Alignments for a candidate for ald-dh-CoA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Pseudarthrobacter sulfonivorans Ar51

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate WP_058931780.1 AU252_RS17310 acetaldehyde dehydrogenase (acetylating)

Query= SwissProt::Q9KWS1
         (316 letters)



>NCBI__GCF_001484605.1:WP_058931780.1
          Length = 310

 Score =  368 bits (945), Expect = e-107
 Identities = 190/310 (61%), Positives = 238/310 (76%), Gaps = 10/310 (3%)

Query: 6   LSVAIIGSGNIGTDLMIKIMRNSKLLKVGAMVGIDPKSDGLARAQRLGVPTTAEGVDGLL 65
           + VAIIGSGNIGTDLM KIMR S+ L++GAMVGIDP SDGL RA  +GVP T++GV GL+
Sbjct: 3   IKVAIIGSGNIGTDLMFKIMRRSRTLEMGAMVGIDPASDGLRRAASMGVPITSDGVQGLI 62

Query: 66  DMPAFRDIKIAFDATSAGAQAIHNQKLQAHGVRVIDLTPAAIGPYVIPVVNFDQHVDAPN 125
           +MP F +I++ FDATSAG    +   L     R++DLTPAA+GP+VIP VN ++H+DAP+
Sbjct: 63  EMPGFDEIEVVFDATSAGGHIANAAALAPFNKRLVDLTPAALGPFVIPAVNLEEHLDAPD 122

Query: 126 INMVTCGGQATIPIVHAVSKVSPVHYAEIVASISSKSAGPGTRANIDEFTETTSKAILEV 185
           INMVTCGGQATIPIV AVS+V PV YAEIVAS++S+SAGPGTRANIDEFTETT+ AI +V
Sbjct: 123 INMVTCGGQATIPIVAAVSRVVPVPYAEIVASVASRSAGPGTRANIDEFTETTAHAIEQV 182

Query: 186 GGAAQGRAIIILNPAEPPLIMRDTVYCFVSAEANIDAITDSVEQMVKSVQEYVPGYRLKQ 245
           GGAA+G+AIIILNPA+PP IMRDTVYC ++ E + + I  S+ +MV +V +YVPGYRLKQ
Sbjct: 183 GGAARGKAIIILNPADPPPIMRDTVYC-LTGEVDHEKIRASITEMVAAVSQYVPGYRLKQ 241

Query: 246 KVQF-----EKIVAGNEQNIPGLGWSTGLKVSVFLEVEGAGHYLPSYAGNLDIMTSAGLT 300
            VQ      E + +   ++  G+ W    K++ FLEVEGA  YLP+YAGNLDIMTSA L 
Sbjct: 242 DVQITPVEPETLASLLGKDAAGIRW----KITTFLEVEGAADYLPAYAGNLDIMTSAALR 297

Query: 301 VAERIAGSGV 310
           V E +A   +
Sbjct: 298 VGELVAARDI 307


Lambda     K      H
   0.317    0.134    0.380 

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: 363
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: 316
Length of database: 310
Length adjustment: 27
Effective length of query: 289
Effective length of database: 283
Effective search space:    81787
Effective search space used:    81787
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate WP_058931780.1 AU252_RS17310 (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.3147836.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-141  455.6   2.9   3.9e-141  455.4   2.9    1.0  1  NCBI__GCF_001484605.1:WP_058931780.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001484605.1:WP_058931780.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.4   2.9  3.9e-141  3.9e-141       2     282 ..       3     305 ..       2     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 455.4 bits;  conditional E-value: 3.9e-141
                             TIGR03215   2 vkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfd 70 
                                           +kvaiiGsGnigtdl++k++r s++le+ ++vGidp+sdGl+ra+++gv ++++Gv++l+e++   +i++vfd
  NCBI__GCF_001484605.1:WP_058931780.1   3 IKVAIIGSGNIGTDLMFKIMRrSRTLEMGAMVGIDPASDGLRRAASMGVPITSDGVQGLIEMPgfdEIEVVFD 75 
                                           79******************99****************************************99999****** PP

                             TIGR03215  71 atsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvky 143
                                           atsa  h +na++l+  +k+++dltPaa+Gp+v+Pavnlee+lda+++n+vtCgGqatiPivaavsrv++v y
  NCBI__GCF_001484605.1:WP_058931780.1  76 ATSAGGHIANAAALAPFNKRLVDLTPAALGPFVIPAVNLEEHLDAPDINMVTCGGQATIPIVAAVSRVVPVPY 148
                                           ************************************************************************* PP

                             TIGR03215 144 aeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeeaiea 216
                                           aeivas+as+saGpgtranideftett++a+eqvgGa++gkaiiilnPa+Pp +mrdtvy+l+ e+d+e+i+a
  NCBI__GCF_001484605.1:WP_058931780.1 149 AEIVASVASRSAGPGTRANIDEFTETTAHAIEQVGGAARGKAIIILNPADPPPIMRDTVYCLTGEVDHEKIRA 221
                                           ************************************************************************* PP

                             TIGR03215 217 sveemveevqkyvpGyrlkqevvld..................gekvsvlleveGagdylPkyaGnldiltaa 271
                                           s++emv++v +yvpGyrlkq+v+++                    k++++leveGa+dylP+yaGnldi+t+a
  NCBI__GCF_001484605.1:WP_058931780.1 222 SITEMVAAVSQYVPGYRLKQDVQITpvepetlasllgkdaagiRWKITTFLEVEGAADYLPAYAGNLDIMTSA 294
                                           *****************************************87778*************************** PP

                             TIGR03215 272 alavaeklaee 282
                                           al+v+e +a++
  NCBI__GCF_001484605.1:WP_058931780.1 295 ALRVGELVAAR 305
                                           ******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (310 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: 18.01
//
[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