Align Fructose-1,6-bisphosphate aldolase/phosphatase; FBP A/P; FBP aldolase/phosphatase; EC 3.1.3.11; EC 4.1.2.13 (uncharacterized)
to candidate WP_013644184.1 METBO_RS02970 fructose 1,6-bisphosphatase
Query= curated2:B6YTP6 (375 letters) >NCBI__GCF_000191585.1:WP_013644184.1 Length = 365 Score = 491 bits (1265), Expect = e-143 Identities = 230/370 (62%), Positives = 293/370 (79%), Gaps = 6/370 (1%) Query: 6 KITISVIKADIGGWPGHSRVHPQLIEAAEEVLAKAKEEGTIIDFYVAYAGDDLQLIMTHK 65 K TISVIKAD+G GH++ H L +EVLAKAKE ++D+++ GDD+ LIMTH+ Sbjct: 2 KTTISVIKADVGSIAGHAKTHVALKNKCDEVLAKAKESELLVDYHITSCGDDIDLIMTHR 61 Query: 66 KGVDSPDIHGLAWKAFEEATEIAKEFGLYGAGQDLLKDAFSGNIRGMGPGIAEMEITLRK 125 G ++ ++H LAW AF EAT++AK LYGAGQDLL D FSGNI+GMGPG AEME R Sbjct: 62 NGEENEEVHELAWNAFLEATQVAKSLKLYGAGQDLLSDTFSGNIKGMGPGCAEMEFKERP 121 Query: 126 SEPIVTFHMDKTEPGAFNLPIFRMFADPFNTAGLVIDPNMHMGFRFEVWDIKEHKRVILN 185 S+P++ F DKTEPGAFN+P+F+MFADPFNTAGLVIDP++H G+ FE++D+ EHK+V ++ Sbjct: 122 SDPVIIFCCDKTEPGAFNMPLFKMFADPFNTAGLVIDPSLHGGYDFEIFDVIEHKKVTMS 181 Query: 186 TPEEIYDLLALIGAKSRYVIKRVYPKEGHKISKDEPVAVISTEKLYEIAGEYVGKDDPVA 245 P+E+YD LAL+G+ RYVIK + + S +E A +STE+L +AG+Y+GKDDPVA Sbjct: 182 CPDEMYDALALLGSTGRYVIKHI-----SRRSDNEIAASVSTERLNLMAGQYIGKDDPVA 236 Query: 246 IVRAQSGLPALGEVLEPFAFPHLVSGWMRGSHNGPIMPVPMHQANPTRFDGPPRVVALGW 305 +VRAQSG PA GEV+EPFAFPHLVSGWMRGSHNGP+MPV ANP RFDGPPRV+ALG+ Sbjct: 237 VVRAQSGFPAAGEVVEPFAFPHLVSGWMRGSHNGPLMPVAQRNANPVRFDGPPRVIALGF 296 Query: 306 QISPEGKLVGPVDLFDDPAFDYARQKALEITEYIRRHGPFEPHRLPLEDMEYTTLPGVLK 365 QI+ +LVGP+D+FDDPAFD +R A E+ EY+RRHGPFEPHRLP ++MEYT+LPGVLK Sbjct: 297 QIN-NSELVGPLDMFDDPAFDRSRDLASEVAEYMRRHGPFEPHRLPADEMEYTSLPGVLK 355 Query: 366 KLEERFEDIE 375 LE+R ED++ Sbjct: 356 MLEDRMEDMD 365 Lambda K H 0.319 0.140 0.425 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: 531 Number of extensions: 23 Number of successful extensions: 4 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: 375 Length of database: 365 Length adjustment: 30 Effective length of query: 345 Effective length of database: 335 Effective search space: 115575 Effective search space used: 115575 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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