Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_011384943.1 AMB_RS12895 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_000009985.1:WP_011384943.1 Length = 430 Score = 219 bits (559), Expect = 9e-62 Identities = 142/424 (33%), Positives = 220/424 (51%), Gaps = 54/424 (12%) Query: 4 KTLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAGQHT---------GYEYSRTANPTRTA 54 +T+++H G D TG+V+VP+YQ ++Y Q + +H G Y+R NPT Sbjct: 9 ETIVLHAGYRADPATGSVAVPVYQTTSY-QFRDSEHAANLFALKELGNIYTRLMNPTTDV 67 Query: 55 LEALVTELESGEAGYAFSSGMAAIT-AVMMLFNSGDHVVLTDDVYGGTYRVMTKVLNRLG 113 LE + LE G A A +SG AA T A++ L +GD+ V + D+YGGT+ + +LG Sbjct: 68 LEQRLAALEGGVAALAVASGQAASTFAILNLAQAGDNFVTSTDLYGGTWNLFANTFKQLG 127 Query: 114 IESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTF 173 IE+ FVD + E +A T+A Y ET NP L++ + +A +A + GV LIVDNT Sbjct: 128 IEARFVDPADPEAFVRATDDKTRAWYAETLPNPKLQVFPIAEVAKLANQVGVPLIVDNT- 186 Query: 174 NTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVV------------------------ 209 +P +PL+LGA IV++S TKY+GGH +GG +V Sbjct: 187 ASPVIAKPLSLGAHIVVYSCTKYIGGHGTSIGGAIVDGGTFDWEKHAKRFPLLNEPDPSY 246 Query: 210 ------TASKELGEELHFVQ------NSTGGVLGPQDSWLLMRGIKTLGLRMEAIDQNAR 257 A K LG + ++ G + P +++ +++G++TL LRM +NA Sbjct: 247 HGAVWTQAVKPLGPIAYIIRARVTLLRDIGAAISPFNAFQVLQGMETLPLRMREHCRNAS 306 Query: 258 KIASFLENHPAVQTLYYPGSSNHPGHELAKTQGA---GFGGMISFDI-GSEERVDAFLGN 313 +A FL H V + +P S G + A G+GG++ F++ G E F+ Sbjct: 307 AVAQFLAGHHKVAHVIHP--SLQDGEYRRRADAALKGGYGGLLGFELKGGAEAGRRFIDA 364 Query: 314 LKLFTIAESLGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIG 373 LKL ++G SL PA TH+ + + +L G+T G +R+S+GIE +D+L D+ Sbjct: 365 LKLLYHVANIGDARSLAIHPASTTHSQLSADDQLASGVTPGYVRLSIGIEHIDDILADLK 424 Query: 374 QALE 377 QAL+ Sbjct: 425 QALD 428 Lambda K H 0.316 0.134 0.375 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: 446 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 379 Length of database: 430 Length adjustment: 31 Effective length of query: 348 Effective length of database: 399 Effective search space: 138852 Effective search space used: 138852 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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