Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate CA265_RS13740 CA265_RS13740 cysteine synthase
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__Pedo557:CA265_RS13740 Length = 348 Score = 186 bits (471), Expect = 9e-52 Identities = 111/301 (36%), Positives = 168/301 (55%), Gaps = 7/301 (2%) Query: 4 QHVQELIGHTPLMALPIEVPNH-SHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAK 62 +H+ L+G+TP++ L IY K E +N GSIKDR+ Y ++ G++ A Sbjct: 18 EHLSLLVGNTPMLELTYTYQGSLGKIYVKCEHYNLTGSIKDRMALYTLKKAYAEGKIKAG 77 Query: 63 TTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEE-GIK 121 I+E T+GNTGI A +A +++P S E+ ++++LGAEI+ EE G Sbjct: 78 DRIVEATSGNTGIAFAAIGKALGHPVTIIMPNWLSKERMDIIKSLGAEIILVSKEEGGFI 137 Query: 122 GAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADM---PAPITAFVAGAGSG 178 G+I+ AE +AA+ N ++P QF+N ANP A+ HT EI + AFVAG G+G Sbjct: 138 GSIKLAEKMAASDPNIFLPKQFENIANPEAHEHTTGKEIWEQLRLKNLSPDAFVAGVGTG 197 Query: 179 GTFAGVAAYLQAQDSATKAVVVEPEGS--ILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQ 236 GT GV +L+ Q++ K +EP S + G +HR +GI EFIP +D+ Sbjct: 198 GTIMGVGNFLRKQNADIKIHPLEPAESPTLTTGYKVGSHRIQGISDEFIPEIVKLNELDE 257 Query: 237 TLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSHIVTIFPDSSERYL 296 L + D DA + LA GL +G SSGA + +++ + A+S +VTIF DS+++YL Sbjct: 258 VLQVNDGDAILMAQKLAEKLGLAVGISSGANVIGAIKQQQKMGADSCVVTIFSDSNKKYL 317 Query: 297 S 297 S Sbjct: 318 S 318 Lambda K H 0.317 0.133 0.378 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: 276 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: 303 Length of database: 348 Length adjustment: 28 Effective length of query: 275 Effective length of database: 320 Effective search space: 88000 Effective search space used: 88000 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: 48 (23.1 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