Align Probable fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Probable fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate WP_013683840.1 ARCVE_RS05825 fructose-bisphosphate aldolase
Query= curated2:Q9YG90 (272 letters) >NCBI__GCF_000194625.1:WP_013683840.1 Length = 266 Score = 163 bits (413), Expect = 3e-45 Identities = 101/268 (37%), Positives = 149/268 (55%), Gaps = 9/268 (3%) Query: 6 DVGKRVRLSRILP--DGRSVIFAFDHGIEHGPGEIPEERLDPRLLIREVVEAGVDAIMTT 63 ++GKRVR+ RIL G +VI DHG+ GP + +D I V E G +A++ Sbjct: 3 EIGKRVRIERILDRNSGNTVIVPMDHGLSMGP---IDGIVDMPKTINAVAEGGANAVVIH 59 Query: 64 PGIARLTWDIWANRVAMIIKVSGKTSIRPQDDQFLQSAISSVDEVVALGGDGVAATVYWG 123 GI + V +I+ +SG TS+ P ++ + + +V+E + LG D V+ + G Sbjct: 60 KGIVPFGHRGYGRDVGLIVHMSGSTSLSPDPNE--KVLVCTVEEAIKLGADAVSVHINIG 117 Query: 124 SQFEDKMLERWTRIRLRAEKLGLPALQLAYPRGPHIKNRYAVDIVAYGARAAMETGADLI 183 S+ E + L + + ++ G+P L + YPRG I N++ VA ARA E GAD++ Sbjct: 118 SKTEAEQLAKLGEVSRACKEWGMPLLAMMYPRGDGI-NQFDEKAVALAARAGAELGADIV 176 Query: 184 KTYYTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVYSVMEAGGGGVVVGRNIFQ 243 KT +TGS ESF+RV +A VPV+++GG + S ++ L V ME G GV +GRNIFQ Sbjct: 177 KTNFTGSVESFKRV-TAGCPVPVVVAGGPKMKSEEDILKMVEMAMEGGARGVAIGRNIFQ 235 Query: 244 AGDIRAMVKAIRAIVHEGFDPEKASKLL 271 A D M KAI IVHE + A + L Sbjct: 236 AEDPTKMTKAIAMIVHENASAKDALEFL 263 Lambda K H 0.320 0.137 0.403 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: 172 Number of extensions: 10 Number of successful extensions: 5 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: 272 Length of database: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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: 47 (22.7 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