Align Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011372397.1 SUDEN_RS04000 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P53780 (464 letters) >NCBI__GCF_000012965.1:WP_011372397.1 Length = 421 Score = 200 bits (508), Expect = 9e-56 Identities = 126/407 (30%), Positives = 208/407 (51%), Gaps = 46/407 (11%) Query: 99 DPFDAMSTPLYQTATFKQPS--------AIENGPYDYTRSGNPTRDALESLLAKLDKADR 150 D M+ P+YQT ++ S +++ YTR NPT D E A L+ + Sbjct: 15 DSQGTMAVPIYQTTAYEFNSVEHAADLFSLKQLGNIYTRLNNPTTDVFEKRFASLEGGEA 74 Query: 151 AFCFTSGMAA-LSAVTHLIKNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTKLDE 209 A +SGM+A A+ + GE IV +YGGS L + + R G+ + + + Sbjct: 75 ALATSSGMSATFFAIVNATAAGENIVCAKQLYGGSLTLNTHTLKRFGIEARYFDVHDMSS 134 Query: 210 VAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGA 269 + + I +T++++ ES TNP ++DI I+++A G L +VDN++ +PVL RP E GA Sbjct: 135 LESLIDDKTRVIFFESLTNPSIDVADIEAITKIADKYGILSVVDNTVATPVLCRPFEFGA 194 Query: 270 DIVMHSATKFIAGHSDVMAGVLAVKG---EKLAKEVYF---------------------- 304 DIV+HSA+K+ G + G+L + EKL + Sbjct: 195 DIVVHSASKYTTGQGLAIGGILVERKNLVEKLRSNPRYEHFNNPDPSYHGLIYVNIGLPP 254 Query: 305 --------LQNSEGSGLAPFDCWLCLRGIKTMALRIEKQQENARKIAMYLSSHPRVKKVY 356 L G+ L+PF+ WL ++GI+T++LR+++ +NA +A +L SHP+VKKV Sbjct: 255 FTLRARLSLSRDLGAVLSPFNSWLFIQGIETLSLRMKEHSKNALALAEFLESHPKVKKVN 314 Query: 357 YAGLPDHPGH---HLHFSQAKGAGSVFSFITGSVALSKHLVETTKYFSIAVSFGSVKSLI 413 Y GL + + +F + +G + SF S+ + +V+ TK +S+ V+ G KS+I Sbjct: 315 YPGLKSNANYKNAQKYFDGGECSG-LLSFEVASLQEATKIVDATKLYSLVVNIGDSKSII 373 Query: 414 SMPCFMSHASIPAEVREARGLTEDLVRISAGIEDVDDLISDLDIAFK 460 + P +H + + A G+ L+RIS G+E + DLI D+ A + Sbjct: 374 THPASTTHQQLNEQELIACGVPSGLIRISCGLESIKDLIDDMKQALE 420 Lambda K H 0.316 0.130 0.369 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: 405 Number of extensions: 14 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: 464 Length of database: 421 Length adjustment: 32 Effective length of query: 432 Effective length of database: 389 Effective search space: 168048 Effective search space used: 168048 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 (21.6 bits) S2: 51 (24.3 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