Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_019865008.1 METMI_RS0104315 hypothetical protein
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_000384075.1:WP_019865008.1 Length = 300 Score = 124 bits (311), Expect = 3e-33 Identities = 94/309 (30%), Positives = 149/309 (48%), Gaps = 44/309 (14%) Query: 25 QYLPNISREIGA--------DVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITV 76 Q+ P+I +I A ++++KRDDL I GNK RKL+Y+L ALS + +I++ Sbjct: 11 QFQPSILTKINAPILDQQQIELWLKRDDLLHPVISGNKWRKLKYILNHALSLKSHTLISM 70 Query: 77 GAVHSNHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLDKIMGIETRVYDAKDSFELMKY 136 G V+SNH + L L I +RG D + + DA+ +K+ Sbjct: 71 GGVYSNHLHALAYVGQLLKLQTIGYIRG----------DPAGPLTPTLQDARAWGMTLKF 120 Query: 137 AEEIAEELKRE--------GRKP--YVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIV 186 + R G +P Y +P GGA + LG V E A++ + FD + Sbjct: 121 VSRGDYRILRNHQNWDGLPGLQPGQYWLPEGGAQALALLG----VAESASEITLPFDWLC 176 Query: 187 VAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRP 246 V G+G TLAGL ++ + R +G A + + +++NL++ + + + Sbjct: 177 VPCGTGTTLAGL---INAIPGHSRAIGFAALKNAGFLNQEVENLLQHPRDNWHINL---- 229 Query: 247 ELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGEL--GEKIL 304 DY FG + + + + I + GIIL+PVYTGK +GL DL +K G+KI+ Sbjct: 230 ---DYHFGGFAQTSAPLMDFISEFQCGTGIILEPVYTGKMLFGLYDLIKKNTFKPGQKII 286 Query: 305 FIHTGGISG 313 IHTGG+ G Sbjct: 287 AIHTGGLQG 295 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: 217 Number of extensions: 12 Number of successful extensions: 3 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: 300 Length adjustment: 27 Effective length of query: 298 Effective length of database: 273 Effective search space: 81354 Effective search space used: 81354 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 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