Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_077274914.1 BW732_RS00300 D-threitol dehydrogenase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_001998885.1:WP_077274914.1 Length = 254 Score = 114 bits (284), Expect = 3e-30 Identities = 73/249 (29%), Positives = 132/249 (53%), Gaps = 12/249 (4%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69 L+ K I+GG +GIG+ + ++++GAK+A DI ++ +LV + T+ ++ F Sbjct: 12 LENKVAIITGGLSGIGSAIGELYVKKGAKLAIFDIN-PDTPELVEEQFGTK---AIGF-- 65 Query: 70 CDLVDIAALKRVIAQVEDDLG---PISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHY 126 VD+ + ++V+ V++ + I +L+N+A + ++ WD N N++ Sbjct: 66 --AVDVTSKEQVMNAVKETMNHFKKIDILVNSAGVCFLDDAENLSETEWDLTFNINVKGS 123 Query: 127 FFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKI 186 F QAV +M + GGG +IN+ S + Y ASK + +T+ LA + + I Sbjct: 124 FLVAQAVGNEMIQSGGGKIINMASQAALVALDNHVAYAASKGAILSMTKVLAYEWAQYSI 183 Query: 187 RINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTA 246 +N L+P V+T+ W + + ++ I + PE++AA ALFLA+D S L T Sbjct: 184 NVNCLSPTIVLTELGKKAWAGQ-VGEDMKQQIPIGRFGYPEEVAASALFLASDASNLMTG 242 Query: 247 QNFIVDGGW 255 +N ++DGG+ Sbjct: 243 ENMVIDGGY 251 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: 157 Number of extensions: 11 Number of successful extensions: 4 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