Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate 16033 b1919 putative 1-aminocyclopropane-1-carboxylate deaminase (VIMSS)
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Keio:16033 Length = 328 Score = 211 bits (537), Expect = 2e-59 Identities = 131/321 (40%), Positives = 183/321 (57%), Gaps = 14/321 (4%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68 L +FPR+E I TP++YLP S +G +++IKRDD+T + +GGNK+RKLE+L DAL + Sbjct: 6 LTRFPRLEFIGAPTPLEYLPRFSDYLGREIFIKRDDVTPMAMGGNKLRKLEFLAADALRE 65 Query: 69 GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRG-------KEELKGNYLLDKIMGIE 121 GAD +IT GA+ SNH T A KLGL + +L GN LL + + Sbjct: 66 GADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQ 125 Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-- 179 + DA + EE+A ++ +G +PYVIP GG++ +G LGYV + EIA Q E Sbjct: 126 IEMCDALT--DPNAQLEELATRVEAQGFRPYVIPVGGSNALGALGYVESALEIAQQCEGA 183 Query: 180 VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLG 239 V S+VVA+GS GT AGL++GL L + +G+ V R K+ NL + A+ L Sbjct: 184 VNISSVVVASGSAGTHAGLAVGLEHLMPESELIGVTVSRSVADQLPKVVNLQQAIAKELE 243 Query: 240 VKVEVRPELYDYSFGE-YGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVD-LARKG 297 + L+D F YG E + ++ + EGI+LDPVYTGKA GL+D +++K Sbjct: 244 LTASAEILLWDDYFAPGYGVPNDEGMEAVKLLARLEGILLDPVYTGKAMAGLIDGISQKR 303 Query: 298 ELGE-KILFIHTGGISGTFHY 317 E ILFIHTGG F Y Sbjct: 304 FKDEGPILFIHTGGAPALFAY 324 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: 272 Number of extensions: 15 Number of successful extensions: 5 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: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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