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_013644184.1 METBO_RS02970 fructose-1,6-bisphosphate aldolase/phosphatase
Query= SwissProt::D9PUH5 (365 letters) >NCBI__GCF_000191585.1:WP_013644184.1 Length = 365 Score = 654 bits (1687), Expect = 0.0 Identities = 310/365 (84%), Positives = 339/365 (92%) Query: 1 MKTTISVIKADVGSVAGHAVAHEALKKKCDEILAEARDTGILEDYYITNCGDDIDLIMTH 60 MKTTISVIKADVGS+AGHA H ALK KCDE+LA+A+++ +L DY+IT+CGDDIDLIMTH Sbjct: 1 MKTTISVIKADVGSIAGHAKTHVALKNKCDEVLAKAKESELLVDYHITSCGDDIDLIMTH 60 Query: 61 RNGEENEEVHQTAWNAFREATEVARGLKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKER 120 RNGEENEEVH+ AWNAF EAT+VA+ LKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKER Sbjct: 61 RNGEENEEVHELAWNAFLEATQVAKSLKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKER 120 Query: 121 PSDPVIIFCCDKTEPGAFNLPLFRMFADPFNTAGLVIDPTLHNGYEFEVFDVVEHKKVTM 180 PSDPVIIFCCDKTEPGAFN+PLF+MFADPFNTAGLVIDP+LH GY+FE+FDV+EHKKVTM Sbjct: 121 PSDPVIIFCCDKTEPGAFNMPLFKMFADPFNTAGLVIDPSLHGGYDFEIFDVIEHKKVTM 180 Query: 181 ACPDEMYDLLALLGSISRYVIKKIHRRDDGEIAASVSTERLNLMAGKYIGKDDPVAIVRA 240 +CPDEMYD LALLGS RYVIK I RR D EIAASVSTERLNLMAG+YIGKDDPVA+VRA Sbjct: 181 SCPDEMYDALALLGSTGRYVIKHISRRSDNEIAASVSTERLNLMAGQYIGKDDPVAVVRA 240 Query: 241 QSGFPAAGEVVEPFAFPHLVGGWMRGSHNGPLMPVAQRDATPVRFDGPPRVIGLGFQIAD 300 QSGFPAAGEVVEPFAFPHLV GWMRGSHNGPLMPVAQR+A PVRFDGPPRVI LGFQI + Sbjct: 241 QSGFPAAGEVVEPFAFPHLVSGWMRGSHNGPLMPVAQRNANPVRFDGPPRVIALGFQINN 300 Query: 301 CKLVGPIDMFDDPSFDRSRQLASEIAEYMRRHGPFEPHRLPSDEMEYTSLPGVLEKLGDR 360 +LVGP+DMFDDP+FDRSR LASE+AEYMRRHGPFEPHRLP+DEMEYTSLPGVL+ L DR Sbjct: 301 SELVGPLDMFDDPAFDRSRDLASEVAEYMRRHGPFEPHRLPADEMEYTSLPGVLKMLEDR 360 Query: 361 FEDMD 365 EDMD Sbjct: 361 MEDMD 365 Lambda K H 0.320 0.139 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: 628 Number of extensions: 15 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: 365 Length of database: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 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