Align Facilitated trehalose transporter Tret1; PvTret1 (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= SwissProt::A5LGM7 (504 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 179 bits (455), Expect = 1e-49 Identities = 134/455 (29%), Positives = 221/455 (48%), Gaps = 34/455 (7%) Query: 44 ILAAIAVSMGSMVVGFASAYTSPALVSMQNTTITSFKVTEQEASWVGGIMPLAGLAGGIA 103 I +I ++G + GF +A S A +Q Q + W G+ L G + Sbjct: 8 IFLSIVAALGGFLFGFDTAVISGAERFIQEKW--------QLSDWTHGMAVAIALYGTVI 59 Query: 104 GGPF----IEYLGRKNTILATAVPFIVAWLLIAFANSIWMVLAGRALSGFCVGIASLSLP 159 G F + GRK ++L V + ++ L A A ++ + R + G VG +S+ P Sbjct: 60 GALFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAP 119 Query: 160 VYLGETVQPEVRGTLGLLPTAFGNIGILICFVAGKYV-------NWSGLAFIGSILPIPF 212 +Y+ E + RG L L GIL+ + + + +W + + +I + + Sbjct: 120 MYISEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNESWRWMMGMEAIPALIY 179 Query: 213 MVLTLLIPETPRWFVTRGREERARKALQWLRGKKADVEPELKGIVKSHCEAERHASQNAI 272 +L++ +P++PRW + + +A Q LR K D E + I + E R + Sbjct: 180 TLLSIRVPKSPRWLIAH--HNKVEEATQILR--KTDPEGVDEAIHLAIEERNREKIKVGF 235 Query: 273 FDLMKRSNLKPLLIALGLMFFQQLSGINAVIFYTVSIFKDAGSTIDEN---LCTIIVGVV 329 L K S+LK L+A+ + F QLSGINA+I++ +F+ AG ID+ L TI +GVV Sbjct: 236 AVLFKHSHLKTTLLAIMIALFNQLSGINAIIYFAPRVFEMAG--IDQKSALLSTIGIGVV 293 Query: 330 NFGATFFATVLIDRLGRKILLYISEVAMVITLLTLGTFFYYKNSGNDVSNIGWLPLASFV 389 N AT LIDR+GRK L+ I + +I+LL + Y SG V N G+LPL FV Sbjct: 294 NMIATMIGLYLIDRIGRKKLMVIGSIGYIISLLLMA----YSFSGG-VINSGYLPLFVFV 348 Query: 390 IYVIGFSSGVGPIPWLMLGEILPGKIRGSAASVATGFNWTCTFIVTKTFADIVAAIGNHG 449 ++ + G G + W+ + E+ P + R S+ +W ++ F + G Sbjct: 349 -FIASHAVGQGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPAS 407 Query: 450 AFWFFGVICLIGLFFVIFFVPETQGKSLEEIERKM 484 F FF V+ + L +V+ +PET+G+SLEEI++ + Sbjct: 408 IFGFFAVMMGLQLLWVLTKMPETKGRSLEEIQQDL 442 Lambda K H 0.326 0.141 0.428 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: 551 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 504 Length of database: 448 Length adjustment: 33 Effective length of query: 471 Effective length of database: 415 Effective search space: 195465 Effective search space used: 195465 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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