Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate WP_002965418.1 BIBO1_RS10685 trimeric intracellular cation channel family protein
Query= reanno::ANA3:7023996 (213 letters) >NCBI__GCF_000182725.1:WP_002965418.1 Length = 218 Score = 128 bits (322), Expect = 7e-35 Identities = 64/189 (33%), Positives = 110/189 (58%), Gaps = 1/189 (0%) Query: 14 GILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLAIA 73 G+ A TGALAA R+Q+D+ G + + TAIGGGT+RD++L + P+ WV YL Sbjct: 11 GVFVFAATGALAASRRQLDIIGFIFLANITAIGGGTMRDLVLAS-PVFWVVQPLYLFVGT 69 Query: 74 FASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFG 133 A++ A + + L +DA+G+A ++++GA K L LGF P++A+V G+ T FG Sbjct: 70 LAAIAVYFTAHKVESRYRTLLWLDAIGMAAYTVMGAAKGLALGFGPSVAIVTGIFTATFG 129 Query: 134 GVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSLRMLAL 193 G++RD++ + ++ ++E+Y ++ A LY+ L + I+ F +R AL Sbjct: 130 GILRDMVVGEPSVLMRREIYVTAAVAGACLYVVLEYLGINPVISAGAAAFAAFFVRGGAL 189 Query: 194 RYHWSMPTF 202 + W++P + Sbjct: 190 YFGWTLPVY 198 Lambda K H 0.330 0.143 0.438 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: 149 Number of extensions: 10 Number of successful extensions: 3 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: 213 Length of database: 218 Length adjustment: 22 Effective length of query: 191 Effective length of database: 196 Effective search space: 37436 Effective search space used: 37436 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: 40 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 24 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