GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Pseudomonas fluorescens FW300-N2E3

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate AO353_19655 AO353_19655 2,5-diketo-D-gluconic acid reductase

Query= BRENDA::C1K8Y9
         (324 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19655
          Length = 267

 Score =  140 bits (354), Expect = 3e-38
 Identities = 102/306 (33%), Positives = 141/306 (46%), Gaps = 46/306 (15%)

Query: 18  MPLVGFGCWKVNNETAADQIYNAIKTGYRLFDGAEDYGNEKEVGEGINRAIKEGLVKREE 77
           +P  G G +++  +   D +   ++ GYR  D A+ Y NE +VG+    AI    + REE
Sbjct: 3   VPAFGLGTFRLQGQVVIDSVSTGLELGYRAIDTAQIYDNEADVGQ----AIAASGIAREE 58

Query: 78  LFITSKLWNNFHDPKNVETALNKTLSDLNLDYVDLFLIHFPIAFKFVPIEEKYPPGFYCG 137
           LFITSK+W        +  +L  +L  L  DY+DL LIH+P     VP+ E      + G
Sbjct: 59  LFITSKIWIANFAKDQLIASLKDSLRKLQTDYLDLTLIHWPSPENQVPVHE------FMG 112

Query: 138 DGDNFHYEDVPLLDTWKALEKLVEAGKIKSIGISNFTGALIYDLIRGATIKP-AVLQIEH 196
                            AL +    G  + IG+SNFT  L+   I        A  QIE 
Sbjct: 113 -----------------ALLEAKALGLTRQIGVSNFTVDLMQQAIDAVGADNIATNQIEL 155

Query: 197 HPYLQQPKLIEYVQKAGIAITGYSSFGPQSFLELESKRALNTPTLFEHETIKSIADKHGK 256
           HPYLQ   ++E+ Q  GI IT Y        + L     L  P       I+ IA++H  
Sbjct: 156 HPYLQNRTVVEFAQSQGIQITSY--------MTLAYGEVLKDPV------IQQIAERHQA 201

Query: 257 SPAQVLLRWATQRNIAVIPKSNNPERLAQNLSVVDFDLTKDDLDNIAKLDIGLRFNDPW- 315
           +PAQV L WA Q+  AVIP S     L  NL+  +  L++ D+  IA L+ G R   P  
Sbjct: 202 TPAQVTLAWAMQQGYAVIPSSTQRANLDSNLAARELTLSEADMTLIAGLERGQRLTSPKG 261

Query: 316 ---DWD 318
              DWD
Sbjct: 262 IAPDWD 267


Lambda     K      H
   0.318    0.139    0.420 

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: 206
Number of extensions: 9
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: 324
Length of database: 267
Length adjustment: 26
Effective length of query: 298
Effective length of database: 241
Effective search space:    71818
Effective search space used:    71818
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: 48 (23.1 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