Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= reanno::pseudo5_N2C3_1:AO356_05505 (236 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 119 bits (298), Expect = 5e-32 Identities = 67/222 (30%), Positives = 118/222 (53%), Gaps = 9/222 (4%) Query: 9 WRPFLYSDGVNITGLAMTLWLLSASLLIGFVVSIPLSIARVSPKFYVRWPVQFYTYLFRG 68 W+ + S I G+ TL + LLIGF + I + ++ K+++RWP Y +FRG Sbjct: 9 WQAAIDSIPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRG 68 Query: 69 TPLYIQLLICYTGIYSIAAVRAQPMLDSFFRDAMNCTILAFALNTCAYTTEIFAGAIRSM 128 TP+ +Q+L + G+ P L D + I A ALN+ AY +E+ G ++S+ Sbjct: 69 TPILVQVLFIFYGL---------PDLIGGPIDPLTAGIAAIALNSGAYISEVVRGGVQSI 119 Query: 129 NHGEVEAAKAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATVPDVLKV 188 + G+ EA + GL+ + + V+ P A RR +P N+ I+ + T++ V ++++ Sbjct: 120 DKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVGELVRQ 179 Query: 189 ARDANSATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLA 230 + + TF F+ + + A++YL +T +L + R ERR LA Sbjct: 180 GQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERRGLA 221 Lambda K H 0.329 0.140 0.433 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: 142 Number of extensions: 9 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: 236 Length of database: 223 Length adjustment: 23 Effective length of query: 213 Effective length of database: 200 Effective search space: 42600 Effective search space used: 42600 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: 46 (22.3 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