Align 2-keto-3-deoxy-galactonokinase (characterized, see rationale)
to candidate H281DRAFT_06294 H281DRAFT_06294 2-keto-3-deoxygalactonate kinase (EC 2.7.1.58)
Query= uniprot:B2SYR9 (350 letters) >FitnessBrowser__Burk376:H281DRAFT_06294 Length = 374 Score = 578 bits (1491), Expect = e-170 Identities = 301/373 (80%), Positives = 318/373 (85%), Gaps = 23/373 (6%) Query: 1 MKRAGSPT----QAAGHAAAVAVDAS-------------------HEHAALIALDWGTTS 37 MK AGSPT Q A AAA V A+ + HAALIALDWGTTS Sbjct: 1 MKHAGSPTPSDAQVAVGAAAAGVPANAGINAEANAEANAEANAEANSHAALIALDWGTTS 60 Query: 38 LRAYLYDASGNVLATRASTAGIMNLPRSAEQGGFDAAFDDTCGAWLAHAPAAPVIAAGMV 97 LRAYLYDASG VLATRASTAGIMNLPRSAEQGGFDAAF+D CGAWL AP APVIAAGMV Sbjct: 61 LRAYLYDASGKVLATRASTAGIMNLPRSAEQGGFDAAFEDACGAWLKAAPGAPVIAAGMV 120 Query: 98 GSAQGWLEAPYVDTPASADALVAGIVRVKAACGVTLHIVPGVLQRGELPNVMRGEETQIF 157 GSAQGWLEAPYVD PA+ADAL AGIVRVKAACG TLHI+PGVLQRGELPNVMRGEETQIF Sbjct: 121 GSAQGWLEAPYVDAPANADALAAGIVRVKAACGATLHIIPGVLQRGELPNVMRGEETQIF 180 Query: 158 GALGEETNTADSGKRSLIGLPGTHAKWAVVQADRIERFHTFMTGEVFAALREHTILGRTM 217 GAL E++ ADS R+LIGLPGTHAKWAVVQA RIERFHTFMTGEVF ALREHTILGRTM Sbjct: 181 GALSEDSRDADSSNRALIGLPGTHAKWAVVQAGRIERFHTFMTGEVFGALREHTILGRTM 240 Query: 218 LTPDSPDTSAFLHGVNIAREKGQAGVLATVFSSRTLGLTGQLSREQQPDYLSGLLIGHEL 277 +TPD PD+ AFL GVNIAR+KGQAGVLATVFSSRTLGLTGQLS EQQPDYLSGLLIGHEL Sbjct: 241 VTPDRPDSEAFLRGVNIARDKGQAGVLATVFSSRTLGLTGQLSPEQQPDYLSGLLIGHEL 300 Query: 278 AGLDAVLAQQQSALAGQSLRLIGNEALCERYRLALAQFGCTQAELVKHATERGLWRVASQ 337 AGL+ VL QQQS+LAGQSLRLIGNEALCERYR+ALA+FGCTQAELVK ATERGLWRVASQ Sbjct: 301 AGLETVLKQQQSSLAGQSLRLIGNEALCERYRVALARFGCTQAELVKQATERGLWRVASQ 360 Query: 338 AGLVKPAAKTARA 350 AGLV PAA+ A+A Sbjct: 361 AGLVNPAARAAQA 373 Lambda K H 0.318 0.131 0.384 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: 512 Number of extensions: 14 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: 350 Length of database: 374 Length adjustment: 29 Effective length of query: 321 Effective length of database: 345 Effective search space: 110745 Effective search space used: 110745 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 (21.7 bits) S2: 49 (23.5 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