Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 321 bits (822), Expect = 4e-92 Identities = 179/477 (37%), Positives = 270/477 (56%), Gaps = 24/477 (5%) Query: 3 NSSNSTTEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMV 62 N E + RGLK RH+ MIA+GG IG GLFL +G I AGP G + +Y + G + Sbjct: 9 NEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGP-GLMLSYAIGGVAI 67 Query: 63 YFLMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIK 122 +F+M +LGE+ Y P SGSF+ Y +V P GFA GW+YW W +T ++TAVA+ + Sbjct: 68 FFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVH 127 Query: 123 FWLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIM 182 +W PDVP WI +L L +++ +N ++V FGE E+W + IK+ +V ++IG IF Sbjct: 128 YWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIF--- 184 Query: 183 GGHIDVAKNLSVGNHGFVGGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAENPEKS 242 G + S N GG F T G +L L + F++QG EL+G+TAGEA+NPEK Sbjct: 185 FGVTPLGPTASFSNLWTHGGFMPFGTLGVVL-TLQIVMFAYQGVELIGVTAGEAQNPEKV 243 Query: 243 IPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASI 302 +P A N + WRIL+FY+ ++ +M A++P+ + SPF VFER+G AA+I Sbjct: 244 LPHATNGVVWRILIFYVGALIIMMALVPWNE------LKPGVSPFVYVFERIGVPGAAAI 297 Query: 303 MNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTA-VALL 361 +N VV+T+ S+ NSG++++ RMLY+LA+ G AP F + S +P IA+ + A + + Sbjct: 298 VNLVVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIG 357 Query: 362 TFLTSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPF 421 L I F ++ S S + W I I+H +R+A +A G+ VK + + P+ Sbjct: 358 VLLNYIVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKA-IAAGR-VKAVAFRMPGAPY 415 Query: 422 GP--ILALIMTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKFKNKTKLI 476 ++A ++ V V L DP V +Y A F +L +GY+F L+ Sbjct: 416 ANWLVVAFMIAVAVLLSLDP--------GTRVALYVAPVWFALLGIGYRFTKSRALL 464 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: 577 Number of extensions: 31 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: 472 Length adjustment: 34 Effective length of query: 454 Effective length of database: 438 Effective search space: 198852 Effective search space used: 198852 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 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