Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate Echvi_3630 Echvi_3630 Entner-Doudoroff aldolase
Query= BRENDA::A0A0B6VQ18 (222 letters) >FitnessBrowser__Cola:Echvi_3630 Length = 222 Score = 196 bits (499), Expect = 2e-55 Identities = 90/219 (41%), Positives = 142/219 (64%), Gaps = 1/219 (0%) Query: 3 QFSRIEVAQVMKETGLVPLFYHKDVEVSKKVLKACYDGGARLLEFTSRGDFAHEIFAALV 62 +FS E+ + M++TG++P+F H D+EV+K V+ A Y+GG R+ EFT+RG+ A E+F L Sbjct: 2 KFSNSEIIEAMEKTGMIPVFNHSDLEVAKNVMDASYNGGVRVFEFTNRGENALEVFRELK 61 Query: 63 KYAVAELPGMILGVGSVTDAAAASLYMQLGANFIVTPVFREDIAIVCNRRKVMWSPGCGS 122 Y+ + G++LG+G++ +++ GA+FIV+P ++A+ R +W PGCG+ Sbjct: 62 AYS-SRHKGLMLGIGTIFTPKEVEDFIEAGADFIVSPALIPNVAVTATRNDTLWIPGCGT 120 Query: 123 LTEIARAEEMGCEVVKLFPGELYGPAFINGIKGPQPWTTIMPTGGVSPTKESLTEWIKAG 182 +TEI A EMG +V+K FPG + GP+FI+ +K P IMPTGGV PT+E+L +W KAG Sbjct: 121 VTEIFNAREMGAQVIKAFPGNVLGPSFISAVKAVLPSLKIMPTGGVEPTEENLGQWFKAG 180 Query: 183 AVCVGMGSKLIKPESDGNFDLNKIQSLTKECIDIIKELK 221 CVGMGS+L K + + ++ E +D I+ ++ Sbjct: 181 VTCVGMGSQLFKKDWIKQKKFDALEKQISEALDTIQRIR 219 Lambda K H 0.320 0.137 0.411 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: 178 Number of extensions: 9 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: 222 Length of database: 222 Length adjustment: 22 Effective length of query: 200 Effective length of database: 200 Effective search space: 40000 Effective search space used: 40000 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: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. 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