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_RS08900 BWI76_RS08900 putative short-chain dehydrogenase/reductase SDR

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



>FitnessBrowser__Koxy:BWI76_RS08900
          Length = 249

 Score =  110 bits (274), Expect = 4e-29
 Identities = 81/250 (32%), Positives = 135/250 (54%), Gaps = 17/250 (6%)

Query: 16  LISGAAA--GIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVA-DVSDCAQV 72
           +I+GAA+  G+G A A+ F + GA+V I D++  A   A  A  + H G+A +V+D  QV
Sbjct: 9   IITGAASARGLGFATAKLFAENGASVVILDLNSEASKAAAAALGEGHLGLAANVADEVQV 68

Query: 73  DRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVPLL 132
              ++   +K G +D+L+NNAGI  P   + D+  A ++  +  +L       +  +P +
Sbjct: 69  QAAMEQILAKYGRVDVLVNNAGITQPLKLM-DIKRANYDAVLDVSLRGTLLMSQAVIPTM 127

Query: 133 KETSANPGIIAMASV-AGRLGYAFRTP-YAASKWAIVGMVKSLAIELGPNNVRVNAILPG 190
           +   +   I+ ++SV A R G  F  P Y+A+K  ++G+ +++A ELGP+NVRVN I PG
Sbjct: 128 RAQKSG-SIVCISSVSAQRGGGIFGGPHYSAAKAGVLGLARAMARELGPDNVRVNCITPG 186

Query: 191 VVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNIS 250
           +++ +     I+A     G   D M    L  I + R+    D+A  ALFL S      +
Sbjct: 187 LIQTD-----ITA-----GKLTDDMTANILAGIPMNRLGDAVDIARAALFLGSDLSSYST 236

Query: 251 GQAISVDGNV 260
           G  + V+G +
Sbjct: 237 GITLDVNGGM 246


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: 135
Number of extensions: 7
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: 263
Length of database: 249
Length adjustment: 24
Effective length of query: 239
Effective length of database: 225
Effective search space:    53775
Effective search space used:    53775
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