Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate Ac3H11_1501 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= SwissProt::P75682 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1501 Length = 309 Score = 104 bits (259), Expect = 3e-27 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 12/246 (4%) Query: 1 MPQSALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEE 60 MP S L+ ++ P DG +D P AAL L GV G GS GE + L E Sbjct: 21 MPFSGLWIALVTPFK-----DGAVDHPALAALTARLRAQGVAGFVACGSTGEAAALDKAE 75 Query: 61 RKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANL 120 + + + + +PV++G G + + ++ Q + G++V P+Y + S+ L Sbjct: 76 QLQVLETVLQAA-QGLPVVMGVSGYHQGQVLQQVQALARYPVAGLLVSAPHYIRPSQEGL 134 Query: 121 IRYFEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMI 180 + +F +AD+ +P+++Y+ P TG +T + LA + I IKD S A +++I Sbjct: 135 LHWFRTLADASAVPLLIYDIPYRTGATITTETLLALA-AHPRIQAIKDCGGSPAKTQALI 193 Query: 181 HTVKGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAG 240 + VL G D +F+TL LGG GAISAS ++ V L+ R GD+ +A Sbjct: 194 -----SDGRLQVLTGEDAQIFHTLALGGAGAISASAHWQTPRFVELMALLRAGDLGEARR 248 Query: 241 YHQTLL 246 + LL Sbjct: 249 VWRALL 254 Lambda K H 0.320 0.138 0.407 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: 222 Number of extensions: 12 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: 302 Length of database: 309 Length adjustment: 27 Effective length of query: 275 Effective length of database: 282 Effective search space: 77550 Effective search space used: 77550 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: 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