Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate AZOBR_RS14115 AZOBR_RS14115 (3S)-malyl-CoA thiolesterase
Query= BRENDA::Q8N0X4 (340 letters) >FitnessBrowser__azobra:AZOBR_RS14115 Length = 291 Score = 136 bits (343), Expect = 6e-37 Identities = 89/294 (30%), Positives = 148/294 (50%), Gaps = 14/294 (4%) Query: 44 PRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDLGPTE 103 PRR+VLY+PG++ + ++K SL D +LD ED VA + K EAR I ++ G E Sbjct: 7 PRRSVLYMPGSNTRALEKGRSLPADGLILDLEDAVAPDAKAEARATIKASIAAGGYGGRE 66 Query: 104 KCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVESPEEIQWFADKFSFHLKGRKLEQP 163 VR N +++ +DL S +++LPKVESP+ ++ + L+ Sbjct: 67 LVVRTNGLNTPWGYDDLVMAASSGA--DAVLLPKVESPDMVR----QAEAVLRANGSPDG 120 Query: 164 MNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRASIGATSSKETLDIL 223 + +ET +G+LN K + + K+G +V G D + A +++ L +L Sbjct: 121 QTIWCMMETPLGMLNTKEIAGASPKLG--------GLVMGTSDLAKDLHAAHTRDRLPML 172 Query: 224 YARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQEQ 283 + ++ A+A+GL +D V++D D AG +G +GF GK +IHP IA Sbjct: 173 TSLGLCLLAARAYGLAILDGVHLDLNDDAGFGESCVQGRELGFDGKTLIHPKTIAACNAA 232 Query: 284 FSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSI 337 F+PS E++ A +I A E GKG G +++ ++ A+ V +A +I Sbjct: 233 FAPSEEEVAQAHRIIQAHAEAVAQGKGVVLVDGRLVENLHVENARRLVAMAEAI 286 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: 9 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: 340 Length of database: 291 Length adjustment: 27 Effective length of query: 313 Effective length of database: 264 Effective search space: 82632 Effective search space used: 82632 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