Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_017597109.1 D471_RS0102170 TRAP transporter fused permease subunit
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000341125.1:WP_017597109.1 Length = 724 Score = 368 bits (944), Expect = e-106 Identities = 240/699 (34%), Positives = 377/699 (53%), Gaps = 46/699 (6%) Query: 10 LPDIEV--GEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSLNIAPLET 67 LPD++ G D L V EE R G + VA+LA+A +AF LY A L+ Sbjct: 38 LPDVDGRDGGDGPLWRRVAEERWGEGRAATAVGAV--VAVLAVALTAFQLYVALFAGLDA 95 Query: 68 WSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLYQTFSFWQ 127 RI+H+ +VL F+L F + G +SA ++ AL + + + Sbjct: 96 RQQRIIHLLFVMVLVFLLMRP--FDLGKASG--------LSALTVVRALIPRRRKGTV-K 144 Query: 128 MVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVCSLAVAAY 187 G R V TGVG V+ DLVL+ ++ V+ Y Sbjct: 145 GEDGGDPRDAAARRV---------LTGVGWVL--------------DLVLVTAAVVVSVY 181 Query: 188 FLVVYNTSMRMSTGTSFAPVGISFA-AIAGTALIMELTRRVAGMALVIIGLVFLAYVFAG 246 + Y + G A G+ + + +++E TRR GM +V++ + F+ Y + G Sbjct: 182 -PIRYQDELAARAG---AYTGLDWVLGLILMIVLLEATRRAVGMIMVLLVVAFVYYAWIG 237 Query: 247 PYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVN 306 P++PG G+ G ++QR + Y GI G T V T++ +FI+F A L + G++FV Sbjct: 238 PFIPGQFGHTGATIQRISTHTYLGDGIYGLTLGVVVTFVFVFILFGALLNKTGGGNFFVG 297 Query: 307 FAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVE 366 A+ GR GGPAK ++ S +MG ++G++ NVV++G TIPLM+KVGY + A VE Sbjct: 298 LAYVVTGRMVGGPAKGAVLGSAMMGSVSGSAIANVVTSGPFTIPLMRKVGYRRADAAGVE 357 Query: 367 AAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGM 426 AAASTGGQI+PPIMGAGAFIMAE TGIPY +I A+IPA++YF ++ VD A K G+ Sbjct: 358 AAASTGGQILPPIMGAGAFIMAERTGIPYADIVKVALIPALMYFGVMFLFVDILARKHGI 417 Query: 427 RGMREDELPKLRTMMKQCYLF-VPIIILIVALFMGYSVIRAGTLATVSAAVVSWL-SPNK 484 R ++LP+LR +M + F +P+++LIV L +AG A + V+ L + ++ Sbjct: 418 GVARNEDLPRLRLVMAAGWHFLLPLLLLIVLLLQYVPPTQAGLYACGALLAVAMLRAGSR 477 Query: 485 MGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALI 544 + +L +A+ + + CA AG+IVG++ LTG+G S +L+ V A + LL L+ Sbjct: 478 LSPSDLLDVFVMAARNTLPVSAACAVAGIIVGMVGLTGLGLTLSNVLVTVFAGNLLLTLV 537 Query: 545 FAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALA 604 S+++G G+P TA+Y V + + P L +LG+ L AH V++++ S +TPPVALA Sbjct: 538 MVAVASLIMGFGLPVTASYVVISVLAVPALGELGLTVLVAHMIVYWYSQDSNVTPPVALA 597 Query: 605 SYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTATFGVY 664 ++AAAGI+GA M A+++ +++P M Y+ L ++ E+A A+++ + Sbjct: 598 AFAAAGIAGAKPMRAGAAAWKFAKGLYLIPVMMAYSALLAVDGPVLELAAAVLSGCVALA 657 Query: 665 MLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDL 703 + + G F + L++AAAL+M+ G W L Sbjct: 658 AAAIAIEGHFLRRTTLGERLGLILAAALVMV-GPEWAAL 695 Lambda K H 0.327 0.139 0.410 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: 1293 Number of extensions: 60 Number of successful extensions: 3 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: 729 Length of database: 724 Length adjustment: 40 Effective length of query: 689 Effective length of database: 684 Effective search space: 471276 Effective search space used: 471276 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 Apr 09 2024. 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