Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate WP_086510924.1 BZY95_RS16165 mannitol dehydrogenase family protein
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >NCBI__GCF_002151265.1:WP_086510924.1 Length = 491 Score = 380 bits (977), Expect = e-110 Identities = 224/473 (47%), Positives = 279/473 (58%), Gaps = 14/473 (2%) Query: 25 IVHLGCGAFHRAHQALYTHHLLE-STDSDWGICEVNLMPGNDRVLIENLKKQQLLYTVAE 83 IVHLG GAFHRAHQA+Y + S D WG+C NL G L++ L+ Y VAE Sbjct: 18 IVHLGLGAFHRAHQAVYLERYRQRSGDGAWGVCSANLRGGV--ALVDALRDAGCRYHVAE 75 Query: 84 KG-AESTELKIIGSMKEALHPEID-------GCEGILNAMARPQTAIVSLTVTEKGYCAD 135 +++ L+ IG +++AL D +L MA P+T IV+LTVTEKGY Sbjct: 76 YADSDTVTLREIGVIEQALFTGRDLAGEWGRDLASLLARMASPETRIVTLTVTEKGYFLS 135 Query: 136 AASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVA 195 A G L ++PLI HD++ P AP++A G +VEAL RR G+ FTV+ CDN+ NG Sbjct: 136 PAEGNLLRDDPLIAHDIDQPQAPRTAPGILVEALARRRSAGVPPFTVLCCDNMPNNGQRT 195 Query: 196 KVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACE 255 + AV+ LA RD +LAAWIE V FPC+MVDRIVPA T +A+ LGV D A+ E Sbjct: 196 RAAVVQLAACRDAELAAWIEREVAFPCSMVDRIVPAMTAADFARLAE-LGVEDLNAVVGE 254 Query: 256 PFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIA 315 F QWV+ED+F GRPDW+ G + V DV PFE MKLRMLNGSHS LAYLG L ET+ Sbjct: 255 AFSQWVVEDDFPLGRPDWEAEGVEMVTDVAPFETMKLRMLNGSHSLLAYLGALDDIETVF 314 Query: 316 DTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGS 375 D V+ M+ E PTL+MPEGTDL AYA L+ RF N SLRHR QIAMDGS Sbjct: 315 DAVSRDDLVALLRRYMLCEAEPTLAMPEGTDLVAYADSLLVRFGNDSLRHRLQQIAMDGS 374 Query: 376 QKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINA 435 QKLPQR L L+ GG ALG+A W+RYT G D GN V DPM F+ ++ Sbjct: 375 QKLPQRWLHGALARLEAGGEVPCTALGLAAWIRYTAGSDLHGNDHVVDDPMAGTFRLLHE 434 Query: 436 QY--QGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 + + V A L L + L ++A F AV AAY+ L G +A L Sbjct: 435 AHGENVEELVPAFLELDAVVPPALAEHAGFTAAVVAAYRCLTTYGLAAALARL 487 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: 654 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 491 Length adjustment: 34 Effective length of query: 452 Effective length of database: 457 Effective search space: 206564 Effective search space used: 206564 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: 52 (24.6 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