Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_012967296.1 KVAR_RS04285 CoA-acylating propionaldehyde dehydrogenase PduP

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_000025465.1:WP_012967296.1
          Length = 461

 Score =  409 bits (1051), Expect = e-118
 Identities = 219/458 (47%), Positives = 292/458 (63%), Gaps = 6/458 (1%)

Query: 9   TITKKILNEINLKEAEEKKEKDNPDLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAA 68
           T+ + IL+E  L  A   +E+     GIF DV  A++ A +A  ++    L+ R  II+A
Sbjct: 8   TLIRTILSE-KLAPAPVSQEQQ----GIFRDVGSAIDAAHQAFLRYQQCPLKTRSAIISA 62

Query: 69  IREACVNNARLLAEIACSETGRGRVEDKVAKNILAAKKTPGTEDLKPTAWTGDRGLTLVE 128
           +RE        LAE + +ETG G  EDK  KN  A + TPG EDL  +A TGD G+ L E
Sbjct: 63  LRETLAPELVTLAEESATETGMGNKEDKYLKNKAALENTPGIEDLTTSALTGDGGMVLFE 122

Query: 129 MAPVGVIASITPVTNPTATIINNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKV 188
            +P GVI ++ P TNPT TIINN+ISMLAAGN+V F+PHP AKK S   +  I E   + 
Sbjct: 123 YSPFGVIGAVAPSTNPTETIINNSISMLAAGNSVYFSPHPGAKKVSLTLIARIEEIAYRC 182

Query: 189 GAPNGLVCSINNPTIQTAQKLMEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVV 248
                LV ++  PT +  Q++M HP + ++ +TGG  +V   ++ GKKVIGAGAGNPP +
Sbjct: 183 SGIRNLVVTVAEPTFEATQQMMAHPLIAVLAITGGPGIVAMGMKSGKKVIGAGAGNPPCI 242

Query: 249 VDETADIVKAAHDIACGASFDNNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDID 308
           VDETAD+VKAA DI  GA+FD NLPCIAEK +I V  +AD L+++M+   A +L  ++ D
Sbjct: 243 VDETADLVKAAEDIISGAAFDYNLPCIAEKSLIVVASVADRLIQQMQDFDALLLSPQETD 302

Query: 309 RMTELIFQGGAINKDLIGRDAHFILSQIGIET-GKDIRLVVMPVDVSHPLVYHEQLMPVI 367
            +  +    GA NK L+G+    +L+  G+    +  RL++  V  + P V  EQLMPV+
Sbjct: 303 TLRAVCLPDGAANKKLVGKSPAELLAAAGLAVPSRPPRLLIAEVQANDPWVTCEQLMPVL 362

Query: 368 PFVTVPTVEEAINLAVKAEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGF 427
           P V V   + A+ LA++ E G  HTA+MHS+NV  +   AR +QT+IFVKN PSYAGIG 
Sbjct: 363 PIVRVADFDSALALALRVEEGLHHTAIMHSQNVSRLNLAARTLQTSIFVKNGPSYAGIGV 422

Query: 428 GGEGYTTFTIAGPTGEGLTSARTFTRQRRCVLVDAFRI 465
           GGEG+TTFTIA PTGEG TSARTF R RRCVL + F I
Sbjct: 423 GGEGFTTFTIATPTGEGTTSARTFARLRRCVLTNGFSI 460


Lambda     K      H
   0.317    0.133    0.377 

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: 529
Number of extensions: 24
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: 466
Length of database: 461
Length adjustment: 33
Effective length of query: 433
Effective length of database: 428
Effective search space:   185324
Effective search space used:   185324
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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