Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate WP_160173842.1 JG50_RS0109790 amino acid permease
Query= TCDB::K7VV21 (488 letters) >NCBI__GCF_000763315.1:WP_160173842.1 Length = 453 Score = 262 bits (670), Expect = 2e-74 Identities = 141/390 (36%), Positives = 225/390 (57%), Gaps = 17/390 (4%) Query: 13 VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72 ++R L R + MI LG IGTGLF+ S IH AGP G L +Y+L +V ++ L + Sbjct: 15 LQRSLSERQMIMIGLGSAIGTGLFMGSSLTIHYAGP-GVLFSYLLSSLIVLAMVFCLSRL 73 Query: 73 ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132 + PT+GSF + Y+ FGFA+ + YW AI + + TA+ L +K+W P +PSWI Sbjct: 74 SVIHPTAGSFGLHAETYLGSWFGFAVRFTYWAANAIVIGGEATAIGLYMKYWFPGLPSWI 133 Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKNL 192 + + +++ INA+SV++FG EYW S +K+ V+ F+++G IFG N Sbjct: 134 WIIAFSLLIIGINAISVQSFGWFEYWFSTLKVVAVIGFILLGIALIFG----------NS 183 Query: 193 SVGNHGFVGGLGSFTTGG--GILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNSI 250 + H ++ G F G G+ +A FSF GTE++ ITAGEA+ P++++ +AM + Sbjct: 184 TQSTH-YLLAYGGFLPHGWKGVWMGSAMAMFSFMGTEIIAITAGEAKKPKQALTRAMKWM 242 Query: 251 FWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLTS 310 R+++FY+LS VM I+P+ +GG +SPF V + + AA +MN ++LT+ Sbjct: 243 VARLVIFYLLSTLVMVCIVPWNQ---IGGEQIQESPFVKVLQSLHIPYAAGVMNFIILTA 299 Query: 311 VVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALLTFLTSIYGV 370 +S N+ +YA TRM++SL+K G AP +F K ++ GIP +AL+ ++ + L +++ Sbjct: 300 ALSTMNANLYACTRMMFSLSKSGYAPAVFGKVNRRGIPLMALIVSSFGLGVAVLLNMFDP 359 Query: 371 SFFTFLVSASGLTGFIAWIGIAISHFRFRR 400 + L S G WI I +S+ R RR Sbjct: 360 QAYNTLFGISIFGGIFTWITIFLSYARLRR 389 Lambda K H 0.326 0.141 0.425 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: 585 Number of extensions: 30 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: 488 Length of database: 453 Length adjustment: 33 Effective length of query: 455 Effective length of database: 420 Effective search space: 191100 Effective search space used: 191100 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 (21.6 bits) S2: 51 (24.3 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