Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate WP_013076931.1 BTUS_RS15100 amino acid permease
Query= TCDB::K7VV21 (488 letters) >NCBI__GCF_000092905.1:WP_013076931.1 Length = 462 Score = 315 bits (808), Expect = 2e-90 Identities = 181/464 (39%), Positives = 268/464 (57%), Gaps = 26/464 (5%) Query: 10 EMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFL-MTS 68 E ++ RGLK RH+ +IALGG IG GLFL S IH AGP ALT L+G +V FL M + Sbjct: 4 ESELVRGLKERHLQLIALGGAIGVGLFLGSARAIHLAGP--ALTISYLVGGLVIFLIMRA 61 Query: 69 LGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDV 128 LGE+A Y P +GSFS Y +V P GF GW YW W T ++TAV + +++W P V Sbjct: 62 LGELALYKPVAGSFSTYAEEFVGPWAGFITGWTYWFMWITTAMAEITAVGVYVRYWFPAV 121 Query: 129 PSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSI-FGIMGGHID 187 P W+ +LIAL+++F +N ++V +GE E+W + IK+ +V +++G L I FG+ + Sbjct: 122 PQWLPALIALVVMFLVNLIAVGAYGEFEFWFALIKVVTIVAMIVVGLLIILFGVWNQGVP 181 Query: 188 VAKNLSVGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKA 246 V + ++ +HG G F TG GG L L + F++ G EL+G+TAGEA +P K+IP A Sbjct: 182 VGFS-NLWSHG-----GFFPTGIGGALLALQMVMFAYVGVELIGVTAGEARDPSKTIPSA 235 Query: 247 MNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAV 306 N I WRIL+FY+ ++ ++ ++ P+ + A SPF + F+R+GF AA ++N V Sbjct: 236 TNKIIWRILIFYVGALVIIMSLYPWNE------LDAQNSPFVLTFQRIGFPAAADVINFV 289 Query: 307 VLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL-TFLT 365 VLT+ +S+ NSG++++ RMLYSLA+ G AP S +P A+ A+ AV L+ L Sbjct: 290 VLTAALSSCNSGVFSTGRMLYSLAQYGQAPRFLRGLSSRRVPAAAIAASAAVMLVGVILN 349 Query: 366 SIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPIL 425 + FT++ S W I ++H +RR VA G+ V+ + Y P + Sbjct: 350 YVVPQQVFTYVTSLGAEAAIWTWGMILVAHMAYRRR-VAAGQ-VQAVKYRMPGSPVTNWI 407 Query: 426 ALIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKF 469 L LV + +LLF V Y A+ F IL + Y+F Sbjct: 408 GLAFLALVVV----LLLFDPD--TRVAFYVALVWFAILVIAYQF 445 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: 534 Number of extensions: 29 Number of successful extensions: 6 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: 462 Length adjustment: 33 Effective length of query: 455 Effective length of database: 429 Effective search space: 195195 Effective search space used: 195195 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