Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate 5210620 Shew_3048 alcohol dehydrogenase (RefSeq)
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__PV4:5210620 Length = 348 Score = 320 bits (819), Expect = 5e-92 Identities = 162/345 (46%), Positives = 230/345 (66%), Gaps = 4/345 (1%) Query: 11 VKAFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVP 70 +K G+AA L P+++ R E DV +++L+ GVCHSD H ++N+WG+T +P VP Sbjct: 1 MKTIGFAAESAHSPLQPYEYDCRPLREDDVAIEILYSGVCHSDLHTVNNDWGWTVFPTVP 60 Query: 71 GHEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCE-NTIDTYGSI-Y 128 GHEIVG V EVGS+V + KVGD V +GC+V SC+SC C E CE TY S+ Sbjct: 61 GHEIVGRVVEVGSQVSRYKVGDQVAVGCMVDSCQSCSQCHSGEEQFCEAGFTQTYNSVDR 120 Query: 129 FDGTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIG 188 +T GG++ +V + F+L PK+L L APLLCAGITTYSPL+ + + PG+++ Sbjct: 121 HTQAITKGGFAKHIVVRQEFVLSIPKSLDLAKAAPLLCAGITTYSPLRTWNVG-PGSQVA 179 Query: 189 VVGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSL 248 ++G+GGLGH+A+K+A A GA VTVI S+ K+ +AL+ LGA+ FLL+S+ E M+ + + Sbjct: 180 IIGMGGLGHMAIKLAVAMGAHVTVISRSQDKQGDALD-LGANDFLLSSEPESMELSANRF 238 Query: 249 DGIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKE 308 D I+DTVPV H + P LLK +G L +VG E+ ++ GR+ + ++ GGI + Sbjct: 239 DLILDTVPVKHDITPYLPLLKVDGTLTLVGQVGPIAEVNTVPMVMGRRRIAASLIGGIAQ 298 Query: 309 TQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDI 353 TQEMLDF AK NI +VE+I M+ +N A ERL ++DVRYRFVID+ Sbjct: 299 TQEMLDFCAKMNILPEVEMIKMEEINQAFERLERADVRYRFVIDM 343 Lambda K H 0.319 0.137 0.415 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: 331 Number of extensions: 18 Number of successful extensions: 4 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: 365 Length of database: 348 Length adjustment: 29 Effective length of query: 336 Effective length of database: 319 Effective search space: 107184 Effective search space used: 107184 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 (21.7 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