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_027699619.1 TT13_RS08680 (S)-acetoin forming diacetyl reductase

Query= BRENDA::Q4J9F2
         (255 letters)



>NCBI__GCF_000691805.2:WP_027699619.1
          Length = 257

 Score =  127 bits (318), Expect = 3e-34
 Identities = 84/255 (32%), Positives = 131/255 (51%), Gaps = 14/255 (5%)

Query: 9   KVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEV-LGVKADVS 67
           +V  VTGAG GIG AI K+ A +   V  V     +L ++  E+  +     L V ADV+
Sbjct: 3   EVAFVTGAGQGIGEAIVKRLADDGFKVAVVGRTLSKLERVANEINAIHPNAALPVLADVA 62

Query: 68  KKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDELWERVLAVNLYSAFYSSRA 127
           K++DV   V +T E +  + V+ NNAG+    TP+ EV +E  +    +N+    +  +A
Sbjct: 63  KREDVFAGVAKTIEAFGDLTVMINNAGVAP-TTPIMEVDEETIDWTFDINIKGTVWGIQA 121

Query: 128 VIPIM--LKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAVA 185
            +     LK G G I+N  S AG+ G      Y  +K  + G+T++ A      GI   A
Sbjct: 122 AVEAFKQLKHG-GKIINATSQAGVEGNPNLTVYGASKFAIRGITQTTAKELAPLGITVNA 180

Query: 186 VLPGTVKT--------NIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDE 237
             PG VKT         +G  + K  E GM   +  ++L  RL+EPE++A+ + FLA  +
Sbjct: 181 FAPGIVKTPMMFDIAHEVGQNAGKSDEWGMEQFSDGIALG-RLSEPEEVASGVAFLAGHD 239

Query: 238 ASFVNGDAVVVDGGL 252
           +S++ G  +V DGG+
Sbjct: 240 SSYMTGQTLVTDGGM 254


Lambda     K      H
   0.318    0.135    0.369 

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: 162
Number of extensions: 10
Number of successful extensions: 4
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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