Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_012113566.1 XAUT_RS07715 NAD(P)-dependent oxidoreductase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_000017645.1:WP_012113566.1 Length = 282 Score = 129 bits (323), Expect = 9e-35 Identities = 87/252 (34%), Positives = 128/252 (50%), Gaps = 12/252 (4%) Query: 10 LQGKTIFISGGA--TGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTF 67 L+GKT ISGGA GIG F QGA+VA +D+ + + A+L Sbjct: 36 LKGKTAVISGGAGARGIGFATAKTFAAQGARVAILDLDAAGAAKAAAELGPEHVGIG--- 92 Query: 68 YHCDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYF 127 CD+ D A R I +V G I +LINNA Q + ++ PE W + + NL+ Sbjct: 93 --CDVTDKADCARAIGEVLAATGQIDILINNAGITQAIKVWDIDPESWARIQDVNLKGVL 150 Query: 128 FAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAG---YTASKAGAMGLTRGLAADLGKD 184 + QAV P M+ G++ + S+S R G+ G Y+A+KAG +GL + +A +LG D Sbjct: 151 YLSQAVMPHMRERKAGAIACMSSVS-AQRGGGILGGAHYSAAKAGVLGLAKAMARELGAD 209 Query: 185 KIRINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLC 244 IR+N +TPG + T D K +EN + +P+D+A + LFLA+D S Sbjct: 210 GIRVNCVTPGLIQTDINAGKISDDARVKILENIP-LNRLGVPQDVANIFLFLASDLSAYV 268 Query: 245 TAQNFIVDGGWI 256 T V+GG + Sbjct: 269 TGAVIDVNGGML 280 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: 178 Number of extensions: 12 Number of successful extensions: 5 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: 282 Length adjustment: 25 Effective length of query: 231 Effective length of database: 257 Effective search space: 59367 Effective search space used: 59367 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