Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Ac3H11_2939 D-arabinitol 4-dehydrogenase (EC 1.1.1.11)
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2939 Length = 463 Score = 238 bits (606), Expect = 4e-67 Identities = 141/392 (35%), Positives = 209/392 (53%), Gaps = 8/392 (2%) Query: 28 IVHFGVGNFFRAHEAFYVEQILEH-APDWAIVGVGLTGSDRSKKKAEEFKAQDCLYSLTE 86 I+H G+G+F RAH+A Y+ Q+ + + DWAI G L A +AQ Y+L Sbjct: 4 ILHLGLGSFHRAHQAVYMHQLRQQGSTDWAIAGGNLRPDMADTIAA--LQAQGGRYTLET 61 Query: 87 TAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIRIVSMTITEGGYNINETTGAFDL 146 P G+ + V+ +++ + D ++ DPA RI+S T+TE GY ++ Sbjct: 62 VTPQGERSYTVIESIQRVIPYQDDLAPLIAAGADPATRIISFTVTEAGYYLDAANQLDWA 121 Query: 147 ENAAVKADLKNPEKPS---TVFGYVVEALRRRWDAGGKAFTVMSCDNLRHNGNVARKAFL 203 A ++ADL + T++G + LR R AG T+M+CDNLRHNG+ +R L Sbjct: 122 TFADLRADLATVQAGQAGHTIYGGLASILRARMRAGAGPVTLMNCDNLRHNGDRSRGGLL 181 Query: 204 GYAKAR-DPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDDLPLVAEDFHQ 262 + A D L W+E+N T PN MVDRITP + ++A+++ A+G DD L+ E F Q Sbjct: 182 QFIDALGDAPLKGWVEQNTTSPNAMVDRITPRPTPDVAERVKTATGWDDKAALMGESFIQ 241 Query: 263 WVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILVGYENVDDAIE 322 WV+ED F GRP EK GV+MV V E KIR+LNA H + + G L GY+ + + Sbjct: 242 WVIEDDFIAGRPAWEKVGVEMVQSVQAHEEAKIRLLNATHSCIAWAGTLAGYQYIHEGTH 301 Query: 323 DSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLRIASDGCSKVQ 382 D+ + +Y+ D IP L P + LE YRD V+ RF N A++D R+A D SK+ Sbjct: 302 DAAIRQMAHDYVTDDAIPVL-LPCPIDLEAYRDVVLDRFGNPAIADTNQRVAMDAFSKIP 360 Query: 383 VFWTETVRRAIEDKRDLSRIAFGIASYLEMLR 414 T+R + + +A A +L L+ Sbjct: 361 GMIAPTIRDKLARNQPFDSVAVLPALFLAYLQ 392 Lambda K H 0.317 0.135 0.398 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: 543 Number of extensions: 21 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: 485 Length of database: 463 Length adjustment: 33 Effective length of query: 452 Effective length of database: 430 Effective search space: 194360 Effective search space used: 194360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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