Align TRAP transporter (characterized, see rationale)
to candidate Pf6N2E2_320 TRAP transporter, 4TM/12TM fusion protein, unknown substrate 1
Query= uniprot:A8LI82 (743 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_320 Length = 675 Score = 338 bits (867), Expect = 5e-97 Identities = 200/526 (38%), Positives = 289/526 (54%), Gaps = 60/526 (11%) Query: 187 VLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVI 246 VL++ GVA A Y L++ S + + I V L+ E RRV G+AL +I Sbjct: 75 VLSLGGVATALYQWVFESDLIQRSGDLTTTDMIMGIVLVV---LVFEAARRVMGIALPII 131 Query: 247 AGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQV-YTDAGILGPTTAVSSTYIILFIIFAAF 305 G+FLAY G+YLPG L + +Q+ + G+ G T VS+TYI LFI+F AF Sbjct: 132 CGLFLAYGLFGEYLPGDLAHRGYGLDQIINQLSFGTEGLYGTPTYVSATYIFLFILFGAF 191 Query: 306 LQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKK 365 L+ + + F +FA G GGPAKVA+ +S LMG I G+ NVV TG TIPLMK+ Sbjct: 192 LEKAGMIKLFTDFAMGLFGHKLGGPAKVAVVSSALMGTITGSGIANVVTTGQFTIPLMKR 251 Query: 366 VGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVY 425 GY AG VEA +S G QIMPP+MGA AFIMAE +P+ EIA AA+IPA LYF SV+ Sbjct: 252 FGYKAAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPACLYFGSVF 311 Query: 426 FMVDLEAAKLGMRGMSRDELPKFNKMVRQV-YLFLPIIILIYALFMGYSVIRAGTLATVA 484 +MV LEA + ++G+ +D+ P V+ +L +P+ +L+Y LF G + + +G + Sbjct: 312 WMVHLEAKRSDLKGLPKDQCPSAWGAVKDSWFLLIPLGVLVYLLFSGRTPLFSGMVGLAL 371 Query: 485 AAVV------------------SWFTP-------FRMGPRSIAKAFEIAGTM-------- 511 A+V W FR+G I F + G + Sbjct: 372 TAIVILGSAIILKVSNYALRCAFWIALGLLCVGFFRLG---IGVVFAVIGVLVVACWFMQ 428 Query: 512 -------------------SVQIIAVCACAGIIVGVISLTGVGARFSAVLLGIADTSQLL 552 +V + CA G I+ V+SLTGV + F+ +L I + LL Sbjct: 429 GTRETLVICLHALVDGARHAVPVGIACALVGSIIAVVSLTGVASTFAGYILAIGRDNLLL 488 Query: 553 ALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFFVFYFAVLSAITPPV 612 +L M ++LGMG+PT Y + +S+ AP L++LG+PL+ +H FVFYF +L+ +TPPV Sbjct: 489 SLILTMLTCLVLGMGIPTIPNYIITSSIAAPALLELGVPLIVSHMFVFYFGILADLTPPV 548 Query: 613 ALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDG 658 ALA +AAA I+ + ++ S + +I +A F++PFM YN A+++ G Sbjct: 549 ALACFAAAPIARESGLKISFWAVRIALAGFVIPFMTVYNPALMLQG 594 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: 1252 Number of extensions: 82 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 743 Length of database: 675 Length adjustment: 39 Effective length of query: 704 Effective length of database: 636 Effective search space: 447744 Effective search space used: 447744 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 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