Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_011307392.1 MBAR_RS12885 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_000195895.1:WP_011307392.1 Length = 457 Score = 253 bits (645), Expect = 1e-71 Identities = 155/417 (37%), Positives = 220/417 (52%), Gaps = 43/417 (10%) Query: 5 TLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAGQHT--------GYEYSRTANPTRTALE 56 TL +H G D TGA SVPIYQ + Y A + G Y+R NPT E Sbjct: 42 TLAVHAGAKPDPATGARSVPIYQTAAYVFKDAEEAADLFGLRKEGNIYTRLMNPTTDVFE 101 Query: 57 ALVTELESGEAGYAFSSGMAAITAVMMLFNS-GDHVVLTDDVYGGTYRVMTKVLNRLGIE 115 + LE G A +SGMAAIT ++ F GD ++ D +YGGTY + +LG Sbjct: 102 KRIAALEGGIGALAVASGMAAITTALLTFTRPGDEIISGDKLYGGTYELFNYTFPKLGRT 161 Query: 116 STFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNT 175 FVD EE + AI TKAIY+E+ NP L I D +A+IA AG+ +VDNT + Sbjct: 162 VKFVDVGKPEEFKNAISEKTKAIYVESIGNPGLDIPDFEKLAEIAHGAGIPFVVDNTV-S 220 Query: 176 PYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTAS----------------------- 212 P +P+ G DIV++SATK++GGH +GG++V + Sbjct: 221 PLILRPIDHGVDIVVYSATKFIGGHGTSIGGVIVDSGNFYWKPEKFPEICEPDPGYHGLK 280 Query: 213 -KELGEELHFVQNS-------TGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLE 264 KE + F+ + TG + P +S+L G++TL LRM+ NA +IA FLE Sbjct: 281 YKEAFGKAAFIAKARVQFIRDTGACISPFNSFLFTLGLETLPLRMKKHCDNALEIAKFLE 340 Query: 265 NHPAVQTLYYPGSSNHPGHELAKTQ-GAGFGGMISFDI-GSEERVDAFLGNLKLFTIAES 322 HP V + YPG +H +ELAK +G+G +I F I G F+ L++F+ + Sbjct: 341 KHPKVSWVSYPGLESHCSYELAKKYLKSGYGALIGFGIKGGARECKKFIEGLEIFSHLAN 400 Query: 323 LGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQALENI 379 +G +SL+ PA TH + +E +L G+T+ IR+S+GIEDA+DL+ DI QAL + Sbjct: 401 IGDAKSLVIHPASTTHEQLSKEEQLACGVTEDFIRLSIGIEDAKDLISDIKQALSEV 457 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: 454 Number of extensions: 25 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: 457 Length adjustment: 31 Effective length of query: 348 Effective length of database: 426 Effective search space: 148248 Effective search space used: 148248 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 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