Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate Ga0059261_2975 Ga0059261_2975 Mannitol-1-phosphate/altronate dehydrogenases
Query= curated2:P39160 (486 letters) >FitnessBrowser__Korea:Ga0059261_2975 Length = 479 Score = 289 bits (740), Expect = 1e-82 Identities = 182/476 (38%), Positives = 249/476 (52%), Gaps = 11/476 (2%) Query: 1 MTTIVDSNLPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNL 60 + T+ D + +P++D + + + +VH G GAFHRAHQA Y +L + D WGI V+L Sbjct: 6 LETLRDVPAAIVKPAYDPATVSTGVVHFGPGAFHRAHQASYFDTVL-ANDPRWGIAAVSL 64 Query: 61 MPGNDRVLIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQT 120 G +E L Q LYT+A E + +++IG+ + + P G + +ARP+ Sbjct: 65 RSGGT---VEALAAQDGLYTLAVLDREPS-MRVIGAHRTWIGP--GGGAQVSALLARPEV 118 Query: 121 AIVSLTVTEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAF 180 IV+ TVTEKGYC A G LD+++P I DL+ P+S +G++V+ L RR G F Sbjct: 119 RIVTSTVTEKGYCL-AGDGTLDMSHPDIVADLQGGE-PRSFVGWLVQGLAARRAAGADPF 176 Query: 181 TVMSCDNVRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEI 240 V+ CDN+ NG + A + LA ARD LA WI + FP TMVD I PA+ + Sbjct: 177 MVLCCDNLSGNGGKLRAATIALAAARDADLAKWIADTAAFPDTMVDSITPASDDALYARV 236 Query: 241 ADQLGVYDPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHS 300 A +LGV D + E F QWVI + PD GA +DV +E KLR+LNG HS Sbjct: 237 AAELGVEDRATVQREAFTQWVIGPYTLADGPDLAGAGATLTSDVGGYERAKLRILNGLHS 296 Query: 301 FLAYLGYLGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSN 360 LAYLG G ET+AD + A L +Q+ P L G D Y ++ERF N Sbjct: 297 SLAYLGLAMGLETVADAMGQAQLAAFAERLALQDIVPVLDPVAGLDHAGYTQAVLERFRN 356 Query: 361 PSLRHRTWQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAI 420 P++RH QIA DGSQKLP RLLD ++ G LA+ VA WM + G AI Sbjct: 357 PAIRHLLSQIAWDGSQKLPYRLLDTTAAAIRAGRPVDRLAVPVAAWMHFVARRAAAGEAI 416 Query: 421 DVVDPMLAEFQKINAQYQGADRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCE 476 DP+ A A A V L +F ++ +A + AVTA + L E Sbjct: 417 --TDPLAAPLADAAAGASPAQLVDRLFAFEAVFRPEIAGHAAYRAAVTAGVEALAE 470 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: 628 Number of extensions: 31 Number of successful extensions: 3 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: 479 Length adjustment: 34 Effective length of query: 452 Effective length of database: 445 Effective search space: 201140 Effective search space used: 201140 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 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