Alignments for a candidate for ald-dh-CoA in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Desulfitobacterium hafniense DCB-2

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10); propanal dehydrogenase (CoA-propanoylating) (EC 1.2.1.87) (characterized)
to candidate WP_015943315.1 DHAF_RS06235 acetaldehyde dehydrogenase

Query= BRENDA::Q53WH9
         (307 letters)



>NCBI__GCF_000021925.1:WP_015943315.1
          Length = 297

 Score =  328 bits (842), Expect = 7e-95
 Identities = 169/297 (56%), Positives = 223/297 (75%), Gaps = 9/297 (3%)

Query: 3   ERVKVAILGSGNIGTDLMYKLLKNPGHMELVAVVGIDPKSEGLARARALGLEASHEGIAY 62
           +R+  AI+G GNIGTDLMYK+L+   ++EL  V GI  +SEGL  AR  G+  S  GI  
Sbjct: 4   QRLNAAIIGPGNIGTDLMYKILRRSEYLELKLVAGIVAESEGLRLAREEGVATSAAGIQA 63

Query: 63  ILERPEIKIVFDATSAKAHVRHAKLLREAGKIAIDLTPAARGPYVVPPVNLKEHLDKDNV 122
           IL+R +I IVFDAT+A AH +HA LL++AG IA+DLTPAA GPYV+P VNL+EH+D  NV
Sbjct: 64  ILDRKDIDIVFDATTAHAHAQHAPLLKDAGIIAVDLTPAAVGPYVMPVVNLEEHIDAMNV 123

Query: 123 NLITCGGQATIPLVYAVHRVAPVLYAEMVSTVASRSAGPGTRQNIDEFTFTTARGLEAIG 182
           NLITCGGQATIP+VYA+ RV P  YAE+V+T+AS+SAGPGTRQNIDEFT TTA+G+  IG
Sbjct: 124 NLITCGGQATIPIVYAISRVVPTAYAEIVATIASKSAGPGTRQNIDEFTLTTAKGIVDIG 183

Query: 183 GAKKGKAIIILNPAEPPILMTNTV-RCIPEDEGFDREAVVASVRAMEREVQAYVPGYRLK 241
            A+KGKAII+LNPA+PP++M NT+   I + +    + +  SV  + +EVQA+VPGY+LK
Sbjct: 184 NAQKGKAIILLNPADPPMMMNNTIYALIDQVDPAIEQKITESVEEIIKEVQAFVPGYKLK 243

Query: 242 ADPVFERLPTPWGERTVVSMLLEVEGAGDYLPKYAGNLDIMTASARRVGEVFAQHLL 298
             P+F+      G +  V++++EVEG+GDYLP+Y+GNLD+ T +A  V E  A+H L
Sbjct: 244 IPPMFD------GNK--VTVMIEVEGSGDYLPQYSGNLDLETCAALAVAEKMAKHKL 292


Lambda     K      H
   0.318    0.136    0.389 

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: 290
Number of extensions: 8
Number of successful extensions: 3
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: 307
Length of database: 297
Length adjustment: 27
Effective length of query: 280
Effective length of database: 270
Effective search space:    75600
Effective search space used:    75600
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_015943315.1 DHAF_RS06235 (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.8013.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-135  436.5   6.1   2.6e-135  436.3   6.1    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015943315.1  DHAF_RS06235 acetaldehyde dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015943315.1  DHAF_RS06235 acetaldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.3   6.1  2.6e-135  2.6e-135       2     284 ..       6     292 ..       5     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 436.3 bits;  conditional E-value: 2.6e-135
                                 TIGR03215   2 vkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleeedidivf 69 
                                               +++aiiG+Gnigtdl++k+lr se lel+l++Gi +es+Gl+ are gv+tsa G++a+l+++didivf
  lcl|NCBI__GCF_000021925.1:WP_015943315.1   6 LNAAIIGPGNIGTDLMYKILRrSEYLELKLVAGIVAESEGLRLAREEGVATSAAGIQAILDRKDIDIVF 74 
                                               689****************999*********************************************** PP

                                 TIGR03215  70 datsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrv 138
                                               dat+a+aha++a ll+++g+i++dltPaavGpyv+P+vnlee+ da nvnl+tCgGqatiPiv+a+srv
  lcl|NCBI__GCF_000021925.1:WP_015943315.1  75 DATTAHAHAQHAPLLKDAGIIAVDLTPAAVGPYVMPVVNLEEHIDAMNVNLITCGGQATIPIVYAISRV 143
                                               ********************************************************************* PP

                                 TIGR03215 139 akvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalve 207
                                               ++ +yaeiva+iasksaGpgtr+nideft tt+k++  +g a+kgkaii+lnPa+Pp++m++t+yal++
  lcl|NCBI__GCF_000021925.1:WP_015943315.1 144 VPTAYAEIVATIASKSAGPGTRQNIDEFTLTTAKGIVDIGNAQKGKAIILLNPADPPMMMNNTIYALID 212
                                               ********************************************************************9 PP

                                 TIGR03215 208 ead...eeaieasveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldiltaaal 273
                                               ++d   e++i++svee+++evq++vpGy+lk  +++dg+kv+v++eveG gdylP+y+Gnld+ t+aal
  lcl|NCBI__GCF_000021925.1:WP_015943315.1 213 QVDpaiEQKITESVEEIIKEVQAFVPGYKLKIPPMFDGNKVTVMIEVEGSGDYLPQYSGNLDLETCAAL 281
                                               99977789************************************************************* PP

                                 TIGR03215 274 avaeklaeell 284
                                               avaek+a++ l
  lcl|NCBI__GCF_000021925.1:WP_015943315.1 282 AVAEKMAKHKL 292
                                               *******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (297 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: 00:00:00.00
# Mc/sec: 11.38
//
[ok]

This GapMind analysis is from Sep 24 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