GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Echinicola vietnamensis KMM 6221, DSM 17526

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::B8H1Z0
         (248 letters)



>FitnessBrowser__Cola:Echvi_3928
          Length = 252

 Score =  121 bits (304), Expect = 1e-32
 Identities = 90/247 (36%), Positives = 123/247 (49%), Gaps = 16/247 (6%)

Query: 9   LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCD 68
           L GK  V+TGG SGIG         +GA+VI    + E      AEL  + I       D
Sbjct: 4   LNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRSAEKVNVAAAELGVTGIT-----AD 58

Query: 69  LMNLEAIKA----VFAEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQ 124
           ++ L AI A    V A+ G VD+L  NAG      +   T   +D+++++NL+  +F  +
Sbjct: 59  VLELAAIDAAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVFTIE 118

Query: 125 AVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCV 184
              P +K   GG++IN  SI+ + G+ +  +Y  +KA +   TR  A EL P  IRV  V
Sbjct: 119 KFLPILKD--GGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRVNAV 176

Query: 185 VPGNVKTKRQEKWYTPEGEAQIVAAQC-----LKGRIVPENVAALVLFLASDDASLCTGH 239
            PG V T    K    E +   +AA       LK    PE++A LV FLASD AS  TG 
Sbjct: 177 NPGPVYTPIFSKTGMSEDQLNGMAAAMQNRIPLKRYGKPEDIAELVAFLASDRASFITGA 236

Query: 240 EYWIDAG 246
           EY ID G
Sbjct: 237 EYNIDGG 243


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: 133
Number of extensions: 7
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: 252
Length adjustment: 24
Effective length of query: 224
Effective length of database: 228
Effective search space:    51072
Effective search space used:    51072
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