GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Lactobacillus silagei IWT126

Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_089136018.1 CES79_RS00720 NAD(P)-dependent oxidoreductase

Query= metacyc::MONOMER-15565
         (287 letters)



>NCBI__GCF_002217945.1:WP_089136018.1
          Length = 288

 Score =  152 bits (384), Expect = 8e-42
 Identities = 85/264 (32%), Positives = 137/264 (51%)

Query: 3   EIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKYTI 62
           +IGF+G G+MG A+A +LL  G ++ V+NRT ++ D LV  GA+  ETPA+V +K     
Sbjct: 2   KIGFIGTGVMGGAIAEHLLDAGHELVVYNRTKAKTDALVAKGATWVETPAQVAEKTDIIF 61

Query: 63  AMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAPVS 122
           +M+  P    ++ F   G    + AGK  IDM+T     + +I+    +     L+APVS
Sbjct: 62  SMVGYPTDVEAIYFGDQGIFSTLTAGKTVIDMTTSTPTLAEKIAVKARALNAHALDAPVS 121

Query: 123 GSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGSMM 182
           G    A++  L ++  GD+  +D V P F+++G K    G  G G   K+   +++   M
Sbjct: 122 GGDVGAKNATLTVMVGGDQATFDAVKPLFELVGSKVHLFGPAGKGQHTKMANQIMIAGTM 181

Query: 183 NAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKDMR 242
               E +V A  +GL+ + +LD L  G   N       P ++K  Y P F  KH  KD+R
Sbjct: 182 TGTVEMMVYAKHAGLNMNDVLDTLSSGGADNWSMDNYAPRILKGDYTPGFFAKHFLKDLR 241

Query: 243 LALALGDENAVPMPVAAAANEAFK 266
           +AL   D+  + +P    A + ++
Sbjct: 242 IALDEADKMKIDLPATKLAKQLYE 265


Lambda     K      H
   0.318    0.135    0.384 

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: 188
Number of extensions: 7
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: 287
Length of database: 288
Length adjustment: 26
Effective length of query: 261
Effective length of database: 262
Effective search space:    68382
Effective search space used:    68382
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: 47 (22.7 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