Align Erythritol/L-threitol dehydrogenase; EC 1.1.1.- (characterized)
to candidate SM_b20853 SM_b20853 sugar-alcohol dehydrogenase
Query= SwissProt::A0QXD8 (362 letters) >FitnessBrowser__Smeli:SM_b20853 Length = 339 Score = 138 bits (348), Expect = 2e-37 Identities = 105/341 (30%), Positives = 155/341 (45%), Gaps = 33/341 (9%) Query: 9 MQAVVCHGPHDYRLEEVAVPQRKPGEALIRVEAVGICASDLKCYHGAAKFWGDENRPAWA 68 M+A+V H P D RLE P PGE L+RV +VG+C SDL + AW Sbjct: 1 MRAIVLHAPGDIRLETRPKPVAGPGEVLLRVASVGVCGSDLPRMLV---------KGAW- 50 Query: 69 ETMVIPGHEFVGRVVELDDEAAQRWGIAVGDRVVSEQIVPCWECLFCKRGQYHMCQPHDL 128 + +I GHEF G + L + G +G+ ++PC +C+ CK G + C+ +D Sbjct: 51 KMPLITGHEFSGHIHALGENVE---GWEIGELTAIAPLMPCNQCIECKTGNFSRCRDYDY 107 Query: 129 YGFKRRTPGAMASYMVYPAEALVHKVSPDIPAQHAAFAEPLSCSLHAVERAQ-ITFEDTV 187 +G +R GA A ++ P E L+ K + + A +P S +LHA+ +A IT T Sbjct: 108 FGSRR--DGAYAEFVAVPVENLI-KTPQHVDPRAIAMTDPASIALHAIWKAGGITAGQTG 164 Query: 188 VVAGCGPIGLGMIAGAKAKSPMRVIALDMAPDKLKLAEKCGADLTINIAEQDAEKIIKDL 247 V GCGPIGL I + RVIA+D+ +KL LA + GADL I A+ K Sbjct: 165 AVVGCGPIGLFAIQWMRIMGTSRVIAVDVTEEKLALARQAGADLCILSADFADNK----- 219 Query: 248 TGGYGADVYIEGTGHTSAVPQGLNLLRKLGRYVEYGVFGSDVTVDWSI--------ISDD 299 AD+ IE G S + + L G G+ DV + + +S Sbjct: 220 ---ERADLVIEAVGIDSTINAAVMLAAPGGHVTFIGIPVPDVKLSNATFQRFLRQEVSLH 276 Query: 300 KELDVLGAHLGPYCWPAAIKMIESGALPMDEICTHQFPLTE 340 + GA W ++ +G L + + +H L E Sbjct: 277 GSWNSFGAPFPGPQWTTTVQKFATGELKWEFMISHDLDLAE 317 Lambda K H 0.320 0.137 0.428 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: 343 Number of extensions: 16 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: 362 Length of database: 339 Length adjustment: 29 Effective length of query: 333 Effective length of database: 310 Effective search space: 103230 Effective search space used: 103230 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: 49 (23.5 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