GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Burkholderia phytofirmans PsJN

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate BPHYT_RS16120 BPHYT_RS16120 sorbitol dehydrogenase

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__BFirm:BPHYT_RS16120
          Length = 260

 Score =  155 bits (391), Expect = 1e-42
 Identities = 93/254 (36%), Positives = 150/254 (59%), Gaps = 17/254 (6%)

Query: 12  ITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK--EDVKDVAAQINPSRTLALQVDI 69
           + DKVA++TGAASGIG+A+A  + ++GA  VL+D+K  +   D        R L +  D+
Sbjct: 5   LQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATYGDRVLTVSADV 64

Query: 70  TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129
           T++++I+++VA   + + +IDIL N+A +  +    +   + +D+   +N+KG F + Q 
Sbjct: 65  TRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQA 124

Query: 130 IGREMIATG-GGKIVNMASQAS--VIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVN 186
           + ++M+  G GGKI+NM+SQA     AL  H  YCA+KAA++S TQ  A+  AP+ INVN
Sbjct: 125 VAQKMVEQGCGGKIINMSSQAGRRGEALVSH--YCATKAAVLSYTQSAALALAPHKINVN 182

Query: 187 AISPTVILTELGKKAWA----------GQVGEDMKKLIPAGRFGYPEEVAACALFLVSDA 236
            I+P V+ T +  +  A          G+    + + +P GR G P+++   ALFL S  
Sbjct: 183 GIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASAD 242

Query: 237 ASLITGENLIIDGG 250
           A  IT + L +DGG
Sbjct: 243 ADYITAQTLNVDGG 256


Lambda     K      H
   0.316    0.133    0.369 

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: 157
Number of extensions: 10
Number of successful extensions: 5
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: 254
Length of database: 260
Length adjustment: 24
Effective length of query: 230
Effective length of database: 236
Effective search space:    54280
Effective search space used:    54280
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 (21.6 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