Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3856 HP15_3797 TRAP-type mannitol/chloroaromatic compound transport system, large permease component
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Marino:GFF3856 Length = 454 Score = 372 bits (956), Expect = e-107 Identities = 192/448 (42%), Positives = 293/448 (65%), Gaps = 15/448 (3%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGA-ALGSFDPIF-------LSAMPQRI 58 +G + GAL+ G YPVA+ LGG A+++ ++G A+ +F + +P+RI Sbjct: 9 IGMFLTFGALLMTG--YPVAWVLGGTAVIWTVVGVVAVENFGANLWFDYQSSMGLVPERI 66 Query: 59 FGIMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAAT 118 + ++++ TL+A+P FIF+G ML++SG+AE+L+ +M + G +RGG A+ VI++G +LAAT Sbjct: 67 WKVVSSETLVALPMFIFMGIMLDQSGVAERLMNSMVKLFGAVRGGYAVTVIVIGVLLAAT 126 Query: 119 TGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGV-- 176 TG++ A+VV +G++SLP+M+ Y K A G A+GTLG +IPPS++L+++AD+L V Sbjct: 127 TGIIGASVVLLGMLSLPVMMENKYDKGFAVGTACATGTLGILIPPSIMLVLMADRLAVPE 186 Query: 177 -SVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVML 235 SVGDLF+G+ PGLM+ + Y +I L+P++AP +P + + + + ++ Sbjct: 187 ASVGDLFMGAFFPGLMLGAMYVAYAIIRPMLQPNIAP-VPEGTEKVSWA-IVWEVAKAVV 244 Query: 236 PPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMV 295 P LIL VLGSIF GIA+PTEA VG++GA+ LA + RLN L T R + + Sbjct: 245 PTAALILGVLGSIFAGIATPTEASGVGALGALLLALMSGRLNLNVLNSSMQQTTRTAAFI 304 Query: 296 MLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFI 355 I LG+TAFS+V RGL GD+ + D L LP G G + + +F+LGFF+D+ EI I Sbjct: 305 FAIFLGATAFSVVLRGLGGDQVIEDALLGLPFGPYGVVLTILFGVFLLGFFLDWVEITLI 364 Query: 356 VLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGA 415 +LPL PV ++L DL+W+ ++ LQTSFLTPP GFALFY++GVAP + IYRG Sbjct: 365 ILPLVAPVVQSLGFDLVWFTILFAMCLQTSFLTPPVGFALFYIKGVAPPEIKVTDIYRGV 424 Query: 416 VPFIGLQVLVLLLIIIFPALINWLPSLS 443 +PFI +Q+ L ++ + P + WLPS++ Sbjct: 425 IPFIIIQLAALAIVFVVPEIATWLPSVA 452 Lambda K H 0.331 0.148 0.443 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: 684 Number of extensions: 41 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: 445 Length of database: 454 Length adjustment: 33 Effective length of query: 412 Effective length of database: 421 Effective search space: 173452 Effective search space used: 173452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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