Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 7024897 Shewana3_2071 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >FitnessBrowser__ANA3:7024897 Length = 256 Score = 252 bits (643), Expect = 7e-72 Identities = 127/255 (49%), Positives = 173/255 (67%), Gaps = 8/255 (3%) Query: 30 KFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRPW 89 ++PSLQG+ +F++GG +GIGA +V AF EQGA+VAFVD+ E S L +AD +P Sbjct: 6 QYPSLQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQL---VADLKQTQPE 62 Query: 90 WRV----CDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAI 145 V CD+ D+ AL+ +A +LG +VL+NN A D RH+++ VTPEY+D+ + Sbjct: 63 ASVTFYHCDLVDIAALKRVIAQVEDDLGP-ISVLINNAACDQRHSIDEVTPEYWDQCLNT 121 Query: 146 NERPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTL 205 N R FFA+QAV P M+RLG GSVINLGS W + G Y +K+ GLTRGLA L Sbjct: 122 NLRHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADL 181 Query: 206 GQDRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDA 265 G+D+IRINT++PGWVMT+RQ+ W+D + K + NQC+ + + P DIA M LFLA+DD+ Sbjct: 182 GKDKIRINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDS 241 Query: 266 AMCTAQEFKVDAGWV 280 +CTAQ F VD GW+ Sbjct: 242 KLCTAQNFIVDGGWI 256 Lambda K H 0.320 0.133 0.405 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: 202 Number of extensions: 4 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: 280 Length of database: 256 Length adjustment: 25 Effective length of query: 255 Effective length of database: 231 Effective search space: 58905 Effective search space used: 58905 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 17 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