GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Sphingomonas koreensis DSMZ 15582

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Ga0059261_2665 Ga0059261_2665 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__Korea:Ga0059261_2665
          Length = 248

 Score =  110 bits (274), Expect = 3e-29
 Identities = 75/245 (30%), Positives = 115/245 (46%), Gaps = 6/245 (2%)

Query: 9   LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGS-PIPPVYKRC 67
           +KG+ V+ TG   G+G   T     +GA V+ +D       ALEA   G  P   +    
Sbjct: 1   VKGRTVLYTGAAGGLGLDTTLLLIERGATVVAIDHDLAKVEALEAAARGKGPGRLIVSTA 60

Query: 68  DLMNLEAIKA----VFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCT 123
           DL +L+ ++     +  E G  DV++NNA         D + A       VN+   +   
Sbjct: 61  DLADLDRLRVTLDILIEETGGFDVVINNAAIYPSKPFEDYSIAEHQAIQRVNVDAGIVAV 120

Query: 124 QAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTC 183
           QA  PGM+ +G G +IN  SI+   G  +L  Y  +K  + G+TRA ARE G   + V  
Sbjct: 121 QAALPGMQAKGFGRIINVSSITISGGWANLSPYVASKMALVGLTRAWAREFGAWGVTVNA 180

Query: 184 VVPGNVKTKRQEKWYTPEG-EAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYW 242
           + PG   T  ++    PEG    ++ AQ +K R    ++A  + F ASD++   TG    
Sbjct: 181 IAPGAFPTDAEKIHPDPEGYNRMVLDAQSIKRRGTARDIANAIAFFASDESGFVTGQTLH 240

Query: 243 IDAGW 247
           ++ GW
Sbjct: 241 VNGGW 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: 146
Number of extensions: 11
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: 248
Length adjustment: 24
Effective length of query: 224
Effective length of database: 224
Effective search space:    50176
Effective search space used:    50176
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