Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate WP_057687361.1 ABB28_RS15950 cysteine synthase A
Query= BRENDA::Q2V0C9 (504 letters) >NCBI__GCF_001431535.1:WP_057687361.1 Length = 319 Score = 218 bits (556), Expect = 2e-61 Identities = 125/304 (41%), Positives = 180/304 (59%), Gaps = 12/304 (3%) Query: 39 ILTAIGQTPLIKLNNIPKSYGIKCEIYAKCEFLNPGGSVKDRIAYRMIQDAEDKGLLKPG 98 IL IG TP++KL+ + ++ +YAK E NPGGSVKDR+A ++ DAE +GLLKPG Sbjct: 7 ILDTIGNTPIVKLHRLAPAH---VTLYAKVESFNPGGSVKDRLALAIVLDAEQRGLLKPG 63 Query: 99 CTIIEPTSGNTGIGLAMAAAVRGYKCIIVMPEKMSDEKISTLYALGAKIIRTPTEASWHS 158 TIIE TSGNTG+ LAM AA RGYK + M E S E+ + A GAK+I TP Sbjct: 64 DTIIEATSGNTGVALAMVAAARGYKFVATMVETFSIERRKLMRAYGAKVILTPAA---ER 120 Query: 159 PEAHISVAQKLQKEIPNSIILDQYTNPGNPLAHYDQTAIEIWKQCEG-KIDYLVAGAGTG 217 + A +L +E + Q+ NP NP H TA EI + G ++DY V+G GTG Sbjct: 121 GSGMVRRAAELAQE-HGWFLASQFANPANPAYHRSTTAAEILRDFAGRRLDYFVSGWGTG 179 Query: 218 GTISGIGRKLKELSPNIKIIAVDPKGSILDPSSDSQNEVGFYEVEGIGYDFIPTVLDRNV 277 GT++G+G LK P +I+A +P G+ L D + ++++G DF+P VL+RNV Sbjct: 180 GTLTGVGEVLKVARPQTRIVATEPAGAALLKGDDWKP----HKIQGWTPDFVPDVLNRNV 235 Query: 278 IDKWIKTEDNESLNAARMLIRQEGLLCGGSSGAALIAALKIAKDIPEEKRMVIILPDGIR 337 +D+ + ED+ +++ AR L +EGL G S+GA L +AL +A+ ++ +LPD Sbjct: 236 VDELLTVEDDRAISTARRLAAEEGLFVGISAGATLASALDVAERAEPGSVILAMLPDTGE 295 Query: 338 NYLT 341 Y + Sbjct: 296 RYFS 299 Lambda K H 0.318 0.135 0.404 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: 319 Number of extensions: 18 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: 504 Length of database: 319 Length adjustment: 31 Effective length of query: 473 Effective length of database: 288 Effective search space: 136224 Effective search space used: 136224 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 (21.7 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