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:
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