Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Synpcc7942_B2623 Synpcc7942_B2623 cysteine synthase A
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__SynE:Synpcc7942_B2623 Length = 329 Score = 219 bits (559), Expect = 5e-62 Identities = 124/304 (40%), Positives = 179/304 (58%), Gaps = 5/304 (1%) Query: 2 LIQHVQELIGHTPLMALPIEVPNH---SHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGR 58 ++ + E IG+TPL+ L + + + KLE NP GS+KDR LI+ +G Sbjct: 4 ILNRLTEWIGNTPLVRLQETAQQYGAIAEVLLKLEYLNPLGSVKDRTALSLIQSARSQGL 63 Query: 59 VNAKTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEE 118 + A TT+IEPT GNTGIGLA A A LR ILV+P++ S E+ L + LGA++V TP+ E Sbjct: 64 ITAGTTLIEPTTGNTGIGLAFAAAAEQLRLILVMPDRVSAERIRLAKLLGAKVVLTPAAE 123 Query: 119 GIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSG 178 + G I KA+AL I +S + QF+NPANP+ + T PEI D + VAG G+G Sbjct: 124 AMLGCIAKAQALQQQIPDSVILQQFQNPANPSIHQATTGPEIWRDTDGEVDIVVAGVGTG 183 Query: 179 GTFAGVAAYLQAQDSATKAVVVEPEGS-ILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQT 237 GT G++ YL+ +++ V+P S +L+GG A +H+ G+G F+ P D+ ID+ Sbjct: 184 GTLMGISRYLKPLRPRLQSIAVQPARSPVLSGGAAGSHQLTGMGPNFVSPLVDRSLIDEI 243 Query: 238 LTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLP-ANSHIVTIFPDSSERYL 296 L+ + DA A +R A G+ +G SSGA + A+LQ+A A IV + P SERYL Sbjct: 244 LSAYEEDAIAVIRTCAAREGIPLGVSSGAIVWAALQVAKRPENAGKRIVAVCPSGSERYL 303 Query: 297 SQKI 300 S + Sbjct: 304 SSTL 307 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: 244 Number of extensions: 12 Number of successful extensions: 3 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: 329 Length adjustment: 27 Effective length of query: 276 Effective length of database: 302 Effective search space: 83352 Effective search space used: 83352 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