Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate PP_1791 PP_1791 putative Aldolase/synthase
Query= curated2:P05345 (381 letters) >FitnessBrowser__Putida:PP_1791 Length = 534 Score = 78.2 bits (191), Expect = 5e-19 Identities = 67/240 (27%), Positives = 107/240 (44%), Gaps = 27/240 (11%) Query: 8 DTTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLVRRQLPDA 67 D TLRDG F + A+ AAGI +E+G ++ + + Sbjct: 5 DCTLRDGGYYNNWNFSEALIAQYITAMQAAGIQTIELGLRSLKNSSFSGA---------C 55 Query: 68 TLMTWCRMNALEIRQSADLGIDWVD----ISIPASDKLRQYKLREPLA---VLLERLAMF 120 T ++ L++ S +G+ V+ + A + Q P + V L R+A Sbjct: 56 AYTTDAFLSTLDLPPSMTIGV-MVNGSELVGKNAGQQALQLLFPSPASESPVDLVRIACH 114 Query: 121 IH-LAHTL---------GLKVCIGCEDASRASGQTLRAIAEVAQNAPAARLRYADTVGLL 170 +H A L G V + S ++A+A++A N P L +AD++G + Sbjct: 115 VHEFAEALPAASWLKERGYDVGFNLMQIANCSESEIKALAKLANNYPLDVLYFADSMGSM 174 Query: 171 DPFTTAAQISALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTVLGLGERAGNA 230 P A I LR W G + +H H++LG+A +NTL A+ G T V++TV G+G GNA Sbjct: 175 SPDDAAQIIQWLRSEWQGALGIHTHDNLGLALSNTLRAMDEGVTWVDSTVTGMGRGPGNA 234 Lambda K H 0.319 0.132 0.384 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: 410 Number of extensions: 22 Number of successful extensions: 1 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: 381 Length of database: 534 Length adjustment: 33 Effective length of query: 348 Effective length of database: 501 Effective search space: 174348 Effective search space used: 174348 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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