Alignments for a candidate for ald-dh-CoA in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Amycolatopsis halophila YIM 93223

Align Acetaldehyde dehydrogenase 1; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 1 (uncharacterized)
to candidate WP_034270588.1 AMYHA_RS10790 acetaldehyde dehydrogenase (acetylating)

Query= curated2:A1UM81
         (310 letters)



>NCBI__GCF_000504245.1:WP_034270588.1
          Length = 306

 Score =  395 bits (1014), Expect = e-115
 Identities = 199/296 (67%), Positives = 237/296 (80%), Gaps = 5/296 (1%)

Query: 8   AIVGSGNISTDLLYKLQRSEYLEPRWMIGIDPESEGLARARKLGLETSHEGVDWLLAQDD 67
           AIVG GNI TDLL KL+RSE ++ R+M+G+ PES+GL RA +LGLETS +GVDWLL +D 
Sbjct: 9   AIVGPGNIGTDLLAKLRRSELVDVRYMVGVVPESDGLTRAAELGLETSADGVDWLLTRDR 68

Query: 68  KPDLVFEATSAYVHRAAAPRYEEAGIRAIDLTPAAVGPAVIPPANLREHLDAPNVNMITC 127
            PDLVFEATSA  H A A RY EAGI A+DLTPAA+GP   P  N+ + LDAPNVNMITC
Sbjct: 69  LPDLVFEATSAKAHAANAQRYAEAGITAVDLTPAALGPFTCPVVNIGDQLDAPNVNMITC 128

Query: 128 GGQATIPIVYAVTRAVTEQGGTVPYAEIVASVSSSSAGPGTRANIDEFTKTTSKGVQTIG 187
           GGQATIPIV+AV+R        VPYAEIVASVSS SAGPGTRANIDEFT+TT+ G++ +G
Sbjct: 129 GGQATIPIVHAVSRVTP-----VPYAEIVASVSSRSAGPGTRANIDEFTETTAAGIEKVG 183

Query: 188 GAARGKAIIILNPADPPMIMRDTIFCAIPEDVDRDAIAQSIRDVVAEVQTYVPGYRLLND 247
           GAA+GKAIII+NP +PPMIMRDT+FCAI  D DRDAI++SI  +V++VQ YVPGYRL  D
Sbjct: 184 GAAKGKAIIIINPVEPPMIMRDTVFCAIDPDADRDAISESIHRMVSDVQVYVPGYRLKAD 243

Query: 248 PQFDDPSINSGGQAVVTTFVEVEGAGDYLPPYAGNLDIMTAAAAKVGEEIAKESLS 303
           PQFDDP  N  G+A V  F+EV G GDYLP YAGNLDIMTAAA++ GE +A++ +S
Sbjct: 244 PQFDDPQPNWNGRARVAVFLEVAGNGDYLPTYAGNLDIMTAAASRAGELLAEKIIS 299


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: 318
Number of extensions: 13
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: 306
Length adjustment: 27
Effective length of query: 283
Effective length of database: 279
Effective search space:    78957
Effective search space used:    78957
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_034270588.1 AMYHA_RS10790 (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.667211.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-137  443.8   0.7   1.5e-137  443.6   0.7    1.0  1  NCBI__GCF_000504245.1:WP_034270588.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034270588.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.6   0.7  1.5e-137  1.5e-137       4     284 ..       8     298 ..       5     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 443.6 bits;  conditional E-value: 1.5e-137
                             TIGR03215   4 vaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleeedi.divfdatsak 75 
                                           +ai+G+Gnigtdll kl rse ++++++vG+ pesdGl ra+elg+etsa+Gvd+ll+++ + d+vf+atsak
  NCBI__GCF_000504245.1:WP_034270588.1   8 AAIVGPGNIGTDLLAKLRRSELVDVRYMVGVVPESDGLTRAAELGLETSADGVDWLLTRDRLpDLVFEATSAK 80 
                                           79**********************************************************999********** PP

                             TIGR03215  76 ahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyaeiva 148
                                           aha+na++++e+g++++dltPaa+Gp+ +P+vn+ ++lda+nvn++tCgGqatiPiv+avsrv++v yaeiva
  NCBI__GCF_000504245.1:WP_034270588.1  81 AHAANAQRYAEAGITAVDLTPAALGPFTCPVVNIGDQLDAPNVNMITCGGQATIPIVHAVSRVTPVPYAEIVA 153
                                           ************************************************************************* PP

                             TIGR03215 149 siasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeaieasvee 220
                                           s++s+saGpgtranideftett+ ++e+vgGa+kgkaiii+nP ePp++mrdtv++++  +ad++ai++s+++
  NCBI__GCF_000504245.1:WP_034270588.1 154 SVSSRSAGPGTRANIDEFTETTAAGIEKVGGAAKGKAIIIINPVEPPMIMRDTVFCAIdPDADRDAISESIHR 226
                                           **********************************************************7799*********** PP

                             TIGR03215 221 mveevqkyvpGyrlkqevvld........gekvsvlleveGagdylPkyaGnldiltaaalavaeklaeell 284
                                           mv++vq yvpGyrlk+++++d          +v+v+lev G+gdylP+yaGnldi+taaa +++e lae+++
  NCBI__GCF_000504245.1:WP_034270588.1 227 MVSDVQVYVPGYRLKADPQFDdpqpnwngRARVAVFLEVAGNGDYLPTYAGNLDIMTAAASRAGELLAEKII 298
                                           ***************************98889************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (306 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: 23.75
//
[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