GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Weissella oryzae SG25

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_027699596.1 TT13_RS08545 alcohol dehydrogenase AdhP

Query= BRENDA::Q9CEN0
         (340 letters)



>NCBI__GCF_000691805.2:WP_027699596.1
          Length = 348

 Score =  410 bits (1053), Expect = e-119
 Identities = 210/349 (60%), Positives = 263/349 (75%), Gaps = 11/349 (3%)

Query: 1   MKAAVVRHNPDGYADLVEK-ELRAIKPNEALLDMEYCGVCHTDLHVAAGDYGNKAGT--- 56
           MKAAVVR N DGY DL++  E RA+   EAL+D+EY G+CHTDLHVA GD+G+ +     
Sbjct: 1   MKAAVVRENLDGYVDLIDNWEPRALSFGEALVDVEYSGLCHTDLHVAGGDFGDPSTINPR 60

Query: 57  ----VLGHEGIGIVKEIGTDVSS-LQVGDRVSVAWFFEGCGHCEYCVSGNETFCREVKNA 111
               V+GHEG+G V ++       L++GDRVS+AWF++ CG+CEYC SGNETFCR+V+NA
Sbjct: 61  PFRRVIGHEGVGRVTKLAEGADDYLKIGDRVSIAWFYDACGNCEYCNSGNETFCRKVRNA 120

Query: 112 GYSVDGGMAEEAIVVADYAVKVPDGLDPIEASSITCAGVTTYKAIKVSGVKPGDWQVIFG 171
           G+SVDG MA++ +V A YAVKVP+GLDP+EASSITCAGVT YK++KV   KPG W  + G
Sbjct: 121 GFSVDGAMAQQVVVNAKYAVKVPEGLDPMEASSITCAGVTMYKSLKVGETKPGQWVSVVG 180

Query: 172 AGGLGNLAIQYAKNVFGAKVIAVDINQDKLNLAKKIGADVIINSGDVNPVDEIKKITGGL 231
           AGGLGNLA+QYA NVFGA V+AVD N DKL  AK++GA+++IN    +    I++  GG+
Sbjct: 181 AGGLGNLAVQYAHNVFGAHVVAVDGNPDKLAAAKEMGAELLINRKTEDVPAVIQEKVGGV 240

Query: 232 GAQSAIVCAVARIAFEQAVASLKPMGKMVAVALPNTEMTLSVPTVVFDGVEVAGSLVGTR 291
              +A V AV   AF Q++ASL+PMGK+VAVALP+ +M L+V   V DG+EV GSLVGTR
Sbjct: 241 --HNAQVTAVNTTAFNQSIASLRPMGKLVAVALPSGDMGLNVVKTVLDGIEVRGSLVGTR 298

Query: 292 LDLAEAFQFGAEGKVKPIVATRKLEEINDIIDEMKAGKIEGRMVIDFTK 340
            DL EAFQFGAEGKVKPIV    + +IND+IDEMK GKI GRMV DFTK
Sbjct: 299 EDLKEAFQFGAEGKVKPIVTRADIRDINDVIDEMKNGKITGRMVFDFTK 347


Lambda     K      H
   0.318    0.136    0.395 

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: 452
Number of extensions: 16
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: 340
Length of database: 348
Length adjustment: 29
Effective length of query: 311
Effective length of database: 319
Effective search space:    99209
Effective search space used:    99209
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: 49 (23.5 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