GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Paraburkholderia bryophila 376MFSha3.1

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate H281DRAFT_00644 H281DRAFT_00644 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family

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



>FitnessBrowser__Burk376:H281DRAFT_00644
          Length = 263

 Score =  506 bits (1302), Expect = e-148
 Identities = 263/263 (100%), Positives = 263/263 (100%)

Query: 1   MSIIDLLKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLH 60
           MSIIDLLKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLH
Sbjct: 1   MSIIDLLKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLH 60

Query: 61  AGIADVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNS 120
           AGIADVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNS
Sbjct: 61  AGIADVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNS 120

Query: 121 QFYFLRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPS 180
           QFYFLRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPS
Sbjct: 121 QFYFLRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPS 180

Query: 181 NVRVNAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALF 240
           NVRVNAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALF
Sbjct: 181 NVRVNAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALF 240

Query: 241 LASPAGSNVTGQAISVDGNVEYL 263
           LASPAGSNVTGQAISVDGNVEYL
Sbjct: 241 LASPAGSNVTGQAISVDGNVEYL 263


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: 327
Number of extensions: 1
Number of successful extensions: 1
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: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
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 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