GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Lactobacillus shenzhenensis LY-73

Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_022528034.1 L248_RS00395 acetoin reductase

Query= reanno::BFirm:BPHYT_RS16120
         (260 letters)



>NCBI__GCF_000469325.1:WP_022528034.1
          Length = 255

 Score =  170 bits (431), Expect = 2e-47
 Identities = 103/251 (41%), Positives = 145/251 (57%), Gaps = 4/251 (1%)

Query: 8   KVAILTGAASGIGEAVARRYLDEGARCVLVDV--KPADSFGDSLRATYGDRVLTVSADVT 65
           K AI+TG   GIG  +A +   +G   V+ D+  K A S  + ++A   D  L V ADV+
Sbjct: 3   KTAIVTGGGQGIGRGIALQLAKDGFNVVVGDLNEKTAASVAEEIKALGVDS-LPVVADVS 61

Query: 66  RRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQAV 125
                Q +V +  ++F  ID+L NNA +  +  I E +   F+R+F +NV  +FF ++AV
Sbjct: 62  DEASFQNLVETAHKQFPTIDVLVNNAGIALVATIQETTTAEFERIFRINVNSVFFGIKAV 121

Query: 126 AQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINVNGIA 185
              M  QG GGKIIN SS AG +G  L+  Y ATK A+   TQ+AA  LA   I VNG A
Sbjct: 122 TPIMQAQG-GGKIINASSIAGHQGIELLGPYSATKFAIRGLTQAAAQELAKDHITVNGYA 180

Query: 186 PGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASADADY 245
           PG+V TPMW+ +D   +     P+G  ++   + + LGR   P+D+ G   FLAS+ +DY
Sbjct: 181 PGIVLTPMWDLIDKRMSEIHGVPIGASRQKFIDGIALGRGEQPEDVAGLVSFLASSKSDY 240

Query: 246 ITAQTLNVDGG 256
           IT QT+ VDGG
Sbjct: 241 ITGQTIVVDGG 251


Lambda     K      H
   0.321    0.135    0.393 

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: 134
Number of extensions: 7
Number of successful extensions: 3
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: 260
Length of database: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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 (21.9 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