Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate PP_4571 PP_4571 cysteine synthase A
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__Putida:PP_4571 Length = 324 Score = 206 bits (525), Expect = 4e-58 Identities = 122/303 (40%), Positives = 173/303 (57%), Gaps = 10/303 (3%) Query: 10 IGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAKTTIIEPT 69 IG+TPL+ + P I AK+E NPG S+K R+GA ++ D G++ TI+EPT Sbjct: 12 IGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMVWDAESSGKLKPGMTIVEPT 71 Query: 70 AGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEA 129 +GNTGIGLA A + +L +P S+E++ +++ALGAE+V T +G+KGAI KA Sbjct: 72 SGNTGIGLAFVAAARGYKLMLTMPASMSLERRKVLKALGAELVLTDPAKGMKGAIEKANE 131 Query: 130 LAATISNSY-VPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYL 188 + A+ Y +P QF+NPANPA + T PEI D I VAG G+GGT GV+ Y+ Sbjct: 132 IVASDPEQYFLPGQFENPANPAIHEKTTGPEIWNDTDGAIDVLVAGVGTGGTITGVSRYI 191 Query: 189 Q-AQDSATKAVVVEPEGSILNGG-------PAHAHRTEGIGVEFIPPFFDQVRIDQTLTI 240 + Q A +V VEP S L H+ +GIG F+P D +DQ T+ Sbjct: 192 KHTQGKAILSVAVEPVASPLISQTLAGEELKPSPHKIQGIGAGFVPKNLDLSIVDQVETV 251 Query: 241 ADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSH-IVTIFPDSSERYLSQK 299 D ++ A L ++ G+L G S GAA+AA+++LA IV I PDS ERYLS Sbjct: 252 TDEESKAMAIRLMQEEGILCGISCGAAMAAAVRLAEKPEMQGKTIVVILPDSGERYLSSM 311 Query: 300 IYT 302 +++ Sbjct: 312 LFS 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: 255 Number of extensions: 11 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