GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudomonas fluorescens FW300-N1B4

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Pf1N1B4_5039 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5039
          Length = 257

 Score =  150 bits (379), Expect = 3e-41
 Identities = 90/261 (34%), Positives = 144/261 (55%), Gaps = 10/261 (3%)

Query: 3   KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62
           K+  GK  L+TG+   IG   A     EG  +A+ D+N   LE+A+A+  E    A +  
Sbjct: 2   KRLEGKSALITGSARGIGRTFAQAYIREGATVAIADIN---LERAQATAAELWPNAYAVE 58

Query: 63  CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFH 122
            DVT ++++ G + +V+   GK+D L NNA      AP+ +   D + R+ +INV+G   
Sbjct: 59  MDVTDQQSIDGAIAAVIATTGKLDILINNAALFD-LAPITEISRDSYERLFSINVSGTLF 117

Query: 123 VLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181
            L+A ++QMI Q +G +I+N AS AG +G   +A Y  +K A+I+LT++A L+L P+NI 
Sbjct: 118 TLQAAAKQMIRQGHGGKIINMASQAGRRGEALVAVYCATKAAVISLTQSAGLNLIPHNIN 177

Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241
           VNAI+PG +  G  W+    L AK  ++      K+  Q+    VP  R G  +++ G+ 
Sbjct: 178 VNAIAPGVV-DGEHWDGVDALFAKYENRPLGEKKKLAGQE----VPYGRMGTADDLVGMA 232

Query: 242 AFLLGDDSSFMTGVNLPIAGG 262
            FL   +S ++      + GG
Sbjct: 233 IFLASAESDYIVAQTYNVDGG 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: 163
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