Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_009122055.1 BUB52_RS10260 gluconate 5-dehydrogenase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_900129655.1:WP_009122055.1 Length = 267 Score = 119 bits (299), Expect = 5e-32 Identities = 78/258 (30%), Positives = 136/258 (52%), Gaps = 10/258 (3%) Query: 5 NQYP--SLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPE 62 NQY SL+GK ++G + GIG + +AF EQGAK+ F DI E + +A + + Sbjct: 2 NQYLNFSLEGKVALVTGASYGIGFAIASAFAEQGAKICFNDINQELVDKGIAAYAEKGIQ 61 Query: 63 ASVTFYHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTN 122 A Y CD+ D A++ ++A +E ++G + +L+NNA +R + E+ + + ++ + Sbjct: 62 AHG--YVCDVTDEPAVQAMVATIEKEVGSVDILVNNAGIIRRIPMHEMEAADFRKVIDID 119 Query: 123 LRHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLG 182 L F +AV P M + G G +IN+ SM + ++ Y A+K G LTR + ++ G Sbjct: 120 LNAPFIVSKAVLPAMMKKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYG 179 Query: 183 KDKIRINTLTPGWVMTKRQL-THWVDKDTAKH-IENNQCIK----EYVMPEDIAAMALFL 236 + I+ N + PG++ T + D ++H ++ C K ++ PE++ A+FL Sbjct: 180 EYNIQCNGIGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFL 239 Query: 237 AADDSKLCTAQNFIVDGG 254 A++ S VDGG Sbjct: 240 ASEASNAVNGHILYVDGG 257 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: 153 Number of extensions: 8 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: 267 Length adjustment: 25 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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