Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_011384252.1 AMB_RS09340 CBS domain-containing protein
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_000009985.1:WP_011384252.1 Length = 455 Score = 157 bits (396), Expect = 6e-43 Identities = 98/309 (31%), Positives = 162/309 (52%), Gaps = 19/309 (6%) Query: 1 MIYD-NILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGK 59 M YD ++L IGNTPL+ + +L+ P +++ KLE NP+GS+KDR AL M+ AE +G Sbjct: 1 MPYDADLLCQIGNTPLIELTNLDTAP-CRLFVKLESRNPSGSIKDRAALSMVRAAERDGL 59 Query: 60 LHPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIIL--TDK 117 L PG ++EAT+GNTG+ LA++ +GY + +V+ + +++ ++A GAE++L +D Sbjct: 60 LRPGGHLVEATAGNTGLALALLAAHRGYRLTLVIPDKAGLDKVSHLRAMGAEVVLARSDV 119 Query: 118 KLGTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAV 177 + VA + G +F +QF+N N AH T E+W Q G V VA Sbjct: 120 PRRHPEHYQNVASRLAGETGAHF-IDQFNNPANPAAHEDGTGPELWEQMGGRVDAVVAGA 178 Query: 178 GTSGTLMGVGKNLREKNPEIKIIEAQP---------TKGHYIQGLKSMEEAI----VPAI 224 G+ GTL G+ + ++P +++ A P G + + E I +P + Sbjct: 179 GSGGTLTGLSRFFARRSPATEMVLADPRGSVLADYVRTGRVGEAGSWLVEGIGGDSIPMV 238 Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA-EKIDSGVIVVLF 283 ++ + E+FA AR ++ EG+ +G SSG + AA + E+ + L Sbjct: 239 SDFSRVTRAYSVSDRESFATARLVLRIEGLLVGSSSGTLLAAALRYCREQTAPKRVATLV 298 Query: 284 ADRGEKYLS 292 D G ++LS Sbjct: 299 CDAGNRHLS 307 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: 320 Number of extensions: 15 Number of successful extensions: 4 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: 455 Length adjustment: 30 Effective length of query: 269 Effective length of database: 425 Effective search space: 114325 Effective search space used: 114325 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 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