Align L-serine dehydratase, beta chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate CA265_RS21785 CA265_RS21785 L-serine ammonia-lyase
Query= uniprot:P33074 (222 letters) >FitnessBrowser__Pedo557:CA265_RS21785 Length = 475 Score = 55.5 bits (132), Expect = 2e-12 Identities = 46/148 (31%), Positives = 70/148 (47%), Gaps = 23/148 (15%) Query: 5 SAFEVMGPIMVGPSSSHTAGACKIANVATSIVSNNY-----NQVEFQLHGSFAHTFKGHG 59 S F++ I +GPSSSHT G + A T+ ++ N+ ++ L+GS A T KGHG Sbjct: 7 SVFDIF-KIGIGPSSSHTLGPWRAAQQFTASLAQNHLIDEIEGIKILLYGSLAKTGKGHG 65 Query: 60 TDRALVGGILGFEP---DDDRIKTSFE---------LAKQAGLNYIFTTTNL-----GDN 102 TD A++ G+ G +P D D + +FE LA +++ + L Sbjct: 66 TDVAILLGLTGADPVTFDVDAVTPTFESIQRDQKLNLAGHLIIDFDYDNDLLFLFAESLP 125 Query: 103 YHPNSVKIVFSYPNGEEEYVIGSSIGGG 130 +HPN+V G+ SIGGG Sbjct: 126 FHPNAVTFQAFLKGGKAFSETYYSIGGG 153 Lambda K H 0.314 0.133 0.373 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: 204 Number of extensions: 8 Number of successful extensions: 2 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: 222 Length of database: 475 Length adjustment: 28 Effective length of query: 194 Effective length of database: 447 Effective search space: 86718 Effective search space used: 86718 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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