Align 6-phosphofructokinase (EC 2.7.1.11); 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) (characterized)
to candidate AO356_24685 AO356_24685 2-dehydro-3-deoxygluconokinase
Query= BRENDA::D4GR05 (318 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24685 Length = 326 Score = 105 bits (262), Expect = 1e-27 Identities = 89/282 (31%), Positives = 127/282 (45%), Gaps = 10/282 (3%) Query: 4 ELVTFGETMIRLSPPEGERIETARSLEFRTAGAESNVAVAASRLGCSAAWLSKLPDSPLG 63 ++++FGETM L + + + R AGA+SNVA+ SRLG AWLS++ LG Sbjct: 5 DVLSFGETMAMLVADQRGDLASVDQFHKRIAGADSNVAIGLSRLGFKVAWLSRVGADSLG 64 Query: 64 RRVTTELRTHGVE-PYVRWDDDARQGAYYIEQGRAPRPTNVIYDRADAAVTTARPDELAV 122 R VT L G++ +V D + G + V Y R +A + +A Sbjct: 65 RFVTQTLENEGLDCRHVAVDPEHPTGFQFKSLTVDGSDPQVEYFRRSSAASHLSVGSIAP 124 Query: 123 DIVEDAAAFYTSGITPALSETLRETTGELLQTATEAGTTTAFDLNYRSKLW-SPSDARDA 181 ++ DA + +GI PALS T RE + EL+ AG + +FD N R LW S S A Sbjct: 125 ALL-DARHVHATGIVPALSGTAREMSFELMSRMRAAGRSLSFDPNLRPSLWGSESTMITA 183 Query: 182 CESLFPKVDVLVAAERDIRAVLELDGDAPTLASELAGDFDFETVVVTRGEDGALARHG-- 239 L ++ + R + D A A L D E VV+ G DGA R Sbjct: 184 INRLAALAHWVLPGLGEGRLLTGFDDPADIAAFYL--DQGAEIVVIKLGADGAYYRTALD 241 Query: 240 -GTVYEQPVFETDTVDAIGTGDAFVGAFLSRLIAGEPVETAL 280 G + PV VD +G GD F +S L+ G + A+ Sbjct: 242 QGVIPGVPV--AQVVDTVGAGDGFAVGLISALLEGRAITEAV 281 Lambda K H 0.315 0.132 0.378 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: 268 Number of extensions: 17 Number of successful extensions: 4 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: 318 Length of database: 326 Length adjustment: 28 Effective length of query: 290 Effective length of database: 298 Effective search space: 86420 Effective search space used: 86420 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: 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