Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase
Query= BRENDA::E5LPF4 (309 letters) >FitnessBrowser__azobra:AZOBR_RS06795 Length = 331 Score = 66.2 bits (160), Expect = 1e-15 Identities = 62/208 (29%), Positives = 90/208 (43%), Gaps = 8/208 (3%) Query: 1 MVTAADNITGLIGNTPLLKLNRVVPEDAADVYVKLEFFNPGGSVKDRIALAMIEDAEYKG 60 +V AA + G TPLL+ + V +K E GS K R A + + Sbjct: 14 IVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLTPE- 72 Query: 61 VLKPGGTIVEPTSGNTGIGLALVAAAKGYHLIITMPETMSVERRALMRGYGAELILTPGA 120 + G +V +SGN G+A AA G +I MP + A RGYGAE++L Sbjct: 73 --ERRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRW 130 Query: 121 DGMPGAIKKAQALSKENGYFLPMQFQNPANPDVHERTTGQEIIRSFD--GGTPDAFVAGV 178 AI A A+++E G + +P + T G EI G PD +A Sbjct: 131 TESREAI--ATAIAEERGAATVPPYDHP-QIMAGQGTVGLEIAAQAQAIGAVPDDVIAPC 187 Query: 179 GTGGTLTGVGRALRKINPQVQIYALEAA 206 GG ++GV A+R P +++A E A Sbjct: 188 SGGGLMSGVATAVRHSFPDARLWAAEPA 215 Lambda K H 0.316 0.137 0.390 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: 261 Number of extensions: 12 Number of successful extensions: 1 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: 309 Length of database: 331 Length adjustment: 28 Effective length of query: 281 Effective length of database: 303 Effective search space: 85143 Effective search space used: 85143 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 (21.6 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