Align Citramalyl-CoA lyase, mitochondrial; (3S)-malyl-CoA thioesterase; Beta-methylmalate synthase; Citrate lyase subunit beta-like protein, mitochondrial; Citrate lyase beta-like; Malate synthase; EC 4.1.3.25; EC 3.1.2.30; EC 2.3.3.-; EC 2.3.3.9 (characterized)
to candidate 3609102 Dshi_2490 Citryl-CoA lyase (RefSeq)
Query= SwissProt::Q8R4N0 (338 letters) >FitnessBrowser__Dino:3609102 Length = 310 Score = 124 bits (312), Expect = 2e-33 Identities = 95/307 (30%), Positives = 147/307 (47%), Gaps = 19/307 (6%) Query: 43 RRAVLYVPGNDEKKIRKIPSLKVDCAVLDCEDGVAENKKNEARLRIAKTLEDFDLGTTEK 102 +R+ L VP ++ I K D LD ED VA +K +AR + L D D K Sbjct: 7 QRSELAVPASNPTMIDKAAESAADFVFLDLEDAVAPPEKVQARKNAIQALNDIDWAAKGK 66 Query: 103 CV--RINSVSSGLAEVDLETFL-QARVLPSSLMLPKVEGPEEIRWFSDKFSLHLKGRKLE 159 V RIN + + D+ + QA +L++PKV ++ + LE Sbjct: 67 TVSVRINGLDTHYMYRDVVDIMEQAGDRVHTLLVPKVGVTADLYMVEAMVNQAEMACGLE 126 Query: 160 QPMNLIPFVETAMGLLNFKAVCEETLKTGPQVGLCLDAVVFGGEDFRAS-------IGAT 212 + L +ETA+G+ N +A+ Q G L+A+ FG D+ AS IG Sbjct: 127 TRVGLEALIETALGMANVEAIA--------QFGGRLEALHFGVADYAASMRARTVNIGGL 178 Query: 213 SNKDTQDILYAR-QKVVVTAKAFGLQAIDLVYIDFRDEDGLLRQSREAAAMGFTGKQVIH 271 + D +A ++V+ +A+GL+AID + DF D DG + +R AAA+G GK IH Sbjct: 179 NPDYPGDQWHASITRMVIACRAYGLRAIDGPFGDFSDPDGYMAGARRAAALGCEGKWAIH 238 Query: 272 PNQIAVVQEQFTPTPEKIQWAEELIAAFKEHQQLGKGAFTFRGSMIDMPLLKQAQNIVTL 331 P+QI + + F+P ++ A +I + + GKGA + G MID K A+N++ Sbjct: 239 PSQIEMANDVFSPPEAEVSKAHRIIEELRNAEAAGKGAASLDGKMIDAASEKMARNVIDT 298 Query: 332 ATSIKEK 338 A +I K Sbjct: 299 ANAIAAK 305 Lambda K H 0.319 0.135 0.385 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: 193 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: 338 Length of database: 310 Length adjustment: 28 Effective length of query: 310 Effective length of database: 282 Effective search space: 87420 Effective search space used: 87420 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