Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate SMc02486 SMc02486 oxidoreductase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__Smeli:SMc02486 Length = 250 Score = 145 bits (367), Expect = 6e-40 Identities = 97/253 (38%), Positives = 136/253 (53%), Gaps = 14/253 (5%) Query: 7 VVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGRRVIA 66 V++VTGGSRGIG A+A+A A+EG VA+NY + D A +VV I G ++ Sbjct: 6 VLLVTGGSRGIGAAVALAAASEGWRVAVNYASNRD-------AAEDVVRRIAEAGGTAVS 58 Query: 67 IEGNVAARETGQQLVRHTVEAFGKVDVLASNAGIC-PFHAFLDMPPEVLESTVAVNLNGA 125 +EGNV E + + AFG++D L +NAGI P ++ PE +E VN+ G+ Sbjct: 59 VEGNVGREEGVRAIFAAVDTAFGRLDGLVNNAGIIGPPQRVDEVSPERIEQLFRVNVTGS 118 Query: 126 FYVTQAAAQQMKLQ--GTGGAIVATSSISALVGG-GMQTHYTPTKAGVHSLMQSCAVALG 182 A +M + G GG+IV SSI+A++G G Y TK + S A + Sbjct: 119 IRCAAEAVLRMSARHGGRGGSIVNLSSIAAVLGAPGQYVDYAATKGAIDSFTVGLAREVA 178 Query: 183 PYGIRCNSVMPGTIATDLNAQ-DLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 GIR N+V PG I T+++A L D A+ IP+ R G +VAD + +L SD+A Sbjct: 179 TEGIRVNAVRPGIIDTEIHASGGLPDRARD--LAPTIPIQRPGTAGEVADAILYLLSDKA 236 Query: 242 RYVTGAALLVDGG 254 YVTG L V GG Sbjct: 237 TYVTGTILTVSGG 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: 179 Number of extensions: 12 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: 250 Length adjustment: 24 Effective length of query: 236 Effective length of database: 226 Effective search space: 53336 Effective search space used: 53336 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