Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Ac3H11_3568 TRAP dicarboxylate transporter, DctM subunit, unknown substrate 6
Query= TCDB::P74224 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3568 Length = 594 Score = 287 bits (735), Expect = 6e-82 Identities = 195/521 (37%), Positives = 279/521 (53%), Gaps = 92/521 (17%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGT 66 L P+MF G + FL G+PVAFSLG + FA IG L L A+P RIFGIM N T Sbjct: 8 LAPIMFAGLICFLLVGFPVAFSLGACGLFFAFIGIELNVLPEALLQAVPLRIFGIMQNDT 67 Query: 67 LLAIPFFIFLGSMLERSGIAEQLLETM------------------GIILGHLRGGLALAV 108 LLAIPFF +G +LERSG+AE LL+T+ G +L G +A +V Sbjct: 68 LLAIPFFTLMGLILERSGMAEDLLDTIGQLFGPIRGGLALAVIFVGALLAATTGVVAASV 127 Query: 109 ILVGTM-------------LAATTGVVAAT-----VVAMGLISLPIMLRYGYSK-ELASG 149 I +G + LAA GV+AA+ ++ L+ + I + G S ++ G Sbjct: 128 ISMGLISLPIMLRYGYDRRLAA--GVIAASGTLAQIIPPSLVLIIIADQMGRSVGDMYKG 185 Query: 150 VIVASGTLGQIIPPSVVLIVL------------ADQLGVSVGDLFIGSLL--PGLMMAGS 195 + L ++L+ + A L G + SLL G+ +A S Sbjct: 186 AFLPGLMLTGFYALYIILLAVFKPQWVPAIPPEARTLRGDDGKSGVPSLLVLTGICVAAS 245 Query: 196 F---------------------ALYVLIIAWLKPDLAPA-LPAEVRNIGGQELRRRIVQ- 232 AL I+ + +A A + A + I L R+ + Sbjct: 246 IYVAKNMPALHSWWSGETVDKVALDETIVVSMCFGVALAFVAASINKITRMGLLSRVAER 305 Query: 233 ---VMLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATL 289 V++PPL+LI LVLG+IF G+A+PTE GA+G++GA +A RL L + T Sbjct: 306 VTFVLIPPLLLIFLVLGTIFLGVATPTEGGAMGALGAGIMAIIRGRLTLSLLKQAITTTT 365 Query: 290 RITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDF 349 +++ V+ IL+G+T F L F+G++G ++ LL LPGGQ+GFL + I +F L FF+DF Sbjct: 366 KLSCFVVFILVGATIFGLTFQGVDGPLWVEHLLTGLPGGQLGFLIVVNIMVFFLAFFLDF 425 Query: 350 FEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPAS---- 405 FE++FIV+PL PVA L +DLIW+GV++ N+QTSF+ PPFGFALFYLR VAPA Sbjct: 426 FELSFIVVPLLAPVAHKLGIDLIWFGVLLAVNMQTSFMHPPFGFALFYLRSVAPAKEYMD 485 Query: 406 ---------LTTGQIYRGAVPFIGLQVLVLLLIIIFPALIN 437 +TT QIY GA+PF+ +Q+L++ LII FP +++ Sbjct: 486 KVTKKMIAPVTTPQIYWGAIPFLCIQLLMVGLIIAFPGIVS 526 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: 781 Number of extensions: 39 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 594 Length adjustment: 35 Effective length of query: 410 Effective length of database: 559 Effective search space: 229190 Effective search space used: 229190 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