Align 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate PP_2689 PP_2689 putative Endoribonuclease
Query= SwissProt::Q9KWS2 (142 letters) >FitnessBrowser__Putida:PP_2689 Length = 123 Score = 55.8 bits (133), Expect = 2e-13 Identities = 28/78 (35%), Positives = 43/78 (55%) Query: 61 IELQTREVISNIRDILQSVGADLGDVVEVCSYLVNMNDFAAYNKVYAEFFDATGPARTTV 120 IE Q R+ + N+R L++ G+ L V +V Y+ + A N VYAE+F A P R V Sbjct: 44 IEAQARQTLDNLRHTLEAAGSSLDAVTQVLIYVTDRRYLATVNAVYAEYFQAPYPNRAAV 103 Query: 121 AVHQLPHPQLVIEIKVVA 138 V L ++++E+ V A Sbjct: 104 VVAGLAREEMLVELVVYA 121 Lambda K H 0.318 0.135 0.389 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: 30 Number of extensions: 2 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: 142 Length of database: 123 Length adjustment: 15 Effective length of query: 127 Effective length of database: 108 Effective search space: 13716 Effective search space used: 13716 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: 41 (20.4 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