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 AZOBR_RS31565 AZOBR_RS31565 hypothetical protein
Query= SwissProt::Q8R4N0 (338 letters) >FitnessBrowser__azobra:AZOBR_RS31565 Length = 278 Score = 114 bits (286), Expect = 2e-30 Identities = 88/291 (30%), Positives = 139/291 (47%), Gaps = 24/291 (8%) Query: 47 LYVPGNDEKKIRKIPSLKVDCAVLDCEDGVAENKKNEARLRIAKTL-EDFDLGTTEKCVR 105 L+VPG + K D ++D ED VA K+ AR + L E G VR Sbjct: 1 LFVPGARPDRFAKALGAGADAVIIDLEDAVAPGDKDSARAAVCSFLREHTGAGGPAVFVR 60 Query: 106 INSVSS--GLAEVDLETFLQARVLP--SSLMLPKVEGPEEIRWFSDKFSLHLKGRKLEQP 161 NSV S GL ++ T L P + ++LPKV+G E++R + L R L P Sbjct: 61 TNSVRSRTGLLDILALTDLPDGTAPRWAGILLPKVDGAEDVRLAAGL----LDERNL--P 114 Query: 162 MNLIPFVETAMGLLNFKAVCEETLKTGPQVGLCLDAVVFGGEDFRASIGATSNKDTQDIL 221 L +E+A GL N A+ + + L ++FGG D A + + ++ Sbjct: 115 GALGALIESADGLENVMAIAAASPR--------LSFLMFGGGDLSAELRVPLA--WEPLV 164 Query: 222 YARQKVVVTAKAFGLQAIDLVYIDFRDEDGLLRQSREAAAMGFTGKQVIHPNQIAVVQEQ 281 AR ++V A FGL A+D+ +I DE+G ++ + GFT + IHP QI + + Sbjct: 165 QARTRIVHAAARFGLDALDMPWIALDDEEGYRQELARSVLHGFTARSAIHPKQITAIHDA 224 Query: 282 FTPTPEKIQWAEELIAAFKEHQQLGKGAFTFRGSMIDMPLLKQAQNIVTLA 332 +TP+P+ + A ++AAF + G G G +++ PL+ + I+ LA Sbjct: 225 YTPSPDAVLRAGRVLAAF---EAAGGGVCVLDGRLVERPLVLGSHRILALA 272 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: 212 Number of extensions: 15 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: 338 Length of database: 278 Length adjustment: 27 Effective length of query: 311 Effective length of database: 251 Effective search space: 78061 Effective search space used: 78061 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 Apr 09 2024. 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