Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate 3608764 Dshi_2156 Fructose-bisphosphate aldolase (RefSeq)
Query= curated2:Q8RGH3 (295 letters) >FitnessBrowser__Dino:3608764 Length = 294 Score = 343 bits (880), Expect = 3e-99 Identities = 176/291 (60%), Positives = 222/291 (76%), Gaps = 1/291 (0%) Query: 4 KLEKMRNGKGFIAALDQSGGSTPKALKLYGVNENEYSNDKEMFDLIHKMRTRIIKSPAFN 63 K +++R+G GFIAALDQSGGSTPKAL+LYG+ E+ Y D EMFDLIH+MR+RI+ +PAF Sbjct: 3 KADQIRSGHGFIAALDQSGGSTPKALRLYGIEEDAYGTDAEMFDLIHQMRSRIVAAPAFT 62 Query: 64 ESKILGAILFEQTMDSKIDGKYTADFLWEEKKVLPFLKIDKGLNDLDADGVQTMKPNPTL 123 K++GAILFE TMD + GK +LWE+K V+PFLKIDKGL + +A+GVQ MKP P L Sbjct: 63 GEKVIGAILFEMTMDREFAGKSAPAYLWEDKGVVPFLKIDKGL-EAEANGVQLMKPMPGL 121 Query: 124 ADLLKRANERHIFGTKMRSVIKKASPAGIARVVEQQFEVAAQVVAAGLIPIIEPEVDINN 183 DLL RA IFGTK RSVI A+P GI +V QQFE+ AQV+A GL+PI+EPEV I Sbjct: 122 DDLLSRAAAMGIFGTKERSVISAANPKGIKAIVAQQFEIGAQVLAHGLVPILEPEVTITI 181 Query: 184 VDKVQCEEILRDEIRKHLNALPETSNVMLKLTLPTVENLYEEFTKHPRVVRVVALSGGYS 243 DK + E++L EI HL+ +PE +MLKL+LP+ N Y +H +V++VVALSGGYS Sbjct: 182 ADKAEAEDMLLAEILAHLDTVPEGLQIMLKLSLPSKPNQYLPLVEHAKVMKVVALSGGYS 241 Query: 244 REKANDILSKNKGVIASFSRALTEGLSAQQTDEEFNKTLAASIDGIYEASV 294 RE+AN L++N GVIASFSRALTEGLSAQQ+D EFN T+AA+ID I+ AS+ Sbjct: 242 REEANAKLAENTGVIASFSRALTEGLSAQQSDAEFNATIAATIDSIHAASI 292 Lambda K H 0.314 0.132 0.362 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: 255 Number of extensions: 2 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: 295 Length of database: 294 Length adjustment: 26 Effective length of query: 269 Effective length of database: 268 Effective search space: 72092 Effective search space used: 72092 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: 42 (22.0 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