Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_057507496.1 ABB28_RS04570 NAD(P)-dependent oxidoreductase
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >NCBI__GCF_001431535.1:WP_057507496.1 Length = 253 Score = 110 bits (276), Expect = 2e-29 Identities = 80/249 (32%), Positives = 116/249 (46%), Gaps = 12/249 (4%) Query: 15 SLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKPLFRH 74 + K V +TG G+GIGAA AF+ GA+V D AL E+AA + L Sbjct: 2 NFNAKTVIVTGAGSGIGAATARAFSNAGANVVLADRDHPDVAALAGELAAE---RTLVHD 58 Query: 75 CDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRPSFFA 134 D+ D QA + + G DV+ NNA E+ +LE WN +A+N F Sbjct: 59 VDVSDEAQVQALVDATVKRFGGLDVIFNNAGILVEGPAEDTSLEDWNRIVAVNLTGVFLG 118 Query: 135 VQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHKIRVN 194 ++ + +++R G I+N +S+S + P Y K + LTR LA D G H +RVN Sbjct: 119 CRAALPELRKRKG-CIVNTASVSGLAADRNMPAYNAVKGAVANLTRALAIDNGRHGVRVN 177 Query: 195 TVTPGWVMTERQIKLWLDEEGKKAIAR---NQCLQGDL-LPWHLARMVLFLAADDSAMCT 250 V P + T + ++E KA+ N+ G L P +A VL LA+D + T Sbjct: 178 AVCPTFTRT----SMTAEKEKDKALVTNFLNRIPMGRLGEPEDIANAVLLLASDHAGFIT 233 Query: 251 AQEFIVDAG 259 VD G Sbjct: 234 GVNLPVDGG 242 Lambda K H 0.321 0.134 0.411 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: 97 Number of extensions: 6 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: 261 Length of database: 253 Length adjustment: 24 Effective length of query: 237 Effective length of database: 229 Effective search space: 54273 Effective search space used: 54273 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 (21.9 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