Align 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Synpcc7942_0972 Synpcc7942_0972 YjgF-like protein
Query= SwissProt::Q9KWS2 (142 letters) >FitnessBrowser__SynE:Synpcc7942_0972 Length = 130 Score = 73.2 bits (178), Expect = 1e-18 Identities = 47/127 (37%), Positives = 68/127 (53%), Gaps = 13/127 (10%) Query: 18 PMGSFPH-VKRAGDFLFVSGTSSRRP-DNTFVGAEPDDTGRPRPNIELQTREVISNIRDI 75 P+G + + +G LFVSG + P T VG + ++E+QT +V+SN++ + Sbjct: 14 PVGPYSQAIAASGRMLFVSGQIALDPATGTMVGGD---------DVEVQTHQVLSNLKAV 64 Query: 76 LQSVGADLGDVVEVCSYLVNMNDFAAYNKVYAEFFD-ATGPARTTVAVHQLPHPQLVIEI 134 L + GA GDVV +L +M DFA N +YA FD AT PAR V +LP +EI Sbjct: 65 LAAAGASFGDVVRTTVFLADMEDFARVNAIYATVFDEATAPARACVQAARLP-KDAKVEI 123 Query: 135 KVVAYKP 141 +A P Sbjct: 124 DCIAVLP 130 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: 50 Number of extensions: 3 Number of successful extensions: 2 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: 130 Length adjustment: 15 Effective length of query: 127 Effective length of database: 115 Effective search space: 14605 Effective search space used: 14605 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