Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate HSERO_RS02215 HSERO_RS02215 D-arabinitol 4-dehydrogenase
Query= curated2:P39160 (486 letters) >FitnessBrowser__HerbieS:HSERO_RS02215 Length = 477 Score = 194 bits (494), Expect = 4e-54 Identities = 130/364 (35%), Positives = 192/364 (52%), Gaps = 16/364 (4%) Query: 26 VHLGCGAFHRAHQALYTHHLLES-TDSDWGICEVNLMPGNDRVLIENLKKQQLLYT---V 81 +H+G G+FHRAHQA+Y + L ES D W + N+ + L+E L +QQ YT V Sbjct: 19 LHIGAGSFHRAHQAVYLNALRESGADRRWQLALANIR-ADMSPLLEALARQQGQYTLETV 77 Query: 82 AEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQL 141 +G S + I S+ L P ++ A A +T I+S TVTE GY D QL Sbjct: 78 TPQGQRSYQR--IASIGRIL-PWDAQLTQLIAAGAEERTRIISFTVTEGGYYLDHQH-QL 133 Query: 142 DLNNPLIKHDL----ENPTAPKSAIGYIVEALRLRREKGLKA-FTVMSCDNVRENGHVAK 196 D +N + DL + AP++ G I L R + +A T+++CDN+R NG + Sbjct: 134 DTSNADLAEDLRCALDGSGAPRTIYGAIAAILHARSQAHPQAALTLLNCDNLRHNGERFR 193 Query: 197 VAVLGLAQAR-DPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACE 255 + R + L +W++ N T P MVDRI P T Q + + G+ DPCA+ E Sbjct: 194 DGLRQFLTLRGETALVSWMQANTTSPNAMVDRITPRPTAAVAQRVKEATGIDDPCALMGE 253 Query: 256 PFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIA 315 F QWVIED+F GRP ++ G + V V+P+E K+R+LN SHS +A+ G L G + I Sbjct: 254 SFIQWVIEDDFKAGRPRLEEAGVEMVQSVLPYEEAKIRILNASHSCIAWAGTLAGLQYIH 313 Query: 316 DTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGS 375 + R+ A+ + Q+ L+ P DL AY + RFSNP+++ ++A DG Sbjct: 314 EGTLRDDIRQMAYDYVTQDVIACLT-PSPIDLAAYRDTTLARFSNPAIQDTNQRVAADGY 372 Query: 376 QKLP 379 K+P Sbjct: 373 SKIP 376 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: 562 Number of extensions: 28 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: 477 Length adjustment: 34 Effective length of query: 452 Effective length of database: 443 Effective search space: 200236 Effective search space used: 200236 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