Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate 3609490 Dshi_2874 Citrate (pro-3S)-lyase (RefSeq)
Query= BRENDA::Q8N0X4 (340 letters) >FitnessBrowser__Dino:3609490 Length = 295 Score = 149 bits (376), Expect = 9e-41 Identities = 91/299 (30%), Positives = 151/299 (50%), Gaps = 15/299 (5%) Query: 40 HKYIPRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDL 99 H+ P R+VLY+PG+ E+ + K SL VD + D ED VA +K AR + +TL + D Sbjct: 7 HRARPYRSVLYIPGSKERALHKAQSLPVDAIIFDLEDAVAVEEKANARHLLARTLAETDY 66 Query: 100 GPTEKCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVESPEEIQWFADKFSFHLKGRK 159 GP K VR+N + + DL+ + +R P +++LPKV + +++ AD+ L R Sbjct: 67 GPRAKIVRINGFDTDWGQADLDVIAAAR--PEAILLPKVNTAADVETLADR----LDARP 120 Query: 160 LEQPMNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRASIGATSSKET 219 + +ET +G+LN + P++ F V G D + + + Sbjct: 121 ETAETTIWTMMETPLGMLNAAQIA-----AAPRMAGF----VMGTNDLAKELDSRFRPDR 171 Query: 220 LDILYARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAV 279 L +L ++ A+A GL A+D VY F+D GL + +G MGF GK +IHP Q+A+ Sbjct: 172 LPMLTGLGLCLLAARAHGLVAVDGVYNAFKDDEGLEAECAQGRDMGFDGKTLIHPAQVAI 231 Query: 280 VQEQFSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSIK 338 F+PS ++ A I AF++ G+G G +++ + A+ + A +I+ Sbjct: 232 ANAVFAPSDSELALASRQILAFEQAAARGQGVAVVDGKIVENLHVATARQLLAKAEAIQ 290 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: 176 Number of extensions: 10 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: 295 Length adjustment: 27 Effective length of query: 313 Effective length of database: 268 Effective search space: 83884 Effective search space used: 83884 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