Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate RR42_RS32990 RR42_RS32990 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Cup4G11:RR42_RS32990 Length = 338 Score = 169 bits (429), Expect = 7e-47 Identities = 110/322 (34%), Positives = 167/322 (51%), Gaps = 20/322 (6%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGA--DVYIKRDDL-TGLGIGGNKIRKLEYLLGDA 65 L +FPR +L TPIQ L +S +G D+Y KR+D +GL GGNK RKLEY++ DA Sbjct: 3 LKRFPRHQLTFGPTPIQPLKRLSAHLGGKVDLYAKREDCNSGLAFGGNKTRKLEYIIPDA 62 Query: 66 LSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLR-------GKEELKGNYLLDKIM 118 L++G D ++++G + SN A LGL +LV + GN + +IM Sbjct: 63 LAQGCDTLVSIGGIQSNQTRQVAAVAAHLGLKCVLVQEDWVNYSDAVYDRVGNIQMSRIM 122 Query: 119 GIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPG-GASPIGTLGYVRAVGEIATQ 177 G + R+ + K EE E +++ G KPY IP G P+G LG+V E+ Q Sbjct: 123 GADVRLVSDGFDIGIRKSWEEAMESVRQAGGKPYPIPAGCSEHPLGGLGFVGFAEEVRAQ 182 Query: 178 SE---VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEA 234 KFD +VV + +G T AG+ +G + R +GI +++ + + Sbjct: 183 EAELGFKFDYVVVCSVTGSTQAGMVVGFAADGRANRVIGIDASAKPAQTRAQILRIARNT 242 Query: 235 AELLGVKVEVRPE--LYDYSFG--EYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGL 290 A L+ + ++ E + D +G EYG + E + IR EG++ DPVY GK+ G+ Sbjct: 243 AHLVDLGRDITDEDVVLDTRYGGPEYGLPSEETLEAIRMSAKLEGMMTDPVYEGKSMQGM 302 Query: 291 VDLARKGEL--GEKILFIHTGG 310 +DL R+GE G K+L+ H GG Sbjct: 303 IDLVRRGEFPEGSKVLYAHLGG 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: 293 Number of extensions: 26 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:
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