GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Phaeobacter inhibens BS107

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__Phaeo:GFF1301
          Length = 257

 Score =  135 bits (341), Expect = 7e-37
 Identities = 87/261 (33%), Positives = 138/261 (52%), Gaps = 10/261 (3%)

Query: 3   KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62
           K+ +GK  L+TGA   IG A A   A EG  + + D++     +AEA+  + G  A +  
Sbjct: 2   KRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTA---RAEATAAQIGAAAIAVE 58

Query: 63  CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFH 122
            DVT + ++   +   V  FG +D L NNA    A AP+ +   + + R   INV+G   
Sbjct: 59  LDVTDQASIDRALSRTVECFGGLDILINNAAVFTA-APLVEVTREAYQRTFDINVSGTLF 117

Query: 123 VLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181
           +++A ++QMITQ  G +I+N AS AG +G P ++ Y  +K A+I+LT++A L+L  + I 
Sbjct: 118 MMQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGIN 177

Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241
           VNAI+PG +  G  W+      AK    Y    P     ++  SVP  R G   ++ G+ 
Sbjct: 178 VNAIAPGVV-DGEHWDGVDAFFAK----YEGKAPGQKKAEVAQSVPYGRMGTAADLTGMA 232

Query: 242 AFLLGDDSSFMTGVNLPIAGG 262
            FL  +D+ ++      + GG
Sbjct: 233 VFLASEDADYVVAQTYNVDGG 253


Lambda     K      H
   0.318    0.135    0.384 

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: 170
Number of extensions: 12
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: 262
Length of database: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
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