Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_057508382.1 ABB28_RS09420 cystathionine beta-synthase
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_001431535.1:WP_057508382.1 Length = 456 Score = 171 bits (434), Expect = 2e-47 Identities = 109/309 (35%), Positives = 169/309 (54%), Gaps = 20/309 (6%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 I+ ++L+ IG TP+V+ L+ +++ KLE NP GS+KDRI L MIE AE G L Sbjct: 3 IHASVLDLIGQTPIVKAQRLDTGV-CELFLKLESANPGGSIKDRIGLSMIEAAEKRGDLK 61 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILT--DKKL 119 PG+T++E T+GNTG+GLA++ + KGY +++V+ + +S E+ +KA GAE+ LT D Sbjct: 62 PGATLVEGTAGNTGLGLALVAQQKGYKLVLVVPDKMSREKIFNLKAMGAEVRLTRSDVAK 121 Query: 120 GTDGAIRKVAELVKEN-PGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVG 178 G + +A+ + + PG YF NQF N N AH T EI Q G + V G Sbjct: 122 GHPEYYQDLAKTIADQIPGAYF-INQFGNPDNPAAHEFGTGPEILEQMGGDLDAIVFGCG 180 Query: 179 TSGTLMGVGKNLREKNPEIKIIEAQPT---KGHYIQG-----------LKSMEEAIVPAI 224 +SGT+ G+ + +P+ +++ A P YI ++ + E +P+I Sbjct: 181 SSGTMTGLSRAFSTLSPKTELVLADPVGSILAEYINDGVLNDKSGSWLVEGIGEDFLPSI 240 Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA-EKIDSGVIVVLF 283 ++ + I E+F ARE++ +EGI G S+G + AA K E+ ++VL Sbjct: 241 SDFSRVKKAYAITDAESFHTARELLGKEGILGGSSTGTLLAAALKYCKEQTTPKKVLVLV 300 Query: 284 ADRGEKYLS 292 D G KYLS Sbjct: 301 CDTGNKYLS 309 Lambda K H 0.315 0.133 0.367 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: 385 Number of extensions: 24 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: 299 Length of database: 456 Length adjustment: 30 Effective length of query: 269 Effective length of database: 426 Effective search space: 114594 Effective search space used: 114594 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: 42 (22.0 bits) S2: 49 (23.5 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