Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3307 HP15_3249 TRAP-type mannitol/chloroaromatic compound transport system, large permease component
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Marino:GFF3307 Length = 431 Score = 438 bits (1126), Expect = e-127 Identities = 215/427 (50%), Positives = 312/427 (73%), Gaps = 6/427 (1%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66 +G +MF ALV L G+PVAF+ GGVA+ F I + F + MP RI +M N Sbjct: 2 IGMIMFGVALVMLMLGFPVAFTFGGVALFFGIFAEGMDLF-----AFMPYRIMSVMQNTV 56 Query: 67 LLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATV 126 L+A+P FIF+G +L+R+ +AEQLL +MG + G L GGLA++ ILVG +LAA+TGVV A+V Sbjct: 57 LMAVPLFIFMGVVLQRTRLAEQLLTSMGRLFGGLPGGLAISTILVGALLAASTGVVGASV 116 Query: 127 VAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSL 186 VAMGLISLP+ML + Y K LA+G I ASGTLGQI+PPS++LI+L D LG+ VGDLF ++ Sbjct: 117 VAMGLISLPVMLAHKYDKRLATGTICASGTLGQIVPPSIILIILGDVLGLPVGDLFKAAV 176 Query: 187 LPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLG 246 PG+++ G + +Y+L++ LKP+ APA+P E +E+ ++ + +PPL LI++VLG Sbjct: 177 WPGVVLVGLYIIYILVLTRLKPETAPAMPDEPGVSRKKEVFNALLAI-IPPLALIVVVLG 235 Query: 247 SIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFS 306 SIF GIA+PTE+ A+G +GA+ LA ++ ++K +W+ T+++T+MV IL+G+TAFS Sbjct: 236 SIFTGIATPTESSALGGVGAVVLAIIYRQFSFKMVWDASKDTVKVTAMVFAILIGATAFS 295 Query: 307 LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEA 366 +VF GD + + L LPG + GF+ ++M+ I +LGFFIDF EI+FI++P+ PVAEA Sbjct: 296 MVFSYTGGDYLLEEWLLQLPGEKWGFIILAMVVILVLGFFIDFVEISFIIVPILAPVAEA 355 Query: 367 LNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVL 426 + ++++W+ +++ NLQTSFLTPPFGF+LFYL+GVAP + T IY+G +PFI +Q+ VL Sbjct: 356 MGINMLWFAILIAMNLQTSFLTPPFGFSLFYLKGVAPPGVRTTDIYKGVLPFILIQMFVL 415 Query: 427 LLIIIFP 433 LI+IFP Sbjct: 416 ALIVIFP 422 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: 637 Number of extensions: 37 Number of successful extensions: 3 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: 431 Length adjustment: 32 Effective length of query: 413 Effective length of database: 399 Effective search space: 164787 Effective search space used: 164787 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