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.
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:
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