Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate WP_057508430.1 ABB28_RS09665 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >NCBI__GCF_001431535.1:WP_057508430.1 Length = 350 Score = 324 bits (831), Expect = 2e-93 Identities = 171/346 (49%), Positives = 230/346 (66%), Gaps = 5/346 (1%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 A +AA TT L PF F RRA DVR+++L+ G+CHSD H ++WG YP+VPGH Sbjct: 4 AKAYAAHSTTAPLVPFTFERRAVAAGDVRIEILYSGICHSDLHQARDDWGGAKYPMVPGH 63 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTY-GSIYFD 130 EI+G V EVG++V K+KVGD G+GC+V SCR CE+C + E +C E + TY G+ Sbjct: 64 EIIGKVVEVGAEVTKLKVGDFAGVGCMVDSCRHCEACNADLEQYCAEGSTFTYNGTDRHT 123 Query: 131 GTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVV 190 G T GGYSD +V ++ F+++ + L L + APLLCAGITTYSPLK++ + PG K+GV+ Sbjct: 124 GEPTQGGYSDHIVVEQRFVVKVSETLDLKAAAPLLCAGITTYSPLKHFKVG-PGQKVGVI 182 Query: 191 GLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDG 250 GLGGLGH+ VK AKA GA V +I + K +A +LGAD L++ D EQMK S D Sbjct: 183 GLGGLGHMGVKFAKALGAHVVMITTTPEKGADA-TRLGADEVLVSRDPEQMKAHAGSFDF 241 Query: 251 IIDTVPVNHPLAPLFDLLKPNGKLVMVGA-PEKPFELPVFSLLKGRKLLGGTINGGIKET 309 +++T+PV H P LLK + + +VG E L S++ GRK L G+ GG+ ET Sbjct: 242 LLNTIPVGHDTNPYMGLLKRDATMCLVGVLTELDPPLTGVSVIFGRKHLTGSAIGGMAET 301 Query: 310 QEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355 QEM+DF A+H I +DVEVI + VN A ER+ K+DVRYRFVID+A+ Sbjct: 302 QEMMDFCAEHGIVSDVEVINIQDVNEAWERMAKNDVRYRFVIDMAS 347 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: 351 Number of extensions: 19 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: 350 Length adjustment: 29 Effective length of query: 336 Effective length of database: 321 Effective search space: 107856 Effective search space used: 107856 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