Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_086508654.1 BZY95_RS03790 TRAP transporter large permease subunit
Query= TCDB::P74224 (445 letters) >NCBI__GCF_002151265.1:WP_086508654.1 Length = 444 Score = 351 bits (901), Expect = e-101 Identities = 192/436 (44%), Positives = 281/436 (64%), Gaps = 9/436 (2%) Query: 10 MMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFG-IMANGTLL 68 +MF G L+ L G+P+AF LGG+A+ IGA LG + + L + I+G M N L+ Sbjct: 11 VMFGGLLIGLFMGHPLAFVLGGIAV----IGAYLGPGERV-LGTIINNIYGNAMDNYVLV 65 Query: 69 AIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVA 128 AIP F+ + L SG+ E++ M ++L +LRGGLAL V++V MLAATTG+V A++ Sbjct: 66 AIPLFVLMARFLNDSGVTEKMFAVMRLLLANLRGGLALTVVIVSVMLAATTGIVGASIAV 125 Query: 129 MGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLP 188 MG+I+L ML++GY+KEL++GVI+ASG LG +IPPS++LI++A VSVG LF G+L+P Sbjct: 126 MGMIALVPMLKHGYNKELSTGVIMASGCLGILIPPSIMLILMASYSPVSVGALFAGALVP 185 Query: 189 GLMMAGSFALYVLIIAWLKPDLAPALPAEVR-NIGGQELRRRIVQVMLPPLVLILLVLGS 247 GLM+ +ALYVL+I ++KP P +P E R +L + + +LPP+ LIL VLG+ Sbjct: 186 GLMLGAMYALYVLVICYIKPAYGPPVPTEERAETSTGQLLLMLAKYVLPPMALILGVLGA 245 Query: 248 IFFGIASPTEAGAVG-SIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFS 306 +F G+A+ TEA A+G +I + F R K + + T+MVML+L+G+TAF+ Sbjct: 246 LFTGVATATEASAIGVAIAFLLFLIFGDR-RLKTCFNTLIEAGKTTTMVMLVLVGATAFT 304 Query: 307 LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366 VF G + DL+ +PGG G L + + +F+LG F+D+ I + P+ P+ Sbjct: 305 GVFSRGGGMTVISDLVLAMPGGTTGALILMLFLVFLLGMFLDWTGIVLLSFPIMLPIVNQ 364 Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVL 426 + +D++W+ V+V LQTSFLTPPFG+ALFYL+GVAP + +YR VPF L VL Sbjct: 365 MGVDVLWFVVMVAVVLQTSFLTPPFGYALFYLKGVAPKGVEIVDLYRAVVPFCALIVLAC 424 Query: 427 LLIIIFPALINWLPSL 442 +L+ FP L+ LPSL Sbjct: 425 VLMAFFPVLVTGLPSL 440 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: 616 Number of extensions: 35 Number of successful extensions: 4 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: 444 Length adjustment: 32 Effective length of query: 413 Effective length of database: 412 Effective search space: 170156 Effective search space used: 170156 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 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