GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Sedimenticola selenatireducens DSM 17993

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_029133105.1 A3GO_RS0108930 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>NCBI__GCF_000428045.1:WP_029133105.1
          Length = 497

 Score =  206 bits (523), Expect = 2e-57
 Identities = 143/470 (30%), Positives = 235/470 (50%), Gaps = 15/470 (3%)

Query: 18  QGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLR 77
           Q   P++ P  G     V L  +A     I  A++AF AWR  P  +R +++  + ++L 
Sbjct: 17  QRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETPPLKRAQVMFRYKQLLE 76

Query: 78  EHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETW 137
           +H  ++  L++ E GK+  + +GE+   I++ ++A G    L G    S  P       +
Sbjct: 77  QHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKGEYSKSVGPAIDSWSEF 136

Query: 138 HPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFG 197
            PLGVV  I+ FNFPV V  W   +A++ GN+ + KPSE+ P  AL    L ++A     
Sbjct: 137 QPLGVVVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSAALRIAELLQQA----- 191

Query: 198 DAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGG-N 256
             P G+  LV G +EA + +++DPRV   S  GST M  E         G+ +  LGG  
Sbjct: 192 GLPDGVFNLVNGDKEAVDTLLNDPRVQAASFVGST-MVAEYIYHTGTAAGKRVQALGGAK 250

Query: 257 NAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLI-VHRSIKDEVVARVKAAYGKVRI 315
           N  ++ P ADLD AV  ++ +A G+ G+RC  +  ++ V  ++ D VV  +      +++
Sbjct: 251 NHAVVMPDADLDNAVNALMGAAYGSCGERCMAISVVVCVGDTVADAVVGGLAEKLAHLKV 310

Query: 316 GDPRKD-NLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAIAE 373
           G  R+  + +GPL+  Q    ++G + +  DEG + V  G  Q  + +   +++   + +
Sbjct: 311 GPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVVDGRGQRVEGHAEGFFLGGCLFD 370

Query: 374 -MPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432
            +  +  + R E F P+L V+  ++ ++A+ L +    G  +CIFT D  EA RF S   
Sbjct: 371 RVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTRD-GEAARFFS-DH 428

Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWKGYMRRQTNT 480
              G+  VNI         +FGG K +  G     G DA + Y RR+T T
Sbjct: 429 IRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTIT 478


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: 548
Number of extensions: 36
Number of successful extensions: 5
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: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
Effective search space:   213906
Effective search space used:   213906
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