Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_037570579.1 BS73_RS07645 glucose 1-dehydrogenase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_000744815.1:WP_037570579.1 Length = 247 Score = 139 bits (349), Expect = 7e-38 Identities = 81/246 (32%), Positives = 132/246 (53%), Gaps = 8/246 (3%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69 + G+T+ I+GGA G+G + +GA+V DIL EE L K+ P+A++ F Sbjct: 7 VSGRTVLITGGARGMGEAHARLLVAEGARVVVGDILEEEGRALA---KELGPDAAL-FQP 62 Query: 70 CDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFA 129 D+ AA ++ ++ E+ GP+S L+NNA I E++ + + ++ N F Sbjct: 63 LDVTSEAAWQQAVSAAEEAFGPVSGLVNNAGIVHVGPIAELSEADYRKVVDVNQVGVFLG 122 Query: 130 VQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRIN 189 +++V P M+R GGGS++N+ S+ +G+ GYTA+K G+T+ A + G+ IR+N Sbjct: 123 MKSVLPSMRRAGGGSIVNISSVGGIIAFSGIVGYTAAKWAVRGMTKTAAQEFGRYGIRVN 182 Query: 190 TLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQNF 249 ++ PG V T + H+ I PE++A M LFL +D+S CT F Sbjct: 183 SVHPGMVATPMTADAPGTEGAVAHLP----IPRQARPEELATMVLFLLSDESSYCTGGEF 238 Query: 250 IVDGGW 255 VDGG+ Sbjct: 239 TVDGGY 244 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: 150 Number of extensions: 7 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: 247 Length adjustment: 24 Effective length of query: 232 Effective length of database: 223 Effective search space: 51736 Effective search space used: 51736 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