Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_012404689.1 BPHY_RS27245 serine dehydratase
Query= BRENDA::P20132 (328 letters) >NCBI__GCF_000020045.1:WP_012404689.1 Length = 306 Score = 256 bits (655), Expect = 4e-73 Identities = 145/307 (47%), Positives = 190/307 (61%), Gaps = 11/307 (3%) Query: 7 LHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAG 66 LH+ TP+ +S LS G V LKMD+ Q GSFKIRGIG+ C++ A G FV SS G Sbjct: 3 LHIDTPLLESQPLSHALGRRVLLKMDALQAPGSFKIRGIGYACEQHANHGKRRFVSSSGG 62 Query: 67 NAGMAAAYAARQLGVPATIVVPSTTPALTIERLKNEGATVKVVGELLDEAFELAKALAKN 126 NAG+A AYA R L + T+VVP +T + ++ +GA + V G EA A AL + Sbjct: 63 NAGIAVAYAGRALSIAVTVVVPQSTGERAKDLIRLQGADLIVHGATWQEAN--AFALEQV 120 Query: 127 NPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQEVGWG 186 P YI PFDDPL+W GHAS++ E+ K A+ LSVGGGGL+ G ++GL+ G G Sbjct: 121 GPDDAYIHPFDDPLLWHGHASMIDEVARA-GAKFDAVVLSVGGGGLMAGAIEGLRRNGLG 179 Query: 187 DVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGAQALKLFQEHPIFSEVI 246 +VPVIA+ET GA S + AGK + LP ITSVA +LG K V QA L Q HP+ V+ Sbjct: 180 NVPVIAVETEGASSLAQSVRAGKRIELPGITSVATSLGAKQVCKQAFTLTQTHPVECVVV 239 Query: 247 SDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGS 306 SD EAV+A +FVDD ++LVEPACGA+LA Y + + S++VIVCGG+ Sbjct: 240 SDAEAVSASRRFVDDHRVLVEPACGASLALAYGQAPALQRFD--------SVLVIVCGGA 291 Query: 307 NISLAQL 313 ++ QL Sbjct: 292 GTTIEQL 298 Lambda K H 0.318 0.134 0.395 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: 228 Number of extensions: 8 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: 328 Length of database: 306 Length adjustment: 27 Effective length of query: 301 Effective length of database: 279 Effective search space: 83979 Effective search space used: 83979 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: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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