Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_084276347.1 B8779_RS08955 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_900176045.1:WP_084276347.1 Length = 396 Score = 167 bits (423), Expect = 5e-46 Identities = 125/395 (31%), Positives = 193/395 (48%), Gaps = 49/395 (12%) Query: 17 KTGAVSVPIYQVS--TYKQPK------AGQHTGYEYSRTANPTRTALEALVTELESGEAG 68 K GA+S PI + +Y PK AG+ Y+R NPT LE L+ ++ G+ Sbjct: 18 KDGAISPPIIGSAAFSYGDPKSAEAVFAGESRKPLYARMGNPTNAKLETLLAGIDQGDGA 77 Query: 69 YAFSSGMAAITAVMMLF-NSGDHVVLTDDVYGGTYRVMTKVLNRLGIESTFVDTSSREEV 127 SSGM AI AV+ F SGD +V ++GGTY T+ L R GI+ F + + Sbjct: 78 VVTSSGMGAIAAVVSAFLQSGDEIVCVGGLFGGTYAFFTQNLPRFGIKVRFF----KADE 133 Query: 128 EKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNTPYFQQPLTLGAD 187 E + P TK I+ E+ NP L + + + +A+K G+L +VDNT TP +P + GAD Sbjct: 134 EVVLSPQTKMIFCESVGNPSLTVVNFVKLGKLAQKHGILFVVDNTI-TPLLFEPFSWGAD 192 Query: 188 IVLHSATKYLGGHSDVVGGLVV--TASKELGEELHFVQN--------------------S 225 I+++S TK + G S +GG ++ K+L F+QN Sbjct: 193 IIVYSTTKVISGQSQALGGAIIYKEPRKDLFIHFPFLQNFYENLGKDAIMGVIKKRALRD 252 Query: 226 TGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHEL 285 G + ++L + G++TL LR++ NA+K+ FL V+ LY P Sbjct: 253 FGMSMQAHAAYLTILGLETLPLRIQKATDNAQKL--FLALKDKVKVLYAKNEQYFP---- 306 Query: 286 AKTQGAGFGGMISFDIGSEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRER 345 G G M+ D S+E FL + K+ I ++G +L ++ R T + Sbjct: 307 -----FGTGQMMGIDFKSKEDAFTFLEHAKIPFITANIGDSRTL-ALHMRSTIYRDFKAN 360 Query: 346 RLE-LGITDGLIRISVGIEDAEDLLEDIGQALENI 379 LE LG+++GL+RISVG+E+ ++ED AL + Sbjct: 361 ELEYLGVSEGLVRISVGLENCAMIIEDFENALRKV 395 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: 348 Number of extensions: 21 Number of successful extensions: 5 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: 379 Length of database: 396 Length adjustment: 30 Effective length of query: 349 Effective length of database: 366 Effective search space: 127734 Effective search space used: 127734 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