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 WP_084703970.1 BS73_RS11395 5-dehydro-2-deoxygluconokinase
Query= reanno::HerbieS:HSERO_RS12125 (657 letters) >NCBI__GCF_000744815.1:WP_084703970.1 Length = 385 Score = 169 bits (427), Expect = 3e-46 Identities = 119/347 (34%), Positives = 171/347 (49%), Gaps = 19/347 (5%) Query: 22 DLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIAFGCARLGLKSAMLARIGDEAN 81 DLI +GR+ VD+Y Q+G PL++V +F K+LGGS+ N+A ARL +SA+++R G + Sbjct: 21 DLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGADPF 80 Query: 82 GQFLKAELAAEGCDVSHVTVDPQRLTALVMLGLKDKDSFPLIFY-RDNCADMALAPEDID 140 G+++ L G D VT + T + + D FP+ FY R D+ + PE++D Sbjct: 81 GEYVHRALREFGVDDRWVTPVQRYPTPVTFCEIFPPDDFPIWFYRRPKAPDLEIHPEELD 140 Query: 141 EAFIASSKALLITGTHF--STPQVHRSSSLALQYARRHNVRTVLDIDYRPVLWGLTSKGD 198 I S+ ITGT + ++LA + AR TV D+D+RP WG G+ Sbjct: 141 LDAIRSAGIFWITGTGLCEEPSRTATLAALAARSARPGAGPTVFDLDWRPAFWG----GE 196 Query: 199 GETRFIASDGVTQHLQGILPQF-------DLVVGTEEEFMIAGGSTDIMAALRAVRALCA 251 G +G + + P + + VG +E +A G D A A+ L A Sbjct: 197 GGASGDGGEGGARAMAEARPIYREALAHATVAVGNLDEAEVATGLRDPQACAEALLELGA 256 Query: 252 ATLVVKRGPLGCVVLHGAIPERLDDGFHYRGVQVEVLNVLGAGDAFISGFLKGWLNEEDD 311 VVK+GP G + LH R V VEV+N LGAGDAF G L Sbjct: 257 ELAVVKQGPKGVLALH-----RDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPL 311 Query: 312 EHCCRYANACGALVVSRHACAPAMPGPIELDYFLQHAHRLQRPDRDA 358 E R+ANA GA+V R AC+ AMP P E++ L P+ +A Sbjct: 312 ERTVRWANAAGAIVAGRLACSSAMPTPEEIEQRLTETETRADPETEA 358 Lambda K H 0.322 0.137 0.414 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: 582 Number of extensions: 28 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: 657 Length of database: 385 Length adjustment: 34 Effective length of query: 623 Effective length of database: 351 Effective search space: 218673 Effective search space used: 218673 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: 52 (24.6 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