Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_086510288.1 BZY95_RS12675 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_002151265.1:WP_086510288.1 Length = 338 Score = 160 bits (405), Expect = 4e-44 Identities = 106/323 (32%), Positives = 164/323 (50%), Gaps = 20/323 (6%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGADV--YIKRDDL-TGLGIGGNKIRKLEYLLGDA 65 L +FPR L +PI L +S +G V Y KR+D +GL GGNK RKLEYL+ +A Sbjct: 3 LQRFPRYPLTFGPSPITPLKRLSEHLGGKVELYAKREDCNSGLAFGGNKTRKLEYLIPEA 62 Query: 66 LSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLR-------GKEELKGNYLLDKIM 118 L +G D ++++G + SN A LG+ +LV + GN + +IM Sbjct: 63 LEQGCDTLVSIGGIQSNQTRQVAAVAAHLGMRCVLVQEDWVNYSDAVYDRVGNIEMSRIM 122 Query: 119 GIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPG-GASPIGTLGYVRAVGEIATQ 177 G E R+ +A + E+ E++++ G KP+ IP G P G LG+V E+ Q Sbjct: 123 GAEVRLDEAGFDIGIRPSWEQALEDVRKRGGKPFPIPAGCSEHPYGGLGFVGFAEEVRQQ 182 Query: 178 SE---VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEA 234 KFD IVV + +G T AG+ +G + R +GI E ++ + + Sbjct: 183 ERELGFKFDYIVVCSVTGSTQAGMVVGFAADGRARRVIGIDASAKPERTREQILRIARHT 242 Query: 235 AELLGVKVEVRPE--LYDYSFG--EYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGL 290 AEL+ ++ + E + D +G EYG + + IR EG++ DPVY GK+ G+ Sbjct: 243 AELVELEGGIADEDVVLDTRYGGPEYGLPSEGTLEAIRLCARLEGVLTDPVYEGKSMQGM 302 Query: 291 VDLARKGEL--GEKILFIHTGGI 311 +D+ R GE G ++L+ H GG+ Sbjct: 303 IDMVRNGEFAEGSRVLYAHLGGV 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: 308 Number of extensions: 25 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 24 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