Align TRAP transporter (characterized, see rationale)
to candidate WP_086508325.1 BZY95_RS01940 permease
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_002151265.1:WP_086508325.1 Length = 673 Score = 359 bits (922), Expect = e-103 Identities = 194/537 (36%), Positives = 307/537 (57%), Gaps = 40/537 (7%) Query: 222 IAAVAGTALIMELTRRVAGMALIVIAGIFLAYVF---------VGQYLPGFLNAPAVTWQ 272 I ++E +RR G+ + +I I + Y F +GQ++PG L Sbjct: 118 IVGCIAVVTVLEASRRAVGLGMTIIGAIAILYAFAGPRGELPWLGQFMPGILEHRGYNLD 177 Query: 273 RFFSQVYT-DAGILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGQSRGGPA 331 R Q+Y GI G V++T+I +F++F AFL+++ G +F++ A+AA G+ RGGPA Sbjct: 178 RVVGQLYLGQEGIFGLPLGVAATFIFVFVLFGAFLESTGAGKFFIDMAYAATGRQRGGPA 237 Query: 332 KVAIFASGLMGMINGTSAGNVVATGSLTIPLMKKVGYHKKTAGAVEAAASTGGQIMPPIM 391 K A+ AS MG I+G++ NVV TG+ TIPLMK++GY AG +EAAASTGGQIMPP+M Sbjct: 238 KAAVIASAGMGSISGSAIANVVTTGAFTIPLMKRLGYKPHQAGGIEAAASTGGQIMPPLM 297 Query: 392 GAGAFIMAEITGIPYTEIALAAIIPAILYFVSVYFMVDLEAAKLGMRGMSRDELPKFNKM 451 GAGAF++AE T PY ++ +I+PAI+YF +VY V + A K GM+G+ + ELP+ + Sbjct: 298 GAGAFLIAEYTNTPYLDVVKVSILPAIMYFATVYLFVHIIALKQGMQGLPKSELPQMRDV 357 Query: 452 VRQVYLF-LPIIILIYALFMGYSVIRAGTLATVAAAVVS------WFTPFRMGPR----- 499 +R+ + F LP+ +L++ L M S +R G A V V+ WF F + PR Sbjct: 358 LREGWHFLLPLAVLVWLLAMHMSPMRVGFYAVVTMVAVAALRYTIWF--FFVAPRQGQPV 415 Query: 500 --------------SIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSAVLLGI 545 + + E+ +V + CA AGIIVGV+ LTG+G +FSA+++ Sbjct: 416 TLASTGRVIWAGFVKLIEGLELGARNAVSVSLACAVAGIIVGVVGLTGLGLKFSAMMMAF 475 Query: 546 ADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGL-VQLGIPLLTAHFFVFYFAV 604 + + +LAL + +++LGMG+P TA+Y V +V P L + GIPLL AH VF+++ Sbjct: 476 SGGNIVLALLMVLLASLILGMGLPVTASYIVLIVLVGPALTAEFGIPLLIAHLVVFWYSQ 535 Query: 605 LSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDGTWFEVL 664 S +TPP+ALA +A A I+G+ PM T V ++K +++P +N I+M G + Sbjct: 536 DSNVTPPIALAGFAGAAIAGSKPMATGVQAWKFAKGLYLIPMFMVFNPEIIMGGPLHILA 595 Query: 665 RAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDLIGVGTAV 721 G A++ + ++ ++G ++ R +W R+ + A + + M + +GV + Sbjct: 596 WNGLIAILALGAFAAALEG-YLFTRMSWLPRIAISGAIVAVFYPNFMVEAVGVAVMI 651 Lambda K H 0.327 0.140 0.419 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: 1441 Number of extensions: 97 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 743 Length of database: 673 Length adjustment: 39 Effective length of query: 704 Effective length of database: 634 Effective search space: 446336 Effective search space used: 446336 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 (21.7 bits) S2: 55 (25.8 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