Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate H281DRAFT_01159 H281DRAFT_01159 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::A3LZU7 (258 letters) >FitnessBrowser__Burk376:H281DRAFT_01159 Length = 266 Score = 151 bits (382), Expect = 1e-41 Identities = 92/249 (36%), Positives = 134/249 (53%), Gaps = 8/249 (3%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVV-VNHLPSEEQAQLAKELKEEISDGENNVL 63 L GKV +TG TG+G +A+ +A+ G +V V+ + + + +D Sbjct: 21 LGGKVAIVTGSNTGLGAGMALALAQAGCDIVGVSRADAGDTPARVEVTGRRFAD------ 74 Query: 64 TIPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGA 123 + D+S IV AVE FG I+V V+NAG+ ++ L+ T + +++NL Sbjct: 75 -VRADLSSTAPVEDIVRAAVEAFGRIDVLVNNAGIIRRQDALDFTEDDWDAVMDLNLKSL 133 Query: 124 FFAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYG 183 FF QAAA+Q VKQ GG II I+S+ + GG YT +K+G+L L + A Sbjct: 134 FFLAQAAARQFVKQQSGGKIINIASMLSFQGGIRVASYTASKSGVLGLTRLLANEWAAKR 193 Query: 184 IRCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNYVN 243 I NAI PG ++TA +D ++ + RIP GR G P D+AGP +FLAS S+YV+ Sbjct: 194 INVNAIAPGYMATANTAALREDAQRNDEILSRIPAGRWGAPDDLAGPVVFLASSASDYVH 253 Query: 244 GAQLLVDGG 252 G L VDGG Sbjct: 254 GHTLAVDGG 262 Lambda K H 0.317 0.136 0.382 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: 135 Number of extensions: 5 Number of successful extensions: 1 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: 258 Length of database: 266 Length adjustment: 25 Effective length of query: 233 Effective length of database: 241 Effective search space: 56153 Effective search space used: 56153 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: 47 (22.7 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