Align L-fuculose-phosphate aldolase (EC 4.1.2.17) (characterized)
to candidate Pf1N1B4_5075 Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases
Query= BRENDA::Q58813 (181 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5075 Length = 212 Score = 87.8 bits (216), Expect = 1e-22 Identities = 57/182 (31%), Positives = 98/182 (53%), Gaps = 8/182 (4%) Query: 3 KKQFIKICRKLYDRKYVVGSGGNVSVKEGDKIYLTPTGSILGFLKEDDIAEMDLDGNVIK 62 +++ ++ R LY+R Y VGS GN+S + D +TPT LG L IA+++L G + Sbjct: 8 REEICQVGRSLYERGYTVGSAGNISARLDDGWLITPTDVCLGRLDPATIAKVNLAGEWVS 67 Query: 63 G-KPTSEKNLHLMIYRKRNDINAIIHTHS--LISTFLSTINKEIELLTPEGKIFLKKIGY 119 G KP+ LH +Y + + ++HTHS L++ L+ + + ++L P + K+G+ Sbjct: 68 GDKPSKTLALHRQVYDRNPSVGGVVHTHSTHLVALTLAGVWQPNDILPPLTPYQVMKVGH 127 Query: 120 ---VDYYEAGSLKLAEETAKRDEDV--IILKNHGVVCLGKDLIDAYIKVEVLEEQAKLTL 174 + Y GS K+AE+ A+ V ++L+ G V + A +E LEE A+L L Sbjct: 128 IPLIGYQRPGSPKVAEQVAQLANSVRGVMLERLGPVVWESSVSRASYALEELEETARLWL 187 Query: 175 LN 176 ++ Sbjct: 188 MS 189 Lambda K H 0.318 0.139 0.385 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: 80 Number of extensions: 5 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: 181 Length of database: 212 Length adjustment: 20 Effective length of query: 161 Effective length of database: 192 Effective search space: 30912 Effective search space used: 30912 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: 45 (21.9 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