GapMind for catabolism of small carbon sources

 

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

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate AO353_24520 AO353_24520 short-chain dehydrogenase

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24520
          Length = 249

 Score =  119 bits (298), Expect = 6e-32
 Identities = 80/243 (32%), Positives = 125/243 (51%), Gaps = 5/243 (2%)

Query: 9   LKGKRVVITGGGS--GIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKR 66
           L+GK  +ITG  S  GIG      FA+QGA V+ LD+ +  +R   A L    +      
Sbjct: 3   LQGKVAIITGAASARGIGRATATTFAQQGARVVILDLDESAARDAAASLGEGHLGIGANV 62

Query: 67  CDLMNL-EAIKAVFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQA 125
            D + + +A+  +    G +D+L+NNAG     K  D+  + +D+ ++V+LR  L  +QA
Sbjct: 63  ADELQVRQAVAKIIEHFGRIDILINNAGITQPLKTLDIRPSDYDKVLDVSLRGTLLMSQA 122

Query: 126 VAPGMKKRGGGAVINFGSISWHL--GLEDLVLYETAKAGIEGMTRALARELGPDDIRVTC 183
           V P M+++  G+++   S+S     G+     Y  AKAG+ G+ +A+ARELGPD +RV  
Sbjct: 123 VIPTMRQQSSGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMARELGPDKVRVNS 182

Query: 184 VVPGNVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYWI 243
           + PG + T         E    I+    L      ++VA   LFLASD +S  TG    +
Sbjct: 183 IAPGLIHTDITGGLMQDERRHAIIDGIPLGRLGEAQDVANAALFLASDLSSYLTGITLDV 242

Query: 244 DAG 246
           + G
Sbjct: 243 NGG 245


Lambda     K      H
   0.319    0.137    0.416 

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: 139
Number of extensions: 8
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: 248
Length of database: 249
Length adjustment: 24
Effective length of query: 224
Effective length of database: 225
Effective search space:    50400
Effective search space used:    50400
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 (21.7 bits)
S2: 46 (22.3 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