Align 2-keto-3-deoxy-galactonokinase (characterized, see rationale)
to candidate Pf1N1B4_400 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)
Query= uniprot:B2SYR9 (350 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_400 Length = 330 Score = 305 bits (780), Expect = 1e-87 Identities = 171/324 (52%), Positives = 210/324 (64%), Gaps = 10/324 (3%) Query: 26 AALIALDWGTTSLRAYLYDASGNVLATRASTAGIMNLPRSAE-------QGGFDAAFDDT 78 A LIALDWGTTSLRAY G VL R+ ++GIM LPR+ GF+ AFD+ Sbjct: 3 AQLIALDWGTTSLRAYKLGFGGQVLEQRSLSSGIMQLPRTPRIIVGQECADGFELAFDEA 62 Query: 79 CGAWLAHAPAAPVIAAGMVGSAQGWLEAPYVDTPASADALVAGIVRVKAACGVTLHIVPG 138 CG WL P PVIA GMVGSAQGW EA Y DTPA+ L + V++ GV +HIVPG Sbjct: 63 CGDWLDAQPDLPVIACGMVGSAQGWREAAYCDTPANVANLGTSLQIVRSLRGVDVHIVPG 122 Query: 139 VLQRGELPNVMRGEETQIFGALGEETNTADSGKRSLIGLPGTHAKWAVVQADRIERFHTF 198 V+QR LPNVMRGEETQ+ G L + + +G LIGLPG+H+KW V I F TF Sbjct: 123 VIQRSRLPNVMRGEETQVLGVL--QHLPSGAGNDLLIGLPGSHSKWVEVADGCIVHFDTF 180 Query: 199 MTGEVFAALREHTILGRTMLTPDSPDTSAFLHGVNIA-REKGQAGVLATVFSSRTLGLTG 257 MTGEVFA L EH+ILGRT S + AF GV +A G+ G L+T+FS+R+LGLTG Sbjct: 181 MTGEVFAVLSEHSILGRTQQRGASFNGEAFDRGVRVALSADGEIGPLSTLFSARSLGLTG 240 Query: 258 QLSREQQPDYLSGLLIGHELAGLDAVLAQQQSALAGQSLRLIGNEALCERYRLALAQFGC 317 +LS QPDYLSGLLIGHELA L V ++++++ S+ LIGN LC RY AL G Sbjct: 241 ELSATAQPDYLSGLLIGHELAALANVQRRRRNSVHLPSIILIGNSQLCARYSRALDACGF 300 Query: 318 TQAELVKHATERGLWRVASQAGLV 341 + L + ATERGLW++A AGL+ Sbjct: 301 ARVTLAEQATERGLWQLAVAAGLI 324 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: 344 Number of extensions: 8 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: 330 Length adjustment: 28 Effective length of query: 322 Effective length of database: 302 Effective search space: 97244 Effective search space used: 97244 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