Align class I fructose-bisphosphate aldolase/sedoheptulose-1,7-bisphosphate aldolase monomer (EC 4.1.2.13) (characterized)
to candidate 3608764 Dshi_2156 Fructose-bisphosphate aldolase (RefSeq)
Query= metacyc::FBABSYN-MONOMER (300 letters) >FitnessBrowser__Dino:3608764 Length = 294 Score = 328 bits (842), Expect = 7e-95 Identities = 167/287 (58%), Positives = 217/287 (75%) Query: 13 KMKSHPGFIAALDQSGGSTPGALADYGIEPNTYSGDDQMFALVHQMRTRIMTSPGFTGDR 72 +++S GFIAALDQSGGSTP AL YGIE + Y D +MF L+HQMR+RI+ +P FTG++ Sbjct: 6 QIRSGHGFIAALDQSGGSTPKALRLYGIEEDAYGTDAEMFDLIHQMRSRIVAAPAFTGEK 65 Query: 73 ILAAILFEDTMNREVDGEPTANYLWQNKQIVPILKVDKGLAQEKDGSQLMKPIPQLDSLL 132 ++ AILFE TM+RE G+ YLW++K +VP LK+DKGL E +G QLMKP+P LD LL Sbjct: 66 VIGAILFEMTMDREFAGKSAPAYLWEDKGVVPFLKIDKGLEAEANGVQLMKPMPGLDDLL 125 Query: 133 MKAKKKGIFGTKMRSFIKHANPAGIEAIVDQQFELAQQIIAAGLVPIIEPEVDIHCSEKA 192 +A GIFGTK RS I ANP GI+AIV QQFE+ Q++A GLVPI+EPEV I ++KA Sbjct: 126 SRAAAMGIFGTKERSVISAANPKGIKAIVAQQFEIGAQVLAHGLVPILEPEVTITIADKA 185 Query: 193 QAEALLKQAMLKHLNQLPKGQWVMLKLTLPEQDNLYSNCIEHANVLRVVALSGGYSQAEA 252 +AE +L +L HL+ +P+G +MLKL+LP + N Y +EHA V++VVALSGGYS+ EA Sbjct: 186 EAEDMLLAEILAHLDTVPEGLQIMLKLSLPSKPNQYLPLVEHAKVMKVVALSGGYSREEA 245 Query: 253 NERLSRNHGVIASFSRALTEGLTAQQTDAEFNTMLDESIEKIYQASI 299 N +L+ N GVIASFSRALTEGL+AQQ+DAEFN + +I+ I+ ASI Sbjct: 246 NAKLAENTGVIASFSRALTEGLSAQQSDAEFNATIAATIDSIHAASI 292 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: 284 Number of extensions: 11 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: 294 Length adjustment: 26 Effective length of query: 274 Effective length of database: 268 Effective search space: 73432 Effective search space used: 73432 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