Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate 15215 b1093 3-oxoacyl-[acyl-carrier-protein] reductase (NCBI)
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__Keio:15215 Length = 244 Score = 127 bits (319), Expect = 2e-34 Identities = 85/257 (33%), Positives = 135/257 (52%), Gaps = 14/257 (5%) Query: 1 MLLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEAL 60 M + K+ +VTG SRGIGRAIA AA GA V +N A+ +++ L Sbjct: 1 MNFEGKIALVTGASRGIGRAIAETLAARGAKVIGTATSENG---------AQAISDY--L 49 Query: 61 GRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAV 120 G + NV + + ++ FG+VD+L +NAGI + + M E + Sbjct: 50 GANGKGLMLNVTDPASIESVLEKIRAEFGEVDILVNNAGITRDNLLMRMKDEEWNDIIET 109 Query: 121 NLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVA 180 NL+ F +++A + M ++ G I+ S+ +G G Q +Y KAG+ +S A Sbjct: 110 NLSSVFRLSKAVMRAM-MKKRHGRIITIGSVVGTMGNGGQANYAAAKAGLIGFSKSLARE 168 Query: 181 LGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDR 240 + GI N V PG I TD+ + L+D+ ++A ++P GRLG +++A+ V FLASD Sbjct: 169 VASRGITVNVVAPGFIETDMT-RALSDD-QRAGILAQVPAGRLGGAQEIANAVAFLASDE 226 Query: 241 ARYVTGAALLVDGGLFV 257 A Y+TG L V+GG+++ Sbjct: 227 AAYITGETLHVNGGMYM 243 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: 139 Number of extensions: 6 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: 260 Length of database: 244 Length adjustment: 24 Effective length of query: 236 Effective length of database: 220 Effective search space: 51920 Effective search space used: 51920 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: 46 (22.3 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