Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate WP_004303336.1 C665_RS06455 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_05505 (236 letters) >NCBI__GCF_000310185.1:WP_004303336.1 Length = 244 Score = 209 bits (531), Expect = 5e-59 Identities = 116/234 (49%), Positives = 146/234 (62%), Gaps = 15/234 (6%) Query: 5 LQEYWRPFLYSDGVNITGLAMTLWLLSASLLIGFVVSIPLSIARVSPKFYVRWPVQFYTY 64 L E+WR GL MT+ L +LL GF V+IPL++ R+SP V PV YTY Sbjct: 13 LPEFWR-----------GLWMTVQLTGLALLFGFFVAIPLAVMRLSPNRLVSAPVAAYTY 61 Query: 65 LFRGTPLYIQLLICYTGI----YSIAAVRAQPMLDSFFRDAMNCTILAFALNTCAYTTEI 120 FRGTP+ +QLL+ Y G + AA A L S FR+ C + AF LNTCAYT EI Sbjct: 62 FFRGTPMLVQLLLVYYGASQWEWMRAAWEAGHPLWSLFREPYFCALFAFGLNTCAYTVEI 121 Query: 121 FAGAIRSMNHGEVEAAKAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTA 180 AG++R+ HGE+EAAKA G+T K +++PSALRR +P YSNEVILML + +A Sbjct: 122 LAGSMRNTPHGELEAAKAMGMTRLKALQRIVIPSALRRMIPSYSNEVILMLQGSAIASAV 181 Query: 181 TVPDVLKVARDANSATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLAFLGP 234 T+ D+ AR+ S F F+SF LIYL +TFALVGLF+LAE RWLA L P Sbjct: 182 TLVDLTGAARNVYSRHFAPFESFVFVGLIYLALTFALVGLFKLAEHRWLAHLAP 235 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: 188 Number of extensions: 8 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: 244 Length adjustment: 23 Effective length of query: 213 Effective length of database: 221 Effective search space: 47073 Effective search space used: 47073 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 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