Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate SM_b20490 SM_b20490 L-fuculose phosphate aldolase
Query= BRENDA::P0AB87 (215 letters) >FitnessBrowser__Smeli:SM_b20490 Length = 232 Score = 182 bits (462), Expect = 4e-51 Identities = 95/213 (44%), Positives = 142/213 (66%), Gaps = 6/213 (2%) Query: 2 ERNKLA--RQIIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFID 59 E +KLA R+++D C M G+NQGTAGN+SVR DG LITP+ +PY+ + +V + Sbjct: 5 ETDKLALRREMVDICRRMNLSGINQGTAGNLSVRTDDGFLITPSSMPYDTMQPDDLVEMG 64 Query: 60 GNGKHEEGKLPSSEWRFHMAAYQSRPDANAVVHNHAVHCTAVSILNRSIPAIHYMIAAAG 119 +G + G PSSEWRFH ++R D + V+H H+++ T ++ +++IP+ HYM AG Sbjct: 65 FDGTYV-GHRPSSEWRFHRDILRARTDIDVVLHCHSIYATTLACHHKTIPSFHYMTGIAG 123 Query: 120 GNSIPCAPYATFGTRELSEHVALALKNRKATLLQHHGLIACEVNLEKALWLAHEVEVLAQ 179 G +I CA YATFGT+ LS++ LALK+R A LL HG I+ LE+ALWLA EVE L++ Sbjct: 124 GTTIRCAEYATFGTQALSDNALLALKDRLACLLGQHGQISLGKTLEQALWLAIEVETLSR 183 Query: 180 LYLTTLAITDPVPVLSDEEIAVVLEKFK--TYG 210 +Y+ L + +P P+L D+E+ V+ + + +YG Sbjct: 184 IYVQALTLGEP-PILPDDEMERVIAQMRRMSYG 215 Lambda K H 0.319 0.134 0.394 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: 133 Number of extensions: 10 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: 215 Length of database: 232 Length adjustment: 22 Effective length of query: 193 Effective length of database: 210 Effective search space: 40530 Effective search space used: 40530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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