Alignments for a candidate for adh in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Herbaspirillum autotrophicum IAM 14942

Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Matured fruit 60 kDa protein; MF-60; EC 1.2.1.3 (characterized)
to candidate WP_050464339.1 AKL27_RS18540 aldehyde dehydrogenase family protein

Query= SwissProt::Q9ZPB7
         (508 letters)



>NCBI__GCF_001189915.1:WP_050464339.1
          Length = 503

 Score =  467 bits (1201), Expect = e-136
 Identities = 241/484 (49%), Positives = 327/484 (67%), Gaps = 9/484 (1%)

Query: 32  SGPVISTVSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDAL 91
           +G  I   SP +   IA +   +  E ++ + + + A+  W++ PAP RGE+VR +G  L
Sbjct: 18  AGQDIPARSPRDGSTIAVLRSHTASEVQQAIDNASQASLQWRNEPAPLRGELVRLLGQVL 77

Query: 92  REKLQHLGKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEV 151
           REK   LG+LV+LE GKIL+EGIGEVQE+I +CDFAVGLSRQL+G  I SERP H M E 
Sbjct: 78  REKRDALGQLVTLESGKILSEGIGEVQEMIDICDFAVGLSRQLHGLTITSERPGHRMMET 137

Query: 152 WNPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLEKN 211
           W+PLG+ GVITAFNFP AV  WNA +ALVCGN V+WK +  TPL  +AV  L+ + + ++
Sbjct: 138 WHPLGVCGVITAFNFPVAVWAWNAALALVCGNAVIWKPSEKTPLTALAVHALLQQAIARH 197

Query: 212 NLPAAIFTAFC----GGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLEL 267
              AA+  A C    GGAE+G A+++   + LVS TGS  +G KV   V +R G+ LLEL
Sbjct: 198 ARQAAVPAALCQVLIGGAEVGVALSRSPAVALVSATGSVAMGRKVAVEVAQRLGRSLLEL 257

Query: 268 SGNNALIVMDDADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQV 327
            GNN +IV   AD+ LA+R+I F+AVGTAGQRCT+ RRL++  S +  +   +  +Y  +
Sbjct: 258 GGNNGMIVAPSADLDLALRAIVFSAVGTAGQRCTSLRRLFVERSKFDTLTAHIERVYATL 317

Query: 328 KIGDPLEEGTLVGPVHTKASRENFEKGISTIKSQGGKILTGGSVIESDGN----FVQPTI 383
            IGDPL  GTLVGP+    +  N +  +S  +S+GG +++GG  I   G     +V+P +
Sbjct: 318 NIGDPLAAGTLVGPLIDAHAYANMQAALSQARSEGG-MVSGGERIAGLGGEHAFYVRPAL 376

Query: 384 VEIASNASVVKEELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPH 443
           V +   ++V+  E F P+LY + +    +AIALNN+VPQGLSS+IFT+       ++  +
Sbjct: 377 VRMPQQSAVMHHETFAPILYALPYDDFSQAIALNNAVPQGLSSAIFTNDIREAELFMSAN 436

Query: 444 GSDCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQ 503
           GSDCG+ NVNI T+GAEIGGAFGGEK TGGGRE+GSD+WK YMRR+T TINY   LPLAQ
Sbjct: 437 GSDCGLANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKTYMRRATNTINYSGALPLAQ 496

Query: 504 GINF 507
           G++F
Sbjct: 497 GVSF 500


Lambda     K      H
   0.317    0.136    0.404 

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: 662
Number of extensions: 19
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: 508
Length of database: 503
Length adjustment: 34
Effective length of query: 474
Effective length of database: 469
Effective search space:   222306
Effective search space used:   222306
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: 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