Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate CA265_RS14425 CA265_RS14425 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Pedo557:CA265_RS14425 Length = 289 Score = 140 bits (352), Expect = 5e-38 Identities = 95/287 (33%), Positives = 149/287 (51%), Gaps = 20/287 (6%) Query: 37 DVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGL 96 ++++KRDDL I GNK RKL+Y+L A + ++T G +SNH T AA + GL Sbjct: 19 NLFVKRDDLIDPYISGNKWRKLKYILARAKAAHKSHLVTFGGAYSNHLVATAAAASRSGL 78 Query: 97 DAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPP 156 A +RG+E LL ++ G++ ++ ++S+ + +++ ++ ++ Y I Sbjct: 79 TATAFVRGEEVKNELLLLCRLFGMKL-IFTDRESY---RDKQKLFQQHFGNDQQAYFIDE 134 Query: 157 GGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAV 216 GGAS T G + E+ +D I AAG+G T AGL G+ + I V Sbjct: 135 GGASAEATTGCAEVISELTE----TYDHIFCAAGTGTTAAGLLNGIQQQGLSTKLHIIPV 190 Query: 217 GRFGEVMTSKLDNLIKEAAELLGVKVEVRPELY-DYSFGEYGKITGEVAQIIRKVGTREG 275 + G + ++ + L EL+ DY FG Y K T E+ I+ ++ G Sbjct: 191 LKGGLFIKDEIAKYTPLSNHL---------ELHLDYHFGGYAKTTPELISFIKTFTSKTG 241 Query: 276 IILDPVYTGKAFYGLVDLARKGELG--EKILFIHTGGISGTFHYGDK 320 ++LDPVYTGK FY + DL ++G +G EK+L IHTGG+ G F DK Sbjct: 242 LLLDPVYTGKMFYAIQDLVKQGIIGKDEKVLAIHTGGLMGIFGMKDK 288 Lambda K H 0.319 0.142 0.402 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: 240 Number of extensions: 13 Number of successful extensions: 3 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: 325 Length of database: 289 Length adjustment: 27 Effective length of query: 298 Effective length of database: 262 Effective search space: 78076 Effective search space used: 78076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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