GapMind for catabolism of small carbon sources

 

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

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase

Query= reanno::ANA3:7024897
         (256 letters)



>FitnessBrowser__Cola:Echvi_4610
          Length = 248

 Score =  127 bits (318), Expect = 3e-34
 Identities = 79/248 (31%), Positives = 129/248 (52%), Gaps = 5/248 (2%)

Query: 10  LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDIL-VEESTQLVADLKQTQPEASVTFY 68
           L GKT  I+G + GIG  +   + ++GA VAF  +  VE+   L  +L +   +A    +
Sbjct: 4   LTGKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKG--F 61

Query: 69  HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFF 128
             D  D  A + ++ +V  + G + VLINNA   + + +  +  E WD  +N NL+  F 
Sbjct: 62  RSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCFN 121

Query: 129 AVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRI 188
            V+A    + +   GS+IN+ S+      AG A Y ASKAG +G T+ +A +LG   IR 
Sbjct: 122 TVKAATRTLMKQKAGSIINITSVVGIKGNAGQANYAASKAGIIGFTKSVALELGSRGIRS 181

Query: 189 NTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQN 248
           N + PG++ T  ++T  +D+ T +   +   +K    PE++A   +FL +D S   + Q 
Sbjct: 182 NAVAPGFIET--EMTEVLDEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSYVSGQV 239

Query: 249 FIVDGGWI 256
             VDG  +
Sbjct: 240 IQVDGAML 247


Lambda     K      H
   0.320    0.134    0.406 

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: 132
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: 256
Length of database: 248
Length adjustment: 24
Effective length of query: 232
Effective length of database: 224
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 (21.8 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