Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate 3608032 Dshi_1439 pyridoxal phosphate-dependent enzyme, D-cysteine desulfhydrase family (RefSeq)
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Dino:3608032 Length = 347 Score = 198 bits (503), Expect = 2e-55 Identities = 124/332 (37%), Positives = 184/332 (55%), Gaps = 18/332 (5%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGA-DVYIKRDDLTGLGIGGNKIRKLEYLLGDALS 67 L +FPR L TPI+ +P +S +G +++KRDD TGL +GGNK RKLE+L+G+A+ Sbjct: 16 LDRFPRTPLCHQPTPIEAMPRLSAALGGPSLFVKRDDCTGLAMGGNKTRKLEFLVGEAME 75 Query: 68 KGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLR----GKE---ELKGNYLLDKIMGI 120 + AD+++T GAV SNH T AA KLG+ ++L G++ E GN LLD + G Sbjct: 76 EKADMLVTQGAVQSNHVRQTAAAACKLGMKCHVLLERRVPGRDASYESTGNVLLDNLFGA 135 Query: 121 ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEV 180 A ++ A + E L+ EG +PY IP GG++P G LGYV EIA S Sbjct: 136 THEFRPA--GLDMNAEARTVTERLQAEGHRPYFIPGGGSNPTGALGYVACAREIAEHSRA 193 Query: 181 ---KFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAEL 237 FD +V++ GS GT AGL G + ++ +G++V + E + L + E Sbjct: 194 TGQSFDWLVMSTGSTGTHAGLVAGFHAMGHELPVMGVSVRQPRERQMQAVHALTQATLEK 253 Query: 238 LGVK-VEVRPELYDYSF-GE-YGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLA 294 LG V ++ + D + GE YG + IR +EG++LDPVY+ K GL+ + Sbjct: 254 LGHDGVPLKKIIVDDGYVGEGYGIPAPSTLEAIRLTARQEGLLLDPVYSAKGMAGLIGMV 313 Query: 295 RKG--ELGEKILFIHTGGISGTFHYGDKLLSL 324 R G + + +LF+HTGG S F Y D++ +L Sbjct: 314 RSGFFKPSDSVLFLHTGGASALFAYEDQITAL 345 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: 247 Number of extensions: 14 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: 347 Length adjustment: 28 Effective length of query: 297 Effective length of database: 319 Effective search space: 94743 Effective search space used: 94743 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