Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate BPHYT_RS10545 BPHYT_RS10545 fructose-1,6-bisphosphate aldolase
Query= curated2:P74309 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS10545 Length = 298 Score = 313 bits (802), Expect = 3e-90 Identities = 161/293 (54%), Positives = 209/293 (71%) Query: 7 NQEQLKKMKSHPGFIAALDQSGGSTPGALADYGIEPNTYSGDDQMFALVHQMRTRIMTSP 66 +++ L ++ GF AALDQSGGSTPGAL YGI Y+GD +MF L+H+MR RI+T+P Sbjct: 3 DEKMLAQVCEKQGFFAALDQSGGSTPGALRLYGIPETAYNGDAEMFKLIHEMRVRIITAP 62 Query: 67 GFTGDRILAAILFEDTMNREVDGEPTANYLWQNKQIVPILKVDKGLAQEKDGSQLMKPIP 126 FTGD+I+ AILFE TM+ + G+P +LW+ + +VP LKVDKGL E DG QLMKPIP Sbjct: 63 AFTGDKIIGAILFEATMDGQAQGKPVPAFLWEERGVVPFLKVDKGLQAEADGVQLMKPIP 122 Query: 127 QLDSLLMKAKKKGIFGTKMRSFIKHANPAGIEAIVDQQFELAQQIIAAGLVPIIEPEVDI 186 LD LL +A K I GTKMRS I + GI AIV QQFELA QI A GL+PI+EPEV I Sbjct: 123 GLDDLLARAAKLSICGTKMRSVINLNSQNGIAAIVKQQFELAAQIDAHGLLPILEPEVSI 182 Query: 187 HCSEKAQAEALLKQAMLKHLNQLPKGQWVMLKLTLPEQDNLYSNCIEHANVLRVVALSGG 246 +K AEA L+ ++K L+ LP + VMLKLT+P+ + Y IEH V RVVALSGG Sbjct: 183 KSPDKPGAEATLRAELIKGLDALPDSRRVMLKLTIPDAADFYRQLIEHPRVARVVALSGG 242 Query: 247 YSQAEANERLSRNHGVIASFSRALTEGLTAQQTDAEFNTMLDESIEKIYQASI 299 Y++A+A +RL+ NHG+IASFSRAL L +D+EFN L++++++IYQAS+ Sbjct: 243 YTRADACQRLASNHGMIASFSRALINELKESMSDSEFNAALEKAVDEIYQASV 295 Lambda K H 0.316 0.132 0.371 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: 264 Number of extensions: 7 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: 300 Length of database: 298 Length adjustment: 27 Effective length of query: 273 Effective length of database: 271 Effective search space: 73983 Effective search space used: 73983 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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