Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_028316922.1 G491_RS0128270 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q96GA7 (329 letters) >NCBI__GCF_000429905.1:WP_028316922.1 Length = 309 Score = 274 bits (700), Expect = 2e-78 Identities = 150/315 (47%), Positives = 197/315 (62%), Gaps = 9/315 (2%) Query: 13 PFHVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQEMAKKGCRHLVCSSG 72 P H+ TPLLE L + G + LK E +QP GSFKIRG+G+ CQ+ ++G HL+ SS Sbjct: 3 PIHIHTPLLEHRLLGEAIGRKILLKMECLQPPGSFKIRGVGYLCQKAVERGVTHLISSSA 62 Query: 73 GNAGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLTGKVWDEANLRAQELAK 132 GNAG A AYA RKLG+ T+V PES+S + + +Q E AE+ + G+ WD+A++RAQE Sbjct: 63 GNAGYATAYAGRKLGVKVTVVAPESSSPRARELIQSEKAELIIHGQAWDDAHVRAQECLL 122 Query: 133 RDGWENVPPFDHPLIWKGHASLVQELKAVLRTPPGALVLAVGGGGLLAGVVAGLLEVGWQ 192 + VPPFDHP +W GH+SLV EL A P A+VL+VGGGGLL GV+ G+ GW+ Sbjct: 123 DEKCAYVPPFDHPDLWTGHSSLVDEL-AEQCGKPDAVVLSVGGGGLLCGVLEGMERHGWK 181 Query: 193 HVPIIAMETHGAHCFNAAITAGKLVTLPDITSVAKSLGAKTVAARALECMQVCKIHSEVV 252 VP+IA ET GA F ++ G LV L ITS+A+SLGAKT + AL+ ++ VV Sbjct: 182 DVPVIAAETRGADSFAQSVAQGSLVHLDAITSIAQSLGAKTASQAALDWTFRHEVRPAVV 241 Query: 253 EDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRRLQAEGCLPPSLTSVVVIVCGGN 312 D +AV A +D ++LVEPACGA+LAA Y LR LQ +VVVIVCGG Sbjct: 242 SDKDAVKACLAFAEDRKVLVEPACGASLAAAYDN-LRELQ-------DAKTVVVIVCGGI 293 Query: 313 NINSRELQALKTHLG 327 + + A K G Sbjct: 294 GVTLNRMWAWKKEFG 308 Lambda K H 0.319 0.134 0.404 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: 11 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: 329 Length of database: 309 Length adjustment: 28 Effective length of query: 301 Effective length of database: 281 Effective search space: 84581 Effective search space used: 84581 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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