Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (characterized)
to candidate WP_067074391.1 MCUHO_RS05000 fructose 1,6-bisphosphatase
Query= SwissProt::Q2RG86 (379 letters) >NCBI__GCF_001602375.1:WP_067074391.1 Length = 365 Score = 472 bits (1215), Expect = e-138 Identities = 229/359 (63%), Positives = 279/359 (77%), Gaps = 3/359 (0%) Query: 4 RITLSVIKADIGGFVGHSSVHPRLLETAERYL--AESKLLIDYRVAHVGDDIDLIMTHKY 61 +IT+SVIKADIG F GHS HP++LE A R L AE +LID V H GDD++LIMTH Sbjct: 3 KITVSVIKADIGSFPGHSRTHPKILEVAARRLKEAEGSILIDSYVTHCGDDLELIMTHTK 62 Query: 62 GVDCPEIHHLAWNVFLQCTEVARELKLYGAGQDLLSDAFSGNVKGMGPGVAEMEFEERKS 121 G D EIH LAW++F++C +A+E+KLYGAGQDLL DAFSGNVKGMGPGVAEMEFEER S Sbjct: 63 GEDNEEIHKLAWDIFMECAGLAKEMKLYGAGQDLLGDAFSGNVKGMGPGVAEMEFEERGS 122 Query: 122 EPIIVFAADKTEPGAWNLPLYKMFADPFNTIGLVIDPKMHQGFRFEVYDLIKNERVEFSL 181 +PI++F ADKTEPGAWN LYK+FADPF+T GLVIDP +H GF FEV+D+IK ++ F+ Sbjct: 123 DPILIFMADKTEPGAWNYFLYKIFADPFSTSGLVIDPSLHDGFTFEVHDVIKKRKILFNT 182 Query: 182 PEELYDLLVFIGAPGRYCIKSVYSKTTGEIAAVSSTQRLNLMAGRYVGKDDPVCIVRCQS 241 PEE Y LL +IGAP RY IK V+ K G I A +STQRLNLMAGRYVGKDDPV I+R QS Sbjct: 183 PEESYSLLAYIGAPSRYVIKYVW-KRNGLIGASTSTQRLNLMAGRYVGKDDPVMIIRAQS 241 Query: 242 GLPAVGEALEPFANPHLVAGWMRGSHIGPLMPVGLDQSAPTRFDGPPRVVAMGFQLSGGR 301 G PAVGE ++PF P LVAGWMRGSH GP MPVG+ + T+FDGPPRV+ +GFQ+ G+ Sbjct: 242 GFPAVGEVIDPFRTPILVAGWMRGSHHGPFMPVGVCDANCTQFDGPPRVICLGFQVCNGK 301 Query: 302 LVGPQDFFGDVAFDKARQTANEIASYLRSLGPFEPHRLPLEDMEYTTMPEVMAKLKNRF 360 L+GP D F D A+++ R E++S LR+ GPFEPHRL LE+MEYTT+P V + K+R+ Sbjct: 302 LIGPADMFDDPAYNRVRDQCCELSSMLRAHGPFEPHRLSLEEMEYTTLPGVEKQFKDRW 360 Lambda K H 0.321 0.140 0.423 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: 535 Number of extensions: 28 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: 379 Length of database: 365 Length adjustment: 30 Effective length of query: 349 Effective length of database: 335 Effective search space: 116915 Effective search space used: 116915 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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