Align Cysteine synthase; CSase; EC 2.5.1.47; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase (uncharacterized)
to candidate BWI76_RS00980 BWI76_RS00980 PLP-dependent threonine dehydratase
Query= curated2:Q59447 (307 letters) >FitnessBrowser__Koxy:BWI76_RS00980 Length = 514 Score = 83.2 bits (204), Expect = 1e-20 Identities = 85/258 (32%), Positives = 120/258 (46%), Gaps = 26/258 (10%) Query: 13 TPVVKINNLFNS-DHEIWIKLEKSNPGGSIKDRIALAMIEDAEAKGLLNKDSTIIEPTSG 71 TP+ K+ L + D+ + +K E P S K R A AM+ + K +I ++G Sbjct: 32 TPLQKMEKLSSRLDNVVLVKREDRQPVHSFKLRGAYAMMAGLTEE---QKSHGVITASAG 88 Query: 72 NTGIGLALVAAVKGYKLILVMPESMSIERRKIMEAYGAEFVLTPREKGMKGAIEKANELA 131 N G+A A+ G K ++VMP + + + + +G E +L A KA ELA Sbjct: 89 NHAQGVAFSASRLGVKALIVMPTATADIKVDAVRGFGGEVLL--HGANFDEAKAKAIELA 146 Query: 132 EETPNSWIPRQFDNPANVKIHVETTAQEILQDFPEGLDYVITGVGTGGHITGIAKALKEK 191 ++ +W+P FD+P V T A E+LQ +D V VG GG G+A +K+ Sbjct: 147 QQQGFTWVP-PFDHPM-VIAGQGTLALELLQQDAH-IDRVFVPVGGGGLAAGVAVLIKQL 203 Query: 192 YPNLKVIAVEPE----LSPVLSGGSPAPHPLQGLGAG--FVPSILDITL------LDGVI 239 P +KVIAVE E L L G P P GL A V I D T LD ++ Sbjct: 204 MPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIV 263 Query: 240 TVGKDEAYEYAINAAKKE 257 TV D AI AA K+ Sbjct: 264 TVDSD-----AICAAMKD 276 Lambda K H 0.315 0.135 0.386 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: 309 Number of extensions: 12 Number of successful extensions: 2 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: 307 Length of database: 514 Length adjustment: 31 Effective length of query: 276 Effective length of database: 483 Effective search space: 133308 Effective search space used: 133308 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: 50 (23.9 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