Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate WP_057507459.1 ABB28_RS04355 trimeric intracellular cation channel family protein
Query= reanno::ANA3:7023996 (213 letters) >NCBI__GCF_001431535.1:WP_057507459.1 Length = 205 Score = 206 bits (525), Expect = 2e-58 Identities = 98/198 (49%), Positives = 140/198 (70%) Query: 7 IGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENV 66 + +++LI I AEAMTGAL+AGR++MDLFGVV+I C TA+GGG+LRD++LG+YPL WV++ Sbjct: 3 LSIIYLIAISAEAMTGALSAGRRRMDLFGVVMIACVTALGGGSLRDIILGHYPLAWVKHP 62 Query: 67 HYLLAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMG 126 YL A+L+ +A M + + FL +D LGL F+++G G + I ++ G Sbjct: 63 EYLGFTVCAALIATWVARWMHHFRRTFLVLDGLGLIAFTLIGCAIAREGGHATPIVLIAG 122 Query: 127 LVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGF 186 ++TG FGGV+RDILCN+VPLIF+KELYA+ISL T Y+ L + +A+ ++ CL GF Sbjct: 123 MLTGAFGGVLRDILCNEVPLIFQKELYAIISLLTGAAYLLLLRWNVADNTAILCCLAGGF 182 Query: 187 SLRMLALRYHWSMPTFDY 204 +LR+LA+ Y W MP F Y Sbjct: 183 ALRLLAIHYRWEMPKFVY 200 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: 178 Number of extensions: 5 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: 213 Length of database: 205 Length adjustment: 21 Effective length of query: 192 Effective length of database: 184 Effective search space: 35328 Effective search space used: 35328 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