Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Pf1N1B4_3374 Cysteine synthase (EC 2.5.1.47)
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374 Length = 324 Score = 205 bits (522), Expect = 1e-57 Identities = 123/306 (40%), Positives = 177/306 (57%), Gaps = 16/306 (5%) Query: 10 IGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAKTTIIEPT 69 IG+TPL+ + P I AK+E NPG S+K R+GA +I D G++ TIIEPT Sbjct: 12 IGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGMTIIEPT 71 Query: 70 AGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRK-AE 128 +GNTGIGLA A R +L +P S+E++ +++ALGAE+V T +G+KGAI K AE Sbjct: 72 SGNTGIGLAFVAAARGYRLVLTMPASMSIERRKVLKALGAELVLTEPAKGMKGAIEKAAE 131 Query: 129 ALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYL 188 LA+ S ++P QF+NPANPA + T PEI +D + VAG G+GGT GV+ Y+ Sbjct: 132 ILASDPSTYFMPGQFENPANPAIHEKTTGPEIWSDTDGAVDVLVAGVGTGGTITGVSRYI 191 Query: 189 Q-AQDSATKAVVVEP----------EGSILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQT 237 + Q +V VEP G + P H+ +GIG F+P D +D+ Sbjct: 192 KNTQGKPIISVAVEPVVSPVITQAMAGEEIKPSP---HKIQGIGAGFVPKNLDLSMVDRV 248 Query: 238 LTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLA-TNLPANSHIVTIFPDSSERYL 296 ++D+++ A L ++ G+L G S GAA+A +++LA T IV I PDS ERYL Sbjct: 249 ELVSDDESKAMALRLMQEEGILSGISCGAAMAVAVRLAETPEMQGKTIVVILPDSGERYL 308 Query: 297 SQKIYT 302 S +++ Sbjct: 309 SSMLFS 314 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: 252 Number of extensions: 10 Number of successful extensions: 4 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: 324 Length adjustment: 27 Effective length of query: 276 Effective length of database: 297 Effective search space: 81972 Effective search space used: 81972 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