GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Gracilibacillus halophilus YIM-C55.5

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_003465338.1 J416_RS04015 aldo/keto reductase

Query= BRENDA::Q8TZM9
         (278 letters)



>NCBI__GCF_000359605.1:WP_003465338.1
          Length = 279

 Score =  135 bits (340), Expect = 1e-36
 Identities = 89/238 (37%), Positives = 138/238 (57%), Gaps = 19/238 (7%)

Query: 40  KESIEAIRYGLELGMNLIDTAEFYGAGHAEEIVGEAIKE--FEREDIFIVSKVWPTHFGY 97
           +E   ++++ LE G   IDTA  Y     E+ VGEAIKE    RE++F+ SK+W  + GY
Sbjct: 31  EEVKNSVKWALEHGYKHIDTAAAY---KNEQGVGEAIKESGIPREELFVTSKLWNGNQGY 87

Query: 98  EEAKKAARASAKRLGT-YIDLYLLHWPVDDFKKIEETLHALEDLVDEGVIRYIGVSNFNL 156
           +E   A   + ++LG  Y+DLYL+HWPV +  K +E+  A+E L  +G IR IGVSNF  
Sbjct: 88  DETIAAFETTLQQLGMDYLDLYLIHWPVPEQNKYKESWKAMEKLYHDGKIRAIGVSNFKE 147

Query: 157 ELLQRSQEVMRKYEIV--ANQVKYSVKDRWPETT--GLLDYMKREGIALMAYTPLEKGTL 212
             L    +++++ ++V   NQV+Y      P  T   L DY K+  I L A++PL++G +
Sbjct: 148 HHL---DDLLQEADVVPMVNQVEYH-----PHLTQKSLHDYCKKHQIQLEAWSPLKQGEI 199

Query: 213 ARNECLAKIGEKYGKTAAQVALNYLIWEENVVAIPKASNKEHLKENFGAMGWRLSEED 270
                L +I E++GK+ AQV L + +  E VV IPK+  +  + EN     + LS+++
Sbjct: 200 LSEPVLKEIAERHGKSPAQVILRWDLQNE-VVTIPKSVKQHRIHENADVFDFELSQQE 256


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: 206
Number of extensions: 10
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: 278
Length of database: 279
Length adjustment: 25
Effective length of query: 253
Effective length of database: 254
Effective search space:    64262
Effective search space used:    64262
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