Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate H281DRAFT_04152 H281DRAFT_04152 D-arabinitol 4-dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__Burk376:H281DRAFT_04152 Length = 470 Score = 213 bits (541), Expect = 1e-59 Identities = 138/365 (37%), Positives = 196/365 (53%), Gaps = 21/365 (5%) Query: 25 IVHLGCGAFHRAHQALYTHHLLEST---DSDWGICEVNLMPGNDRVLIENLKKQQLLYT- 80 I+H+G G+FHRAHQA Y H L E+ + W + N+ + VL E L Q +YT Sbjct: 14 ILHIGAGSFHRAHQAWYLHRLNEANLPGEPHWSLTVGNIRSDMNAVL-EALAAQDGVYTL 72 Query: 81 --VAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAAS 138 V +G + E I S++ + P + + ++ A A P I+S TVTE GY D Sbjct: 73 ETVTPQGERAYET--IRSIERVV-PWTESLDALIEAGADPACKIISFTVTEGGYYLDEHD 129 Query: 139 GQLDLNNPLIKHDLENP-TAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENG---HV 194 QLD NP + DL+ T A+ I+EA R + G T+ +CDN+R NG H Sbjct: 130 -QLDTANPDLSTDLKGGHTTIYGALAAILEA---RMKNGAGPVTLQTCDNLRRNGERFHA 185 Query: 195 AKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIAC 254 A L L A + LA W ++N P +MVDRI P TP+ + + GV D C + Sbjct: 186 GMSAFLELRGAGE--LAQWFDDNTACPSSMVDRITPRPTPDVRERVKAATGVDDACPVMG 243 Query: 255 EPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETI 314 E F QWVIE+ F+ GRP W+KVGA+ V V+P+E K+R+LN +HS +A+ G L G I Sbjct: 244 EAFIQWVIEERFIAGRPAWEKVGAELVDSVLPYEEAKIRILNATHSCIAWAGTLVGLNYI 303 Query: 315 ADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDG 374 + + RK AF + ++ P LS P DL Y +++ERF NP ++ ++A DG Sbjct: 304 HEGTQDADIRKFAFDYVTEDVIPCLS-PSPLDLERYRDVVLERFGNPYIQDTNQRVAADG 362 Query: 375 SQKLP 379 KLP Sbjct: 363 FSKLP 367 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: 589 Number of extensions: 32 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: 486 Length of database: 470 Length adjustment: 34 Effective length of query: 452 Effective length of database: 436 Effective search space: 197072 Effective search space used: 197072 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 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