Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate GFF2360 PGA1_c23910 fructose-bisphosphate aldolase class 1
Query= curated2:Q8RGH3 (295 letters) >FitnessBrowser__Phaeo:GFF2360 Length = 300 Score = 330 bits (847), Expect = 2e-95 Identities = 175/291 (60%), Positives = 212/291 (72%), Gaps = 1/291 (0%) Query: 4 KLEKMRNGKGFIAALDQSGGSTPKALKLYGVNENEYSNDKEMFDLIHKMRTRIIKSPAFN 63 +L+++ NGKGFIAALDQSGGSTPKAL LYGV E+ Y ND EMF I KMR RII +P FN Sbjct: 11 QLDRIANGKGFIAALDQSGGSTPKALALYGVTEDAYGNDDEMFGEIQKMRARIITAPDFN 70 Query: 64 ESKILGAILFEQTMDSKIDGKYTADFLWEEKKVLPFLKIDKGLNDLDADGVQTMKPNPTL 123 KILGAILFE+TMD+ IDG +LW+ V+PFLK+DKGL D +AD QTMKP P L Sbjct: 71 SDKILGAILFEKTMDAAIDGTPVPAYLWDNCGVVPFLKVDKGLAD-EADDAQTMKPMPDL 129 Query: 124 ADLLKRANERHIFGTKMRSVIKKASPAGIARVVEQQFEVAAQVVAAGLIPIIEPEVDINN 183 LL RA + IFGTKMRSVIK A+ GI VV QQF V Q+ AAGL+PIIEPEVDIN+ Sbjct: 130 DALLSRAVKAGIFGTKMRSVIKGANATGIKNVVGQQFIVGRQIAAAGLLPIIEPEVDINS 189 Query: 184 VDKVQCEEILRDEIRKHLNALPETSNVMLKLTLPTVENLYEEFTKHPRVVRVVALSGGYS 243 K + E +L+D I LNALP + V LKLT+PT LY++ H VVRVVALSGGY+ Sbjct: 190 TTKAEAEALLKDAILAELNALPADTKVALKLTIPTEAGLYDDLAAHANVVRVVALSGGYT 249 Query: 244 REKANDILSKNKGVIASFSRALTEGLSAQQTDEEFNKTLAASIDGIYEASV 294 + A + LS+NK +IASFSRALTEGL+ +DE++N L ++ID IY AS+ Sbjct: 250 TDDACEKLSQNKTMIASFSRALTEGLNVAMSDEDYNAALGSNIDKIYRASI 300 Lambda K H 0.314 0.132 0.362 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: 269 Number of extensions: 5 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: 295 Length of database: 300 Length adjustment: 26 Effective length of query: 269 Effective length of database: 274 Effective search space: 73706 Effective search space used: 73706 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: 42 (22.0 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