Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate WP_059151132.1 V474_RS08780 mannitol dehydrogenase family protein
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >NCBI__GCF_001046635.1:WP_059151132.1 Length = 476 Score = 307 bits (786), Expect = 6e-88 Identities = 197/468 (42%), Positives = 257/468 (54%), Gaps = 21/468 (4%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70 VARP +D + L +VH G GAFHRAHQA LL D WGI V+L N R + + Sbjct: 16 VARPQYDRAALRGGVVHFGPGAFHRAHQAAAFDTLL-GHDPRWGITGVSL---NSRGVAD 71 Query: 71 NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130 L Q LYT+A E TE ++IGS+ L + G IL A+A T IVS TVTEK Sbjct: 72 ALNPQGGLYTLALL-EEQTEFRVIGSIGRVLTRDEPGA--ILGALAHGDTRIVSSTVTEK 128 Query: 131 GYCADAASGQLDLNNPLIKHDLENPTA----PKSAIGYIVEALRLRREKGLKAFTVMSCD 186 GYC +A G LD +P I+ DL+ + P S IG++V LR RR GL TV+SCD Sbjct: 129 GYCL-SADGTLDFAHPAIRADLDAAKSADWVPGSFIGWLVHGLRARRLAGLLGVTVLSCD 187 Query: 187 NVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGV 246 N+ +NG + A + LA+A DP+ A WI V FP MVD I PA +A G+ Sbjct: 188 NLTDNGRKLEAATIALAEAIDPETARWIAGEVCFPNAMVDSITPATDDALRARVAAATGL 247 Query: 247 YDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLG 306 D I E F QWVIED F RP + G F +V PFE KLR+LNG+HS LAY+G Sbjct: 248 EDAWPIQRERFTQWVIEDRFAGERPALECAGVTFAGEVRPFETAKLRLLNGAHSSLAYIG 307 Query: 307 YLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHR 366 G+ET+A+ + +P A LM ++ AP++S P G DL Y ++ RF+NP++RH Sbjct: 308 LGLGFETVAEAMADPGLAAFAERLMREDIAPSVSAPPGLDLPVYIADVLARFANPAIRHL 367 Query: 367 TWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPM 426 QIA DGSQKLP RLLD R L G LAL +A W+R+ G +I DP+ Sbjct: 368 LSQIAWDGSQKLPYRLLDTTRDALVAGRPVDRLALPIAAWLRFLDRAARSGGSI--TDPL 425 Query: 427 LAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQL 474 + A + ++G+ IF DL ++A F+ AV A L Sbjct: 426 SGPL------LERAGDWRRVVGMREIFG-DLGEDARFLRAVEAGLAAL 466 Lambda K H 0.320 0.135 0.408 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: 623 Number of extensions: 30 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: 486 Length of database: 476 Length adjustment: 34 Effective length of query: 452 Effective length of database: 442 Effective search space: 199784 Effective search space used: 199784 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 (21.8 bits) S2: 51 (24.3 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