Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate GFF709 PGA1_c07240 putative 5-dehydro-2-deoxygluconokinase
Query= reanno::pseudo5_N2C3_1:AO356_23160 (645 letters) >FitnessBrowser__Phaeo:GFF709 Length = 330 Score = 149 bits (375), Expect = 2e-40 Identities = 103/323 (31%), Positives = 158/323 (48%), Gaps = 25/323 (7%) Query: 15 ICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLRSAMLSRVGDDHMGR 74 + +GR+G+DL G D +GGSSANIA G ++G RSA+++ V DD +G Sbjct: 17 LVIGRVGMDLCPTPAGTATADAQDMMVAMGGSSANIAAGLVKMGCRSALVTSVSDDAVGW 76 Query: 75 FLVESLAREGCDVSGIK-VDPERLTAMVLL--GIKDRETFPLVFYRENCADMALRAEDID 131 + + L G D + +K + E T++ + ++D ++ V YR N AD + D++ Sbjct: 77 YCLNQLDHYGVDRTHVKRITGEYRTSLAVYESRVEDHQS---VIYRNNAADFQMTIADVE 133 Query: 132 ETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPVLWGLASKADGE 191 + AL+ GT F+ + A+ +A D A+ + + D+DYRP W A Sbjct: 134 AVDYSQYSALITAGTVFAAEPSRSATFRAFDLARAAGLPIIFDVDYRPYSWPSPEVA--- 190 Query: 192 TRFVADQKVSQHVQSILPRFDLIVGTEEEF-LIAGGSEDLLTALRTVRSLTAATLVVKLG 250 AD S D+IVG +EEF +AGG + R + +A+ +V K+G Sbjct: 191 ----ADVLSRAGAMS-----DIIVGNDEEFGFMAGGIDKGRAKARALAETSASVVVYKMG 241 Query: 251 PQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDASDERCCQLAN 310 P+G R IYP V+ L GAGD+FM+GFLA E + + Sbjct: 242 PKGAVTFADGQEIRT---GIYP---VDALKPTGAGDSFMAGFLASLSEGRPMKDAILRGS 295 Query: 311 ACGGLVVSRHACAPAMPTRAELD 333 AC +VV++ CAPAMP A L+ Sbjct: 296 ACASVVVAKPGCAPAMPDLAALE 318 Lambda K H 0.322 0.137 0.413 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: 495 Number of extensions: 22 Number of successful extensions: 5 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: 645 Length of database: 330 Length adjustment: 33 Effective length of query: 612 Effective length of database: 297 Effective search space: 181764 Effective search space used: 181764 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 (21.9 bits) S2: 51 (24.3 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