Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate Echvi_1573 Echvi_1573 Predicted sugar isomerase
Query= reanno::Cola:Echvi_1573 (427 letters) >FitnessBrowser__Cola:Echvi_1573 Length = 427 Score = 853 bits (2205), Expect = 0.0 Identities = 427/427 (100%), Positives = 427/427 (100%) Query: 1 MRIDKQKIKEVNDQALSEHRESFGHLSSVLGKKGIDVNVLVEKLKEFQVAVPSWALGTGG 60 MRIDKQKIKEVNDQALSEHRESFGHLSSVLGKKGIDVNVLVEKLKEFQVAVPSWALGTGG Sbjct: 1 MRIDKQKIKEVNDQALSEHRESFGHLSSVLGKKGIDVNVLVEKLKEFQVAVPSWALGTGG 60 Query: 61 TRFGRFSGGGEPGTLEDKISDVGLLHQLSQSAGAISLHIPWDIPNDVQAIKELAASHGLI 120 TRFGRFSGGGEPGTLEDKISDVGLLHQLSQSAGAISLHIPWDIPNDVQAIKELAASHGLI Sbjct: 61 TRFGRFSGGGEPGTLEDKISDVGLLHQLSQSAGAISLHIPWDIPNDVQAIKELAASHGLI 120 Query: 121 FDAVNSNTFQDQPDQELSYKFGSLCHADKKVRDQAVKHNLEVIKYGDALGSKSLTVWLAD 180 FDAVNSNTFQDQPDQELSYKFGSLCHADKKVRDQAVKHNLEVIKYGDALGSKSLTVWLAD Sbjct: 121 FDAVNSNTFQDQPDQELSYKFGSLCHADKKVRDQAVKHNLEVIKYGDALGSKSLTVWLAD 180 Query: 181 GSSFPGQLNFKKAFQRTLESLQEIYAGMPEDWKLFVEYKPYEPNFYSTVIQDWGTSHMLA 240 GSSFPGQLNFKKAFQRTLESLQEIYAGMPEDWKLFVEYKPYEPNFYSTVIQDWGTSHMLA Sbjct: 181 GSSFPGQLNFKKAFQRTLESLQEIYAGMPEDWKLFVEYKPYEPNFYSTVIQDWGTSHMLA 240 Query: 241 DKLGDRAYSLVDLGHHLPNTNIEQIVATLMMVGKLGGFHFNDSKYGDDDVTVGSLKPYQL 300 DKLGDRAYSLVDLGHHLPNTNIEQIVATLMMVGKLGGFHFNDSKYGDDDVTVGSLKPYQL Sbjct: 241 DKLGDRAYSLVDLGHHLPNTNIEQIVATLMMVGKLGGFHFNDSKYGDDDVTVGSLKPYQL 300 Query: 301 FLIFNELVDGMEDPSSNNPYPAWMIDASHNLKDPLEDLLQSLEAIKLAYAQALLVDRDAL 360 FLIFNELVDGMEDPSSNNPYPAWMIDASHNLKDPLEDLLQSLEAIKLAYAQALLVDRDAL Sbjct: 301 FLIFNELVDGMEDPSSNNPYPAWMIDASHNLKDPLEDLLQSLEAIKLAYAQALLVDRDAL 360 Query: 361 EEARENNDPALAQEILQAAYRTDVRSLLAEARLQADGALDPIAAYRKLNVRKELIAQRGE 420 EEARENNDPALAQEILQAAYRTDVRSLLAEARLQADGALDPIAAYRKLNVRKELIAQRGE Sbjct: 361 EEARENNDPALAQEILQAAYRTDVRSLLAEARLQADGALDPIAAYRKLNVRKELIAQRGE 420 Query: 421 KVISTGL 427 KVISTGL Sbjct: 421 KVISTGL 427 Lambda K H 0.316 0.135 0.391 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: 804 Number of extensions: 33 Number of successful extensions: 1 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: 427 Length of database: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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