Align TRAP transporter (characterized, see rationale)
to candidate 7023222 Shewana3_0456 TRAP transporter, 4TM/12TM fusion protein (RefSeq)
Query= uniprot:A8LI82 (743 letters) >FitnessBrowser__ANA3:7023222 Length = 677 Score = 347 bits (890), Expect = 1e-99 Identities = 218/594 (36%), Positives = 325/594 (54%), Gaps = 59/594 (9%) Query: 187 VLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVI 246 VL + G+A A Y L++ S A + I + + L+ E RRV G AL +I Sbjct: 75 VLGLAGMATAAYQWFFEADLIQRSGELTDADMVIGVVLIV---LVFEAARRVMGWALPII 131 Query: 247 AGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQV-YTDAGILGPTTAVSSTYIILFIIFAAF 305 IFLAY GQYLPG L + +Q+ + G+ G T VS+TYI LFI+F AF Sbjct: 132 CCIFLAYGLFGQYLPGDLMHRGYGVDQIINQLSFGTEGLYGTPTYVSATYIFLFILFGAF 191 Query: 306 LQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKK 365 L+ + + F +FA G GGPAKVA+ +S +MG I G+ NVV TG TIPLMK+ Sbjct: 192 LEQAGMIRLFTDFAMGLFGHKLGGPAKVAVVSSAMMGTITGSGVANVVTTGQFTIPLMKR 251 Query: 366 VGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVY 425 GY AG VEA +S G QIMPPIMGA AFIMAE +P+ EIA AA+IPA+LYF SV+ Sbjct: 252 FGYRPAFAGGVEATSSMGSQIMPPIMGAVAFIMAETINVPFIEIAKAALIPALLYFSSVF 311 Query: 426 FMVDLEAAKLGMRGMSRDELP-KFNKMVRQVYLFLPIIILIYALFMGYSVIRAGT--LAT 482 +MV LEA + + G+ +D+ P + + + YL +P+ ILIY LF G + + +G LA Sbjct: 312 WMVHLEAKRANLCGLPKDQCPDPWAAVKERWYLLIPLFILIYLLFSGRTPLFSGMVGLAL 371 Query: 483 VAAAVVSWFTPFRMGPRSIAKAFEIA-----------------GTMSVQIIAVC------ 519 + ++ R+ ++ AF IA G +++ ++AVC Sbjct: 372 TSIVILGSAIVLRLPSNAMRFAFWIALGVLCAGFFQMGIAVVFGVIAL-LVAVCWFIKGG 430 Query: 520 -----------------------ACA--GIIVGVISLTGVGARFSAVLLGIADTSQLLAL 554 ACA G+I+G++SLTG+ + F++ +L + + L+L Sbjct: 431 KDTLTICLHALVDGARHAVPVGIACALVGVIIGIVSLTGIASTFASYILAVGQDNLFLSL 490 Query: 555 FFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFFVFYFAVLSAITPPVAL 614 M ++LGMG+P+ Y + +S+ AP L+ LG+PL+ +H FVFYF +++ +TPPVAL Sbjct: 491 VLTMLTCMVLGMGIPSIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVAL 550 Query: 615 ASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDG-TWFEVLRAGATAVVG 673 A +AAA I+ + ++ S+ + +I IA F++PFM Y A+++ +W + A VG Sbjct: 551 ACFAAAPIAKESGLKISLWAIRIAIAGFVIPFMAVYEPALMLQSDSWLAIGFVMLKATVG 610 Query: 674 VFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDLIGVGTAVAIFLIQ 727 + G F+ + W+ RV A LI +SD IG G A+ +F++Q Sbjct: 611 IGIWGVIFTG-FLLQKLYWWERVIGFLAGASLILATPLSDEIGFGLAL-LFIVQ 662 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: 1288 Number of extensions: 86 Number of successful extensions: 5 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: 677 Length adjustment: 39 Effective length of query: 704 Effective length of database: 638 Effective search space: 449152 Effective search space used: 449152 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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