GapMind for catabolism of small carbon sources

 

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

Align Pentulose/hexulose kinase (characterized, see rationale)
to candidate Echvi_1875 Echvi_1875 Sugar (pentulose and hexulose) kinases

Query= uniprot:L0FZT0
         (496 letters)



>FitnessBrowser__Cola:Echvi_1875
          Length = 496

 Score =  998 bits (2581), Expect = 0.0
 Identities = 496/496 (100%), Positives = 496/496 (100%)

Query: 1   MRKLFIGYDIGSSSVKATLLDGDTGKVVASDGQPKIEMPIDSPQKDWAEQDPQMWWKYVI 60
           MRKLFIGYDIGSSSVKATLLDGDTGKVVASDGQPKIEMPIDSPQKDWAEQDPQMWWKYVI
Sbjct: 1   MRKLFIGYDIGSSSVKATLLDGDTGKVVASDGQPKIEMPIDSPQKDWAEQDPQMWWKYVI 60

Query: 61  ETTQAIIQQGGVKPGELQAIGISYQMHGLVMVDKEQQVIRPSIIWCDSRAVETGNSAFEA 120
           ETTQAIIQQGGVKPGELQAIGISYQMHGLVMVDKEQQVIRPSIIWCDSRAVETGNSAFEA
Sbjct: 61  ETTQAIIQQGGVKPGELQAIGISYQMHGLVMVDKEQQVIRPSIIWCDSRAVETGNSAFEA 120

Query: 121 LGSEFCLSHLLNSPGNFTASKLKWVKDHEPANYEKIHKVMLPGDFIAMKLTGEIFTSESG 180
           LGSEFCLSHLLNSPGNFTASKLKWVKDHEPANYEKIHKVMLPGDFIAMKLTGEIFTSESG
Sbjct: 121 LGSEFCLSHLLNSPGNFTASKLKWVKDHEPANYEKIHKVMLPGDFIAMKLTGEIFTSESG 180

Query: 181 LSEGVFWDFKENRVSQPLLDHYGIDREILATAIPSFAEGGKVNAAAAKVLGIAEGIPVTY 240
           LSEGVFWDFKENRVSQPLLDHYGIDREILATAIPSFAEGGKVNAAAAKVLGIAEGIPVTY
Sbjct: 181 LSEGVFWDFKENRVSQPLLDHYGIDREILATAIPSFAEGGKVNAAAAKVLGIAEGIPVTY 240

Query: 241 RAGDQPNNAFSLNVLEAGELATTAGTSGTVYGVSSSPVYDPQSRVNTFLHVNHMADNPHY 300
           RAGDQPNNAFSLNVLEAGELATTAGTSGTVYGVSSSPVYDPQSRVNTFLHVNHMADNPHY
Sbjct: 241 RAGDQPNNAFSLNVLEAGELATTAGTSGTVYGVSSSPVYDPQSRVNTFLHVNHMADNPHY 300

Query: 301 GVLLCVNGTGILNSWLKKMLGGESIDYEAMNKLAAEVPVGAEGLSFVPFGNGAERIMENK 360
           GVLLCVNGTGILNSWLKKMLGGESIDYEAMNKLAAEVPVGAEGLSFVPFGNGAERIMENK
Sbjct: 301 GVLLCVNGTGILNSWLKKMLGGESIDYEAMNKLAAEVPVGAEGLSFVPFGNGAERIMENK 360

Query: 361 TVGAHLAGLNLLKHDKRHVLRAGQEGIVSALTFGFNIMKNMGLTLDTVKAGRANMFLSPL 420
           TVGAHLAGLNLLKHDKRHVLRAGQEGIVSALTFGFNIMKNMGLTLDTVKAGRANMFLSPL
Sbjct: 361 TVGAHLAGLNLLKHDKRHVLRAGQEGIVSALTFGFNIMKNMGLTLDTVKAGRANMFLSPL 420

Query: 421 FREAFVNMNEVNLEFYDTDGSQGAARGAGVGAKHFASPQEAFNGLEKVASYVPEPKLVSA 480
           FREAFVNMNEVNLEFYDTDGSQGAARGAGVGAKHFASPQEAFNGLEKVASYVPEPKLVSA
Sbjct: 421 FREAFVNMNEVNLEFYDTDGSQGAARGAGVGAKHFASPQEAFNGLEKVASYVPEPKLVSA 480

Query: 481 YKEVYQQWEERLRKIQ 496
           YKEVYQQWEERLRKIQ
Sbjct: 481 YKEVYQQWEERLRKIQ 496


Lambda     K      H
   0.316    0.134    0.396 

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: 1004
Number of extensions: 27
Number of successful extensions: 1
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: 496
Length of database: 496
Length adjustment: 34
Effective length of query: 462
Effective length of database: 462
Effective search space:   213444
Effective search space used:   213444
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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