Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 5209489 Shew_1959 short chain dehydrogenase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >FitnessBrowser__PV4:5209489 Length = 271 Score = 86.7 bits (213), Expect = 5e-22 Identities = 74/247 (29%), Positives = 118/247 (47%), Gaps = 4/247 (1%) Query: 35 QGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADA-GLPRPWWRVC 93 QG+ VFV GG SGI I AFA+ GA VA +E +A + + + G + Sbjct: 5 QGKNVFVVGGTSGINLGIAKAFAKAGANVAVASRRQEKVDAAVEALREINGQGKMLGVAF 64 Query: 94 DVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINERPAFFA 153 DVRD++AL+ A G VLV+ A + T ++ + M I+ +F Sbjct: 65 DVRDLEALKTGFKQIADAYG-QLDVLVSGAAGNFPATAAELSENGFKSVMDIDLLGSFQV 123 Query: 154 IQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQDRIRIN 213 ++ P MRR G G+++ + + + AK+ V+ LT+ LA G + IR+N Sbjct: 124 LKQAYPLMRRPG-GAIVQISAPQAYIAMPMQSHVSAAKAGVDMLTKSLALEWGIEGIRVN 182 Query: 214 TVSPGWVM-TERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAMCTAQE 272 ++ PG + TE +L ++ +A++ L DIA V+F+AS+ A+ T Sbjct: 183 SIVPGPISGTEGFSRLAPSDALQQAVAQSVPLKRNGSTDDIANAVMFIASEMASYITGTV 242 Query: 273 FKVDAGW 279 VD GW Sbjct: 243 LPVDGGW 249 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: 137 Number of extensions: 8 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: 271 Length adjustment: 25 Effective length of query: 255 Effective length of database: 246 Effective search space: 62730 Effective search space used: 62730 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