Align 2-keto-3-deoxygalactonate kinase protein; EC 2.7.1.58 (characterized, see rationale)
to candidate GFF30 PS417_00155 2-dehydro-3-deoxygalactonokinase
Query= uniprot:D8J0Z3 (319 letters) >FitnessBrowser__WCS417:GFF30 Length = 319 Score = 315 bits (806), Expect = 1e-90 Identities = 172/311 (55%), Positives = 209/311 (67%), Gaps = 6/311 (1%) Query: 10 LIALDWGTSSLRCYRYDGSGQVVERRAHPWGIMNLPAVEH---GDDAQAPYRAALEAACG 66 LIALDWGTSSLR Y+ +G V+E+RA WGIM+LP+ G + A +AACG Sbjct: 5 LIALDWGTSSLRAYKLGLAGVVLEQRALAWGIMHLPSEPRDIAGVRCGNGFELAFDAACG 64 Query: 67 DWIAAAPEAALIAAGMVGSKQGWREAAYLTVPLAPDGIGRKLTEVDTGLGRSLWIIPGLL 126 DW+ A P +IA GMVGS QGW EAAY P+ +G+ L +V + G + I+PG++ Sbjct: 65 DWLDAEPGLPVIACGMVGSAQGWSEAAYRPTPVDVASLGQALHKVRSLRGVDVHIVPGVI 124 Query: 127 QNSALPNVMRGEETQVIGALQQQRQSELLIGLPGTHSKWVRVVEGRIEHFDTFMTGEVYG 186 + LPNVMRGEETQV+G LQ +++LIGLPG+HSKWV VVEGRI HFDTFMTGEV+ Sbjct: 125 EQVGLPNVMRGEETQVLGVLQGLG-ADMLIGLPGSHSKWVEVVEGRITHFDTFMTGEVFA 183 Query: 187 ALCGHTILGRTMHKPDVPDDAAFVRGARVAQGPQGQAGVLSNIFSSRTLGLTGELAPEAQ 246 L H+ILGRT + AF RG VA+ GQ GVLS +FS+RTLGLTGELAP+ Q Sbjct: 184 VLSKHSILGRTQQPSERFQAEAFDRGVHVARSNDGQRGVLSTLFSARTLGLTGELAPDQQ 243 Query: 247 PDYLSGLLIGHEIAALKSLYPAQQAPIVLIGDAGLCRRYRLALELYGLGPVSEADAATEA 306 PDYLSGLLIGHE+A L A+ PI+L+G A LC RY+ AL L G VS A A E Sbjct: 244 PDYLSGLLIGHELAGLPD--SAKHKPIILVGAAPLCARYQRALALCGFAHVSLAQEAAER 301 Query: 307 GLWILARHAGL 317 GLW LA AGL Sbjct: 302 GLWQLAVAAGL 312 Lambda K H 0.320 0.137 0.423 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: 411 Number of extensions: 22 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: 319 Length of database: 319 Length adjustment: 28 Effective length of query: 291 Effective length of database: 291 Effective search space: 84681 Effective search space used: 84681 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: 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