GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Bacteroides thetaiotaomicron VPI-5482

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 349937 BT0409 putative short-chain dehydrogenase (NCBI ptt file)

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__Btheta:349937
          Length = 256

 Score = 84.0 bits (206), Expect = 3e-21
 Identities = 74/237 (31%), Positives = 110/237 (46%), Gaps = 15/237 (6%)

Query: 9   LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYK--- 65
           +K K V ITG  SGIG G    FA++G  +I           L+AEL       VY    
Sbjct: 1   MKAKIVFITGASSGIGEGCARKFAKEGWNLILNARTVSKLEELKAELEKEYGIQVYVLPF 60

Query: 66  --RCDLMNLEAIKAVFAEIGDVDVLVNNAG---NDDRHKLADVTGAYWDERINVNLRHML 120
             R       A++A+  E   +DVL+NNAG     D+     +    WD  I+ N+R +L
Sbjct: 61  DVRDRKQAAAALEALPEEWKSIDVLINNAGLVIGVDKEFEGSLDE--WDIMIDTNIRGLL 118

Query: 121 FCTQAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIR 180
             T+ V PGM +RG G +IN GSI+         +Y   KA ++ ++  L  +L    +R
Sbjct: 119 AMTRLVVPGMVERGCGHIINIGSIAGDAAYPGGSVYCATKAAVKALSDGLRIDLVDTPLR 178

Query: 181 VTCVVPGNVKTKRQEKWYTPEGEAQIVAAQCLKG--RIVPENVAALVLFLASDDASL 235
           VT + PG V+T      Y  + +A   A    KG   +  +++A  V + AS  A +
Sbjct: 179 VTNIKPGMVETNFTVVRYRGDKQA---ADNFYKGIRPLTGDDIAETVYYAASAPAHI 232


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: 147
Number of extensions: 7
Number of successful extensions: 3
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: 256
Length adjustment: 24
Effective length of query: 224
Effective length of database: 232
Effective search space:    51968
Effective search space used:    51968
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.

Links

Downloads

Related tools

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