Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_028584555.1 G494_RS0110775 D-cysteine desulfhydrase
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_000429965.1:WP_028584555.1 Length = 332 Score = 194 bits (494), Expect = 2e-54 Identities = 128/328 (39%), Positives = 177/328 (53%), Gaps = 18/328 (5%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIG--ADVYIKRDDLTGLGIGGNKIRKLEYLLGDAL 66 L +FPR + TPI+ LP S +G +++IKRDDL GGNK RKL++ + DAL Sbjct: 3 LTQFPRRNYVQDATPIEALPAFSAALGNKVNLFIKRDDLLPGCAGGNKTRKLDFCIADAL 62 Query: 67 SKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRG------KEELKGNYLLDKIMGI 120 KGAD +IT GAV SNH +T A K G+D LVL +E+ GN L K+MG+ Sbjct: 63 EKGADTIITCGAVQSNHCRLTLSWAVKEGMDCHLVLEERVAGSYREDGSGNNFLFKLMGV 122 Query: 121 ETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQ--- 177 ++ + ++M E++A E++ GRKPY+IP G ++ IG GYV EI Q Sbjct: 123 KS-ITVVPGGSDMMAAMEQLAAEVEGSGRKPYIIPGGASNAIGATGYVACAQEIQQQLFA 181 Query: 178 SEVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAEL 237 +K D +VV +GS GT AG+ +G+ N I GI V R V + L E A Sbjct: 182 RNLKIDHMVVPSGSAGTHAGMVVGMYGSNAGIPVSGINVSRTKPVQEEIVHKLALETAAR 241 Query: 238 LGVKVEVRPE---LYDYSFGE-YGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDL 293 LGV+ V E +D G Y T + + ++ + E I+LDPVY+GKA GL+DL Sbjct: 242 LGVRESVPAEEITCFDGYVGPGYSLPTESMVEAVKLLAQTESILLDPVYSGKAMAGLIDL 301 Query: 294 ARKGEL--GEKILFIHTGGISGTFHYGD 319 R G +LF+HTGG + Y D Sbjct: 302 VRNDHFAPGANVLFLHTGGSPALYAYLD 329 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: 254 Number of extensions: 12 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: 332 Length adjustment: 28 Effective length of query: 297 Effective length of database: 304 Effective search space: 90288 Effective search space used: 90288 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