Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate SM_b20749 SM_b20749 D-mannonate oxidoreductase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Smeli:SM_b20749 Length = 487 Score = 428 bits (1101), Expect = e-124 Identities = 243/470 (51%), Positives = 291/470 (61%), Gaps = 7/470 (1%) Query: 11 VARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIE 70 V RP +D + IVHLG GAFHRAHQA+YT LL S D WGIC V+L R + Sbjct: 15 VKRPHYDLGTVTVGIVHLGIGAFHRAHQAVYTDGLL-SEDPSWGICGVSLRSPETR---D 70 Query: 71 NLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEK 130 L Q LYT+A + E +EL ++GS+ E L D E +L MA P T IVSLT+TEK Sbjct: 71 ALHPQDGLYTLAVQDGEGSELSVVGSVVELLCAP-DDPEAVLRRMADPGTRIVSLTITEK 129 Query: 131 GYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRE 190 GYC + A+G LD +P I HDL NP P+SAIG+IVEA+ R G+ FT++SCDN+ Sbjct: 130 GYCHNPATGTLDEGHPDIVHDLANPARPRSAIGFIVEAISRRVSAGIAPFTLLSCDNLPG 189 Query: 191 NGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPC 250 NGHV K V A+ARDP LAA + NV P TMVDRIVPA T +A +G+ D Sbjct: 190 NGHVLKRIVTQFAEARDPALAA-VVRNVASPSTMVDRIVPATTDSDRSAVASAMGLEDAW 248 Query: 251 AIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGG 310 I EPFRQWVIE++F GRP W+K GA FV DV FE MKLR+LNGSHS LAYLGYL G Sbjct: 249 PIMTEPFRQWVIEEDFPLGRPAWEKAGALFVQDVSAFEFMKLRLLNGSHSTLAYLGYLAG 308 Query: 311 YETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQI 370 ET+AD + LM E +PTL G DL AY L++RF NP+LRHRTWQI Sbjct: 309 AETVADAMALAGMEALVEGLMRHEVSPTLPELPGFDLPAYRAELLQRFRNPALRHRTWQI 368 Query: 371 AMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEF 430 AMDGSQKLPQRLL +R LQ G + LALGVA WMRY +G+DE G IDV DP A Sbjct: 369 AMDGSQKLPQRLLGSIRDRLQAGAGYDRLALGVAAWMRYARGLDEAGRPIDVRDPHAARI 428 Query: 431 QKINAQYQGADR-VKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGA 479 + DR V A L ++ +F DLP +A F A+ A L GA Sbjct: 429 AGLARGIDEPDRIVDAFLTMTDVFGTDLPASAPFRAALIKALDGLLRIGA 478 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: 723 Number of extensions: 35 Number of successful extensions: 6 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: 487 Length adjustment: 34 Effective length of query: 452 Effective length of database: 453 Effective search space: 204756 Effective search space used: 204756 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