Alignments for a candidate for ald-dh-CoA in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Nocardioides daejeonensis MJ31

Align Acetaldehyde dehydrogenase 1; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 1 (uncharacterized)
to candidate WP_110205394.1 DNK54_RS02755 acetaldehyde dehydrogenase (acetylating)

Query= curated2:A1UM81
         (310 letters)



>NCBI__GCF_003194585.1:WP_110205394.1
          Length = 300

 Score =  429 bits (1104), Expect = e-125
 Identities = 218/300 (72%), Positives = 246/300 (82%), Gaps = 5/300 (1%)

Query: 4   KLQVAIVGSGNISTDLLYKLQRSEYLEPRWMIGIDPESEGLARARKLGLETSHEGVDWLL 63
           K   AIVG GNI TDL+YKL RSE +EPRWMIG+DP SEGL  AR  GLE++HEGVDWLL
Sbjct: 3   KATAAIVGPGNIGTDLMYKLLRSEVIEPRWMIGVDPSSEGLKLARDKGLESTHEGVDWLL 62

Query: 64  AQDDKPDLVFEATSAYVHRAAAPRYEEAGIRAIDLTPAAVGPAVIPPANLREHLDAPNVN 123
            QD+ PDL+FEATSAYVHR  APRY+EAGIRA+DLTPAAVGPAVIPP N  EH+ A NVN
Sbjct: 63  KQDELPDLIFEATSAYVHRDYAPRYQEAGIRAVDLTPAAVGPAVIPPVNGEEHVGAWNVN 122

Query: 124 MITCGGQATIPIVYAVTRAVTEQGGTVPYAEIVASVSSSSAGPGTRANIDEFTKTTSKGV 183
           MITCGGQATIP+V AV+R        V YAEIVASVSS+SAGPGTRANIDEFT+TTS GV
Sbjct: 123 MITCGGQATIPMVAAVSRVTP-----VSYAEIVASVSSASAGPGTRANIDEFTRTTSNGV 177

Query: 184 QTIGGAARGKAIIILNPADPPMIMRDTIFCAIPEDVDRDAIAQSIRDVVAEVQTYVPGYR 243
            TIGGA RGKAIIILNPA+PPMIMRDTIFCA+  D DRDAIA+S+  +   VQ YVPGYR
Sbjct: 178 MTIGGAERGKAIIILNPAEPPMIMRDTIFCAVEPDADRDAIAESVHRMERAVQEYVPGYR 237

Query: 244 LLNDPQFDDPSINSGGQAVVTTFVEVEGAGDYLPPYAGNLDIMTAAAAKVGEEIAKESLS 303
           LL +PQFDD S  + G+  V+ FVEVEGAGD+LPPYAGNLDIMTAAAA+VG+ IA+  L+
Sbjct: 238 LLQEPQFDDASEATLGKVKVSIFVEVEGAGDFLPPYAGNLDIMTAAAARVGDHIARSLLT 297


Lambda     K      H
   0.315    0.133    0.381 

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: 324
Number of extensions: 10
Number of successful extensions: 2
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: 310
Length of database: 300
Length adjustment: 27
Effective length of query: 283
Effective length of database: 273
Effective search space:    77259
Effective search space used:    77259
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_110205394.1 DNK54_RS02755 (acetaldehyde dehydrogenase (acetylating))
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.1524178.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-138  446.3   0.1   2.5e-138  446.1   0.1    1.0  1  NCBI__GCF_003194585.1:WP_110205394.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110205394.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.1   0.1  2.5e-138  2.5e-138       1     284 [.       3     296 ..       3     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 446.1 bits;  conditional E-value: 2.5e-138
                             TIGR03215   1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleeedi.divfdat 72 
                                           k+++ai+G+Gnigtdl++kllrsev+e+++++G+dp+s+Gl+ ar+ g+e ++eGvd+ll+++++ d++f+at
  NCBI__GCF_003194585.1:WP_110205394.1   3 KATAAIVGPGNIGTDLMYKLLRSEVIEPRWMIGVDPSSEGLKLARDKGLESTHEGVDWLLKQDELpDLIFEAT 75 
                                           5689********************************************************************* PP

                             TIGR03215  73 sakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyae 145
                                           sa++h++ a +++e+g++++dltPaavGp v+P+vn ee++ a nvn++tCgGqatiP+vaavsrv++v+yae
  NCBI__GCF_003194585.1:WP_110205394.1  76 SAYVHRDYAPRYQEAGIRAVDLTPAAVGPAVIPPVNGEEHVGAWNVNMITCGGQATIPMVAAVSRVTPVSYAE 148
                                           ************************************************************************* PP

                             TIGR03215 146 ivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeaieas 217
                                           ivas++s saGpgtranideft+tts+++ ++gGa++gkaiiilnPaePp++mrdt++++v  +ad++ai++s
  NCBI__GCF_003194585.1:WP_110205394.1 149 IVASVSSASAGPGTRANIDEFTRTTSNGVMTIGGAERGKAIIILNPAEPPMIMRDTIFCAVePDADRDAIAES 221
                                           *************************************************************6789******** PP

                             TIGR03215 218 veemveevqkyvpGyrlkqevvld........gekvsvlleveGagdylPkyaGnldiltaaalavaeklaee 282
                                           v++m ++vq+yvpGyrl qe+++d        + kvs+++eveGagd+lP yaGnldi+taaa++v++++a++
  NCBI__GCF_003194585.1:WP_110205394.1 222 VHRMERAVQEYVPGYRLLQEPQFDdaseatlgKVKVSIFVEVEGAGDFLPPYAGNLDIMTAAAARVGDHIARS 294
                                           ******************************97789***********************************998 PP

                             TIGR03215 283 ll 284
                                           ll
  NCBI__GCF_003194585.1:WP_110205394.1 295 LL 296
                                           65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (300 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.81
//
[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 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