Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate GFF357 PGA1_c03680 putative citrate lyase subunit beta
Query= BRENDA::Q8N0X4 (340 letters) >FitnessBrowser__Phaeo:GFF357 Length = 284 Score = 124 bits (311), Expect = 3e-33 Identities = 88/294 (29%), Positives = 140/294 (47%), Gaps = 21/294 (7%) Query: 44 PRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDLGPTE 103 P R+VLY+PG+ + ++K SL VD + D ED V+A +K AR + + L G Sbjct: 7 PYRSVLYIPGSKLRALEKARSLPVDAIIFDLEDAVSAEEKVNARQTLEEALRAGGYGARM 66 Query: 104 KCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVESPEEIQWFADKFSFHLKGRKLEQP 163 K VR+N + + D +R+ +++LPKV SPE++ A + G K Sbjct: 67 KIVRINGLDTVWGRADAAAA--ARMDCDAILLPKVSSPEDLDALAV-----ITGDK---- 115 Query: 164 MNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRASIGATSSKETLDIL 223 L +ET G+LN A+ L L +V G D + + L ++ Sbjct: 116 -PLWAMMETPRGMLNAAAIAAHPL---------LQGMVMGTNDLAKELQTRFRPDRLPLM 165 Query: 224 YARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQEQ 283 + ++ AKA G+ +D VY F+D GL + +G MGF GK +IHP Q+ V Sbjct: 166 AGLGQCLLAAKAKGIIIVDGVYNAFKDAEGLEAECDQGRDMGFDGKTLIHPAQVDVANSA 225 Query: 284 FSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSI 337 F+PS ++I A IAAF + G+G G +++ + A+ + A +I Sbjct: 226 FAPSEDEIDLARRQIAAFDAAEAEGQGVAVVDGKIVENLHVATAREILAKADAI 279 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: 192 Number of extensions: 12 Number of successful extensions: 3 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: 284 Length adjustment: 27 Effective length of query: 313 Effective length of database: 257 Effective search space: 80441 Effective search space used: 80441 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