Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Ga0059261_2975 Ga0059261_2975 Mannitol-1-phosphate/altronate dehydrogenases
Query= BRENDA::Q9KWR5 (485 letters) >FitnessBrowser__Korea:Ga0059261_2975 Length = 479 Score = 238 bits (607), Expect = 3e-67 Identities = 147/419 (35%), Positives = 217/419 (51%), Gaps = 9/419 (2%) Query: 2 ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAPDWAIVGVG 61 +T ETL+ +PA + P YD + G+VHFG G F RAH+A Y + +L + P W I V Sbjct: 4 LTLETLRDVPAAIVKPAYDPATVSTGVVHFGPGAFHRAHQASYFDTVLANDPRWGIAAVS 63 Query: 62 LTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDP 121 L RS E AQD LY+L + ++RV+GA R ++ P V L P Sbjct: 64 L----RSGGTVEALAAQDGLYTLAVL--DREPSMRVIGAHRTWI-GPGGGAQVSALLARP 116 Query: 122 AIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGK 181 +RIV+ T+TE GY + G D+ + + ADL+ E P + G++V+ L R AG Sbjct: 117 EVRIVTSTVTEKGYCL-AGDGTLDMSHPDIVADLQGGE-PRSFVGWLVQGLAARRAAGAD 174 Query: 182 AFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAK 241 F V+ CDNL NG R A + A ARD +LAKWI + A FP+ MVD ITP + Sbjct: 175 PFMVLCCDNLSGNGGKLRAATIALAAARDADLAKWIADTAAFPDTMVDSITPASDDALYA 234 Query: 242 KLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAG 301 ++ A G++D + E F QWV+ P L AG + DV +E K+R+LN Sbjct: 235 RVAAELGVEDRATVQREAFTQWVIGPYTLADGPDLAGAGATLTSDVGGYERAKLRILNGL 294 Query: 302 HVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRF 361 H L + G+ +G E V DA+ ++L + +D++P L +G+ GY +V+ RF Sbjct: 295 HSSLAYLGLAMGLETVADAMGQAQLAAFAERLALQDIVPVLDPVAGLDHAGYTQAVLERF 354 Query: 362 SNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKG 420 N A+ +IA DG K+ +T AI R + R+A +A+++ + R G Sbjct: 355 RNPAIRHLLSQIAWDGSQKLPYRLLDTTAAAIRAGRPVDRLAVPVAAWMHFVARRAAAG 413 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: 533 Number of extensions: 18 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: 485 Length of database: 479 Length adjustment: 34 Effective length of query: 451 Effective length of database: 445 Effective search space: 200695 Effective search space used: 200695 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: 52 (24.6 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