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_012966023.1 FERP_RS07635 fructose 1,6-bisphosphatase
Query= curated2:B6YTP6 (375 letters) >NCBI__GCF_000025505.1:WP_012966023.1 Length = 370 Score = 573 bits (1477), Expect = e-168 Identities = 275/369 (74%), Positives = 319/369 (86%), Gaps = 1/369 (0%) Query: 6 KITISVIKADIGGWPGHSRVHPQLIEAAEEVLAKAKEEGTIIDFYVAYAGDDLQLIMTHK 65 KIT+S+IKAD+G GH+ V +LI+ AE L++AKE G IIDF V AGDDL+L+MTH Sbjct: 3 KITVSLIKADVGSVAGHTTVADELIKIAENNLSEAKESGLIIDFRVFKAGDDLELLMTHT 62 Query: 66 KGVDSPDIHGLAWKAFEEATEIAKEFGLYGAGQDLLKDAFSGNIRGMGPGIAEMEITLRK 125 KGVD+ +IH LAW+ FE+A E AKE LYGAGQDLL DAFSGN+RGMGPG+AEME T RK Sbjct: 63 KGVDNEEIHRLAWETFEKAAEKAKELKLYGAGQDLLADAFSGNVRGMGPGVAEMEFTERK 122 Query: 126 SEPIVTFHMDKTEPGAFNLPIFRMFADPFNTAGLVIDPNMHMGFRFEVWDIKEHKRVILN 185 +EP++ F MDKTEPGAFNLPIFR+FADPFNTAGLVIDP+MH GF FE+WDI EHKRV + Sbjct: 123 AEPLIAFMMDKTEPGAFNLPIFRIFADPFNTAGLVIDPSMHQGFVFEIWDIMEHKRVFMK 182 Query: 186 TPEEIYDLLALIGAKSRYVIKRVYPKEGHKISKDEPVAVISTEKLYEIAGEYVGKDDPVA 245 PEE+YD+LALIGAKSR+VIKRVYPK G K+ +DEPVAV+STEKLY++AGEYVGKDDPVA Sbjct: 183 APEEMYDILALIGAKSRFVIKRVYPKPGGKLPEDEPVAVVSTEKLYQVAGEYVGKDDPVA 242 Query: 246 IVRAQSGLPALGEVLEPFAFPHLVSGWMRGSHNGPIMPVPMHQANPTRFDGPPRVVALGW 305 +VRAQSGLPA+GEVLE FAFPHLVSGWMRGSHNGP+MPV A TRFDGPPRVVA G+ Sbjct: 243 LVRAQSGLPAVGEVLEAFAFPHLVSGWMRGSHNGPLMPVSFKYAKCTRFDGPPRVVAAGF 302 Query: 306 QISPEGKLVGPVDLFDDPAFDYARQKALEITEYIRRHGPFEPHRLPLEDMEYTTLPGVLK 365 Q+S GKL+GPVDLFDDPAFDY RQKA+EI EY+RRHGPFEPHRLP E+MEYTTLP V++ Sbjct: 303 QLS-NGKLIGPVDLFDDPAFDYTRQKAMEIAEYMRRHGPFEPHRLPREEMEYTTLPKVME 361 Query: 366 KLEERFEDI 374 KL+ERFE+I Sbjct: 362 KLKERFEEI 370 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: 591 Number of extensions: 25 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: 370 Length adjustment: 30 Effective length of query: 345 Effective length of database: 340 Effective search space: 117300 Effective search space used: 117300 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: 50 (23.9 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