Align Membrane protein containing probable solute: sodium symporter, small subunit domain (characterized, see rationale)
to candidate 5209924 Shew_2372 hypothetical protein (RefSeq)
Query= uniprot:E4PHQ1 (88 letters) >FitnessBrowser__PV4:5209924 Length = 88 Score = 91.3 bits (225), Expect = 2e-24 Identities = 43/88 (48%), Positives = 59/88 (67%) Query: 1 MSAGHSYDAEAYWKANLRLIFGSLIVWALVSYGFAILLRPMLAGIPIGGTDLGFWFAQQG 60 M+ ++ AE YW+ NLRL+ G L +WA VS+G ILL +L I G LGFWFAQQG Sbjct: 1 MAFENNEKAEGYWRENLRLVLGLLAIWAAVSFGCGILLVDVLNEIHFMGFKLGFWFAQQG 60 Query: 61 SILTFIALIFHYAWRMNKIDEKFGVHEE 88 ++ F+ALIF Y + N +D+K+ VHE+ Sbjct: 61 AMYVFVALIFVYVAKANALDKKYNVHED 88 Lambda K H 0.329 0.143 0.473 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: 54 Number of extensions: 1 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: 88 Length of database: 88 Length adjustment: 9 Effective length of query: 79 Effective length of database: 79 Effective search space: 6241 Effective search space used: 6241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.3 bits) S2: 39 (19.6 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