GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Klebsiella michiganensis M5al

Align D-sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate BWI76_RS23630 BWI76_RS23630 acetoin(diacetyl) reductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1959
         (257 letters)



>FitnessBrowser__Koxy:BWI76_RS23630
          Length = 259

 Score =  177 bits (450), Expect = 1e-49
 Identities = 100/253 (39%), Positives = 145/253 (57%), Gaps = 3/253 (1%)

Query: 4   LEGKSALITGSARGIGRSFAQAYIGEGATVAIADINLERAQATASE---LGPQAYAVEMD 60
           +E K AL+TG+ +GIGR  A     +GA++ + D+N E   A A+E   LG +A     +
Sbjct: 3   IENKVALVTGAGQGIGRGIALRLAKDGASLMLVDVNPEGIAAVAAEVEALGRKAATFVAN 62

Query: 61  VTRQASIDAAIAEVVARAGKLDILVNNAALFDLAPITEITRESYDKLFAINVSGTLFTLQ 120
           +  +A + AAI E   + G  DI+VNNA +  +  + ++T E  D++  INV GTL+ +Q
Sbjct: 63  IADRAQVYAAIDEAEKQLGGFDIIVNNAGIAQVQALADVTPEEVDRIMRINVQGTLWGIQ 122

Query: 121 AAAKQMISQGHGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIKHKINVNA 180
           AAAK+ I +   GKIIN  S AG  G AL+GVY ATK AV +LTQ+A        I VNA
Sbjct: 123 AAAKKFIDRQQKGKIINACSIAGHDGFALLGVYSATKFAVRALTQAAAKEYASRGITVNA 182

Query: 181 IAPGVVDGEHWDGVDALFAKHENRPLGEKKRLVGLEVPYGRMGTAEDLVGMAIFLAGSES 240
             PG+V    W  +D  FA+    P+GE  +     +  GR  T +D+  +  +LAG +S
Sbjct: 183 YCPGIVGTGMWTEIDKRFAEITGAPVGETYKKYVEGIALGRAETPDDVASLVSYLAGPDS 242

Query: 241 DYIVAQTYNVDGG 253
           DY+  Q+  +DGG
Sbjct: 243 DYVTGQSILIDGG 255


Lambda     K      H
   0.317    0.132    0.368 

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: 191
Number of extensions: 7
Number of successful extensions: 2
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: 257
Length of database: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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