Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Synpcc7942_1466 Synpcc7942_1466 cysteine synthase
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__SynE:Synpcc7942_1466 Length = 334 Score = 227 bits (578), Expect = 3e-64 Identities = 127/307 (41%), Positives = 189/307 (61%), Gaps = 8/307 (2%) Query: 2 LIQHVQELIGHTPLMAL---PIEVPNHSHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGR 58 + Q++ ELIG TPL+ L P+ + I KLE FNP S+KDR+G +I + ++G Sbjct: 17 IAQNITELIGRTPLVQLNRIPVADGCLARIVVKLESFNPSASVKDRIGISMILEAERKGL 76 Query: 59 VNA-KTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSE 117 + +TT++EPT+GNTGI LA+A A R IL +P+ S E++ +++A GA + TP Sbjct: 77 IAPDRTTLVEPTSGNTGIALAMAAAARGYRLILTMPDTMSSERRAMLRAYGATLELTPGI 136 Query: 118 EGIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGS 177 EG+ G I++A+ + A+ +Y+ QFKNPANP + T A EI AD + ++G G+ Sbjct: 137 EGMAGCIQRAQEIVASHPEAYMLQQFKNPANPKIHRETTAEEIWADTDGTVDILISGVGT 196 Query: 178 GGTFAGVAAYLQAQDSATKAVVVEPEGS-ILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQ 236 GGT GVA L+ + + +A VEP S +L+GG H+ +GIG F+P ID+ Sbjct: 197 GGTITGVAEVLKERKPSFQAFAVEPANSPVLSGGRPGPHKIQGIGAGFVPEVLATQLIDE 256 Query: 237 TLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSH--IVTIFPDSSER 294 +T++D++A A R LAR+ GLL G SSGAA+AA++Q+A P N+ IV I P ER Sbjct: 257 VVTVSDDEAIAYGRRLAREEGLLSGISSGAAVAAAVQVARR-PENTDKLIVVILPSFGER 315 Query: 295 YLSQKIY 301 YLS ++ Sbjct: 316 YLSTPLF 322 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: 269 Number of extensions: 21 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: 334 Length adjustment: 27 Effective length of query: 276 Effective length of database: 307 Effective search space: 84732 Effective search space used: 84732 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