Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate 6937211 Sama_1381 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__SB2B:6937211 Length = 252 Score = 116 bits (290), Expect = 5e-31 Identities = 92/266 (34%), Positives = 134/266 (50%), Gaps = 27/266 (10%) Query: 1 MLLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGR-RSAVAEVVAEIEA 59 M LKDKV+++TGG+ G+G A+A AA GA +A+ DV R A A++ E Sbjct: 1 MELKDKVIVITGGAGGLGLAMAKDLAAHGAKLALI-----DVDQERLERACADIGDATEV 55 Query: 60 LGRRV-IAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLD---------M 109 G + I E +V A R+ +E FG + L +NAGI + M Sbjct: 56 QGYALDITDEEDVVAG------FRYILEDFGVIHGLVNNAGILRDGLLIKAKDGVVTDRM 109 Query: 110 PPEVLESTVAVNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAG 169 + +S + VNL G F + AA M G GG IV SS+ A G QT+Y +KAG Sbjct: 110 SLDQFQSVINVNLTGTFLCGREAAAAMIESGQGGVIVNISSL-ARAGNMGQTNYAASKAG 168 Query: 170 VHSLMQSCAVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDV 229 V ++ A L + IR +V PG IAT++ A + ++ EK +P+GRLG+ E++ Sbjct: 169 VATMAVGWAKELARFNIRAAAVAPGVIATEMTAAMKPEALER--LEKMVPVGRLGQAEEI 226 Query: 230 ADCVTFLASDRARYVTGAALLVDGGL 255 A V F+ + YV G +DGG+ Sbjct: 227 ASTVRFIMEN--DYVNGRVFEIDGGI 250 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: 156 Number of extensions: 9 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: 260 Length of database: 252 Length adjustment: 24 Effective length of query: 236 Effective length of database: 228 Effective search space: 53808 Effective search space used: 53808 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