Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate RR42_RS24325 RR42_RS24325 citryl-CoA lyase
Query= BRENDA::Q8N0X4 (340 letters) >FitnessBrowser__Cup4G11:RR42_RS24325 Length = 307 Score = 144 bits (364), Expect = 2e-39 Identities = 94/296 (31%), Positives = 151/296 (51%), Gaps = 18/296 (6%) Query: 45 RRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDLGPTEK 104 RR L PG+ EK ++K S N D LD ED VA N+K AR +I+ L +D + Sbjct: 12 RRVQLATPGSSEKMMEKAASSNADHVFLDLEDAVAPNQKVAARKKIIDALNHLDWQGKVR 71 Query: 105 CVRVNSVSSGLAEEDLETLLQSRVLP-SSLMLPKVESPEEIQWFADKF-SFHLKGRKLEQ 162 CVR+N +S+ A ED+ +++ ++M+ KV P ++ FAD+ S K +L + Sbjct: 72 CVRINDLSTEYAYEDIIEIVEGAGHNLDTIMMTKVNGPADVL-FADRLLSMMEKKLRLPR 130 Query: 163 PMNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRA-------SIGATS 215 + L +E GL N +A+ + T + L+ ++FG DF A SIG T Sbjct: 131 RIGLEALIEEVPGLQNVEAIAQSTER--------LECLIFGMGDFSAAMGVNLESIGNTG 182 Query: 216 SKETLDILYARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPN 275 YAR ++++ +A + +D + +FRD G + R +G GK IHP+ Sbjct: 183 GYPGDIWHYARFRLIMACRAADIDPVDGPWAEFRDSEGYRNECRRAGTLGCVGKWAIHPS 242 Query: 276 QIAVVQEQFSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTV 331 QI + +FSP P K+ A +L +A+ + + G GA G M+D+ ++ +NTV Sbjct: 243 QIEIALAEFSPDPAKVAQARKLESAYVQAEAEGLGAINVDGVMVDVATMRLLRNTV 298 Lambda K H 0.319 0.135 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: 188 Number of extensions: 12 Number of successful extensions: 2 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: 340 Length of database: 307 Length adjustment: 28 Effective length of query: 312 Effective length of database: 279 Effective search space: 87048 Effective search space used: 87048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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