Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate Echvi_0643 Echvi_0643 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Cola:Echvi_0643 Length = 309 Score = 121 bits (304), Expect = 2e-32 Identities = 92/291 (31%), Positives = 144/291 (49%), Gaps = 16/291 (5%) Query: 26 YLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHSNHAF 85 +LP I +E+G +++KR D GNK KL+Y L A G V+T G SNH Sbjct: 17 FLPEI-KEMGVRLFVKRLDKIHPLASGNKFYKLKYNLEAAKQSGNSTVLTFGGAFSNHIL 75 Query: 86 VTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELK 145 T +A+ GL +I ++RG+ + N L + + + K+ +EI + L+ Sbjct: 76 ATAASAEAAGLKSIGIIRGECPAEPNPTLKQARANGMTLSFMDRTTYRKKHEKEIIDRLQ 135 Query: 146 REGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLSLGLSIL 205 E Y+IP GG + + ++ EI T + D I + G+GGT+AGL + Sbjct: 136 EEFGNFYLIPEGGTNALA----IKGTAEILTDEDQTMDFICCSIGTGGTIAGL---IKSA 188 Query: 206 NEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYD-YSFGEYGKITGEVA 264 + +G + + GE + ++ NL+ +A E + + + L+ Y FG Y K E+ Sbjct: 189 MPHQKVLGFSALK-GEFIHQEIANLL-QAHE---IPSQNQYALFSTYHFGGYAKHKPELI 243 Query: 265 QIIRKVGTREGIILDPVYTGKAFYGLVDLARKGEL--GEKILFIHTGGISG 313 I+K GI LDPVYTGK FYG++D + G IL IH+GG+ G Sbjct: 244 AFIKKFKQATGIPLDPVYTGKLFYGVMDNIKSSFFPPGSHILLIHSGGLQG 294 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: 243 Number of extensions: 15 Number of successful extensions: 4 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: 309 Length adjustment: 27 Effective length of query: 298 Effective length of database: 282 Effective search space: 84036 Effective search space used: 84036 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