GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Lactobacillus pobuzihii E100301

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_017867317.1 LACPOB_RS0102810 3-oxoacyl-[acyl-carrier-protein] reductase

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>NCBI__GCF_000349725.1:WP_017867317.1
          Length = 243

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 77/255 (30%), Positives = 125/255 (49%), Gaps = 24/255 (9%)

Query: 12  GLRVFVSAGAAGIGLAIAEAFIEAQAEVYIC---DVNQAAIDEATSRFPKLHAGIADVSK 68
           G   F++  + GIG  IA AF +A+A V +    +V     +E  S   +    + D+S+
Sbjct: 5   GKTAFITGSSRGIGKQIALAFAQAKANVILNARKEVPAQLEEEIKSYGVQCVTILGDISR 64

Query: 69  QAQVDQIIDDARRKLGGLDVLVNNAGIAGPT---GAVEELDPAQWESTVSTNLNSQFYFL 125
              V +++ +A      +DVLVNNAGI       G  EE     + S +  NL    Y +
Sbjct: 65  ADDVKRMVKEAYGSFPQIDVLVNNAGITNDKLLIGMKEE----DFRSVIDVNLVGT-YSM 119

Query: 126 RKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185
            +A+           II ++SV G  G   +  YA++K  ++GL K++A E    N+R N
Sbjct: 120 TRAILKKMNKKRTGVIINLASVVGLHGNVGQANYAASKAGVIGLTKTVAKEGALRNIRCN 179

Query: 186 AILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPA 245
           AI PG++E +  D V+S          + ++ + +  I L+R    +++A  A+FLA   
Sbjct: 180 AIAPGMIESDMTD-VLS----------DKVKNQLMAGIPLKRFGDSNEVAKTAVFLAQ-- 226

Query: 246 GSNVTGQAISVDGNV 260
              +TGQ ISVDG +
Sbjct: 227 NDYITGQVISVDGGM 241


Lambda     K      H
   0.318    0.134    0.375 

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: 134
Number of extensions: 8
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: 243
Length adjustment: 24
Effective length of query: 239
Effective length of database: 219
Effective search space:    52341
Effective search space used:    52341
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: 46 (22.3 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