Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_022949747.1 H035_RS0114785 D-cysteine desulfhydrase family protein
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_000421465.1:WP_022949747.1 Length = 339 Score = 194 bits (494), Expect = 2e-54 Identities = 123/324 (37%), Positives = 175/324 (54%), Gaps = 12/324 (3%) Query: 10 AKFPRVELIPWETPIQYLPNISREIGAD-VYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68 A P + LI TP+ LP++++ + + ++IKRDDL G GGNKIR LE+L+GDAL + Sbjct: 14 AVLPWLPLIRHLTPMHPLPSLAKRLRRERLWIKRDDLIAFGFGGNKIRGLEFLVGDALVR 73 Query: 69 GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEE--LKGNYLLDKIMGIETRVYD 126 GAD +IT SNH T K GL V G+++ GNY L +++G ET Sbjct: 74 GADTLITGAGPLSNHVRATAAVGAKYGLRTAAVYWGEDKGHESGNYALVRMLGAETTFTG 133 Query: 127 AKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQ---SEVKFD 183 D + + +AEEL + G+KPYVIP GGASP+G +G+ AV E+ Q D Sbjct: 134 CSDRSSVDRRMASLAEELAKRGQKPYVIPRGGASPLGVVGHFLAVEELLKQFAKGAAMPD 193 Query: 184 SIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVE 243 ++V+ GSG TLAG LG S R + V R ++ L+++ +LLG+ + Sbjct: 194 TVVLPVGSGATLAGWLLGTSYYRAPWRVEAVTVSRPAAEAKRQVLQLVRDTEKLLGIDTD 253 Query: 244 VRP---ELYD-YSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKG-- 297 V ++D Y YG + E + IR EG+ LDPVYTGK GL+ L +G Sbjct: 254 VAEGSVRIHDGYIGAGYGAPSPEGSAAIRLAAVEEGVFLDPVYTGKTLAGLIALCDRGYF 313 Query: 298 ELGEKILFIHTGGISGTFHYGDKL 321 + + +LF+HTGG G F G L Sbjct: 314 DSSKHVLFLHTGGQPGLFVPGQYL 337 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: 278 Number of extensions: 13 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: 339 Length adjustment: 28 Effective length of query: 297 Effective length of database: 311 Effective search space: 92367 Effective search space used: 92367 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