Align TRAP transporter (characterized, see rationale)
to candidate 199647 SO0455 hypothetical transporter (NCBI ptt file)
Query= uniprot:A8LI82 (743 letters) >FitnessBrowser__MR1:199647 Length = 677 Score = 345 bits (884), Expect = 6e-99 Identities = 218/613 (35%), Positives = 327/613 (53%), Gaps = 68/613 (11%) Query: 187 VLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVI 246 +L + G+A A Y L++ S A + + I + L+ E RRV G AL +I Sbjct: 75 LLGLAGMATAAYQWIFEADLIQRSGELTDADMVMGIILIV---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 LMG I G+ NVV TG TIPLMK+ Sbjct: 192 LEQAGMIRLFTDFAMGLFGHKLGGPAKVAVVSSALMGTITGSGVANVVTTGQFTIPLMKR 251 Query: 366 VGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVY 425 GY AG VEA +S G QIMPPIMGA AFIMAE +P+ EIA AA++PA+LYF SV+ Sbjct: 252 FGYRPAFAGGVEATSSMGSQIMPPIMGAVAFIMAETINVPFIEIAKAALLPALLYFCSVF 311 Query: 426 FMVDLEAAKLGMRGMSRDELP-KFNKMVRQVYLFLPIIILIYALFMGYSVIRAGT--LAT 482 +MV LEA + + G+ +D+ P + + + YL +P+ IL+Y LF G + + +G LA Sbjct: 312 WMVHLEAKRANLCGLPKDQCPDPWAAVKARWYLLIPLFILVYLLFSGRTPLFSGMVGLAL 371 Query: 483 VAAAVVSWFTPFRMGPRSIAKAFEIA-----------------GTMSVQIIAVC------ 519 + ++ R+ ++ AF IA G +++ ++A+C Sbjct: 372 TSIVILGSAIVLRLPSNALRFAFWIALGVLCAGFFQMGIGVVFGVIAI-LVAICWFIKGG 430 Query: 520 -----------------------ACA--GIIVGVISLTGVGARFSAVLLGIADTSQLLAL 554 ACA G+I+G++SLTG+ + F++ +L + + L+L Sbjct: 431 KDTLTICLHALVEGARHAVPVGIACALVGVIIGIVSLTGIASTFASYILAVGQDNLFLSL 490 Query: 555 FFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFFVFYFAVLSAITPPVAL 614 M ++LGMG+PT Y + +S+ AP L+ LG+PL+ +H FVFYF +++ +TPPVAL Sbjct: 491 VLTMITCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVAL 550 Query: 615 ASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDG-TWFEVLR-----AGA 668 A +AAA I+ + + S+ + +I IA F++PFM Y+ A+++ +W + A Sbjct: 551 ACFAAAPIAKESGFKISLWAIRIAIAGFVIPFMAVYDPALMLQSDSWLATIYVLIKVTVA 610 Query: 669 TAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDLIGVGTAVAIFLIQK 728 + GV F +Q ++ R FL G + A L SD IG G A+ + Sbjct: 611 IGIWGVVFTGYLLQKLYLWERVIGFLAGGSLILATPL------SDEIGFGLALLFIVQHS 664 Query: 729 LAAPKGGAIPVRG 741 L A K + +G Sbjct: 665 LRARKLKRLAAQG 677 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: 1311 Number of extensions: 83 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: 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