Alignments for a candidate for ald-dh-CoA in Verminephrobacter eiseniae EF01-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Verminephrobacter eiseniae EF01-2

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10); propanal dehydrogenase (CoA-propanoylating) (EC 1.2.1.87) (characterized)
to candidate WP_041950033.1 VEIS_RS13550 acetaldehyde dehydrogenase (acetylating)

Query= BRENDA::Q79AF6
         (304 letters)



>NCBI__GCF_000015565.1:WP_041950033.1
          Length = 309

 Score =  538 bits (1387), Expect = e-158
 Identities = 266/302 (88%), Positives = 287/302 (95%)

Query: 3   KKIKCALIGPGNIGTDLLAKLQRSPVLEPIWMVGIDPESDGLKRAREMGIKTTADGVDGL 62
           KKIKCALIGPGNIGTDLLAKLQRSPVLEP+WMVGIDP SDGLKRA EMGIKTTA+GVDGL
Sbjct: 8   KKIKCALIGPGNIGTDLLAKLQRSPVLEPVWMVGIDPASDGLKRASEMGIKTTAEGVDGL 67

Query: 63  IPHMQADGVQIVFDATSAYVHADNSRKVNALGALMIDLTPAAIGPFCVPTVNLKEHVGKG 122
           IPHM+ADGVQIVFDATSAYVHA+NS KVNA GA+MIDLTPAAIGP+CVP VNLK+HVG+ 
Sbjct: 68  IPHMKADGVQIVFDATSAYVHAENSAKVNAQGAMMIDLTPAAIGPYCVPPVNLKQHVGRR 127

Query: 123 EMNVNMVTCGGQATIPMVAAVSRVQPVAYGEIVATVSSKSAGPGTRKNIDEFTRTTAGAV 182
           EMNVNMVTCGGQATIPMV AVSRVQPVAYGEIVATVSS+S GPGTRKNIDEFTRTTAGAV
Sbjct: 128 EMNVNMVTCGGQATIPMVYAVSRVQPVAYGEIVATVSSRSVGPGTRKNIDEFTRTTAGAV 187

Query: 183 EKVGGAKKGKAIIILNPAEPPLIMRDTVHCLLESEPDQAKITESIHAMIKEVQKYVPGYK 242
           EKVGGA++GKAIII+NPAEPPLIMRDTVHCL+E +PD+A IT+SIH MI+EVQKYVPGYK
Sbjct: 188 EKVGGARQGKAIIIINPAEPPLIMRDTVHCLVEGKPDEAAITQSIHDMIREVQKYVPGYK 247

Query: 243 LVNGPVFDGLRVSVYLEVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEILAGQLTLQPV 302
           LVNGPVFDG RVSV++EVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEIL G+L L+PV
Sbjct: 248 LVNGPVFDGQRVSVFMEVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEILKGELVLEPV 307

Query: 303 HA 304
            A
Sbjct: 308 AA 309


Lambda     K      H
   0.317    0.135    0.388 

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: 414
Number of extensions: 7
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: 304
Length of database: 309
Length adjustment: 27
Effective length of query: 277
Effective length of database: 282
Effective search space:    78114
Effective search space used:    78114
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_041950033.1 VEIS_RS13550 (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.351294.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-147  475.0   2.4   4.5e-147  474.8   2.4    1.0  1  NCBI__GCF_000015565.1:WP_041950033.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015565.1:WP_041950033.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.8   2.4  4.5e-147  4.5e-147       1     284 [.       9     298 ..       9     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 474.8 bits;  conditional E-value: 4.5e-147
                             TIGR03215   1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfd 70 
                                           k+k+a+iG+Gnigtdll kl+rs vle++++vGidp+sdGl+ra e+g++t+aeGvd+l+ +     ++ivfd
  NCBI__GCF_000015565.1:WP_041950033.1   9 KIKCALIGPGNIGTDLLAKLQRSPVLEPVWMVGIDPASDGLKRASEMGIKTTAEGVDGLIPHMkadGVQIVFD 81 
                                           79*********************************************************998877679***** PP

                             TIGR03215  71 atsakahaenaklleelgkividltPaavGpyvvPavnleevldak..nvnlvtCgGqatiPivaavsrvakv 141
                                           atsa++haen+++++++g ++idltPaa+Gpy+vP+vnl++++ ++  nvn+vtCgGqatiP+v+avsrv++v
  NCBI__GCF_000015565.1:WP_041950033.1  82 ATSAYVHAENSAKVNAQGAMMIDLTPAAIGPYCVPPVNLKQHVGRRemNVNMVTCGGQATIPMVYAVSRVQPV 154
                                           ******************************************987767************************* PP

                             TIGR03215 142 kyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeea 213
                                           +y+eiva+++s+s+Gpgtr+nideft+tt+ a+e+vgGa++gkaiii+nPaePpl+mrdtv++lv  ++de+a
  NCBI__GCF_000015565.1:WP_041950033.1 155 AYGEIVATVSSRSVGPGTRKNIDEFTRTTAGAVEKVGGARQGKAIIIINPAEPPLIMRDTVHCLVeGKPDEAA 227
                                           *****************************************************************789***** PP

                             TIGR03215 214 ieasveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldiltaaalavaeklaeell 284
                                           i++s+++m++evqkyvpGy+l++ +v+dg++vsv++eveG gdylPkyaGnldi+taaa+++ae++aee+l
  NCBI__GCF_000015565.1:WP_041950033.1 228 ITQSIHDMIREVQKYVPGYKLVNGPVFDGQRVSVFMEVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEIL 298
                                           *******************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (309 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: 25.00
//
[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