Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate BWI76_RS26950 BWI76_RS26950 2-dehydro-3-deoxygluconokinase
Query= BRENDA::Q97U29 (313 letters) >FitnessBrowser__Koxy:BWI76_RS26950 Length = 312 Score = 149 bits (377), Expect = 6e-41 Identities = 104/312 (33%), Positives = 160/312 (51%), Gaps = 19/312 (6%) Query: 2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEF 61 +DVI +GE + F + G L V +F K VAG+ELN + R LS ++RVG D F Sbjct: 5 LDVITIGEAMAMFVATETGELSAVEHFMKRVAGAELNVATGLARLGLSVGWVSRVGKDSF 64 Query: 62 GKNIIEYSRAQGIDTSHIKVDNESFTGIYF---IQRGY-PIPMKSELVYYRKGSAGSRLS 117 G+ ++ +GID + +D+ TG ++ G PI + Y+RKGSA S LS Sbjct: 65 GRFVLNALAKEGIDARGVSIDDRYATGFQLKSKVENGTDPI-----VEYFRKGSAASHLS 119 Query: 118 PEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSR----SLDTNIRPKLWSSL 173 PED NE+Y +R +H +G+ A+S+++ + +A K++ S D N+RP LW S Sbjct: 120 PEDFNESYFAGARHLHLSGVAAALSESSYALLERAAHTMKAQGKTISFDPNLRPTLWKSE 179 Query: 174 EKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAI 233 + E + + + + ++ + IL + P+ Y GV+ ++ K GS GA Sbjct: 180 AEMVEKLNQL--AFQADWVLPGLKEGMILTGLQTPEAIADFYLGHGVRAVIIKTGSDGA- 236 Query: 234 AYK--DNVKAFKDAYKVP-VEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVIT 290 YK D + A KV V D GAGD A +S L+GK + ++ G +L I Sbjct: 237 WYKTADGEQGAVAAIKVDNVVDTVGAGDGFAVGVISALLEGKPLRQAVKRGNKIGSLAIQ 296 Query: 291 VRGDNELTPTLE 302 V+GD+E PT E Sbjct: 297 VQGDSEGLPTRE 308 Lambda K H 0.317 0.136 0.383 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: 253 Number of extensions: 11 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: 313 Length of database: 312 Length adjustment: 27 Effective length of query: 286 Effective length of database: 285 Effective search space: 81510 Effective search space used: 81510 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 (21.6 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