Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Dsui_1262 Dsui_1262 TRAP transporter, DctM subunit
Query= TCDB::P74224 (445 letters) >FitnessBrowser__PS:Dsui_1262 Length = 488 Score = 508 bits (1307), Expect = e-148 Identities = 248/432 (57%), Positives = 334/432 (77%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66 + P+MF ++FL GYPVAF+L ++F IG LG P A+P+R+FGIMAN T Sbjct: 8 MAPVMFGALVLFLLFGYPVAFALAANGMVFGFIGMELGLLHPALFQALPERVFGIMANDT 67 Query: 67 LLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATV 126 LLAIPFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LAATTGVVAA+V Sbjct: 68 LLAIPFFTFMGLVLERSGMAEDLLDTIGQLFGPMRGGLAYAVIFVGALLAATTGVVAASV 127 Query: 127 VAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSL 186 ++MGLISLPIMLRYGY K LASGVI ASGTL QIIPPS+VLI++ADQLG SVGD++ G++ Sbjct: 128 ISMGLISLPIMLRYGYDKRLASGVIAASGTLAQIIPPSLVLIIMADQLGKSVGDMYEGAM 187 Query: 187 LPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLG 246 +PGL++ + YV+I+ +KP+ APALP E R++ G +L R++ ++PPLVLI LVLG Sbjct: 188 VPGLILTSLYVGYVVILTLIKPNAAPALPLEARSLRGAKLLMRVLTSLVPPLVLIFLVLG 247 Query: 247 SIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFS 306 +IF GIA+PTE GA+G+ GA+ LA +RL+ L + D T +++S V+ IL+GST F Sbjct: 248 TIFMGIATPTEGGAMGASGALILALMRKRLSVSLLKQAMDTTAKLSSFVVFILVGSTVFG 307 Query: 307 LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366 LVFR + GD ++ LL +LPGGQ+GFL + I +F+L FF+DFFE++FI++PL PVAE Sbjct: 308 LVFRAVNGDLWVEHLLTSLPGGQLGFLIVVNILVFVLAFFLDFFELSFIIVPLLGPVAEK 367 Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVL 426 L +DLIW+GV++G N+QTSF+ PPFGFALFYLR VAPAS+ T IY GAVPF+ +Q++++ Sbjct: 368 LGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAPASIKTTDIYWGAVPFVCIQIIMV 427 Query: 427 LLIIIFPALINW 438 LIIIFP ++++ Sbjct: 428 ALIIIFPGIVSY 439 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: 680 Number of extensions: 23 Number of successful extensions: 1 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: 488 Length adjustment: 33 Effective length of query: 412 Effective length of database: 455 Effective search space: 187460 Effective search space used: 187460 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