Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate AZOBR_RS26450 AZOBR_RS26450 short-chain dehydrogenase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__azobra:AZOBR_RS26450 Length = 249 Score = 150 bits (379), Expect = 2e-41 Identities = 107/262 (40%), Positives = 141/262 (53%), Gaps = 17/262 (6%) Query: 1 MLLKDKVVIVTGGS--RGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIE 58 MLL +KV ++TG + RGIGRA A A G I D+ G+ AE AE Sbjct: 1 MLLSNKVCVITGAASQRGIGRATARLFALHGGRAIIL-----DLDGGQ---AAEAAAE-- 50 Query: 59 ALGRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTV 118 LG I +V + VE FG++DVL +NAGI F+D+ P+ E+ Sbjct: 51 -LGEAHRGIACDVTDKAACVNAAARVVEEFGRIDVLVNNAGITQPLKFMDIEPKNYEAVT 109 Query: 119 AVNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGM--QTHYTPTKAGVHSLMQS 176 V+L G Y++QA M+ Q G+IV SS+SA GGG+ HY+ KAGV L ++ Sbjct: 110 DVSLRGTLYMSQAVVPHMRAQ-KSGSIVCISSVSAQRGGGIFGGPHYSAAKAGVLGLAKA 168 Query: 177 CAVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFL 236 A LGP +R NSV PG I TD+ L E +A K IPL RLG EDVA FL Sbjct: 169 MARELGPDNVRVNSVTPGLIQTDITGGKLTPEL-RADILKGIPLNRLGDAEDVARSCLFL 227 Query: 237 ASDRARYVTGAALLVDGGLFVN 258 AS+ + YVTGA L V+GG+ ++ Sbjct: 228 ASELSSYVTGATLDVNGGMLIH 249 Lambda K H 0.319 0.134 0.386 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: 172 Number of extensions: 8 Number of successful extensions: 5 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: 260 Length of database: 249 Length adjustment: 24 Effective length of query: 236 Effective length of database: 225 Effective search space: 53100 Effective search space used: 53100 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: 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