Alignments for a candidate for paaH in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Azohydromonas australica DSM 1124

Align 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-) (characterized)
to candidate WP_029001786.1 H537_RS0136320 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::Marino:GFF2749
         (506 letters)



>NCBI__GCF_000430725.1:WP_029001786.1
          Length = 515

 Score =  427 bits (1098), Expect = e-124
 Identities = 252/496 (50%), Positives = 303/496 (61%), Gaps = 7/496 (1%)

Query: 12  VVGAGAMGSGIAQVAAQAGHQVYLHDQREGAAEAGRDGIAKQLQRRVDKGKMQQQELDDV 71
           VVGAG MG+GIAQVAAQAGH V L D REGAA   R  + K L+    KGK+  QE    
Sbjct: 13  VVGAGIMGAGIAQVAAQAGHAVMLFDLREGAAAEARAKLGKGLEALAAKGKLTAQEAAQT 72

Query: 72  IGRIHPVAKLDDVADAGLVIEAIIEDLQIKRQLLASLEDLCTADAILATNTSSISVTALG 131
           + RI  V  L+  A A LV+EA++E L  KR L   LE +  AD +LATNTSSISVTA+ 
Sbjct: 73  LARIEAVPSLEAAASARLVVEAVVEKLDAKRALFRQLEGIVGADCVLATNTSSISVTAIA 132

Query: 132 ADMSKPERLVGMHFFNPAPLMALVEVVMGLATSKTVADTVHATATAWGKKPVYATSTPGF 191
             +  P RLVGMHFFNP PLM LVEVV GL T   VA  +HA +  WGK PV+A STPGF
Sbjct: 133 NGLQCPGRLVGMHFFNPVPLMKLVEVVSGLQTEPAVAQAIHALSRRWGKVPVFARSTPGF 192

Query: 192 IVNRVARPFYAESLRLLQEQATDAATLDAIIREAGQFRMGAFELTDLIGHDVNYAVTSSV 251
           IVNR+ARP+YAE+L LLQEQA   A LDA +R AG FRMG  EL DLIGHD N++VT SV
Sbjct: 193 IVNRIARPYYAETLALLQEQAGTPALLDACLRAAG-FRMGPCELMDLIGHDTNFSVTQSV 251

Query: 252 FNSYYQDPRFLPSLIQKELVEAGRLGRKSGQGFYPYGESAEKPQ-PKTEPAHQSDESVII 310
           F + + D RF+PSL+Q+ELV+ G LGRKSG+GFY Y E A KP  P+  PA     +++ 
Sbjct: 252 FEANFFDKRFVPSLVQRELVDGGLLGRKSGRGFYDYAEGAAKPALPEHVPAELPAATLLS 311

Query: 311 AEGNPGVAAPLLERLKAAGL---TIIERDGPGQIRFGDAVLALTDGRMATERAACEGVAN 367
             G   VA  L + L AAG     + + D  G +    A L LTDGR A++  A  GVA 
Sbjct: 312 LHGQGPVARCLGDALAAAGRGFEPVPDSDWIG-LEIDGAQLRLTDGRPASQVGA-GGVAE 369

Query: 368 LVLFDLAFDYSKASRLALAPADQASDAAVSCACALLQKAGIEVSLIADRPGLVIMRTVAM 427
           + +FDL       S LA APA QAS A    A   L+  G     +AD PGLV+ RT+AM
Sbjct: 370 VAVFDLPLSAQPGSVLAWAPALQASPAWCELAPRWLRALGFNAQRLADAPGLVVARTIAM 429

Query: 428 LANEAADAALHGVATVADIDLAMKAGLNYPDGPLSWSDRLGAGHVFKVLTNIQTSYAEDR 487
           L NEAADA   GV      D AMK G+NYP GP  W     A  V  +L  +   Y  +R
Sbjct: 430 LINEAADAVHQGVCDEGGADAAMKLGVNYPQGPFEWLRGWDAAAVIALLDALDAHYRGER 489

Query: 488 YRPALLLRKNAFAQKG 503
           YR +  LR  A+ Q G
Sbjct: 490 YRVSPGLRLRAWGQGG 505


Lambda     K      H
   0.318    0.133    0.375 

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: 661
Number of extensions: 24
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: 506
Length of database: 515
Length adjustment: 35
Effective length of query: 471
Effective length of database: 480
Effective search space:   226080
Effective search space used:   226080
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: 52 (24.6 bits)

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