GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Gallaecimonas xiamenensis 3-C-1

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= metacyc::MONOMER-11802
         (255 letters)



>NCBI__GCF_000299915.1:WP_008486155.1
          Length = 249

 Score =  108 bits (271), Expect = 8e-29
 Identities = 86/249 (34%), Positives = 117/249 (46%), Gaps = 17/249 (6%)

Query: 6   KHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVE---AKARELGDNARFAVADISD 62
           K  +V+GA+ GLG A A  L E GA+V+         +   AK   LG  AR   AD+ D
Sbjct: 7   KRALVTGASRGLGQAMALGLAENGAEVICASSREGGCDDTVAKILALGGKARALAADLGD 66

Query: 63  EQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLL 122
            QA Q+  + A++A G +  LVN  G +  E  L       L +F  VI VNL  +F L 
Sbjct: 67  SQAVQALAEQALAA-GPVDVLVNNGGCIYREAALD----FPLDAFDAVIKVNLNAAFQLS 121

Query: 123 RLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARF 182
           +L   AM    +      G I+N AS+ +Y G I   AY ASK AIA LT   A E  + 
Sbjct: 122 QLLGRAMVTKGS------GKIVNIASMLSYSGGIRVPAYTASKHAIAGLTKALANEWGQH 175

Query: 183 GIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPP-RLGRPQEYAALARHIIE--NSML 239
           GI+V  IAPG F T     + D+   S       P  R G P +       +    +  +
Sbjct: 176 GIQVNAIAPGYFRTDNTQALQDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKASDYV 235

Query: 240 NGEVIRLDG 248
           NG ++ +DG
Sbjct: 236 NGHILAVDG 244


Lambda     K      H
   0.318    0.131    0.358 

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: 123
Number of extensions: 5
Number of successful extensions: 1
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: 255
Length of database: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. 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