Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate PfGW456L13_2132 Alcohol dehydrogenase (EC 1.1.1.1)
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2132 Length = 350 Score = 351 bits (900), Expect = e-101 Identities = 177/346 (51%), Positives = 242/346 (69%), Gaps = 7/346 (2%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 A G+AA+ T L+P KF RR+ DV +++L+CGVCHSD H N WG YP++PGH Sbjct: 4 AIGYAAQSATTPLAPVKFERRSPRPDDVAIEILYCGVCHSDIHQARNEWGIAVYPLMPGH 63 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTYGS-IYFD 130 EIVG VT VG+ V + KVGD VG+GC+V SCRSCE+C N E +C E TY + D Sbjct: 64 EIVGKVTAVGASVTQHKVGDLVGVGCMVDSCRSCEACQANLEQYCLEGPTMTYATPDRVD 123 Query: 131 GTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVV 190 G+ T GGYSD++V EHF++R P+ LPL S AP+LCAGITTYSPLK+YG+ K G K+G++ Sbjct: 124 GSNTMGGYSDSIVVSEHFVVRIPEKLPLASAAPILCAGITTYSPLKHYGV-KAGDKVGIL 182 Query: 191 GLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDG 250 G+GGLGH+ +K AKA GA+VT+ S SK +EA + GAD ++++D QM+ A D Sbjct: 183 GMGGLGHMGIKFAKAMGAEVTLFTRSASKAEEA-RRQGADHVIVSTDDAQMQAAAGHFDF 241 Query: 251 IIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFS--LLKGRKLLGGTINGGIKE 308 ++DT+PV H L P D L+ +G ++VG E P E PV + L+ GR++L G++ GGI E Sbjct: 242 LLDTIPVQHDLNPYLDTLRFDGVHILVGLIE-PVEPPVHAAKLVLGRRVLAGSLIGGIAE 300 Query: 309 TQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIA 354 TQE+LDF A+HNIT D+E++ + +N A R++ DV+YRFVID+A Sbjct: 301 TQEVLDFCAEHNITCDIEMLDIRQINEAYARMIAGDVKYRFVIDMA 346 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: 374 Number of extensions: 18 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 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