Align 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.178; EC 2.7.1.58) (characterized)
to candidate BWI76_RS03905 BWI76_RS03905 2-oxo-3-deoxygalactonate kinase
Query= ecocyc::DEHYDDEOXGALACTKIN-MONOMER (292 letters) >FitnessBrowser__Koxy:BWI76_RS03905 Length = 290 Score = 288 bits (737), Expect = 1e-82 Identities = 144/285 (50%), Positives = 188/285 (65%), Gaps = 2/285 (0%) Query: 5 YIAIDWGSTNLRAWLYQGDHCLESRQSEAGVTRLNGKSPAAVLAEVTTDWREEKT-PVVM 63 YIA+DWGST LR WL + C+E++Q G+TRLNG++PA V E WR T PV+M Sbjct: 4 YIAVDWGSTQLRGWLIRNGQCVETKQLPLGITRLNGRAPADVFEEHLAPWRGAATLPVLM 63 Query: 64 AGMVGSNVGWKVAPYLSVPACFSSIGEQLTSVGDNIWIIPGLCVSHDDNHNVMRGEETQL 123 AGM+GS+ GW+ PYL+ PA + G+QL +V +++WIIPGL + ++NVMRGEETQL Sbjct: 64 AGMIGSDAGWQAVPYLACPAAIDAPGQQLCAVAEDVWIIPGLKMDQAGDYNVMRGEETQL 123 Query: 124 IGARALAPSSLYVMPGTHCKWVQADSQQINDFRTVMTGELHHLLLNHSLIGAGLPPQENS 183 +GA LAP+ YV+PGTHCKWVQ + + F T MTGELHHLL+ SL+G GLP Q+ Sbjct: 124 LGAWQLAPAECYVLPGTHCKWVQMEDGAVRHFVTAMTGELHHLLMTQSLLGKGLPAQQPD 183 Query: 184 ADAFTAGLERGLNTPAILPQLFEVRASHVLGTLPREQVSEFLSGLLIGAEVASMRDYVAH 243 AF GLE+GL P+++ +LF RA+ VLG L VS++LSGLLIGAEVA M Sbjct: 184 EAAFERGLEKGLAQPSLVSELFVARAARVLGALAATSVSDYLSGLLIGAEVAVMGQRY-R 242 Query: 244 QHAITLVAGTSLTARYQQAFQAMGCDVTAVAGDTAFQAGIRSIAH 288 +TLV +L ARY +A +A G V +GD A G+ I H Sbjct: 243 PSTVTLVGDPALNARYSRAMRARGMTVKRCSGDEALLNGMARIMH 287 Lambda K H 0.319 0.132 0.399 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: 298 Number of extensions: 12 Number of successful extensions: 3 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: 292 Length of database: 290 Length adjustment: 26 Effective length of query: 266 Effective length of database: 264 Effective search space: 70224 Effective search space used: 70224 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