Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate H281DRAFT_02886 H281DRAFT_02886 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Burk376:H281DRAFT_02886 Length = 338 Score = 160 bits (405), Expect = 4e-44 Identities = 105/323 (32%), Positives = 159/323 (49%), Gaps = 20/323 (6%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGADV--YIKRDDL-TGLGIGGNKIRKLEYLLGDA 65 L +FPR L TPIQ L +S +G V Y KR+D +G GGNK RKLEYL+ +A Sbjct: 3 LQRFPRYPLTFGPTPIQPLKRLSDHLGGKVHLYAKREDCNSGFAFGGNKTRKLEYLIPEA 62 Query: 66 LSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLR-------GKEELKGNYLLDKIM 118 L++G D ++++G + SN A LG+ +LV + GN + +I+ Sbjct: 63 LAQGCDTLVSIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYSDAVYDRVGNIQMSRIL 122 Query: 119 GIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGAS-PIGTLGYVRAVGEIATQ 177 G + R+ K E+ E ++ G KPY IP G + P+G LG+V E+ Q Sbjct: 123 GADVRLVPDGFDIGFRKSWEDALESVRAAGGKPYAIPAGCSDHPLGGLGFVGFAEEVRQQ 182 Query: 178 SE---VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEA 234 KFD IVV + +G T AG+ +G + R +GI ++ + Sbjct: 183 EAELGFKFDYIVVCSVTGSTQAGMVVGFAADGRADRVIGIDASAKPAQTREQITRIASRT 242 Query: 235 AELLGV--KVEVRPELYDYSFG--EYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGL 290 AE +G+ + + D FG EYG + IR EG++ DPVY GK+ +G+ Sbjct: 243 AEKVGLGRDITANDVVLDERFGGPEYGLPNDGTLEAIRLCARLEGVLTDPVYEGKSMHGM 302 Query: 291 VDLARKGEL--GEKILFIHTGGI 311 +D+ R GE G ++L+ H GG+ Sbjct: 303 IDMVRNGEFPEGSRVLYAHLGGV 325 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: 283 Number of extensions: 23 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: 338 Length adjustment: 28 Effective length of query: 297 Effective length of database: 310 Effective search space: 92070 Effective search space used: 92070 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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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