Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_041099653.1 SUTH_RS12460 bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_000828635.1:WP_041099653.1 Length = 423 Score = 238 bits (606), Expect = 3e-67 Identities = 149/421 (35%), Positives = 217/421 (51%), Gaps = 46/421 (10%) Query: 1 MKKKTLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAGQH---------TGYEYSRTANPT 51 MK +T+ +HGG + D T AV+VPIYQ ++Y QH G Y+R NPT Sbjct: 1 MKIETIAVHGGYSPDPTTKAVAVPIYQTTSYAFDDT-QHGADLFDLKVAGNIYTRIMNPT 59 Query: 52 RTALEALVTELESGEAGYAFSSGMAAIT-AVMMLFNSGDHVVLTDDVYGGTYRVMTKVLN 110 LE + ELE G +SGMAAIT A+ + +GD++V +YGGTY + L Sbjct: 60 TDVLEKRMAELEGGIGALGVASGMAAITYAIQTIAEAGDNIVSVGTLYGGTYNLFAHTLP 119 Query: 111 RLGIESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVD 170 + GIE F D + E I TKA++ E+ NPL + DL +A IA AGV LIVD Sbjct: 120 QYGIEVRFADYRNPESFRPLIDGRTKALFCESIGNPLGNVVDLAALAKIAHDAGVPLIVD 179 Query: 171 NTFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASK----------------- 213 NT +PY +P GADIV+H+ TKYLGGH + +GG++V + K Sbjct: 180 NTVPSPYLCRPFEHGADIVVHALTKYLGGHGNSIGGVIVDSGKFPWAEHKERFKRLNTPD 239 Query: 214 ----------------ELGEELHFVQNSTGGVLGPQDSWLLMRGIKTLGLRMEAIDQNAR 257 +G +TG + P +S+L+++GI+TL LRM+ I N Sbjct: 240 VSYHGVVYTEALGPAAFIGRARVVPLRNTGAAISPFNSFLILQGIETLALRMDRICDNTL 299 Query: 258 KIASFLENHPAVQTLYYPGSSNHPGHEL-AKTQGAGFGGMISFDI-GSEERVDAFLGNLK 315 +A++L+ H V+ + Y G +H H L K G G++SF + G F LK Sbjct: 300 AVANYLKGHAKVKWVNYAGLPDHADHALIRKYMGGRASGILSFGVAGGMAGGGRFQDALK 359 Query: 316 LFTIAESLGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQA 375 L T ++G +SL PA TH + E + G+++ ++R+S+GIE +D+ D+ QA Sbjct: 360 LVTRLVNIGDAKSLACHPASTTHRQLSAEEMKKAGVSEDMVRLSIGIEHIDDIKADLEQA 419 Query: 376 L 376 L Sbjct: 420 L 420 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: 463 Number of extensions: 30 Number of successful extensions: 5 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: 423 Length adjustment: 31 Effective length of query: 348 Effective length of database: 392 Effective search space: 136416 Effective search space used: 136416 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