GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Shewanella amazonensis SB2B

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate 6936200 Sama_0389 short chain dehydrogenase (RefSeq)

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



>FitnessBrowser__SB2B:6936200
          Length = 270

 Score = 82.8 bits (203), Expect = 7e-21
 Identities = 63/202 (31%), Positives = 101/202 (50%), Gaps = 9/202 (4%)

Query: 15  VLISGAAAGIGAAIAQAFLDVGANVYICD-----VDPAAIDRARTAHPQLHAGV--ADVS 67
           V+++GA+ GIG A+A+    +G ++ +       +   A++ A+    Q    V  AD++
Sbjct: 9   VILTGASEGIGRALARELARLGCHLVLTARSETRLQSLALELAQEQGAQADVLVHSADLT 68

Query: 68  DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127
              +   +ID   ++ G LD+LINNAG+   +   E  D A  E+ +  N  +       
Sbjct: 69  HPHECRELIDACIARFGRLDILINNAGMTMWSRFDELEDLAILEQIMAVNYLAPARLTHM 128

Query: 128 AVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187
           A+P LK +     ++A+ASVAG  G   R+ YAASK A++G   SL IEL  + V V  I
Sbjct: 129 ALPHLKHSQGQ--VVAIASVAGLTGVPTRSGYAASKHAMMGFFDSLRIELADDKVAVTVI 186

Query: 188 LPGVVEGERMDRVISARAESLG 209
            P  V  +   R +  +   LG
Sbjct: 187 CPDFVVSQIHKRALDGKGNPLG 208


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: 138
Number of extensions: 9
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: 263
Length of database: 270
Length adjustment: 25
Effective length of query: 238
Effective length of database: 245
Effective search space:    58310
Effective search space used:    58310
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