Align 2-keto-3-deoxy-galactonokinase (characterized, see rationale)
to candidate AO356_20280 AO356_20280 2-dehydro-3-deoxygalactonokinase
Query= uniprot:B2SYR9 (350 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20280 Length = 326 Score = 305 bits (781), Expect = 1e-87 Identities = 172/328 (52%), Positives = 208/328 (63%), Gaps = 13/328 (3%) Query: 26 AALIALDWGTTSLRAYLYDASGNVLATRASTAGIMNLPRSAEQ-------GGFDAAFDDT 78 A LIALDWGTTSLRAY A G VL R+ ++GIM LP GF+ AFD+ Sbjct: 3 AQLIALDWGTTSLRAYKLAAGGEVLEQRSLSSGIMQLPSGPRNVAGQVCIDGFELAFDEA 62 Query: 79 CGAWLAHAPAAPVIAAGMVGSAQGWLEAPYVDTPASADALVAGIVRVKAACGVTLHIVPG 138 CG WL P PVIA GMVGSAQGW EAPY DTPA+ L + V++ GV +HIVPG Sbjct: 63 CGDWLDAQPGLPVIACGMVGSAQGWREAPYCDTPANVANLGHSLQTVRSLRGVDVHIVPG 122 Query: 139 VLQRGELPNVMRGEETQIFGALGEETNTADSGKRSLIGLPGTHAKWAVVQADRIERFHTF 198 V+QR LPNVMRGEETQ+ GAL + A LIGLPG+H+KW V RI F TF Sbjct: 123 VIQRSRLPNVMRGEETQVLGALHSLPDEA-----VLIGLPGSHSKWVEVADGRIVHFDTF 177 Query: 199 MTGEVFAALREHTILGRTMLTPDSPDTSAFLHGVNIARE-KGQAGVLATVFSSRTLGLTG 257 MTGE+FA L +H+ILGRT + D AF GV +A GQ G L+TVFS+R+LGLTG Sbjct: 178 MTGEIFAVLSDHSILGRTQQRSVTFDGVAFDRGVQVALSVDGQIGPLSTVFSARSLGLTG 237 Query: 258 QLSREQQPDYLSGLLIGHELAGLDAVLAQQQSALAGQSLRLIGNEALCERYRLALAQFGC 317 +L Q DYLSGLLIGHEL L V +++ +L ++ LIGN LC RY+ AL G Sbjct: 238 ELGASAQADYLSGLLIGHELTALAQVQRRRRDSLHLPTVVLIGNSQLCVRYQRALDACGF 297 Query: 318 TQAELVKHATERGLWRVASQAGLVKPAA 345 + L + ATERGLW++A AGL+ A Sbjct: 298 ARVVLAEQATERGLWQLAVAAGLLDSTA 325 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: 320 Number of extensions: 12 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: 350 Length of database: 326 Length adjustment: 28 Effective length of query: 322 Effective length of database: 298 Effective search space: 95956 Effective search space used: 95956 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