Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate PfGW456L13_2810 Oxidoreductase
Query= BRENDA::O68965 (330 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2810 Length = 327 Score = 88.2 bits (217), Expect = 3e-22 Identities = 83/281 (29%), Positives = 126/281 (44%), Gaps = 42/281 (14%) Query: 3 VRFGLLGAGRIG---------KVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRT 53 VR+G++G G + K A+ RL AV D A IA Y Sbjct: 4 VRWGMIGCGSVAERKSGPAFYKAPGSALVAVMGRRLEAVTDY--ATRHGIARVY----TD 57 Query: 54 IDAIEAAADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTK 113 A+ ++DAV I TP D+H + A AGK EKP+ L+A + R +V +D Sbjct: 58 AQALINDPEVDAVYIATPPDSHHAYALQVAAAGKHCCVEKPMALNAGQSREMQQVFADAG 117 Query: 114 AKLMVGFNRRFDPHFMAVRKAIDDGRIGEVEMVTIT-SRDPSAPP--------VDYIKRS 164 L V + RR P F VR+ +++GRIGEV ++ T ++ PSA D Sbjct: 118 LHLFVSYYRRSLPRFRQVRQWLEEGRIGEVRHLSWTLTKAPSAADRSGTDNWRTDPAIAG 177 Query: 165 GGIFRDMTIHDFDMARFLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAI 224 GG F D+ H D+ ++L G+ A L + G D+VS + ASG + Sbjct: 178 GGYFADLASHGLDLFQYLFGD-----IVEVAGLTARQAGLYAAEDAVSATWRFASGALGM 232 Query: 225 -----ISNSRRATYGYDQRIEVHGSKGAV--AAENQRPVSI 258 +++ R + R+EV GSKG + + ++ PV + Sbjct: 233 GCWNFVADRR------EDRVEVIGSKGRITFSVFDEHPVEL 267 Lambda K H 0.320 0.134 0.379 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: 215 Number of extensions: 14 Number of successful extensions: 2 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: 330 Length of database: 327 Length adjustment: 28 Effective length of query: 302 Effective length of database: 299 Effective search space: 90298 Effective search space used: 90298 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: 49 (23.5 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