Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate H281DRAFT_01519 H281DRAFT_01519 fructuronate reductase
Query= ecocyc::MANNONOXIDOREDUCT-MONOMER (486 letters) >FitnessBrowser__Burk376:H281DRAFT_01519 Length = 498 Score = 395 bits (1016), Expect = e-114 Identities = 213/464 (45%), Positives = 278/464 (59%), Gaps = 5/464 (1%) Query: 25 IVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLKKQQLLYTVAEK 84 IVHLG G FHRAHQALYT + + DWGIC V L D L +Q+ +Y+V E+ Sbjct: 37 IVHLGIGNFHRAHQALYTEEAMLAEGGDWGICGVTLQ--GDVAKRNALMEQEGVYSVVER 94 Query: 85 GAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQLDLN 144 G E ++ ++ +++E L D + + +A P IVSLTVTEKGYC +A +G + L+ Sbjct: 95 GPEGAKVTVVRALREVLAMPHDH-DALFARLADPSVRIVSLTVTEKGYCRNAKTGDVALD 153 Query: 145 NPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVLGLAQ 204 NP + HDL +P AP+S G +V ALR RR+ + FTV+SCDN+ NG + V A+ Sbjct: 154 NPAVVHDLSHPHAPRSVPGILVAALRQRRDAAREPFTVLSCDNLAHNGAALRQVVCSFAR 213 Query: 205 ARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQWVIED 264 DP LA WI V FP TMVDRI PA T +A LG D + CEPFRQWVIED Sbjct: 214 EFDPALADWIAVEVAFPSTMVDRIAPATTDFEHATVAAALGYRDAAPVPCEPFRQWVIED 273 Query: 265 NFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTNPAYR 324 F GRP W VGAQ V DV PFE+ KLRMLNG+HS LAYL LGG+ TI + + +PA R Sbjct: 274 RFPAGRPAWHAVGAQLVDDVTPFELAKLRMLNGTHSTLAYLSMLGGFTTIDEAIADPAMR 333 Query: 325 KAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQRLLD 384 A+M +E APTL+MP D+ Y L+ R++NP+L+HR QIAMDGSQK+P RLL Sbjct: 334 NLIHAMMTEEIAPTLNMPASFDVANYRDALLARYANPALKHRCAQIAMDGSQKIPPRLLG 393 Query: 385 PVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGADR-- 442 + + G + LAL VAGWM + +G + G+ D+ DP+ + + A G R Sbjct: 394 TIAARIDAGQPFTRLALAVAGWMTFLRGYADDGSRYDISDPLAENLKALAASANGDPRAL 453 Query: 443 VKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486 + LLG+ IF +L F A+ A Q L + GAR VAAL Sbjct: 454 MDTLLGVREIFTAELAAQPAFRAALLHALQLLQDNGARAAVAAL 497 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: 678 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: 498 Length adjustment: 34 Effective length of query: 452 Effective length of database: 464 Effective search space: 209728 Effective search space used: 209728 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