Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate BWI76_RS27560 BWI76_RS27560 hypothetical protein
Query= BRENDA::Q9RHA2 (305 letters) >FitnessBrowser__Koxy:BWI76_RS27560 Length = 286 Score = 201 bits (510), Expect = 2e-56 Identities = 121/305 (39%), Positives = 170/305 (55%), Gaps = 22/305 (7%) Query: 1 MLVTGLEILKKAREEGYGVGAFNVNNMEFLQAVLEAAEEQRSPVILALSEGAMKYGGRAL 60 MLV+ E+LK RE G+ +GAFNV + F++AV+E AE +P I+++ + G A Sbjct: 1 MLVSMHELLKPTREHGFAIGAFNVADSCFIRAVVEEAEATNTPAIISIHPSEHDFVGDAF 60 Query: 61 TLMAVELAKEARVPVAVHLDHGSSYESVLRALRAGFTSVMIDKSHEDFETNVRETRRVVE 120 ++ + +RVP +HLDHG+S E VLRA++ GFTSVMID S +E NV TR VV Sbjct: 61 FSYVRDITQRSRVPFTLHLDHGASVEHVLRAIQCGFTSVMIDGSLLPYEENVALTREVVR 120 Query: 121 AAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGA 180 AHAVGV+VE ELG + V + T+P +A F+ RTG D LAVAIGT+HG Sbjct: 121 LAHAVGVSVEGELGTIGQTGTSVEGGVSEVTYTDPAQAEDFVARTGVDTLAVAIGTAHGI 180 Query: 181 YKGKGRPFIDHARLERIARLVPAPLVLHGASAVPPELVERFRASGGEIGEAAGIHPEDIK 240 Y +P + L IA + PLVLHG SA P +I Sbjct: 181 YPKGMQPKLQMHILRDIAGRLSIPLVLHGGSANP---------------------DAEIA 219 Query: 241 KAISLGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPAREAVKEVVKSRMELFG 300 ++++LG+ KIN +D++ A+ RE L K +DP A +EV++ +M+LFG Sbjct: 220 ESVTLGVGKINISSDMKYAYFQKAREILAKE-TWWDPNVIYPEPINAAREVIRHKMKLFG 278 Query: 301 SVGRA 305 S G+A Sbjct: 279 STGKA 283 Lambda K H 0.317 0.134 0.369 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: 219 Number of extensions: 9 Number of successful extensions: 3 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: 305 Length of database: 286 Length adjustment: 26 Effective length of query: 279 Effective length of database: 260 Effective search space: 72540 Effective search space used: 72540 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