Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_055437269.1 ASC41_RS13975 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_001418085.1:WP_055437269.1 Length = 248 Score = 127 bits (319), Expect = 2e-34 Identities = 82/248 (33%), Positives = 129/248 (52%), Gaps = 5/248 (2%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFV-DILVEESTQLVADLKQTQPEASVTFY 68 L+GKT I+G + GIG + F +QGA VAF VE + L +L +A Y Sbjct: 4 LEGKTAIITGASRGIGKGIAEVFAQQGANVAFTYSSSVEAANALEKELNALGVKAKG--Y 61 Query: 69 HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFF 128 + + +++ V + G I +LINNA + + + + +D+ + NL+ F Sbjct: 62 KSNAANFDESQKLAEDVLAEFGSIDILINNAGITKDNLLMRMGEADFDKVIEVNLKSVFN 121 Query: 129 AVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRI 188 +AV+ M + GS+IN+ S+ AG Y ASKAG +G ++ +A +LG IR Sbjct: 122 MTKAVQRTMLKQRKGSIINMSSVVGVKGNAGQTNYAASKAGIIGFSKSVALELGSRNIRS 181 Query: 189 NTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQN 248 N + PG++ T ++T +D++T K N +K PEDIA + +FLA+D S T Q Sbjct: 182 NVIAPGFIET--EMTAKLDEETVKSWRNAIPLKRGGTPEDIANVCVFLASDMSAYVTGQT 239 Query: 249 FIVDGGWI 256 VDGG + Sbjct: 240 INVDGGML 247 Lambda K H 0.320 0.134 0.406 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: 128 Number of extensions: 10 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: 256 Length of database: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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 24 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