Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_068008542.1 PsAD2_RS16875 D-cysteine desulfhydrase family protein
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_001623255.1:WP_068008542.1 Length = 344 Score = 151 bits (382), Expect = 2e-41 Identities = 105/333 (31%), Positives = 167/333 (50%), Gaps = 18/333 (5%) Query: 5 IFALLAKFPRVELIPWETPIQYLPNISREIGAD-VYIKRDDLTGLGIGGNKIRKLEYLLG 63 + + L +FP V L TP++ L N+S+ +G ++ KR+D+TG G+GGNK+RKL+ +L Sbjct: 6 LLSRLERFPTVGLCDLPTPLRPLKNLSQHLGGPMIWEKREDVTGQGMGGNKLRKLDRVLH 65 Query: 64 DALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVL--------RGKEELKGNYLLD 115 A+ GAD +++ G V SN AA LGLD L + + GN LL+ Sbjct: 66 RAVQDGADTLVSGGVVQSNSQRQVAAAAAILGLDCHLAVYHGRVTPPTAQYNTSGNALLN 125 Query: 116 KIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIA 175 + G ++ + + + +A+EL EG++P+V+P G + +G +GY A+ EIA Sbjct: 126 HLYG--ATLHPKTWTGDRNGPVQALAQELLAEGKRPFVVPYGVSDALGAVGYSSAIAEIA 183 Query: 176 TQSEVKF---DSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIK 232 QS S+V GSG T AGL++G D + VGI + E + + Sbjct: 184 AQSAQNGFTPTSVVHCTGSGATQAGLAMGAQSALPDCKIVGIDIDAEPERVKGDVIEYAI 243 Query: 233 EAAELLGVKVEVR--PELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGL 290 A LLG+ + + ++ YG ++ G E + LDPVY+ K GL Sbjct: 244 GGAALLGIPFDASQIEVIAGHAGPAYGIPNDATIHALQIAGRFEALTLDPVYSAKGMAGL 303 Query: 291 VDLARKG--ELGEKILFIHTGGISGTFHYGDKL 321 + L R G + + ++F++TGG F Y D L Sbjct: 304 IALIRTGHWKNDDNVIFLNTGGTPSLFAYADAL 336 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: 287 Number of extensions: 20 Number of successful extensions: 6 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: 344 Length adjustment: 28 Effective length of query: 297 Effective length of database: 316 Effective search space: 93852 Effective search space used: 93852 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