Alignments for a candidate for ald-dh-CoA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Marinobacter adhaerens HP15

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate GFF4095 HP15_4035 acetaldehyde dehydrogenase

Query= SwissProt::Q52060
         (312 letters)



>FitnessBrowser__Marino:GFF4095
          Length = 311

 Score =  498 bits (1282), Expect = e-146
 Identities = 250/311 (80%), Positives = 280/311 (90%)

Query: 1   MNQKLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGV 60
           M++K+K AIIGSGNIGTDLMIK+LRN K +EMGAMVGID  SDGLARA RMGV TT+ GV
Sbjct: 1   MSKKIKAAIIGSGNIGTDLMIKILRNGKNIEMGAMVGIDPESDGLARAARMGVATTHEGV 60

Query: 61  EGLIKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEE 120
           +GL+K+PEFADID VFDATSA AH+ NE  LR  K  I++ID+TPAAIGPYCVPVVNLE+
Sbjct: 61  DGLVKMPEFADIDIVFDATSAKAHMHNEVFLRGHKESIKIIDMTPAAIGPYCVPVVNLEQ 120

Query: 121 HLGKLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS 180
            L + NVNMVTCGGQATIPMVAAVSRVAK HYAEIVASISSKSAGPGTRANIDEFT+TTS
Sbjct: 121 QLQEGNVNMVTCGGQATIPMVAAVSRVAKAHYAEIVASISSKSAGPGTRANIDEFTQTTS 180

Query: 181 KAIEVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPG 240
           +AIEV+GGA KGKAIII+NPAEPPL+MRDTVYVLS AAD+A V ASV EMVQAV +YVPG
Sbjct: 181 RAIEVVGGAQKGKAIIILNPAEPPLLMRDTVYVLSDAADKAEVEASVEEMVQAVNSYVPG 240

Query: 241 YRLKQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALA 300
           YRLKQ+VQFD IPE  P+N+PGLGRFSGLKTS+FLEVEGAAHYLPAYAGNLDIMTSAAL 
Sbjct: 241 YRLKQKVQFDDIPEDQPMNVPGLGRFSGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALG 300

Query: 301 TAERMAQSMLN 311
           TAER+A+S++N
Sbjct: 301 TAERIAESLVN 311


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: 348
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: 312
Length of database: 311
Length adjustment: 27
Effective length of query: 285
Effective length of database: 284
Effective search space:    80940
Effective search space used:    80940
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 GFF4095 HP15_4035 (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.4980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.7e-145  469.6   5.3     2e-145  469.4   5.3    1.0  1  lcl|FitnessBrowser__Marino:GFF4095  HP15_4035 acetaldehyde dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4095  HP15_4035 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.4   5.3    2e-145    2e-145       1     283 [.       4     309 ..       4     311 .] 0.98

  Alignments for each domain:
  == domain 1  score: 469.4 bits;  conditional E-value: 2e-145
                           TIGR03215   1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfda 71 
                                         k+k+aiiGsGnigtdl+ik+lr ++++e+ ++vGidpesdGlara+++gv+t++eGvd+l++++   didivfda
  lcl|FitnessBrowser__Marino:GFF4095   4 KIKAAIIGSGNIGTDLMIKILRnGKNIEMGAMVGIDPESDGLARAARMGVATTHEGVDGLVKMPefaDIDIVFDA 78 
                                         79********************99***************************************99999******* PP

                           TIGR03215  72 tsakahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkya 144
                                         tsakah++n+ +l+ +   +++id+tPaa+Gpy+vP+vnle++l++ nvn+vtCgGqatiP+vaavsrvak++ya
  lcl|FitnessBrowser__Marino:GFF4095  79 TSAKAHMHNEVFLRGHkeSIKIIDMTPAAIGPYCVPVVNLEQQLQEGNVNMVTCGGQATIPMVAAVSRVAKAHYA 153
                                         *************876437899***************************************************** PP

                           TIGR03215 145 eivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeeaieasve 219
                                         eivasi+sksaGpgtranideft+tts+a+e vgGa+kgkaiiilnPaePpllmrdtvy+l+++ad++++easve
  lcl|FitnessBrowser__Marino:GFF4095 154 EIVASISSKSAGPGTRANIDEFTQTTSRAIEVVGGAQKGKAIIILNPAEPPLLMRDTVYVLSDAADKAEVEASVE 228
                                         *************************************************************************** PP

                           TIGR03215 220 emveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylPkyaGnldiltaaalavae 277
                                         emv++v++yvpGyrlkq+v++d                 g k+s++leveGa++ylP+yaGnldi+t+aal +ae
  lcl|FitnessBrowser__Marino:GFF4095 229 EMVQAVNSYVPGYRLKQKVQFDdipedqpmnvpglgrfsGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALGTAE 303
                                         *************************************************************************** PP

                           TIGR03215 278 klaeel 283
                                         ++ae+l
  lcl|FitnessBrowser__Marino:GFF4095 304 RIAESL 309
                                         ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (311 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: 00:00:00.01
# Mc/sec: 7.94
//
[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