GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Klebsiella michiganensis M5al

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate BWI76_RS23630 BWI76_RS23630 acetoin(diacetyl) reductase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__Koxy:BWI76_RS23630
          Length = 259

 Score =  126 bits (317), Expect = 4e-34
 Identities = 80/251 (31%), Positives = 128/251 (50%), Gaps = 5/251 (1%)

Query: 16  LISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAG----VADVSDCAQ 71
           L++GA  GIG  IA      GA++ + DV+P  I         L       VA+++D AQ
Sbjct: 9   LVTGAGQGIGRGIALRLAKDGASLMLVDVNPEGIAAVAAEVEALGRKAATFVANIADRAQ 68

Query: 72  VDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVPL 131
           V   ID+A  +LGG D+++NNAGIA    A+ D+ P E +R +  N+    + ++ A   
Sbjct: 69  VYAAIDEAEKQLGGFDIIVNNAGIA-QVQALADVTPEEVDRIMRINVQGTLWGIQAAAKK 127

Query: 132 LKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILPGV 191
             +      II   S+AG  G+A    Y+A+K+A+  + ++ A E     + VNA  PG+
Sbjct: 128 FIDRQQKGKIINACSIAGHDGFALLGVYSATKFAVRALTQAAAKEYASRGITVNAYCPGI 187

Query: 192 VEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNISG 251
           V       +    AE  G    +   +Y++ I+L R  T  DVA++  +LA P    ++G
Sbjct: 188 VGTGMWTEIDKRFAEITGAPVGETYKKYVEGIALGRAETPDDVASLVSYLAGPDSDYVTG 247

Query: 252 QAISVDGNVEY 262
           Q+I +DG + Y
Sbjct: 248 QSILIDGGIVY 258


Lambda     K      H
   0.320    0.136    0.391 

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: 169
Number of extensions: 11
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: 263
Length of database: 259
Length adjustment: 25
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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