************************* PP

                       TIGR03215 232 yrlkqevvld.................gekvsvlleveGagdylPkyaGnldiltaaalavaeklaeel 283
                                     yrlkq+v+++                 g k++v+leveGa++ylP+yaGnldi+t++ala+aek+a++l
  lcl|FitnessBrowser__Keio:14489 240 YRLKQRVQFEvipqdkpvnlpgvgqfsGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALATAEKMAQSL 308
                                     ******************************************************************986 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: 10.76
//
[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