Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Ac3H11_2592 TRAP dicarboxylate transporter, DctM subunit, unknown substrate 5
Query= TCDB::P74224 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2592 Length = 434 Score = 215 bits (547), Expect = 3e-60 Identities = 136/431 (31%), Positives = 228/431 (52%), Gaps = 11/431 (2%) Query: 10 MMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLLA 69 ++ + + LG G + +L GVA IG L S P AM I+G ++ TL A Sbjct: 9 LLVLSLFLILGSGVWIGLTLSGVAW----IGMQLFSARPAG-DAMAVTIWGSASSWTLTA 63 Query: 70 IPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAM 129 +P FI++G +L R+ +++ + + + + L G L ++ T+ AA +G AAT + Sbjct: 64 LPLFIWMGEILFRTRLSQDMFKGLAPWVQALPGRLLHTNVVGCTIFAAVSGSSAATCATI 123 Query: 130 GLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLPG 189 G ++LP + R GY + + G + + TLG +IPPS+++IV VS+ LFI +LPG Sbjct: 124 GKMTLPELTRRGYPEHMVVGTLAGASTLGLLIPPSIIMIVYGVSAEVSISQLFIAGVLPG 183 Query: 190 LMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLGSIF 249 +++A F+ Y+++ A PD PA A+VR Q+L + ++P ++LI VLGSI+ Sbjct: 184 ILLAALFSGYIMLWALRHPDQVPA--ADVRMTFMQKLAES--RSLIPVVLLIAAVLGSIY 239 Query: 250 FGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFSLVF 309 G A+ TEA AVG +G++ L+ +NW R+ M+ LIL G+ +L Sbjct: 240 TGFATATEAAAVGVVGSLILSAVQGSMNWGTFKASLMGATRLYCMIALILAGAAFLTLSM 299 Query: 310 RGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEALNL 369 + R + + +A+L + +A + ILG F+D + + + + P +A + Sbjct: 300 GYIGLPRHLAEWIASLGLNKAQLIAALAVFFIILGCFLDGISMVVLTMGVLMPTVQAAGI 359 Query: 370 DLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLI 429 D IW+G+ + ++ + +TPP GF LF L+G+ L I + VP L + LI Sbjct: 360 DPIWFGIFIVLVVEMAQITPPVGFNLFVLQGMTGRQLP--WIAKVTVPMFLLMCGAVALI 417 Query: 430 IIFPALINWLP 440 IFP ++ WLP Sbjct: 418 YIFPGIVTWLP 428 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: 531 Number of extensions: 22 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: 434 Length adjustment: 32 Effective length of query: 413 Effective length of database: 402 Effective search space: 166026 Effective search space used: 166026 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