Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 282 bits (721), Expect = 2e-80 Identities = 154/401 (38%), Positives = 239/401 (59%), Gaps = 20/401 (4%) Query: 7 STTEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLM 66 ST ++K GLK RH++MIALGG IG GLF+ SG V+ AGP A+ ++++ GA+V +M Sbjct: 4 STDTTELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGP-AAVLSFLITGALVVLVM 62 Query: 67 TSLGEMATYLPTSGSFSDY------GTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALC 120 LGEMA +P GSF +Y G R GF GW YW W I VAV+ A A Sbjct: 63 RMLGEMACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKL 122 Query: 121 IKFWLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFG 180 ++FWLPDVP+W SL+ L+ + + N +SV ++GE E+W ++IK+ +++FL +G + + G Sbjct: 123 VQFWLPDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLG 182 Query: 181 IMGGHIDVAKNL-SVGNHGFVGGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAENP 239 + V L ++ +H GGL G + G + GF F G E++ I A EA+ P Sbjct: 183 LWPAAKHVTAVLPTLLSH---GGLMPKGIGPVLSGAVAATGFYF-GAEIVTIAAAEAQEP 238 Query: 240 EKSIPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIA 299 K++ KA NS+ R+LVFY+ SI ++ A++P+ P + +P+ + +G A Sbjct: 239 AKAVAKATNSVITRVLVFYVGSILLVVALVPWNSPKMA-------TPYVSALDAMGIPAA 291 Query: 300 ASIMNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVA 359 AS+MNA+VLT+V+SA NSG+YA++RM+++L + G AP +K ++ G+P A+L T Sbjct: 292 ASVMNAIVLTAVLSALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFG 351 Query: 360 LLTFLTS-IYGVSFFTFLVSASGLTGFIAWIGIAISHFRFR 399 + + S + + F FLV++ G ++ IAIS + R Sbjct: 352 YASVVMSYVSPDTVFAFLVNSYGTVAIFVYVLIAISQLKLR 392 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: 544 Number of extensions: 27 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: 476 Length adjustment: 34 Effective length of query: 454 Effective length of database: 442 Effective search space: 200668 Effective search space used: 200668 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: 52 (24.6 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