Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Koxy:BWI76_RS23705 Length = 244 Score = 144 bits (363), Expect = 2e-39 Identities = 95/251 (37%), Positives = 139/251 (55%), Gaps = 9/251 (3%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L KT IVTGA+RGIG A+ AR+GARV+I + G A A SL E G A Sbjct: 1 MKLASKTAIVTGAARGIGFGIAQVLAREGARVIIADRDA-HGEAAAASLRES----GAQA 55 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 + + + D E L + A EAFG+VD++VNNAGI + + + NL G Sbjct: 56 LFISCNIGDKAQVEALFSQAEEAFGAVDIVVNNAGINRDAMLHKLSEADWDTVIDVNLKG 115 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 + +Q AA RM+E+G G II ++S S L G QT+Y+ +KAG++ + ++ L Sbjct: 116 TFLCMQQAAIRMRERG-AGRIINIASASWL-GNVGQTNYSASKAGVVGMTKTACRELAKK 173 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 G+ NA+ PG I TD+ + ++ + M +++P G GE D+ + FLASD ARY+ Sbjct: 174 GVTVNAICPGFIDTDMTRGVPENV--WQIMINKIPAGYAGEAKDVGECVAFLASDGARYI 231 Query: 241 TGASLLVDGGL 251 G + V GG+ Sbjct: 232 NGEVINVGGGM 242 Lambda K H 0.319 0.136 0.383 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: 145 Number of extensions: 10 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: 256 Length of database: 244 Length adjustment: 24 Effective length of query: 232 Effective length of database: 220 Effective search space: 51040 Effective search space used: 51040 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