Align putative transporter, required for L-alanine utilization (characterized)
to candidate 350729 BT1201 conserved hypothetical protein (NCBI ptt file)
Query= reanno::MR1:202450 (213 letters) >FitnessBrowser__Btheta:350729 Length = 209 Score = 141 bits (356), Expect = 8e-39 Identities = 74/195 (37%), Positives = 117/195 (60%), Gaps = 1/195 (0%) Query: 6 FIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLVWVEN 65 F+ +L IG A A++G A K+ D FG ++G ATAIGGGT+RD+LL P W+ N Sbjct: 4 FVQILDFIGTFAFAISGIRLASAKRFDWFGAYVVGLATAIGGGTIRDVLLDVTP-GWMTN 62 Query: 66 VHYLIAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVM 125 YLI A + + + L+ F D +GLA+F++VG K++ LG+ +A++M Sbjct: 63 PIYLICTGLALIWVICFGRWLIRLNNTFFIFDTIGLALFTVVGVGKSIALGYPFWVAIIM 122 Query: 126 GLVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLEEWINLVICLTLG 185 G +TG GGVIRD+ N++PLIF+KE+YA+ + Y +A +E ++ ++ + Sbjct: 123 GSITGAAGGVIRDVFINEIPLIFRKEIYAMACVVGGIAYWLCDAAGMESYVCQLVGGSAV 182 Query: 186 FSLRMLALRYHWSMP 200 F R+LA++YH +P Sbjct: 183 FVTRILAVKYHICLP 197 Lambda K H 0.330 0.143 0.436 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: 157 Number of extensions: 10 Number of successful extensions: 4 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: 209 Length adjustment: 21 Effective length of query: 192 Effective length of database: 188 Effective search space: 36096 Effective search space used: 36096 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 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