GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Bacillus altitudinis 41KF2b

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-12387
         (496 letters)



>NCBI__GCF_000691145.1:WP_019744147.1
          Length = 486

 Score =  211 bits (538), Expect = 4e-59
 Identities = 130/385 (33%), Positives = 202/385 (52%), Gaps = 6/385 (1%)

Query: 38  HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97
           +P TG  +  +   T  DV+ AV+AA  AF TW  T  P R  ++ ++ +LL E   +LA
Sbjct: 30  NPATGEVIAEVPLSTKTDVEHAVQAAQEAFTTWSKTAVPRRARILFKYQQLLVEKWDELA 89

Query: 98  DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157
           +LVT+E GK  +EA GEVQ  I+  +FA G    + G+ +P    G       +P+GV+G
Sbjct: 90  ELVTLENGKSVTEAKGEVQRGIECVEFAAGAPTLMMGKQLPDIATGLESGMYRYPIGVIG 149

Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217
            I+ FNFP+ V  W   +A+ CG+T V KPSE TP+  A  A L +    +AG PKG+  
Sbjct: 150 GITPFNFPMMVPCWMFPLAIACGNTFVLKPSERTPILAARLAELFE----EAGLPKGVLN 205

Query: 218 VVVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPSA 277
           +V GA DV   L++  +V  +S  GS  +   V  +  A   R     G  N ++V   A
Sbjct: 206 IVNGAHDVVNGLLEHEKVKAISFVGSQPVAEYVYKKGTAHGKRVQALAGAKNHSIVLKDA 265

Query: 278 DLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLV 337
           DL+      + AA G+AG+RC     + V ED+AD ++++L     +L IG+       +
Sbjct: 266 DLESATKQIIGAAFGSAGERCMAAAVVAVEEDVADDLIQQLVDESNQLVIGNGINKDVFL 325

Query: 338 GPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALV-RMPAQTAVVR 396
           GP++ +    R  + ++    EG +L   G RQ  +     Y+V P +   +  Q  + +
Sbjct: 326 GPVIRKEHKERTLQYIQSGIEEGASLIRDG-RQDNETNGEGYFVGPTIFDHVTNQMKIWQ 384

Query: 397 EETFAPILYVLTYRDLDEAIRLNNE 421
           +E FAP+L ++    L EAI L+N+
Sbjct: 385 DEIFAPVLSIVRVSSLAEAIDLSNQ 409


Lambda     K      H
   0.320    0.135    0.406 

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: 379
Number of extensions: 10
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: 496
Length of database: 486
Length adjustment: 34
Effective length of query: 462
Effective length of database: 452
Effective search space:   208824
Effective search space used:   208824
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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