GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Lactobacillus delbrueckii ZN7a-9

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_002879650.1 B506_RS06460 aldo/keto reductase

Query= BRENDA::Q8TZM9
         (278 letters)



>NCBI__GCF_000387565.1:WP_002879650.1
          Length = 285

 Score =  130 bits (328), Expect = 2e-35
 Identities = 96/266 (36%), Positives = 139/266 (52%), Gaps = 31/266 (11%)

Query: 17  KVTAIGMGTWGIGGRETPDYSRDKESIEAIRYGLELGMNLIDTAEFYGAGHAEEIVGEAI 76
           K+  IG GTW     +TPD    +E++E     L  G   IDTA  YG    E  VG AI
Sbjct: 17  KIPVIGFGTW-----QTPDGDVAQEAVET---ALNAGYRHIDTAAVYGN---EASVGRAI 65

Query: 77  KE--FEREDIFIVSKVWPTHFGYEEAKKAARASAKRLGT-YIDLYLLHWP----VDDF-- 127
           K    +R D+F+ SK+W     YE AK A   S  +L T Y+DLYL+HWP    + D   
Sbjct: 66  KRSGVKRSDLFVTSKLWNGSHSYEGAKAAIDDSLLKLDTDYLDLYLIHWPNPVAIRDHWA 125

Query: 128 KKIEETLHALEDLVDEGVIRYIGVSNF---NLELLQRSQEVMRKYEIVANQVKYSVKDRW 184
           +   E   A+E+ V  G IR IGVSNF   +LE L ++ E+    + V NQ+  +  D  
Sbjct: 126 EGNAEAWRAMEEAVQAGKIRAIGVSNFRRHHLEALLKTAEI----KPVVNQICLNPNDLQ 181

Query: 185 PETTGLLDYMKREGIALMAYTPLEKGTLARNECLAKIGEKYGKTAAQVALNYLIWEENVV 244
            E T      K  G+   AY+PL  G L  NE +  +G KYGK++AQV + + + + N +
Sbjct: 182 AEVTAA---NKEYGLLSEAYSPLGTGGLLGNETIKAVGAKYGKSSAQVLIRWSL-QHNFL 237

Query: 245 AIPKASNKEHLKENFGAMGWRLSEED 270
            +PK+ + +++K N     + L+ +D
Sbjct: 238 PLPKSVHPDYIKANAEVFDFALTADD 263


Lambda     K      H
   0.317    0.136    0.400 

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: 222
Number of extensions: 19
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: 278
Length of database: 285
Length adjustment: 26
Effective length of query: 252
Effective length of database: 259
Effective search space:    65268
Effective search space used:    65268
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.

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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