Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AZOBR_RS29760 AZOBR_RS29760 C4-dicarboxylate ABC transporter
Query= TCDB::P74224 (445 letters) >FitnessBrowser__azobra:AZOBR_RS29760 Length = 596 Score = 251 bits (642), Expect = 3e-71 Identities = 124/211 (58%), Positives = 161/211 (76%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66 + P+MF + L GYPVAF+L +LF +IG +G F P A+P+R++G M N Sbjct: 1 MAPIMFATLVGMLLLGYPVAFALAANGLLFGLIGIEIGLFRPDLFQALPERVYGTMNNDV 60 Query: 67 LLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATV 126 LLA+PFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LAATTGVVAA+V Sbjct: 61 LLAVPFFTFMGLVLERSGMAEDLLDTIGQLFGSIRGGLAYAVIFVGALLAATTGVVAASV 120 Query: 127 VAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSL 186 ++MGLISLPIMLRYGY + LASGVI ASGTL QIIPPS+VLIV+ADQLG SVGD++ + Sbjct: 121 ISMGLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIVMADQLGRSVGDMYEAAF 180 Query: 187 LPGLMMAGSFALYVLIIAWLKPDLAPALPAE 217 +PGL++AG +ALYV +++ + P AP LP E Sbjct: 181 IPGLLLAGLYALYVFVVSMIWPKAAPGLPPE 211 Score = 224 bits (571), Expect = 6e-63 Identities = 131/352 (37%), Positives = 205/352 (58%), Gaps = 36/352 (10%) Query: 102 GGLALAVILVGTMLAATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQII 161 G LAL V T + T V + + L+S+ +++ + LA+ G ++ Sbjct: 228 GLLALFSGAVATWVMGRTDVKSGADYVVLLLSVAVLVAF-----LAAAFNRGFGAQRLVL 282 Query: 162 PPSVVLIVLADQLGVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNI 221 + A ++V + +L+ + AG ALY L +A V Sbjct: 283 QTVATAALTAAAAWLTVNEWTTLALIGDSIAAG--ALYALAVA------------VVERA 328 Query: 222 GGQELRRRIVQ----VMLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLN 277 G+ L R+ + VM+PPL LI LVLG+IF G+A+PTE GA+G++GA+ALA +RLN Sbjct: 329 TGRRLISRMAEQATFVMVPPLALIFLVLGTIFIGLATPTEGGAMGAVGALALAAMKKRLN 388 Query: 278 WKALWEVCDATLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISM 337 + + + +T ++ + V+ IL+G+ FSL F G+ G ++ +L+ +LPGGQ+GFL Sbjct: 389 FDMVRQATYSTAKLAAFVLFILIGARVFSLTFYGVNGHIWVEELMVSLPGGQMGFLIAVS 448 Query: 338 ITIFILGFFIDFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFY 397 + +F+L FF+DFFE+AFIV+PL P A+ L +DL+W+GVI+ N+QTSF+ PPFGF+LF+ Sbjct: 449 VMVFLLAFFLDFFELAFIVIPLLAPAADRLGIDLVWFGVILAVNMQTSFMHPPFGFSLFF 508 Query: 398 LRGVAP-------------ASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436 LR VAP A + T QIY GAVPF+ +Q++++ L+I FP ++ Sbjct: 509 LRSVAPKLPYIDRITKKETAPVLTSQIYWGAVPFVVIQLVMVALVIAFPQMV 560 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: 788 Number of extensions: 43 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 596 Length adjustment: 35 Effective length of query: 410 Effective length of database: 561 Effective search space: 230010 Effective search space used: 230010 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: 52 (24.6 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