Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate GFF1955 Psest_1998 Entner-Doudoroff aldolase
Query= metacyc::MONOMER-15645 (213 letters) >FitnessBrowser__psRCH2:GFF1955 Length = 214 Score = 195 bits (496), Expect = 5e-55 Identities = 96/201 (47%), Positives = 133/201 (66%) Query: 9 EQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPDAI 68 E+I ++PVI I E +P+A AL AGG+R LE+TLR+ + AIR + +E PD Sbjct: 11 ERICVDARILPVITIGSEEQILPLADALAAGGLRTLEITLRSSHGLTAIRRLREERPDLC 70 Query: 69 VGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYG 128 VGAGTV + + + EV A GAQF ++PG T +L+A ++PL+PGIS+ S+LM G G Sbjct: 71 VGAGTVLDRRMMDEVEATGAQFIVTPGSTREILEAGVSCSVPLLPGISSASDLMEGYALG 130 Query: 129 LREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGSWLVP 188 R FK FPAE GGV AL+A+ GPF +RFCPTGG++ N YLAL +V+CVGG+W++ Sbjct: 131 YRRFKLFPAEVCGGVAALKALGGPFADVRFCPTGGVTAANAASYLALPNVMCVGGTWMID 190 Query: 189 ADALESGDYDRITALAREAVA 209 + +L GD+ I EA+A Sbjct: 191 STSLGEGDWPSIQQRTAEALA 211 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: 170 Number of extensions: 7 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: 214 Length adjustment: 22 Effective length of query: 191 Effective length of database: 192 Effective search space: 36672 Effective search space used: 36672 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