Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate PfGW456L13_2119 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::A3LZU7 (258 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2119 Length = 272 Score = 127 bits (320), Expect = 2e-34 Identities = 87/259 (33%), Positives = 137/259 (52%), Gaps = 23/259 (8%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64 L KVV +TG GIG AI A A+++++ + E+ ++A +++ +D V+ Sbjct: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGAD----VVA 74 Query: 65 IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124 I D+S + + LA++ G I+V V+ AGV FR+ LE+T E + I+L+GA+ Sbjct: 75 IKADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAW 134 Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTP-------TKAGILSLMQSTAC 177 + +A QM++QG GSII I+S H TH P K G+L L ++ Sbjct: 135 YGCKAVLPQMIEQGI-GSIINIAS-------THSTHIIPGCFPYPVAKHGLLGLTRALGI 186 Query: 178 ALGKYGIRCNAILPGTISTALNEE---DLKDPE-KRKYMEGRIPLGRVGDPKDIAGPAIF 233 G+R NAI PG I T LN + DP +R+ P R+G P ++A A+F Sbjct: 187 EYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVF 246 Query: 234 LASDMSNYVNGAQLLVDGG 252 LASD + ++N + + +DGG Sbjct: 247 LASDEAPFINASCITIDGG 265 Lambda K H 0.317 0.136 0.382 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: 121 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: 258 Length of database: 272 Length adjustment: 25 Effective length of query: 233 Effective length of database: 247 Effective search space: 57551 Effective search space used: 57551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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