Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate HSERO_RS14210 HSERO_RS14210 homocitrate synthase
Query= curated2:O26819 (496 letters) >FitnessBrowser__HerbieS:HSERO_RS14210 Length = 376 Score = 278 bits (710), Expect = 3e-79 Identities = 146/345 (42%), Positives = 213/345 (61%), Gaps = 1/345 (0%) Query: 3 VRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITSE 62 V + DTTLRDGEQT GV+ T EEK+ IA +D +G +E G I + E E I+ I + Sbjct: 2 VTINDTTLRDGEQTAGVAFTAEEKIDIARALDEIGVPEMEIGIPIMGQAEIEVIQAIAAL 61 Query: 63 GLRAEICSFARAVREDIDAAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAVDCTEY 122 LR++ + R D+ AA C+ D V+L +P SD+H++HKL++ R+ VL Q Sbjct: 62 PLRSKTMVWGRMCEADLAAAARCNADIVNLSMPVSDIHIQHKLQRDRDWVLAQIRHFLPK 121 Query: 123 AVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEFYRGL- 181 A+D G+ V L EDS+R+D+DF+ + AGA R DT+G+L P +YE R L Sbjct: 122 ALDLGMEVCLGGEDSSRADLDFMLRVIETAQAAGARRFRFADTLGLLDPFATYEVIRQLR 181 Query: 182 SELGAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEEVVVALKSLY 241 E+ L +H HND GLA AN+LA + AGAS V+ T+NG+GERAGNA LEEVV+ L+ L+ Sbjct: 182 QEVDIELEMHAHNDLGLATANTLAAINAGASHVNTTVNGLGERAGNAPLEEVVMGLRHLH 241 Query: 242 DVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADGVLKKAETYEPIT 301 ++T ++ L SR+VA+ +G + PNK+IVGE F HESGIH DG+LK YE + Sbjct: 242 GIETQVDTRSLPAISRLVAKASGKAVAPNKSIVGEAVFTHESGIHVDGLLKNPANYEHFS 301 Query: 302 PEMVGHGRGFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVK 346 P +G V+GKH G+ ++ ++G+ ++D + + R++ Sbjct: 302 PAELGRSHHIVLGKHSGSRGVKDAFAKMGILLSDSQAQAMLMRIR 346 Lambda K H 0.317 0.135 0.373 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: 450 Number of extensions: 18 Number of successful extensions: 2 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: 496 Length of database: 376 Length adjustment: 32 Effective length of query: 464 Effective length of database: 344 Effective search space: 159616 Effective search space used: 159616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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