Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate N515DRAFT_3178 N515DRAFT_3178 2-dehydro-3-deoxyphosphogluconate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase
Query= metacyc::MONOMER-15645 (213 letters) >FitnessBrowser__Dyella79:N515DRAFT_3178 Length = 216 Score = 213 bits (541), Expect = 3e-60 Identities = 111/212 (52%), Positives = 146/212 (68%), Gaps = 3/212 (1%) Query: 1 MKNWKTSAEQI---LTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAI 57 M + +T +Q+ L PVVPV++I+ AVPMA+ALVAGG+ +E+TLRT A++AI Sbjct: 1 MSSIETKQQQVEATLRLAPVVPVVIIDDARAAVPMARALVAGGIPAIEVTLRTPAALDAI 60 Query: 58 RLIAQEVPDAIVGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGIST 117 R IA EV A+VG GTV P+ L AGA+FA+SPG++ LL AA + +PL+PG++T Sbjct: 61 RAIAAEVEGAVVGVGTVLTPRDLEHARQAGAKFAVSPGVSPKLLAAADDSDLPLLPGVAT 120 Query: 118 VSELMLGMDYGLREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKS 177 SE M ++ G R KFFPA GG K L A A P +IRFCPTGGISL + ++L+L + Sbjct: 121 ASEAMSLLERGYRHLKFFPAVPAGGHKLLGAWASPLPQIRFCPTGGISLTSAPEFLSLPN 180 Query: 178 VLCVGGSWLVPADALESGDYDRITALAREAVA 209 V+CVGGSWL P D L+SGD+ I ALAREA A Sbjct: 181 VVCVGGSWLTPVDKLKSGDWAGIEALAREAAA 212 Lambda K H 0.318 0.135 0.390 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: 177 Number of extensions: 5 Number of successful extensions: 1 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: 213 Length of database: 216 Length adjustment: 22 Effective length of query: 191 Effective length of database: 194 Effective search space: 37054 Effective search space used: 37054 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 (21.7 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