GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Desulfobacter vibrioformis DSM 8776

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  199 bits (505), Expect = 2e-55
 Identities = 134/454 (29%), Positives = 221/454 (48%), Gaps = 12/454 (2%)

Query: 23  VHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKAD 82
           V  P  G  + +V   G  ET   I+ A  + +AWRS  A  R  ++R + ++L E++ D
Sbjct: 31  VTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERSAILRKWYDLLMENQED 90

Query: 83  LGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLGV 142
           L  +++ E GK   E  GE+       ++    ++++YG  I        +     P+GV
Sbjct: 91  LAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVYGDVIPQTVASQRLVVIKQPVGV 150

Query: 143 VGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPAG 202
           V  I+ +NFP A+       AL AG ++V KP+  TP +ALA   L ++A       P G
Sbjct: 151 VAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIAKLGQQA-----GVPKG 205

Query: 203 LAQLVIGGREA-GEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNAMIL 261
           +  +V G   A G  +  +P V  ++ TGST++G+++    A    R  +ELGGN   I+
Sbjct: 206 VFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLSMELGGNAPFIV 265

Query: 262 APSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRKD 321
              AD+D AV G +      +GQ C    R+ V   + DE   ++ AA  ++++G+   D
Sbjct: 266 FDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAVQELKVGNGFDD 325

Query: 322 NL-VGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPNAYYVSPAIAEMPAQSDV 380
            +  GPLID  + + ++  +  A D+GG+V  G  + A      ++    IA++     V
Sbjct: 326 GVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHA--LGRTFFAPTIIADVTDDMRV 383

Query: 381 VRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIANV 440
            R ETF P+  V  +D  EE +R  N+   GL++  +T D+  A  ++     + G+  +
Sbjct: 384 AREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDM--ARSWRIGEKLEYGLVGI 441

Query: 441 NIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474
           N G     +   FGG KE+G GRE        Y+
Sbjct: 442 NSGIISNPV-APFGGVKESGNGREGSKYGLDDYL 474


Lambda     K      H
   0.318    0.135    0.396 

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: 523
Number of extensions: 32
Number of successful extensions: 4
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: 496
Length of database: 484
Length adjustment: 34
Effective length of query: 462
Effective length of database: 450
Effective search space:   207900
Effective search space used:   207900
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:

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:

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:

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:

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