Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_066329803.1 BLR17_RS09120 SDR family oxidoreductase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_900100165.1:WP_066329803.1 Length = 254 Score = 108 bits (270), Expect = 1e-28 Identities = 74/259 (28%), Positives = 129/259 (49%), Gaps = 22/259 (8%) Query: 9 SLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFY 68 SL+ K I+GG +GIG + F +QGA+V +++ E + V ++ E F Sbjct: 3 SLKDKKAIITGGGSGIGKAISVLFAKQGAEVHIIELTAESAQSTVDEITA---EGGKVFA 59 Query: 69 HCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFF 128 H ++A V+A E +G I +L+NNA +D +D+ ++ N++ + Sbjct: 60 HA--CNVAKHDEVVATFEK-IGNIHILVNNAGIAHVGKVDTTPEADFDRIMDVNVKGVYN 116 Query: 129 AVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRI 188 + A PQ ++ GGGS++N+ S++ + Y+ +K M +T +A D + IR Sbjct: 117 CLFASIPQFRKSGGGSIVNMASIASWVGISDRFAYSTAKGAVMSMTLSVARDYINENIRC 176 Query: 189 NTLTPGWVMTKRQLTHWVDKDTAKHIENN-----------QCIKEYVMPEDIAAMALFLA 237 N+++P R T +VD AK+ N Q I PE+IA +ALFLA Sbjct: 177 NSISPA-----RVHTPFVDGFIAKNYPGNEAEIFDKLSKSQPIGRMGKPEEIATLALFLA 231 Query: 238 ADDSKLCTAQNFIVDGGWI 256 ++++ T ++ +DGG+I Sbjct: 232 SEEAGFITGSDYPIDGGFI 250 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: 163 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: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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 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