Align Lmo2664 protein (characterized, see rationale)
to candidate RR42_RS35005 RR42_RS35005 L-idonate 5-dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS35005 Length = 342 Score = 164 bits (414), Expect = 4e-45 Identities = 114/335 (34%), Positives = 169/335 (50%), Gaps = 24/335 (7%) Query: 6 LYENNVIKAEQIDEATCGKDQVRVEVKAVGICGSDIHKM----QTRWKYPLPAVMGHEFA 61 ++ + ++ Q++ A G +V V + A GICGSD+H + P GHE A Sbjct: 7 IHASEDLRFTQVEPAAPGPFEVEVRLGAAGICGSDLHYYFHGKVGAFVIREPLTPGHEAA 66 Query: 62 GVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGS-----HFHGGF 116 G+++ +GS VT VA G++VA P C +C+YC+AG LC + R +GS H G F Sbjct: 67 GIVSRVGSAVTRVAPGNKVAINPSHACGQCDYCRAGRDNLCRSMRFLGSASIYPHVQGMF 126 Query: 117 AENVVMKADNVISI-GDLDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGIGTIGILVV 175 E+ +M + + D+ E A EPL+V++HGV LG TV+V G GTIG L V Sbjct: 127 REHFLMHERQLTPVDSDISLGELAFAEPLSVALHGVNRAGELLGKTVLVTGGGTIGSLAV 186 Query: 176 QCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLGADIALECA 235 LAG IIA DI+D+ L A G I E + AD+ LE A Sbjct: 187 MAARLAGAAHIIACDIADRPLEVALRVGADQVIRTDREPPRALQDL------ADVCLEAA 240 Query: 236 GSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWNSYSAPFPGE 295 GS + CLL ++ ++ +G A+ LH A NI REL G + G Sbjct: 241 GSGAALDTCLLAARRGARIVQIGTLPAEG-LHFPA-NNIMARELEYVGAFRF------GR 292 Query: 296 EWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDM 330 E+ ++ ++ QGR+ ++PL+S + L + EAF + Sbjct: 293 EFDWAVRYLTQGRLDVRPLLSAQLPLAQAVEAFTL 327 Lambda K H 0.321 0.139 0.417 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: 259 Number of extensions: 10 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: 350 Length of database: 342 Length adjustment: 29 Effective length of query: 321 Effective length of database: 313 Effective search space: 100473 Effective search space used: 100473 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