Align 2-aminomuconate deaminase (EC 3.5.99.5) (characterized)
to candidate 200579 SO1404 endoribonuclease L-PSP, putative (NCBI ptt file)
Query= metacyc::MONOMER-13362 (143 letters) >FitnessBrowser__MR1:200579 Length = 128 Score = 63.9 bits (154), Expect = 8e-16 Identities = 40/120 (33%), Positives = 65/120 (54%), Gaps = 10/120 (8%) Query: 16 GKFPHIKRAGDFLFVSGTSSRRPDNTLVGVEVDAMGTTRLDIVAQTTAVIENIRDILGSV 75 G + H R G+ +F SG + V D G I Q+ +EN++ +L + Sbjct: 16 GPYSHGTRYGNLIFTSGQ---------LPVCKDKGGVVDGGISEQSVQCLENLKYVLEAG 66 Query: 76 GATLDDVVEISTFLVNMNDFAGYNEVYGTYFGYEGPTRTTVAVHQLPHPHLLIEIKAVAY 135 G +LD V++ + +L ++DFA +NEVY TYF + P R+ AV LP + +EI+A+A+ Sbjct: 67 GGSLDTVLKTTCYLSEISDFAAFNEVYKTYFKTDCPARSCFAVKDLP-LGVKVEIEAIAH 125 Lambda K H 0.318 0.136 0.388 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: 45 Number of extensions: 4 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: 143 Length of database: 128 Length adjustment: 15 Effective length of query: 128 Effective length of database: 113 Effective search space: 14464 Effective search space used: 14464 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 (21.7 bits) S2: 42 (20.8 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