Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate Ga0059261_2135 Ga0059261_2135 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Korea:Ga0059261_2135 Length = 355 Score = 305 bits (782), Expect = 9e-88 Identities = 167/351 (47%), Positives = 221/351 (62%), Gaps = 7/351 (1%) Query: 10 PVKAFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIV 69 P A +AA+ T L+PF F RR DV + +LFCGVCHSD H + W T +P V Sbjct: 2 PSPAKAYAAQSATTPLAPFSFERRDVQPDDVAIDILFCGVCHSDLHQARSEWEGTLFPCV 61 Query: 70 PGHEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENT--IDTY-GS 126 PGHEIVG VT +GS V VGD VG+GC+V SC +C SC + E +CE T + TY G Sbjct: 62 PGHEIVGRVTAIGSDVTTFAVGDLVGVGCMVDSCGTCPSCHEGEEQYCEGTGFVGTYNGP 121 Query: 127 IYFDGTMTHGGYSDTMVADEHFILR-WPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGT 185 G T GGYSDT+V + F+LR L + APLLCAGITTYSPLK++G PG Sbjct: 122 DAHLGGHTFGGYSDTIVVKQGFVLRIGHDEQDLAAVAPLLCAGITTYSPLKHWGAG-PGK 180 Query: 186 KIGVVGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGAR 245 K+GVVG+GGLGH+ VK+A A GA V SE KR +AL LGA +++ + ++M Sbjct: 181 KVGVVGIGGLGHMGVKIAAAMGAHVVAFTTSEGKRADAL-ALGAHEVVVSRNADEMAAHA 239 Query: 246 SSLDGIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELP-VFSLLKGRKLLGGTING 304 S D I++TV +H L +LLK +G + +VG PE P V +L+ R+ + G++ G Sbjct: 240 GSFDFILNTVAASHDLDAFTNLLKRDGTMTLVGVPEHAHPSPSVLNLVFRRRSIAGSLIG 299 Query: 305 GIKETQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355 GI ETQEMLDF H ITAD+E I + ++ + +R+VK DV+YRFVID+A+ Sbjct: 300 GIAETQEMLDFCRDHGITADIETIAIQDIDASFDRMVKGDVKYRFVIDMAS 350 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: 362 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: 365 Length of database: 355 Length adjustment: 29 Effective length of query: 336 Effective length of database: 326 Effective search space: 109536 Effective search space used: 109536 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