Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate WP_094573773.1 CEV32_RS01970 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >NCBI__GCF_002252475.1:WP_094573773.1 Length = 348 Score = 329 bits (844), Expect = 6e-95 Identities = 177/344 (51%), Positives = 221/344 (64%), Gaps = 3/344 (0%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 A G+AA D L PF F RR DV + + +CGVCHSD H + N W YPIVPGH Sbjct: 4 ARGYAATDADQPLVPFTFERREPNADDVVISIQYCGVCHSDIHTVRNEWKNAVYPIVPGH 63 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDG- 131 EIVGVV+ VGS V K KVGD VG+GC V SC C + + E + + TY S+ DG Sbjct: 64 EIVGVVSAVGSNVTKFKVGDKVGVGCFVDSCVGCATRDLDNEHYLPGLVQTYNSVDADGK 123 Query: 132 TMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVG 191 T T GGYSD +V E ++L P NLPLD+ APLLCAGIT YSPL+++ PG K+ +VG Sbjct: 124 TPTQGGYSDQIVVREGYVLSIPDNLPLDASAPLLCAGITLYSPLRHWQAG-PGKKVAIVG 182 Query: 192 LGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGI 251 +GGLGH+ VK+A A GA VTV+ S SK+ + L KLGA + SD E + + D I Sbjct: 183 MGGLGHMGVKLANAMGAHVTVLSQSLSKKDDGL-KLGAKEYYATSDSETFEKLAGTFDLI 241 Query: 252 IDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQE 311 I TV V LLK NG +V+VGAPE + FSL+ GRK L G++ G IKETQE Sbjct: 242 ICTVGVAIDWNAYLGLLKVNGTMVVVGAPEDMVPVHAFSLIPGRKSLAGSMIGSIKETQE 301 Query: 312 MLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355 MLDF KHNI +++E I + +N A ER++KSDVRYRFVIDIA+ Sbjct: 302 MLDFCGKHNIVSEIEKINIQDINEAYERVLKSDVRYRFVIDIAS 345 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: 332 Number of extensions: 13 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 24 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