Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_017868407.1 LACPOB_RS0108455 SDR family oxidoreductase
Query= reanno::ANA3:7024897 (256 letters) >NCBI__GCF_000349725.1:WP_017868407.1 Length = 242 Score = 122 bits (306), Expect = 7e-33 Identities = 84/252 (33%), Positives = 121/252 (48%), Gaps = 19/252 (7%) Query: 10 LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEA-----S 64 + + I I+G A+G+ AFLEQG V D + LKQ + A S Sbjct: 1 MASRNIIITGAASGMAKAQTEAFLEQGDTVFGFDFNEQ-------GLKQEEQNAGAFKGS 53 Query: 65 VTFYHCDLVDIAALKRVIAQVEDDLGPISVLINNAAC-DQRHSIDEVTPEYWDQCLNTNL 123 Y D+ + + V + + I VLIN A D+ E T E WD LNTNL Sbjct: 54 FYGYKVDISSKIQIDNALKNVWEKVDRIDVLINTAGIFDKYQKFLETTEEMWDAVLNTNL 113 Query: 124 RHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGK 183 + F QAV +M + GGG+VIN+ S++ + G YT +K G +GLT+ ++ +LG Sbjct: 114 KGMFLLTQAVTAKMIKNGGGNVINVASVAGLQQDGGGVAYTVAKHGVIGLTKKISYELGT 173 Query: 184 DKIRINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKL 243 IR+N + PG + T ++ +T+ I +N + EDI LFLA+D S Sbjct: 174 QGIRVNAIAPGRITTN------MNNNTSDLIVDNLPAQRNGKVEDIVNATLFLASDKSSY 227 Query: 244 CTAQNFIVDGGW 255 Q VDGGW Sbjct: 228 IHGQVITVDGGW 239 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: 160 Number of extensions: 9 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: 242 Length adjustment: 24 Effective length of query: 232 Effective length of database: 218 Effective search space: 50576 Effective search space used: 50576 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