Align Cysteine synthase; CSase; EC 2.5.1.47; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase (uncharacterized)
to candidate 17824 b3772 threonine dehydratase (NCBI)
Query= curated2:Q59447 (307 letters) >FitnessBrowser__Keio:17824 Length = 514 Score = 83.2 bits (204), Expect = 1e-20 Identities = 89/262 (33%), Positives = 123/262 (46%), Gaps = 34/262 (12%) Query: 13 TPVVKINNLFNS-DHEIWIKLEKSNPGGSIKDRIALAMI----EDAEAKGLLNKDSTIIE 67 TP+ K+ L + D+ I +K E P S K R A AM+ E+ +A G +I Sbjct: 32 TPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHG-------VIT 84 Query: 68 PTSGNTGIGLALVAAVKGYKLILVMPESMSIERRKIMEAYGAEFVLTPREKGMKGAIEKA 127 ++GN G+A +A G K ++VMP + + + + +G E +L A KA Sbjct: 85 ASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLL--HGANFDEAKAKA 142 Query: 128 NELAEETPNSWIPRQFDNPANVKIHVETTAQEILQDFPEGLDYVITGVGTGGHITGIAKA 187 EL+++ +W+P FD+P V T A E+LQ LD V VG GG G+A Sbjct: 143 IELSQQQGFTWVP-PFDHPM-VIAGQGTLALELLQQDAH-LDRVFVPVGGGGLAAGVAVL 199 Query: 188 LKEKYPNLKVIAVEPE----LSPVLSGGSPAPHPLQGLGAG--FVPSILDITL------L 235 +K+ P +KVIAVE E L L G P P GL A V I D T L Sbjct: 200 IKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYL 259 Query: 236 DGVITVGKDEAYEYAINAAKKE 257 D +ITV D AI AA K+ Sbjct: 260 DDIITVDSD-----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: 313 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