Align class I fructose-bisphosphate aldolase/sedoheptulose-1,7-bisphosphate aldolase monomer (EC 4.1.2.13) (characterized)
to candidate Ga0059261_0725 Ga0059261_0725 Fructose-1,6-bisphosphate aldolase
Query= metacyc::FBABSYN-MONOMER (300 letters) >FitnessBrowser__Korea:Ga0059261_0725 Length = 301 Score = 308 bits (790), Expect = 8e-89 Identities = 158/286 (55%), Positives = 212/286 (74%), Gaps = 1/286 (0%) Query: 13 KMKSHPGFIAALDQSGGSTPGALADYGIEPNTYSGDDQMFALVHQMRTRIMTSPGFTGDR 72 K+ GFIAALDQSGGSTP AL YGIE + YSGD++MF L+H MR+RI+TSP F GD+ Sbjct: 9 KIAEGNGFIAALDQSGGSTPKALKGYGIEEDAYSGDEEMFDLIHAMRSRIITSPSFNGDK 68 Query: 73 ILAAILFEDTMNREVDGEPTANYLWQNKQIVPILKVDKGLAQEKDGSQLMKPIPQLDSLL 132 ++ AILFE TM+ +VDGEPT L + + +VP +K+DKGL E++G QLMKP+P+LD+LL Sbjct: 69 VIGAILFERTMDGQVDGEPTPQALIE-RGVVPFIKIDKGLEAEENGVQLMKPMPELDALL 127 Query: 133 MKAKKKGIFGTKMRSFIKHANPAGIEAIVDQQFELAQQIIAAGLVPIIEPEVDIHCSEKA 192 +AK G+FGTK RS + AN GI AIV QQFE+ +Q++AAGL+PI+EPEV+I E+A Sbjct: 128 ARAKGLGVFGTKERSVVNLANAQGIAAIVAQQFEVGRQVLAAGLMPILEPEVNIKSPERA 187 Query: 193 QAEALLKQAMLKHLNQLPKGQWVMLKLTLPEQDNLYSNCIEHANVLRVVALSGGYSQAEA 252 QA+A+L+ +LKHL+ + VMLKL++P Q L+ ++H VLRVVALSGG+ + EA Sbjct: 188 QADAILRDEILKHLDAMTGDDKVMLKLSIPAQPGLFDALVDHPRVLRVVALSGGFKRPEA 247 Query: 253 NERLSRNHGVIASFSRALTEGLTAQQTDAEFNTMLDESIEKIYQAS 298 L++N G+IASFSRAL E L TDAEF+ L +I++I+ AS Sbjct: 248 CAELAKNRGMIASFSRALLEDLRHGMTDAEFDASLGAAIDEIHAAS 293 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: 294 Number of extensions: 18 Number of successful extensions: 2 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: 301 Length adjustment: 27 Effective length of query: 273 Effective length of database: 274 Effective search space: 74802 Effective search space used: 74802 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 Apr 09 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